Get 20M+ Full-Text Papers For Less Than $1.50/day. Subscribe now for You or Your Team.

Learn More →

COMPANION ANIMALS SYMPOSIUM: Development of the mammalian gastrointestinal tract, the resident microbiota, and the role of diet in early life

COMPANION ANIMALS SYMPOSIUM: Development of the mammalian gastrointestinal tract, the resident... ABSTRACT Mammalian gastrointestinal (GI) development is guided by genetic determinants established during the evolution of mammals and matched to the natural diet and environment. Coevolution of the host GI tract (GIT) and the resident bacteria has resulted in commensal relationships that are species and even individual specific. The interactions between the host and the GI bacteria are 2-way and of particular importance during the neonatal period, when the GIT needs to adapt rapidly to the external environment, begin processing of oral foods, and acquire the ability to differentiate between and react appropriately to colonizing commensal and potentially pathogenic bacteria. During this crucial period of life, the patterns of gene expression that determine GI structural and functional development are modulated by the bacteria colonizing the previously sterile GIT of fetuses. The types and amounts of dietary inputs after birth influence GI development, species composition, and metabolic characteristics of the resident bacteria, and the interactions that occur between the bacteria and the host. This review provides overviews of the age-related changes in GIT functions, the resident bacteria, and diet, and describes how interactions among these 3 factors influence the health and nutrition of neonates and can have lifelong consequences. Necrotizing enterocolitis is a common GI inflammatory disorder in preterm infants and is provided as an example of interactions that go awry. Other enteric diseases are common in all newborn mammals, and an understanding of the above interactions will enhance efforts to support neonatal health for infants and for farm and companion animals. INTRODUCTION “We must cultivate our garden,” says Candide (from Candide; Voltaire, 1759). When Candide left sheltered castle life and entered into the external world, he faced challenges and hardships, and his survival was dependent on discriminating between good and evil. Similarly, when the fetus emerges from the shelter of the womb, the immature gastrointestinal tract (GIT) must adapt rapidly to oral feeding, the challenges of extrauterine life, and cultivating the garden of colonizing bacteria. Complex interactions have evolved between the mammalian host and the gastrointestinal (GI) microbiota (Ley et al., 2008). Apparently, the extreme costs that would be imposed on the host by trying to maintain a sterile GIT are outweighed by the benefits of instead establishing commensal relationships with bacteria that provide health and nutritional benefits and that pose little or no risk to the host. Hence, the GIT has come to accept the presence of numerous species of bacteria at densities such that shortly after birth, GI bacterial cells outnumber those of the host by about 10-fold. Much like the challenges faced by Candide, after birth the GIT must establish and maintain a delicate balance between the recognition and exclusion of pathogens and the tolerance of commensal bacteria. The GI disorder necrotizing enterocolitis (NEC) is exemplary of the consequences when the balance is disrupted between exclusion and tolerance and when members of the commensal bacteria trigger excessive inflammatory responses, thereby compromising the health of the neonate (Claud, 2009). The interactions among the GIT, the resident microbiota, and diet begin at birth, when the sterile epithelium of the GIT first encounters the colonizing bacteria and begins processing the first meals. During this critical period of life, genetic determinants of immune responses play a central role in the recognition and responses of the developing GIT to the colonizing bacteria. Although dietary inputs influence postnatal development of the GIT, less understood are how dietary inputs have the potential to influence the interactions between the GI epithelium and the colonizing bacteria. The contrasting responses of the neonatal GIT and the resident bacteria among infants fed breast milk and those fed formula (Hanson, 2007; Penders et al., 2007) highlight how interactions among the genetic determinants of GI characteristics, the resident bacteria, and dietary inputs must be considered together to understand postnatal GI development in health and disease. The objective of our review is to acquaint readers with the responses of the neonatal mammalian GIT to the bacteria that colonize and become established, and how diet is an important factor in those interactions. We first provide readers with a general understanding of mammalian GI development, the postnatal changes in the resident bacteria, and shifts in dietary inputs. Although the changes described are shared among different mammalian species, there are differences in the timing and specifics of the developmental events. Next, we describe the interactions that exist among genetic determinants of GI structure and function, the resident bacteria, and diet. A subsequent section uses NEC, often observed in preterm infants, as an example to describe the consequences when the interactions among GI development, the resident bacteria, and diet go awry. We conclude by discussing some dietary strategies to improve mammalian health by optimizing the interactions between the developing GIT and the resident microbiota. DEVELOPMENT OF THE GIT The GIT represents a critical and expansive interface between the external environment and the host. Organogenesis and maturation of the GIT during prenatal life prepare the fetus for the transition at birth from the sterile intrauterine environment and reliance on placental nutrition to the immediate and dramatic changes in the functional demands placed on the GIT by exposure to the contaminated environment, by digesting food, and by other challenges of extrauterine life. The importance of the GIT being functional at the time of birth is evident by the complications of preterm birth and the consequences of immature GI functions. A notable example is the increased risk of NEC among preterm infants, as discussed subsequently. During prenatal development, the GIT acquires the capacities to 1) digest food; 2) defend against pathogens; 3) contribute to osmoregulation; 4) secrete hormones and other signaling molecules that regulate the GIT and other host systems, and 5) detoxify and eliminate toxins produced by metabolism and acquired from the external environment. Some of the GIT capabilities that develop prenatally are vital for the fetus to process the large volumes of amniotic fluid swallowed (up to 750 mL/d by human fetuses; Pritchard 1966). At term, the GIT is able to process milk, respond to bacterial colonization, and tolerate extrauterine environmental conditions. However, the specific structural and functional characteristics of the GIT at birth vary among species. This is exemplified by comparisons of the GIT among newborns of altricial and precocial species with different adult feeding habits and from different environments (Stevens and Hume, 1995). The changes in the GIT associated with weaning can be accelerated by advancing the transition from milk to the adult diet and can be delayed, but not prevented, by extending suckling. This highlights how the patterns and trajectories of GI development are established by genetic determinants (i.e., are “hard wired”), yet the programmed series of events are responsive to dietary inputs (Drozdowski et al., 2010) and environmental conditions (Bailey and Haverson, 2006) and are capable of some flexibility, to allow the developing GIT to adapt to existing conditions (Lebenthal and Lebenthal, 1999). Evidence also exists for “critical period programming” of GI characteristics, whereby dietary inputs early in life can induce epigenetic changes that persist past the period of exposure and can last for the lifetime of an individual (Drozdowski et al., 2010). This includes early programming of the GI immune system by the colonizing bacteria and environmental antigens (Mulder et al., 2009). Digestion At term, the GIT is adapted for and ready to process the first food, which, for most mammals, is colostrum (Drozdowski et al., 2010). The immature digestive functions of preterm infants are considered to contribute to the increased risk of NEC (reviewed by Claud, 2009) and are why total parenteral nutrition (TPN) is used to meet nutrient and energy needs until the GIT develops adequate capacities to process food. Suckling mammals have a minimal capacity to modulate digestive processes adaptively in response to changes in diet composition (Buddington, 1994) and do not acquire the ability to process the adult diet until just before weaning (Drozdowski et al., 2010). When neonates are not fed breast milk, diarrhea can result when the alternate diet includes ingredients such as sucrose, for which there is inadequate expression of sucrase. Defense The GI immune system provides a comprehensive, multilayered defense (Winkler et al., 2007). Much like a gardener, the GI immune system is able to differentiate among the numerous types of GI bacteria that represent a threat and that should be tolerated, and this contributes to the selection of an assemblage of commensal bacteria (Ogra, 2010). This is the culmination of coevolution between the resident bacteria and the innate and adaptive components of the GI immune system, and is dependent on a diversity of extracellular Toll-like receptors (TLR) and intracellular nucleotide-binding oligomerization domain receptors (Shibolet and Podolsky, 2007; Richardson et al., 2010). Aberrant and excessive reactions of the GI immune system to commensal bacteria and other antigens in the GIT causes inflammation and has been associated with several pathologies, including NEC in preterm infants and inflammatory bowel disease, celiac disease, and various food allergies in children and adults. Conversely, inadequate recognition of or responses to pathogens pose obvious health risks. The GI immune functions develop prenatally, and at term, they are capable of recognizing and responding to pathogens, including bacterial DNA motifs and vaccines (Lacroix-Lamandé et al., 2009). Additional development and maturation occur after birth, and the several phases described for the porcine GI immune system (Bailey and Haverson, 2006) are relevant to most mammals. The innate GI defenses include secretions of acid, antimicrobial peptides, lysozyme, and mucus; as well as the tight junctions that link epithelial cells and provide a physical barrier; activated defense cells (e.g., macrophages, neutrophils); and intestinal motility (Eckmann, 2006). These are supplemented at birth by the transient ability of the enterocytes of neonates to absorb antibodies intact and transfer the antibodies present in colostrum to the systemic circuit of newborns (transcytosis), conferring passive immunity. This is dependent on the expression of a receptor (Fc) on the apical membrane that binds the IgG in breast milk (Van de Perre, 2003). The adaptive component of the GI defenses includes the organized lymphoid tissues (e.g., Peyer's patches, mesenteric lymph nodes) that are associated with the GIT, the B and T classes of lymphocytes, and the antigen-presenting dendritic cells (Rumbo and Schiffrin, 2005). A key difference between the adaptive components of the GI and systemic immune systems, despite sharing similar cell types, is the development of oral tolerance, whereby the GI immune system learns to discriminate between bacteria and antigens that pose little or no risk and those that are dangerous (Magalhaes et al. 2007). The learning process has occurred during the coevolution of hosts with their GI bacteria, resulting in receptors and associated signaling pathways and innate defense mechanisms that can discriminate between “the good, the bad, and the ugly.” At birth, the cellular and tissue elements of the adaptive component are less abundant and immature compared with those in the adult, with maturation and learning occurring after birth (Rumbo and Schiffrin, 2005; Mshvildadze and Neu, 2010). The even more immature status of the GI defenses of preterm infants with increased and less regulated nuclear factor-κB signaling contributes to the hyperresponsiveness of the GIT, the increased risk of GI inflammatory disorders such as NEC, and the increased incidence of sepsis (Claud 2009). Osmoregulation The osmoregulatory challenges facing the GI tract differ markedly between fetuses dependent on placental exchange of water and electrolytes and neonates dependent on processing of milk to obtain electrolytes and water. Chloride channels exist in the fetal GI epithelium (Murray et al., 1996), but colonic expression of the sodium channel (also known as ENaC) and absorption of sodium are underdeveloped or are suppressed in fetuses (Watanabe et al., 1998). This may contribute to the osmoregulatory problems, including sodium imbalances, and the special nutritional needs of premature infants. Postnatally, the osmoregulatory functions of the GIT respond to inflammatory cytokines by a combination of decreased ion absorption and increased chloride secretion. The resulting diarrhea and the loss of electrolytes and water are the major cause of morbidity and mortality among newborn animals and infants. Endocrine Secretion Collectively, the regions of the GI tract and the associated organs (e.g., pancreas) represent the largest endocrine system in the vertebrate body. Furthermore, a linkage exists between the GI endocrine and immune functions, leading to the concept of the GI immunoendocrine axis. Specifically, enteroendocrine cells express TLR and respond to luminal antigens by the production of cytokines and defensins (Palazzo et al., 2007; Selleri et al., 2008), and they respond to cytokines and other regulatory molecules originating from GI immune cells. Hence, GI immune responses to colonizing bacteria can alter endocrine secretions by the neonatal GI tract, thereby having GI and systemic implications. The vast diversity of secreted peptides is critical for regulating GI (e.g., gastrin, secretin, cholecystokinin) and systemic functions (e.g., insulin, glucagon, ghrelin). Despite reports of prenatal development of GI endocrine cells (Alumets et al., 1983) and expression of receptors for epidermal growth factor (Chailler and Ménard, 1999), glucagon-like peptide 2 (Burrin et al., 2003), and cholecystokinin (Bourassa et al., 1999), there is only a fragmentary understanding of ontogenetic development of the GI endocrine functions. Detoxification The GIT plays a role in the detoxification and elimination of ingested toxins, including drugs and metabolic wastes from the host and the resident bacteria (Buddington, 2009). This is accomplished by a combination of enzymes that convert and detoxify noxious molecules and export transporters that eliminate the resulting xenobiotic compounds. Although xenobiotic-converting enzymes are expressed in the liver during late gestation, ontogenetic patterns of development for the numerous enzymes and transporters responsible for the detoxification functions of the GIT are not well characterized (Myllynen et al., 2009). THE ASSEMBLAGES OF BACTERIA IN THE GIT The adult GIT is estimated to harbor 400 to 500 species of bacteria, with some estimates of >800 species and >7,000 strains (O'Keefe, 2008). The majority of the GI bacteria have yet to be cultured, and although molecular-based approaches of detection have increased our understanding of the bacterial diversity, these methods have provided few insights into the functional characteristics of the bacteria and their influences on host health (Flint et al., 2007). The GI microbiota also include fungi, protozoa, yeasts, viruses, and bacteriophages (Mackie et al., 1999) that influence host health and nutrition. Of critical interest are the interactions that develop between the microbiome and the GIT of infants (Mshvildadze and Neu, 2010). Regional Distribution The GIT can be considered a small ecosystem (Buddington and Weiher, 1999), with multiple habitats (regions). Within each region, there are dynamic interactions among the resident bacteria, dietary inputs, and the structure and functions of the region that determine the physical, chemical, and biotic characteristics (Kelly et al., 2007). The interactions are even more pronounced during the postnatal period, when the combination of dietary inputs, developing GI functions, and interbacterial interactions play central roles in determining the densities, diversities, and distributions of species that become established within the different regions of the GIT ecosystem. The acidic stomach of adult nonruminant mammals harbors a decreased density (<104 cfu/g) and diversity of bacterial species compared with the small intestine and colon, despite the increased input of nutrients. Bacterial densities and diversity are similarly small in the acid-secreting portion of the ruminant stomach (abomasum), despite the complex and numerically abundant assemblages of bacteria present in the preceding rumen (Nelson et al. 2003). The densities and diversity of bacteria increase distally along the small intestine, with the greatest densities (1011 to 1012 cfu/g) and diversities being in the colon. The declining gradient for oxygen from the proximal small intestine to the colon is paralleled by a reciprocal decline in the aerotolerant bacteria and an increase in the anaerobic species of bacteria. Additional environmental factors that contribute to the proximal-to-distal gradients along the small intestine and colon for the densities and diversities of species include more rapid movement of the digesta proximally and the introduction into the duodenum of bile acids from the gall bladder and antibacterial peptides secreted by the pancreas and the intestine itself (e.g., defensins from Paneth cells). Even within the colon, there is a proximal-to-distal distribution of species and metabolic activities. The proportions of saccharolytic bacteria and short-chain fatty acid (SCFA) production are greater in the proximal colon, whereas proteolytic bacteria and the production of putrefactive metabolites are more prevalent in the distal colon (Macfarlane and Macfarlane, 2003). This distribution corresponds with the greater distal production of ammonia, phenols, indoles, amines, and other toxic and carcinogenic metabolites, which, in adults, contributes to a greater incidence of colorectal cancer in the distal colon. Vertical gradients that extend from the epithelium into the lumen also exist for the distribution of species in the GIT (Kleessen and Blaut, 2005). The populations of bacteria adherent to or immediately adjacent to the epithelium have a profound impact on the GIT and the host, yet they are less understood. Colonization of the Neonatal GIT The sterile GIT of fetuses is rapidly colonized, and within 12 h after delivery, bacteria can be detected throughout the entire GIT and at densities (i.e., cfu/g) that are comparable with those of adults (Mackie et al., 1999). The similar fecal densities of bacteria enumerated in the colons of infants and adults may reflect a maximum density of bacteria that can be supported by the GIT (i.e., “carrying capacity”). Colonization is a stochastic process and results in individual variation in GI bacterial assemblages. This is true even among littermates (Tannock et al., 1990), monozygotic twins (Stewart et al., 2005), and even identical twins (Dicksved et al., 2008). Infants delivered vaginally are colonized by bacteria originating from the maternal GIT, vagina, skin, and surrounding environment (Mackie et al. 1999; Huurre et al., 2008). Infants delivered by caesarian section are not immediately exposed to maternal fecal and vaginal bacteria. Instead, the initial colonizers are nosocomial, originating from medical staff and the hospital environments. Additional bacteria are eventually acquired from the mother (skin, mammary glands) and from outside the hospital environment. Corresponding with the different sources and timing of colonization, the assemblages of GI bacteria differ between infants born vaginally and by caesarian section. The influence of delivery mode on the assemblages is still apparent up to 7 yr after birth (Salminen et al., 2004). Other nondiet factors considered to influence the GI assemblages that colonize and become established are gestational age at delivery, diet, antibiotic use, and the external environment (Penders et al., 2006). Infants with assemblages considered to be beneficial, with fewer pathogens, are typically delivered vaginally outside of hospitals and are exclusively fed breast milk. Which bacteria persist in the GIT is less random, providing supporting evidence for species-specific host-bacteria relations. Notable are the different species of Helicobacter that have been isolated from different vertebrates (Schrenzel et al., 2010). Hence, not all species of bacteria entering the GIT, including probiotic species, are able to persist. Ecological Principles and the GI Bacteria After the initial period of colonization, interbacterial interactions contribute to the changes in species composition and metabolic activities of the resident bacteria (Mackie et al., 1999; Flint et al., 2007). This includes the competitive exclusion of pathogens, probiotics, and other bacteria by commensal bacteria. The mechanisms of exclusion include competition for nutrients and binding sites and the production of metabolites that are toxic to other groups. The process of facilitation, which can be described as cooperative relationships among organisms, leads to further changes in the GI environment, resulting in assemblages with different dominant species. In the GIT, the aerotolerant species that initially dominate reduce the oxygen tension and thereby favor the emergence of anaerobic groups. Another example of interbacterial interactions is a metabolic cross-feeding, whereby one group of bacteria produces metabolites that are used by other groups (Flint et al., 2007). This includes the conversion of lactate produced by bifidobacteria into butyrate and other SCFA by other anaerobic members of the GI bacteria. Recent studies have described quorum sensing among the GI bacteria, triggering adaptive changes in the characteristics of individual bacterial species (Allen and Torres, 2008) and perhaps host cells (Sperandio et al., 2003). The gradual changes in the species composition and distributions of the resident bacteria that occur with increasing age are representative of the ecological principle of succession. Eventually the changes culminate in a “climax community” of species. The composition and productivity of the resident species are also influenced by the stability and extremes of the local environment (Buddington and Weiher, 1999). Environments that are harsh (e.g., stomach) or subject to frequent and large disturbances (e.g., proximal small intestine) have decreased densities and diversities of species. Ecosystems with the greatest densities and diversities of species are characterized by benign conditions and with intermittent disturbances of intermediate magnitude that are sufficient to prevent one or a few species from becoming dominant. In the GIT, the proximal colon provides such an environment and correspondingly has the greatest densities, diversities, and species evenness of bacteria. Among infants, the greatest disturbances to the GI ecosystem are caused by diarrhea and the administration of antibiotics. Both cause dramatic declines in the densities and diversities of the resident bacteria, with a shift in the dominant species (Tanaka et al., 2009). This has the potential to influence GI development (Mshvildadze and Neu, 2010) and actually increase the risk of NEC (Cotten et al., 2009). It is important to note that the disturbances caused by even short-term antibiotic administration may persist for at least 2 yr (Jernberg et al., 2010). DIETARY INPUTS DURING POSTNATAL DEVELOPMENT There is growing appreciation of the influences of diet on the ontogeny of the GIT and the assemblages of bacteria that colonize it and become established (Newburg and Walker, 2007). Neonatal mammals are dependent on breast milk to varying degrees, ranging from the extreme dependency of altricial species, such as marsupials and many laboratory rodents, to the very short periods of suckling for precocial species, such as guinea pigs, which begin to eat the adult diet shortly after birth. Milk composition varies widely among species (Jenness and Sloan, 1970). Notable is the absence of lactose in the milk of pinnipeds, the greater concentration of oligosaccharides in human milk (Newburg, 2009), and the wide species variation in protein, carbohydrate, and fat content. Milk composition is also not consistent during lactation. Colostrum, the first milk produced after birth, has greater protein content because of the increased concentration of immunoglobulins and a diversity of regulatory proteins. Within days after birth, the composition begins to shift from colostrum to mature milk, with the composition typical of the species. Apparently, milk composition has been refined over evolutionary time to match the unique species, age, and individual demands of infants. Manufacturers of formulas for human infants and milk replacers for companion and production animals attempt to mimic the composition of the milk of the target species. The present formulas are relatively simple, with far fewer components than breast milk. There are intense efforts to identify ingredients that can be added to formulas and milk replacers that will promote patterns of GI development and the establishment of commensal assemblages of bacteria that are similar to those when infants are fed breast milk and when neonates of other species are allowed to nurse their dams. For most species and individuals, weaning is a gradual process, with a progressive decline in milk consumption and an increased dependency on the adult diet to provide energy and nutrients. During this period, GI functions and the resident assemblages of bacteria gradually become adult-like. When weaning is sudden or early, diarrhea often results and is accompanied by changes in the species composition and metabolic activities of the GI bacteria (Lallès et al., 2007). Influences of Diet on GI development The rapid postnatal growth and maturation of the GIT are dependent on dietary inputs and are delayed when neonates are provided TPN rather than fed enterally. The importance of luminal nutrients for development of the neonatal GIT has led to the concept of minimal enteral nutrition (atrophic feeding), whereby small amounts of oral nutrients are provided during TPN to encourage GI growth and maturation and reduce the risk of bacterial translocation and sepsis (Bombell and McGuire, 2009). The composition of the food fed to neonates is a determinant of GI growth, maturation, and health. Colostrum includes immunoglobulins that provide passive immunity to the neonate and numerous hormones, cytokines, and other regulatory molecules that stimulate GI growth and maturation, including immune functions (Hanson, 2007). Even coating the mouth of preterm neonates with colostrum may be adequate to stimulate the development of GI and systemic immune functions (Rodriguez et al., 2010). The change in diet composition at weaning triggers changes in enterocyte cytokinetics and patterns of gene expression, coinciding with changes in absorptive and secretory functions (Drozdowski et al., 2010). The secretory characteristics of GI accessory organs, including the pancreas, are also responsive to the diet change at weaning. Influence of Diet on the Developing Assemblages of Bacteria The inputs into ecosystems are key determinants of the abundances, diversity, and production of the resident organisms. Similarly, the assemblages of GI bacteria are responsive to dietary and host inputs (Buddington and Weiher, 1999; Koenig et al., 2010). This is evident from the disturbance to the assemblages of GI bacteria induced by prolonged administration of TPN (Alverdy et al., 2005), causing increases in pathogens and risks of secondary diseases (Harvey et al., 2006). It is not surprising that the amount and composition of the diet fed to infants influence the postnatal changes in the GI bacteria. By doing so, diet indirectly influences postnatal GIT development and disease resistance (Amarri et al., 2006). A central question surrounding neonatal health and nutrition is, “How does breast milk adventitiously influence the developing assemblage of bacteria?” The majority of studies report that infants fed breast milk have less incidence of disease. This corresponds to greater fecal densities of lactic acid-producing bacteria (e.g., bifidobacteria and lactobacilli) compared with infants receiving formula (Penders et al., 2006). Breast milk also reduces the densities of bacteria adherent to the mucosa, and this may contribute to the reduced risk of NEC (Van Haver et al., 2009). It is interesting that providing infants with only a small volume of formula can elicit dramatic changes in the GI bacteria (Mackie et al., 1999). The different patterns of microbial gene expression among piglets fed by the sow or given milk replacer (Poroyko et al., 2010) raises an intriguing possibility that milk has evolved attributes that favor the establishment and dominance of commensal bacteria that provide health and nutritional benefits and that remove undesired species. The discovery of the immune modulation and health benefits of nucleotides (Yu, 2002), which include beneficially modulating the GI bacteria (Singhal et al., 2008), led to the inclusion of nucleotides in infant formulas. Other components of milk reported to provide more than energy and nutrients to infants that can modify the resident bacteria include IgA, human milk oligosaccharides (HMO), lactose, lysozyme, and lactoferrin (Newburg, 2009). A portion of the lactose in milk is not hydrolyzed during transit of the small intestine and is metabolized by colonic bacteria, causing an increase in breath hydrogen. This is particularly true among preterm infants (Kien et al., 1998) and exemplifies how diet influences bacterial metabolism (González et al., 2008). Although lactose fermentation has been interpreted as lactase insufficiency, it may contribute to shifting the luminal environment to be more conducive to commensal bacteria. The multifunctional and diverse HMO are the third most abundant component of human milk, with species and individual differences in the amounts, types, and proportions (Newburg, 2009). The majority of HMO are not digested during transit of the GIT and are considered to encourage the establishment of commensal, health-promoting bacteria by a combination of having prebiotic properties, serving as receptor mimics for pathogens, and modulating mucosal immune functions (Newburg, 2009; Eiwegger et al., 2010). The protein lactoferrin, although abundant in human, but not cow, milk (Coppa et al., 2006), is absent from present infant formulas. Lactoferrin is considered to be immunomodulatory (Suzuki et al., 2005), to have the potential to influence the assemblages of bacteria by being bifidogenic (Coppa et al., 2006), and to have the ability to reduce sepsis among preterm infants (Venkatesh and Abrams, 2010). Collectively, the components of milk highlight a coevolution between milk composition, the developing GIT, and the resident bacteria. Combined, they effectively enhance the ability of the neonate to “cultivate a garden” of health-promoting bacteria. There is also interest in novel ingredients that are not milk based but that may beneficially influence the species composition of the GI bacteria when fed to infants [e.g., prebiotics and probiotics (Sherman et al., 2009)]. The historical emphasis has been on formula ingredients that improve the species composition of the GI microbiota. Less considered, but of critical importance, is the influence of diet on bacterial enzymes (Grönlund et al., 1999), hence metabolism. Bacterial metabolism and the production of SCFA and other metabolites are related to the types and amounts of substrates (Macfarlane and Macfarlane, 2003), such as the responses of the GI bacteria to lactose (Mäkivuokko et al., 2006). Although total concentrations of fecal SCFA are similar for preterm infants fed expressed breast milk or a commercial infant formula (P > 0.9), those fed breast milk have greater concentrations of propionate but relatively less acetate (P < 0.05; R. K. Buddington, unpublished data). It is interesting that the SCFA profiles of the preterm infants fed expressed breast milk are similar to those we have measured for healthy adults. INTERACTIONS BETWEEN THE BACTERIA AND THE INTESTINE The interactions between the resident bacteria and the host GIT involve 2-way communication. This results in gene expression being modulated in the bacteria and the host (Allen and Torres, 2008; Sharma et al., 2010). Moreover, by modulating the expression of host genes, the resident bacteria modify the GI environment, which in turn alters the interactions and balances among the GI bacteria (Mahowald et al., 2009). The complex interactions result in GIT ecosystems that are unique for species, individuals, life history stages, and health states (Dunne 2001), and these can have long-term immune and health implications (Conroy et al., 2009). The interactions between the host and the GI bacteria occur over 3 time scales. There are rapid and reversible interactions that span minutes to hours, other interactions that occur during the life history of individuals, and those that occur over evolutionary time scales. There is ample evidence for the coevolution of the host GIT and the resident bacteria (Ley et al., 2008). This results in commensal and symbiotic relationships that are species specific and that involve genetic adaptations of the bacteria to the host GIT (Schell et al., 2002). The cooperative responses of the GI immune system to the different bacteria have established mutualisms (Slack et al., 2009). The interactions that occur during the life of an individual influence the characteristics of the host and the assemblages of bacteria (densities, diversity, evenness, regional distribution, and functional attributes). These interactions are particularly relevant to neonates and have been the subject of numerous studies and reviews. Specifically, the early responses of the GIT and the resident bacteria can have lifelong health consequences through epigenetic mechanisms. These include the ability of some bacteria to alter the patterns of host gene expression, such as patterns of glycosylation for extracellular proteins (Freitas et al., 2002) in ways that benefit both the commensal bacteria and the host (Bry et al. 1996). Another relevant example is the relationship between early antigen exposure and the risk of allergies and asthma later in life (the “hygiene hypothesis”; Shreiner et al., 2008). Less understood are the rapid and reversible interactions during infancy between the GIT and the bacteria. These transient interactions occur over periods of minutes to hours and allow the GIT and the resident bacteria to adapt to changing conditions, such as those that occur during and between meals of varying size and composition. The interactions between the bacteria and the GIT can be direct, via cell-to-cell contacts. Typically, the adverse influences of pathogenic bacteria require direct contact with epithelial cells and are mediated by surface molecules (Zoumpopoulou et al., 2009). Exemplary is how the attachment of pathogenic Escherichia coli, Salmonella, clostridia, and other pathogens is required to trigger the expression of virulence genes, such as those coding for toxins, invasive mechanisms, or Type III secretion systems that alter the characteristics or cause the death of the attached enterocytes. Members of the commensal bacteria and some probiotic strains are considered to inhibit pathogen adherence and pathogenesis by occupying sites of attachment and by inducing enterocyte expression of the mucin-encoding gene MUC2 and other defense genes that inhibit attachment (Kim et al., 2008) by the production of immunomodulatory molecules (Mazmanian et al., 2005). The influences of the bacteria can also be indirect and mediated by metabolites that alter host gene expression, beneficially or adversely. Some species of bifidobacteria release soluble factors that decrease epithelial cell secretion of inflammatory cytokines (Heuvelin et al., 2009) and chloride (Heuvelin et al., 2010). The SCFA produced by bacterial fermentation of undigested feedstuffs provide up to 10% of the total metabolic energy requirement of humans and even greater percentages among animals with larger hindguts or rumens (Rechkemmer et al., 1988). Corresponding with this, gnotobiotic rodents require 30% more dietary energy and vitamin supplements compared with conventional rodents harboring commensal bacteria capable of fermenting undigested feedstuffs. The SCFA influence colon health (Wong et al., 2006), alter patterns of epithelial cell gene expression (Sanderson, 2004; Vanhoutvin et al., 2009), and stimulate secretion of regulatory peptides that enhance growth and functions of the proximal small intestine (Bartholome et al., 2004). The responses to butyrate are more pronounced than those to acetate and propionate (Basson et al., 2000). However, excessive production of SCFA, including butyrate, has been associated with damage to the GI epithelium and may contribute to NEC (Lin et al., 2005). Often overlooked is the competition between the GIT and the resident bacteria for nutrients. Maintaining reduced densities of bacteria in the proximal small intestine by peristalsis and antibacterial secretions from the pancreas and intestine provides the GIT with the first access to readily available, digestible nutrients. Food not available to the host can and will be metabolized by the bacteria. The Resident Bacteria Influence the Developing GIT Profound differences exist between germ-free and conventional rodents with respect to villus architecture, and enterocyte patterns of proliferation, differentiation, and gene expression (Zocco et al., 2007) and mucosal immune responses (Williams et al., 2006; Hrncir et al., 2008). Bacteria isolated from the GIT of neonates are reported to enhance maturation of the GIT by modulating gene expression (Are et al., 2008). This includes the age-related shifts in the activities of the fucosyl- and sialyltransferases responsible for the weaning-related changes in the glycosylation of enterocyte glycoproteins (Nanthakumar et al., 2005). Even patterns of intestinal motility are responsive to the resident bacteria (Lesniewska et al. 2006). The interactions between the colonizing bacteria and the developing GI immune functions have immediate and long-term consequences on host health (Dimmitt et al., 2010; Mshvildadze and Neu, 2010). The combination of colonizing bacteria, food, and environmental antigens activate the immature GI immune system of the neonate by triggering the rapid maturation, proliferation, and migration of the cellular components of the adaptive immune division. The interactions during infancy are critical for the development of tolerance and to avoid the risk of allergies to food and other environmental antigens later in life (Kukkonen et al. 2008), and are a key factor in the risk of atopic disorders (Penders et al., 2007). The interactions between the bacteria and GI epithelial cells also influence innate immune functions, such as the secretion of mucous and antimicrobial peptides. Additional immunologic challenges at weaning caused by the concurrent shifts in diet and the GI bacteria trigger further changes in GI defense functions. Different species of colonizing bacteria have varying influences on the expression of proinflammatory genes (Zeuthen et al., 2010), the balance between T helper 1 (antibody-mediated) and T helper 2 (cell-mediated) immune responses (Ogra, 2010), including immunoglobulin production (Huurre et al., 2008), the patterns of expression for the TLR and nucleotide-binding oligomerization domain receptors that are critical for antigen discrimination (Lundin et al., 2008), and the development of tolerance to endotoxins (Lotz et al., 2006). These findings have stimulated interest in providing probiotics to infants to modulate the developing immune responses adventitiously. Conversely, changes in the GI bacteria caused by administration of antibiotics during suckling increases the densities and responses of mast cells, apparently predisposing the infant to the development of allergies (Nutten et al., 2007) and potentially altering GI immune development (Schumann et al., 2005). Much less is known about whether and how the assemblages of bacteria influence the postnatal development of other GI functions. Despite the impact of pathogen-induced diarrheas on neonates, the short- and long-term responses of the osmoregulatory functions to the colonizing bacteria have not been described. There is evidence that enteroendocrine cells can respond directly to resident bacteria by the secretion of hormones (Palazzo et al., 2007). The hyperactive immune responses of the neonate, if stimulated, can be expected to influence the other GI functions. For example, inflammatory cytokines secreted in response to pathogenic bacteria are likely to reduce digestive secretions and nutrient absorption and increase the secretion of electrolytes and water. The Developing GIT Influences the Resident Bacteria The GIT functions are key determinants of the chemical characteristics of the luminal environment. Digestive secretions present barriers to the introduction of species, even probiotics, as well as pathogens. Therefore, the changes in the physicochemical environment of the developing GIT (Sanderson, 1999) and the developing innate and adaptive components of the GI immune system have the potential to influence the developing assemblages of bacteria (Salzman et al., 2010). The immature gastric acid production of neonates (Grahnquist et al., 2000) coincides with greater densities of bacteria in the stomach until acid production increases. Postnatal changes in patterns of enterocyte glycosylation of apical membrane glycoproteins (Nanthakumar et al., 2005) influence bacterial metabolism and may represent a coevolved symbiosis between the host and the commensal GI bacteria. NEC: WHEN THE INTERACTIONS GO AWRY The interactions among the resident bacteria, the developing GIT, and the diet are of key importance for the adaptation of neonates to postnatal life (Mshvildadze and Neu, 2010). They are even more important after preterm birth because of the immature state of GI development, the intolerance of many preterm infants to feeding, and the adverse reactions they have to colonizing bacteria. Necrotizing enterocolitis is an inflammatory reaction that is the most common GIT disorder of neonates, particularly those born premature, with the incidence varying from 1 to 8% among neonatal intensive care units (Kosloske, 1994). The NEC disease process is multifactorial, with prematurity, bacterial colonization of the GIT, and feeding recognized as the key contributors. Necrotizing enterocolitis has also been associated with altered GI bacterial assemblages (Hällström et al., 2004), an immature epithelial barrier and immune defenses, and fetal enterocytes that are hyperresponsive (Claud, 2009). This has led to the routine prophylactic administration of antibiotics to preterm, low-birth-weight infants. Unfortunately, this may actually predispose preterm infants to NEC (Cotten et al., 2009) by destabilizing the assemblages of GI bacteria. Additionally, the majority of preterm infants are delivered by caesarian section, which may compromise the normal postnatal spontaneous activation of intestinal epithelial cells (Lotz et al., 2006) and the already impaired recognition of lipopolysaccharide characteristic of preterm birth (Wolfs et al., 2010). Another issue facing preterm infants is the initial dependence many have on parenteral nutrition, which delays GI growth and maturation (Hay, 2008). As a consequence, development of the GI ecosystem is often compromised among preterm infants (Mshvildadze and Neu, 2010). The absence of NEC among germ-free animals demonstrates the essential role of the resident bacteria in the disease process. Moreover, the risk of NEC is increased when formula is fed, whereas infants fed breast milk are protected. This has been corroborated in studies with animal models (newborn mice and rats) that indicate diet is a determinant of NEC risk via effects on both microbiota composition and the response pathways of the host (Sodhi et al., 2008). Because newborn laboratory rodents have limited physiological, anatomical, and developmental relevance to preterm humans, we recently developed a preterm pig model of NEC to better understand the diet-microbiota interactions during early GI development in humans (Sangild et al., 2006). Our studies confirmed that caesarean section and vaginal birth of preterm pigs (at 92% of gestation) resulted in widely different patterns of GI bacterial colonization, yet resulted in similar incidences of NEC (Siggers et al., 2010). When preterm, caesarean-delivered pigs were reared in infant incubators and fed an infant formula, 50% or more spontaneously developed NEC symptoms and the characteristic lesions. The incidence of NEC was about 5% when preterm pigs were instead fed sow or cow colostrum (Bjornvad et al., 2008). This parallels the benefits of providing colostrum to preterm human infants. The protection provided by colostrum vs. the increased risk associated with formula indicates dietary inputs play a central role in NEC. Whether and how diet influences bacterial colonization of the GIT and the role in NEC has been investigated in the pig model in several studies (reviewed by Siggers et al., 2010). Overall, there were few diet-dependent differences in gut colonization, except that certain pathogenic species (e.g., Clostridium perfringens) were consistently associated with intestinal lesions associated with NEC. Moreover, the patterns of bacterial colonization correlated more closely with the degree of intestinal lesions and gestational age at birth (maturity of the epithelium) than with specific diets (colostrum vs. formula). Reviews of clinical trials with human preterm infants that evaluated the efficacy of probiotics as a prophylactic for NEC suggest the NEC risk is reduced (Alfaleh et al., 2010). However, the use of different strains of probiotics and administration regimens confounds interpretations. The administration of probiotics to preterm pigs did not induce notable changes in the GI bacteria, nor did it consistently reduce the incidence of NEC (Siggers et al., 2010). Although the potential benefits of including prebiotics in formula fed to preterm infants have not been adequately investigated and remain uncertain (Sherman et al., 2009), studies with animal models suggest adding prebiotics may reduce the risk of NEC (Butel et al., 2002). However, the addition of prebiotic compounds to the formula fed to preterm pigs failed to improve NEC resistance relative to the formula alone (Møller et al., 2011). Collectively, these studies lead to the conclusion that the presence of bacteria is essential for intestinal inflammatory reactions in newborns. Furthermore, the state of the mucosa is an important determinant of whether the contact with the colonizing bacteria results in severe inflammation and NEC. Controlling the process of bacterial colonization in preterm newborns through diet is difficult. Even so, the species composition of the GI bacteria appears to be less important for NEC risk than the digestive capacity and immune responses of the immature GIT. The detrimental effects of feeding formula may be related to the absence of immunomodulatory factors and nutrients that are present in breast milk and the responses of the preterm GI ecosystem to novel, nonmilk ingredients that are present in formula (e.g., corn syrup solids). Preterm pigs fed formula prepared with corn syrup solids had a greater incidence of NEC compared with when lactose was the predominant source of carbohydrate (Buddington et al., 2008). The beneficial effects of the lactose-based formula were more closely related to improved functions of the intestinal mucosa rather than to improved gut microbiota (Thymann et al., 2009). Even though bacteria colonize the GIT immediately after delivery and are present during the period of TPN, the onset of NEC-related inflammatory reactions in the majority of preterm pigs occurred within hours after the onset of enteral feeding with formula (Oste et al., 2010). The importance of diet is again evident from the overfed, preterm rat pup as a model for NEC (Okada et al., 2010). The importance of diet for inducing NEC in animal models is similar to the development of NEC in preterm human infants after the beginning of enteral feeding. These findings highlight how adverse interactions between the colonizing bacteria and diet in conjunction with immaturity of the GIT are central to the NEC disease process. Despite the role of the GI microbiome in contributing to disease in infants, it is very likely that the metabolic functions of the GI bacteria and the responses to enteral nutrients are more important in triggering NEC. Rectal introduction of SCFA induces mucosal damage (Lin et al., 2005), and introducing a combination of lactose and lactose-fermenting bacteria that generate increased concentrations of SCFA (Waligora-Dupriet et al., 2009) induces mucosal damage and NEC-like characteristics in animal models. Although the etiology of NEC remains uncertain, the interactions between the GI bacteria and diet are key determinants of the sensitivity of the immature GIT to stimuli that elicit detrimental inflammatory reactions. PERSPECTIVES FOR DIETARY MANAGEMENT OF THE DEVELOPING GIT ECOSYSTEM The type (breast milk or formulas with novel ingredients) and amount (full, minimal, or absence) of enteral diet in conjunction with bacterial colonization play significant roles in mediating postnatal development of the GI structure, functions, and resident microbiota. Present infant formulas fail to replicate the important protective effects of breast milk, which can be attributed to the lack of bioactive constituents that modulate GI gene expression, modulate the growth and maturation of GI functions, possess antimicrobial functions and provide the neonate with passive immunity, and others with prebiotic properties that contribute to the selection and dominance of the commensal microbiota. In addition to providing adequate energy and nutrients, the optimal diet for the neonate, term or preterm, needs to include components that reduce or prevent the harmful actions of the resident GI microbiota on the neonatal mucosa. There is understandable interest in increasing the proportion of beneficial bacteria in the GIT of infants to modulate enteric immune functions and thereby improve resistance to GIT pathogens and other health challenges (Dogi et al., 2008). Three principal approaches have been used to date. Although antibiotics remain a mainstay for neonatal care, there is a growing appreciation of and concern about the long-term consequences associated with the disturbances they cause in the developing GI ecosystem (Cotten et al., 2009; Jernberg et al., 2010). Probiotics are of widespread interest, and there are numerous reports of efficacy. However, the benefits are generally transient and do not persist after the probiotic is no longer administered. It has proven possible to provide probiotic bacteria during pregnancy to facilitate colonization of infants born vaginally (Buddington et al., 2010). However, the numerous strains available, the varying responses that can be elicited, and the likely individual-specific responses complicate the selection of strains that provide benefits. The emergence of prebiotics as ingredients in infant formulas mimics the presence of oligosaccharides in breast milk and has shown promise for encouraging the growth of beneficial bacteria already resident in and presumably adapted to the host GIT (Veereman, 2007), thereby providing health benefits (Arslanoglu et al., 2008). Animal models will remain important for investigating the development of the GI ecosystem of human infants, agricultural species, and companion animals and for evaluating the influences of bacteria and diet. The variation in the GI microbiota among species, individuals, ages, and health states will complicate extrapolating results from one species to another. It is not surprising that responses to probiotics and prebiotics vary among species and even individuals (Sullivan and Nord, 2005). A better understanding of how diet influences host-microbiome interactions during the neonatal period will greatly enhance efforts to improve management of the GIT ecosystem, and thereby the health and nutrition of newborns. LITERATURE CITED Alfaleh K. Anabrees J. Bassler D. 2010. Probiotics reduce the risk of necrotizing enterocolitis in preterm infants: A meta-analysis. Neonatology  97: 93– 99. https://doi.org/19707025 Google Scholar CrossRef Search ADS PubMed  Allen C. A. Torres A. G. 2008. Host-microbe communication within the GIT. Adv. Exp. Med. Biol.  635: 93– 101. https://doi.org/18841706 Google Scholar CrossRef Search ADS PubMed  Alumets J. Håkanson R. Sundler F. 1983. Ontogeny of endocrine cells in porcine gut and pancreas. An immunocytochemical study. Gastroenterology  85: 1359– 1372. https://doi.org/6138293 Google Scholar PubMed  Alverdy J. Zaborina O. Wu L. 2005. The impact of stress and nutrition on bacterial-host interactions at the intestinal epithelial surface. Curr. Opin. Clin. Nutr. Metab. Care  8: 205– 209. https://doi.org/15716801 Google Scholar CrossRef Search ADS PubMed  Amarri S. Benatti F. Callegari M. L. Shahkhalili Y. Chauffard F. Rochat F. Acheson K. J. Hager C. Benyacoub J. Galli E. Rebecchi A. Morelli L. 2006. Changes of gut microbiota and immune markers during the complementary feeding period in healthy breast-fed infants. J. Pediatr. Gastroenterol. Nutr.  42: 488– 495. https://doi.org/16707969 Google Scholar CrossRef Search ADS PubMed  Are A. Aronsson L. Wang S. Greicius G. Lee Y. K. Gustafsson J. A. Pettersson S. Arulampalam V. 2008. Enterococcus faecalis from newborn babies regulate endogenous PPARγ activity and IDL10 levels in colonic epithelial cells. Proc. Natl. Acad. Sci. USA  105: 1943– 1948. https://doi.org/18234854 Google Scholar CrossRef Search ADS   Arslanoglu S. Moro G. E. Schmitt J. Tandoi L. Rizzardi S. Boehm G. 2008. Early dietary intervention with a mixture of prebiotic oligosaccharides reduces the incidence of allergic manifestations and infections during the first two years of life. J. Nutr.  138: 1091– 1095. https://doi.org/18492839 Google Scholar CrossRef Search ADS PubMed  Bailey M. Haverson K. 2006. The postnatal development of the mucosal immune system and mucosal tolerance in domestic animals. Vet. Res.  37: 443– 453. https://doi.org/16611557 Google Scholar CrossRef Search ADS PubMed  Bartholome A. L. Albin D. M. Baker D. H. Holst J. J. Tappenden K. A. 2004. Supplementation of total parenteral nutrition with butyrate acutely increases structural aspects of intestinal adaptation after an 80% jejunoileal resection in neonatal piglets. J. Parenter. Enteral Nutr.  28: 210– 222. https://doi.org/15291402 Google Scholar CrossRef Search ADS   Basson M. D. Liu Y. W. Hanly A. M. Emenaker N. J. Shenoy S. G. Gould Rothberg B. E. 2000. Identification and comparative analysis of human colonocyte short-chain fatty acid response genes. J. Gastrointest. Surg.  4: 501– 512. https://doi.org/11077326 Google Scholar CrossRef Search ADS PubMed  Bjornvad C. R. Thymann T. Deutz N. E. Burrin D. G. Jensen S. K. Jensen B. B. Molbak L. Boye M. Larsson L. I. Schmidt M. Michaelsen K. F. Sangild P. T. 2008. Enteral feeding induces diet-dependent mucosal dysfunction, bacterial proliferation, and necrotizing enterocolitis in preterm pigs on parenteral nutrition. Am. J. Physiol. Gastrointest. Liver Physiol.  295: G1092– G1103. https://doi.org/18818317 Google Scholar CrossRef Search ADS PubMed  Bombell S. McGuire W. 2009. Early trophic feeding for very low birth weight infants. Cochrane Database Syst. Rev.  8: CD000504. https://doi.org/19588318 Bourassa J. Lainé J. Kruse M. L. Gagnon M. C. Calvo E. Morisset J. 1999. Ontogeny and species differences in the pancreatic expression and localization of the CCK(A) receptors. Biochem. Biophys. Res. Commun.  260: 820– 828. https://doi.org/10403848 Google Scholar CrossRef Search ADS PubMed  Bry L. Falk P. G. Midtvedt T. Gordon J. L. 1996. A model of host-microbial interactions in an open mammalian ecosystem. Science  273: 1380– 1383. https://doi.org/8703071 Google Scholar CrossRef Search ADS PubMed  Buddington R. K. 1994. Nutrition and ontogenetic development of the intestine. Can. J. Physiol. Pharmacol.  72: 251– 259. https://doi.org/8069771 Google Scholar CrossRef Search ADS PubMed  Buddington, R. K. 2009. Using probiotics and prebiotics to manage the gastrointestinal tract ecosystem. Pages 1– 31 in Prebiotics and Probiotics Science and Technology.  D. Charalampopoulos and R. A. Rastall ed. Springer Science Publishing, New York, NY. Google Scholar CrossRef Search ADS   Buddington R. K. Bering S. B. Thymann T. Sangild P. T. 2008. Aldohexose malabsorption in preterm pigs is directly related to the severity of necrotizing enterocolitis. Pediatr. Res.  63: 382– 387. https://doi.org/18356743 Google Scholar CrossRef Search ADS PubMed  Buddington R. K. Weiher E. 1999. The application of ecological principles and fermentable fibers to manage the gastrointestinal tract ecosystem. J. Nutr.  129( Suppl.): 1446S– 1450S. https://doi.org/10395618 Google Scholar PubMed  Buddington R. K. Williams C. H. Kostek B. M. Buddington K. K. Kullen M. J. 2010. Maternal-to-infant transmission of probiotics: Concept validation in mice, rats, and pigs. Neonatology  97: 250– 256. https://doi.org/19887854 Google Scholar CrossRef Search ADS PubMed  Burrin D. Guan X. Stoll B. Petersen Y. M. Sangild P. T. 2003. Glucagon-like peptide 2: A key link between nutrition and intestinal adaptation in neonates? J. Nutr.  133: 3712– 3716. https://doi.org/14608101 Google Scholar CrossRef Search ADS PubMed  Butel M. J. Waligora-Dupriet A. J. Szylit O. 2002. Oligofructose and experimental model of neonatal necrotising enterocolitis. Br. J. Nutr.  87( Suppl. 2): S213– S219. https://doi.org/12088521 Google Scholar CrossRef Search ADS PubMed  Chailler P. Ménard D. 1999. Ontogeny of EGF receptors in the human gut. Front. Biosci.  4: D87– D101. https://doi.org/9889180 Google Scholar CrossRef Search ADS PubMed  Claud E. C. 2009. Neonatal necrotizing enterocolitis—Inflammation and intestinal immaturity. Antiinflamm. Antiallergy Agents Med. Chem.  8: 248– 259. https://doi.org/20498729 Google Scholar CrossRef Search ADS PubMed  Conroy M. E. Shi H. N. Walker W. A. 2009. The long-term health effects of neonatal microbial flora. Curr. Opin. Allergy Clin. Immunol.  9: 197– 201. https://doi.org/19398905 Google Scholar CrossRef Search ADS PubMed  Coppa G. V. Zampini L. Galeazzi T. Gabrielli O. 2006. Prebiotics in human milk: A review. Dig. Liver Dis.  38( Suppl. 2): S291– S294. https://doi.org/17259094 Google Scholar CrossRef Search ADS PubMed  Cotten, C. M., S. Taylor, B. Stoll, R. N. Goldberg, N. I. Hansen, P. J. Sánchez, N. Ambalavanan, D. K. Benjamin Jr. and NICHD Neonatal Research Network 2009. Prolonged duration of initial empirical antibiotic treatment is associated with increased rates of necrotizing enterocolitis and death for extremely low birth weight infants. Pediatrics  123: 58– 66. Google Scholar CrossRef Search ADS PubMed  Dicksved J. Halfvarson J. Rosenquist M. Järnerot G. Tysk C. Apajalahti J. Engstrand L. Jansson J. K. 2008. Molecular analysis of the gut microbiota of identical twins with Crohn's disease. ISME J.  2: 716– 727. https://doi.org/18401439 Google Scholar CrossRef Search ADS PubMed  Dimmitt R. A. Staley E. M. Chuang G. Tanner S. M. Soltau T. D. Lorenz R. G. 2010. Role of postnatal acquisition of the intestinal microbiome in the early development of immune function. J. Pediatr. Gastroenterol. Nutr.  51: 262– 273. https://doi.org/20639773 Google Scholar PubMed  Dogi C. A. Galdeano C. M. Perdigón G. 2008. Gut immune stimulation by non pathogenic Gram(+) and Gram(−) bacteria. Comparison with a probiotic strain. Cytokine  41: 223– 231. https://doi.org/18248820 Google Scholar CrossRef Search ADS PubMed  Drozdowski L. A. Clandinin T. Thomson A. B. 2010. Ontogeny, growth and development of the small intestine: Understanding pediatric gastroenterology. World J. Gastroenterol.  16: 787– 799. https://doi.org/20143457 Google Scholar PubMed  Dunne C. 2001. Adaptation of bacteria to the intestinal niche: Probiotics and gut disorder. Inflamm. Bowel Dis.  7: 136– 145. https://doi.org/11383587 Google Scholar CrossRef Search ADS PubMed  Eckmann, L. 2006. Innate immunity. Pages 1033– 1066 in Physiology of the Gastrointestinal Tract.  4th ed. L. R. Johnson, K. E. Barrett, F. K. Ghishan, J. L. Merchant, H. M. Said, and J. Wood ed. Elsevier, Amsterdam, the Netherlands. Google Scholar CrossRef Search ADS   Eiwegger T. Stahl B. Haidl P. Schmitt J. Boehm G. Dehlink E. Urbanek R. Szépfalusi Z. 2010. Prebiotic oligosaccharides: In vitro evidence for gastrointestinal epithelial transfer and immunomodulatory properties. Pediatr. Allergy Immunol.  21: 1179– 1188. https://doi.org/20444147 Google Scholar CrossRef Search ADS PubMed  Flint H. J. Duncan S. H. Scott K. P. Louis P. 2007. Interactions and competition within the microbial community of the human colon: Links between diet and health. Environ. Microbiol.  9: 1101– 1111. https://doi.org/17472627 Google Scholar CrossRef Search ADS PubMed  Freitas M. Axelsson L. G. Cayuela C. Midtvedt T. Trugnan G. 2002. Microbial-host interactions specifically control the glycosylation pattern in intestinal mouse mucosa. Histochem. Cell Biol.  118: 149– 161. https://doi.org/12189518 Google Scholar PubMed  González R. Klaassens E. S. Malinen E. de Vos W. M. Vaughan E. E. 2008. Differential transcriptional response of Bifidobacterium longum to human milk, formula milk, and galactooligosaccharide. Appl. Environ. Microbiol.  74: 4686– 4694. https://doi.org/18539808 Google Scholar CrossRef Search ADS PubMed  Grahnquist L. Ruuska T. Finkel Y. 2000. Early development of human gastric H,K-adenosine triphosphatase. J. Pediatr. Gastroenterol. Nutr.  30: 533– 537. https://doi.org/10817284 Google Scholar CrossRef Search ADS PubMed  Grönlund M. M. Salminen S. Mykkänen H. Kero P. Lehtonen O. P. 1999. Development of intestinal bacterial enzymes in infants—Relationship to mode of delivery and type of feeding. APMIS  107: 655– 660. https://doi.org/10440061 Google Scholar CrossRef Search ADS PubMed  Hällström M. Eerola E. Vuento R. Janas M. Tammela O. 2004. Effects of mode of delivery and necrotising enterocolitis on the intestinal microflora in preterm infants. Eur. J. Clin. Microbiol. Infect. Dis.  23: 463– 470. https://doi.org/15168141 Google Scholar CrossRef Search ADS PubMed  Hanson L. A. 2007. Feeding and infant development breast-feeding and immune function. Proc. Nutr. Soc.  66: 384– 396. https://doi.org/17637091 Google Scholar CrossRef Search ADS PubMed  Hay W. W. 2008. Strategies for feeding the preterm infant. Neonatology  94: 245– 254. https://doi.org/18836284 Google Scholar CrossRef Search ADS PubMed  Heuvelin E. Lebreton C. Bichara M. Cerf-Bensussan N. Heyman M. 2010. A Bifidobacterium probiotic strain and its soluble factors alleviate chloride secretion by human intestinal epithelial cells. J. Nutr.  140: 7– 11. https://doi.org/19889806 Google Scholar CrossRef Search ADS PubMed  Heuvelin E. Lebreton C. Grangette C. Pot B. Cerf-Bensussan N. Heyman M. 2009. Mechanisms involved in alleviation of intestinal inflammation by Bifidobacterium breve soluble factors. PLoS ONE  4: e5184. https://doi.org/19381276 Google Scholar CrossRef Search ADS PubMed  Hrncir T. Stepankova R. Kozakova H. Hudcovic T. Tlaskalova-Hogenova H. 2008. Gut microbiota and lipopolysaccharide content of the diet influence development of regulatory T cells: Studies in germ-free mice. BMC Immunol.  9: 65. https://doi.org/18990206 Google Scholar CrossRef Search ADS PubMed  Huurre A. Kalliomäki M. Rautava S. Rinne M. Salminen S. Isolauri E. 2008. Mode of delivery—Effects on gut microbiota and humoral immunity. Neonatology  93: 236– 240. https://doi.org/18025796 Google Scholar CrossRef Search ADS PubMed  Jenness R. Sloan R. E. 1970. The composition of milks of various species: A review. Dairy Sci.  32: 599– 612. Jernberg C. Löfmark S. Edlund C. Jansson J. K. 2010. Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology  156: 3216– 3223. https://doi.org/20705661 Google Scholar CrossRef Search ADS PubMed  Kelly D. King T. Aminov R. 2007. Importance of microbial colonization of the gut in early life to the development of immunity. Mutat. Res.  622: 58– 69. https://doi.org/17612575 Google Scholar CrossRef Search ADS PubMed  Kien C. L. McClead R. E. Cordero L.Jr 1998. Effects of lactose intake on lactose digestion and colonic fermentation in preterm infants. J. Pediatr.  133: 401– 405. https://doi.org/9738725 Google Scholar CrossRef Search ADS PubMed  Kim Y. Kim S. H. Whang K. Y. Kim Y. J. Oh S. 2008. Inhibition of Escherichia coli O157:H7 attachment by interactions between lactic acid bacteria and intestinal epithelial cells. J. Microbiol. Biotechnol.  18: 1278– 1285. https://doi.org/18667857 Google Scholar PubMed  Kleessen B. Blaut M. 2005. Modulation of gut mucosal biofilms. Br. J. Nutr.  93( Suppl. 1): S35– S40. https://doi.org/15877893 Google Scholar CrossRef Search ADS PubMed  Koenig J. E. Spor A. Scalfone N. Fricker A. D. Stombaugh J. Knight R. Angenent L. T. Ley R. E. 2010. Microbes and Health Sackler Colloquium: Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. USA  https://doi.org/10.1073/pnas.1000081107. Kosloske A. M. 1994. Epidemiology of necrotizing enterocolitis. Acta Paediatr.  83:( Suppl. s396): 2– 7. https://doi.org/10.1111/j.1651-2227.1994.tb13232.x. https://doi.org/8086675 Google Scholar CrossRef Search ADS   Kukkonen K. Savilahti E. Haahtela T. Juntunen-Backman K. Korpela R. Poussa T. Tuure T. Kuitunen M. 2008. Long-term safety and impact on infection rates of postnatal probiotic and prebiotic (synbiotic) treatment: Randomized, double-blind, placebo-controlled trial. Pediatrics  122: 8– 12. https://doi.org/18595980 Google Scholar CrossRef Search ADS PubMed  Lacroix-Lamandé S. Rochereau N. Mancassola R. Barrier M. Clauzon A. Laurent F. 2009. Neonate intestinal immune response to CpG oligodeoxynucleotide stimulation. PLoS ONE  4: e8291. https://doi.org/20011519 Google Scholar CrossRef Search ADS PubMed  Lallès J. P. Bosi P. Smidt H. Stokes C. R. 2007. Nutritional management of gut health in pigs around weaning. Proc. Nutr. Soc.  66: 260– 268. https://doi.org/17466106 Google Scholar CrossRef Search ADS PubMed  Lebenthal A. Lebenthal E. 1999. The ontogeny of the small intestinal epithelium. J. Parenter. Enteral. Nutr.  23( Suppl.): S3– S6. Google Scholar CrossRef Search ADS   Lesniewska V. Rowland I. Laerke H. N. Grant G. Naughton P. J. 2006. Relationship between dietary-induced changes in intestinal commensal microflora and duodenojejunal myoelectric activity monitored by radiotelemetry in the rat in vivo. Exp. Physiol.  91: 229– 237. https://doi.org/16263800 Google Scholar CrossRef Search ADS PubMed  Ley R. E. Hamady M. Lozupone C. Turnbaugh P. J. Ramey R. R. Bircher J. S. Schlegel M. L. Tucker T. A. Schrenzel M. D. Knight R. Gordon J. I. 2008. Evolution of mammals and their gut microbes. Science  320: 1647– 1651. https://doi.org/18497261 Google Scholar CrossRef Search ADS PubMed  Lin J. Peng L. Itzkowitz S. Holzman I. R. Babyatsky M. W. 2005. Short-chain fatty acid induces intestinal mucosal injury in newborn rats and down-regulates intestinal trefoil factor gene expression in vivo and in vitro. J. Pediatr. Gastroenterol. Nutr.  41: 607– 611. https://doi.org/16254517 Google Scholar CrossRef Search ADS PubMed  Lotz M. Gütle D. Walther S. Ménard S. Bogdan C. Hornef M. W. 2006. Postnatal acquisition of endotoxin tolerance in intestinal epithelial cells. J. Exp. Med.  203: 973– 984. https://doi.org/16606665 Google Scholar CrossRef Search ADS PubMed  Lundin A. Bok C. M. Aronsson L. Björkholm B. Gustafsson J. A. Pott S. Arulampalam V. Rafter J. Pettersson S. 2008. Gut flora, Toll-like receptors and nuclear receptors: A tripartite communication that tunes innate immunity in large intestine. Cell. Microbiol.  10: 1093– 1103. https://doi.org/18088401 Google Scholar CrossRef Search ADS PubMed  Macfarlane S. Macfarlane G. T. 2003. Regulation of short-chain fatty acid production. Proc. Nutr. Soc.  62: 67– 72. https://doi.org/12740060 Google Scholar CrossRef Search ADS PubMed  Mackie R. I. Sghir A. Gaskins H. R. 1999. Developmental microbial ecology of the neonatal gastrointestinal tract. Am. J. Clin. Nutr.  69: 1035S– 1045S. https://doi.org/10232646 Google Scholar PubMed  Magalhaes J. G. Tattoli I. Girardin S. E. 2007. The intestinal epithelial barrier: How to distinguish between the microbial flora and pathogens. Semin. Immunol.  19: 106– 115. https://doi.org/17324587 Google Scholar CrossRef Search ADS PubMed  Mahowald M. A. Rey F. E. Seedorf H. Turnbaugh P. J. Fulton R. S. Wollam A. Shah N. Wang C. Magrini V. Wilson R. K. Cantarel B. L. Coutinho P. M. Henrissat B. Crock L. W. Russell A. Verberkmoes N. C. Hettich R. L. Gordon J. I. 2009. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc. Natl. Acad. Sci. USA  106: 5859– 5864. https://doi.org/19321416 Google Scholar CrossRef Search ADS   Mäkivuokko H. A. Saarinen M. T. Ouwehand A. C. Rautonen N. E. 2006. Effects of lactose on colon microbial community structure and function in a four-stage semi-continuous culture system. Biosci. Biotechnol. Biochem.  70: 2056– 2063. https://doi.org/16960357 Google Scholar CrossRef Search ADS PubMed  Mazmanian S. K. Liu C. H. Tzianabos A. O. Kasper D. L. 2005. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell  122: 107– 118. https://doi.org/16009137 Google Scholar CrossRef Search ADS PubMed  Møller H. K. Thymann T. Fink L. N. Frokiaer H. Kvistgaard A. S. Sangild P. T. 2011. Bovine colostrum is superior to enriched formulas in stimulating intestinal function and necrotising enterocolitis resistance in preterm pigs. Br. J. Nutr.  105: 44– 53. https://doi.org/20723273 Google Scholar CrossRef Search ADS PubMed  Mshvildadze M. Neu J. 2010. The infant intestinal microbiome: Friend or foe? Early Hum. Dev.  86( Suppl. 1): 67– 71. https://doi.org/20116944 Google Scholar CrossRef Search ADS PubMed  Mulder I. E. Schmidt B. Stokes C. R. Lewis M. Bailey M. Aminov R. I. Prosser J. I. Gill B. P. Pluske J. R. Mayer C. D. Musk C. C. Kelly D. 2009. Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces. BMC Biol.  7: 79. https://doi.org/19930542 Google Scholar CrossRef Search ADS PubMed  Murray C. B. Chu S. Zeitlin P. L. 1996. Gestational and tissue-specific regulation of C1C-2 chloride channel expression. Am. J. Physiol.  271: L829– L837. https://doi.org/8944727 Google Scholar PubMed  Myllynen P. Immonen E. Kummu M. Vähäkangas K. 2009. Developmental expression of drug metabolizing enzymes and transporter proteins in human placenta and fetal tissues. Expert Opin. Drug Metab. Toxicol.  5: 1483– 1499. https://doi.org/19785513 Google Scholar CrossRef Search ADS PubMed  Nanthakumar N. N. Dai D. Meng D. Chaudry N. Newburg D. S. Walker W. A. 2005. Regulation of intestinal ontogeny: Effect of glucocorticoids and luminal microbes on galactosyltransferase and trehalase induction in mice. Glycobiology  15: 221– 232. https://doi.org/15483270 Google Scholar CrossRef Search ADS PubMed  Nelson K. E. Zinder S. H. Hance I. Burr P. Odongo D. Wasawo D. Odenyo A. Bishop R. 2003. Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tract: Insights into an unexplored niche. Environ. Microbiol.  5: 1212– 1220. https://doi.org/14641599 Google Scholar CrossRef Search ADS PubMed  Newburg D. S. 2009. Neonatal protection by an innate immune system of human milk consisting of oligosaccharides and glycans. J. Anim. Sci.  87( Suppl.): 26– 34. https://doi.org/19028867 Google Scholar CrossRef Search ADS PubMed  Newburg D. S. Walker W. A. 2007. Protection of the neonate by the innate immune system of developing gut and of human milk. Pediatr. Res.  61: 2– 8. https://doi.org/17211132 Google Scholar CrossRef Search ADS PubMed  Nutten S. Schumann A. Donnicola D. Mercenier A. Rami S. Garcia-Rodenas C. L. 2007. Antibiotic administration early in life impairs specific humoral responses to an oral antigen and increases intestinal mast cell numbers and mediator concentrations. Clin. Vaccine Immunol.  14: 190– 197. https://doi.org/17151185 Google Scholar CrossRef Search ADS PubMed  O'Keefe S. J. 2008. Nutrition and colonic health: The critical role of the microbiota. Curr. Opin. Gastroenterol.  24: 51– 58. https://doi.org/18043233 Google Scholar CrossRef Search ADS PubMed  Ogra P. L. 2010. Ageing and its possible impact on mucosal immune responses. Ageing Res. Rev.  9: 101– 106. https://doi.org/19664726 Google Scholar CrossRef Search ADS PubMed  Okada K. Fujii T. Ohtsuka Y. Yamakawa Y. Izumi H. Yamashiro Y. Shimizu T. 2010. Overfeeding can cause NEC-like enterocolitis in premature rat pups. Neonatology  97: 218– 224. https://doi.org/19887849 Google Scholar CrossRef Search ADS PubMed  Oste M. Van Haver E. Thymann T. Sangild P. T. Weyns A. Van Ginneken C. J. 2010. Formula induces intestinal apoptosis in preterm pigs within a few hours of feeding. J. Parenter. Enteral. Nutr.  34: 271– 279. Google Scholar CrossRef Search ADS   Palazzo M. Balsari A. Rossini A. Selleri S. Calcaterra C. Gariboldi S. Zanobbio L. Arnaboldi F. Shirai Y. F. Serrao G. Rumio C. 2007. Activation of enteroendocrine cells via TLRs induces hormone, chemokine, and defensin secretion. J. Immunol.  178: 4296– 4303. https://doi.org/17371986 Google Scholar CrossRef Search ADS PubMed  Penders J. Stobberingh E. E. van den Brandt P. A. Thijs C. 2007. The role of the intestinal microbiota in the development of atopic disorders. Allergy  62: 1223– 1236. https://doi.org/17711557 Google Scholar CrossRef Search ADS PubMed  Penders J. Thijs C. Vink C. Stelma F. F. Snijders B. Kummeling I. van den Brandt P. A. Stobberingh E. E. 2006. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics  118: 511– 521. https://doi.org/16882802 Google Scholar CrossRef Search ADS PubMed  Poroyko V. White J. R. Wang M. Donovan S. Alverdy J. Liu D. C. Morowitz M. J. 2010. Gut microbial gene expression in mother-fed and formula-fed piglets. PLoS ONE  5: e12459. https://doi.org/20805981 Google Scholar CrossRef Search ADS PubMed  Pritchard J. A. 1966. Fetal swallowing and amniotic fluid volume. Obstet. Gynecol.  28: 606– 610. https://doi.org/5332288 Google Scholar PubMed  Rechkemmer G. Rönnau K. von Engelhardt W. 1988. Fermentation of polysaccharides and absorption of short chain fatty acids in the mammalian hindgut. Comp. Biochem. Physiol. A  90: 563– 568. https://doi.org/2902962 Google Scholar CrossRef Search ADS   Richardson W. M. Sodhi C. P. Russo A. Siggers R. H. Afrazi A. Gribar S. C. Neal M. D. Dai S. Prindle T. Branca M. Ma C. Ozolek J. Hackam D. J. 2010. Nucleotide-binding oligomerization domain-2 inhibits toll-like receptor-4 signaling in the intestinal epithelium. Gastroenterology  139: 904– 917. https://doi.org/20580721 Google Scholar CrossRef Search ADS PubMed  Rodriguez N. A. Meier P. P. Groer M. W. Zeller J. M. Engstrom J. L. Fogg L. 2010. A pilot study to determine the safety and feasibility of oropharyngeal administration of own mother's colostrum to extremely low-birth-weight infants. Adv. Neonatal Care  10: 206– 212. https://doi.org/20697221 Google Scholar CrossRef Search ADS PubMed  Rumbo M. Schiffrin E. J. 2005. Ontogeny of intestinal epithelium immune functions: Developmental and environmental regulation. Cell. Mol. Life Sci.  62: 1288– 1296. https://doi.org/15971104 Google Scholar CrossRef Search ADS PubMed  Salminen S. Gibson G. R. McCartney A. L. Isolauri E. 2004. Influence of mode of delivery on gut microbiota composition in seven year old children. Gut  53: 1388– 1389. https://doi.org/15306608 Google Scholar CrossRef Search ADS PubMed  Salzman N. H. Hung K. Haribhai D. Chu H. Karlsson-Sjöberg J. Amir E. Teggatz P. Barman M. Hayward M. Eastwood D. Stoel M. Zhou Y. Sodergren E. Weinstock G. M. Bevins C. L. Williams C. B. Bos N. A. 2010. Enteric defensins are essential regulators of intestinal microbial ecology. Nat. Immunol.  11: 76– 83. https://doi.org/19855381 Google Scholar CrossRef Search ADS PubMed  Sanderson I. R. 1999. The physicochemical environment of the neonatal intestine. Am. J. Clin. Nutr.  69: 1028S– 1034S. https://doi.org/10232645 Google Scholar PubMed  Sanderson I. R. 2004. Short chain fatty acid regulation of signaling genes expressed by the intestinal epithelium. J. Nutr.  134: 2450S– 2454S. https://doi.org/15333741 Google Scholar CrossRef Search ADS PubMed  Sangild P. T. Siggers R. H. Schmidt M. Elnif J. Bjornvad C. R. Thymann T. Grondahl M. L. Hansen A. K. Jensen S. K. Boye M. Moelbak L. Buddington R. K. Westrom B. R. Holst J. J. Burrin D. G. 2006. Diet- and colonization-dependent intestinal dysfunction predisposes to necrotizing enterocolitis in preterm pigs. Gastroenterology  130: 1776– 1792. https://doi.org/16697741 Google Scholar CrossRef Search ADS PubMed  Schell M. A. Karmirantzou M. Snel B. Vilanova D. Berger B. Pessi G. Zwahlen M. C. Desiere F. Bork P. Delley M. Pridmore R. D. Arigoni F. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. USA  99: 14422– 14427. https://doi.org/12381787 Google Scholar CrossRef Search ADS   Schrenzel M. D. Witte C. L. Bahl J. Tucker T. A. Fabian N. Greger H. Hollis C. Hsia G. Siltamaki E. Rideout B. A. 2010. Genetic characterization and epidemiology of helicobacters in non-domestic animals. Helicobacter  15: 126– 142. https://doi.org/20402815 Google Scholar CrossRef Search ADS PubMed  Schumann A. Nutten S. Donnicola D. Comelli E. M. Mansourian R. Cherbut C. Corthesy-Theulaz I. Garcia-Rodenas C. 2005. Neonatal antibiotic treatment alters gastrointestinal tract developmental gene expression and intestinal barrier transcriptome. Physiol. Genomics  23: 235– 245. https://doi.org/16131529 Google Scholar CrossRef Search ADS PubMed  Selleri S. Palazzo M. Deola S. Wang E. Balsari A. Marincola F. M. Rumio C. 2008. Induction of pro-inflammatory programs in enteroendocrine cells by the Toll-like receptor agonists flagellin and bacterial LPS. Int. Immunol.  20: 961– 970. https://doi.org/18544573 Google Scholar CrossRef Search ADS PubMed  Sharma R. Young C. Neu J. 2010. Molecular modulation of intestinal epithelial barrier: Contribution of microbiota. J. Biomed. Biotechnol.  2010: 305879. https://doi.org/20150966 Google Scholar PubMed  Sherman P. M. Cabana M. Gibson G. R. Koletzko B. V. Neu J. Veereman-Wauters G. Ziegler E. E. Walker W. A. 2009. Potential roles and clinical utility of prebiotics in newborns, infants, and children: Proceedings from a global prebiotic summit meeting. J. Pediatr.  155: S61– S70. https://doi.org/19840609 Google Scholar CrossRef Search ADS PubMed  Shibolet O. Podolsky D. K. 2007. TLRs in the gut. IV. Negative regulation of Toll-like receptors and intestinal homeostasis: Addition by subtraction. Am. J. Physiol. Gastrointest. Liver Physiol.  292: G1469– G1473. https://doi.org/17554134 Google Scholar CrossRef Search ADS PubMed  Shreiner A. Huffnagle G. B. Noverr M. C. 2008. The “Microflora Hypothesis” of allergic disease. Adv. Exp. Med. Biol.  635: 113– 134. https://doi.org/18841708 Google Scholar CrossRef Search ADS PubMed  Siggers R. H. Siggers J. Thymann T. Boye M. Sangild P. T. 2010. Nutritional modulation of the gut microbiota and immune system in preterm neonates susceptible to necrotizing enterocolitis. J. Nutr. Biochem.  https://doi.org/10.1016/j.jnutbio.2010.08.002. https://doi.org/21193301 Singhal A. Macfarlane G. Macfarlane S. Lanigan J. Kennedy K. Elias-Jones A. Stephenson T. Dudek P. Lucas A. 2008. Dietary nucleotides and fecal microbiota in formula-fed infants: A randomized controlled trial. Am. J. Clin. Nutr.  87: 1785– 1792. https://doi.org/18541569 Google Scholar PubMed  Slack E. Hapfelmeier S. Stecher B. Velykoredko Y. Stoel M. Lawson M. A. Geuking M. B. Beutler B. Tedder T. F. Hardt W. D. Bercik P. Verdu E. F. McCoy K. D. Macpherson A. J. 2009. Innate and adaptive immunity cooperate flexibly to maintain host-microbiota mutualism. Science  325: 617– 620. https://doi.org/19644121 Google Scholar CrossRef Search ADS PubMed  Sodhi C. Richardson W. Gribar S. Hackam D. J. 2008. The development of animal models for the study of necrotizing enterocolitis. Dis. Model. Mech.  1: 94– 98. https://doi.org/19048070 Google Scholar CrossRef Search ADS PubMed  Sperandio V. Torres A. G. Jarvis B. Nataro J. P. Kaper J. B. 2003. Bacteria-host communication: The language of hormones. Proc. Natl. Acad. Sci. USA  100: 8951– 8956. https://doi.org/12847292 Google Scholar CrossRef Search ADS   Stevens, C. E., and I. D. Hume 1995. Comparative Physiology of the Vertebrate Digestive System.  2nd ed. Cambridge Univ. Press, New York, NY. Stewart J. A. Chadwick V. S. Murray A. 2005. Investigations into the influence of host genetics on the predominant eubacteria in the faecal microflora of children. J. Med. Microbiol.  54: 1239– 1242. https://doi.org/16278440 Google Scholar CrossRef Search ADS PubMed  Sullivan A. Nord C. E. 2005. Probiotics and gastrointestinal diseases. J. Intern. Med.  257: 78– 92. https://doi.org/15606379 Google Scholar CrossRef Search ADS PubMed  Suzuki Y. A. Lopez V. Lönnerdal B. 2005. Mammalian lactoferrin receptors: Structure and function. Cell. Mol. Life Sci.  62: 2560– 2575. https://doi.org/16261254 Google Scholar CrossRef Search ADS PubMed  Tanaka S. Kobayashi T. Songjinda P. Tateyama A. Tsubouchi M. Kiyohara C. Shirakawa T. Sonomoto K. Nakayama J. 2009. Influence of antibiotic exposure in the early postnatal period on the development of intestinal microbiota. FEMS Immunol. Med. Microbiol.  56: 80– 87. https://doi.org/19385995 Google Scholar CrossRef Search ADS PubMed  Tannock G. W. Fuller R. Pedersen K. 1990. Lactobacillus succession in the piglet digestive tract demonstrated by plasmid profiling. Appl. Environ. Microbiol.  56: 1310– 1316. https://doi.org/2339885 Google Scholar PubMed  Thymann T. Møller H. K. Stoll B. Støy A. C. Buddington R. K. Bering S. B. Jensen B. B. Olutoye O. O. Siggers R. H. Mølbak L. Sangild P. T. Burrin D. G. 2009. Carbohydrate maldigestion induces necrotizing enterocolitis in preterm pigs. Am. J. Physiol. Gastrointest. Liver Physiol.  297: G1115– G1125. https://doi.org/19808655 Google Scholar CrossRef Search ADS PubMed  Van de Perre P. 2003. Transfer of antibody via mother's milk. Vaccine  21: 3374– 3376. https://doi.org/12850343 Google Scholar CrossRef Search ADS PubMed  Van Haver E. R. Sangild P. T. Oste M. Siggers J. L. Weyns A. L. Van Ginneken C. J. 2009. Diet-dependent mucosal colonization and interleukin-1β responses in preterm pigs susceptible to necrotizing enterocolitis. J. Pediatr. Gastroenterol. Nutr.  49: 90– 98. https://doi.org/19516189 Google Scholar CrossRef Search ADS PubMed  Vanhoutvin S. A. Troost F. J. Hamer H. M. Lindsey P. J. Koek G. H. Jonkers D. M. Kodde A. Venema K. Brummer R. J. 2009. Butyrate-induced transcriptional changes in human colonic mucosa. PLoS ONE  4: e6759. https://doi.org/19707587 Google Scholar CrossRef Search ADS PubMed  Veereman G. 2007. Pediatric applications of inulin and oligofructose. J. Nutr.  137( Suppl.): 2585S– 2589S. https://doi.org/17951508 Google Scholar CrossRef Search ADS PubMed  Venkatesh M. P. Abrams S. A. 2010. Oral lactoferrin for the prevention of sepsis and necrotizing enterocolitis in preterm infants. Cochrane Database Syst. Rev.  12: CD007137. https://doi.org/20464748 Voltaire 1929. Candide.  Random House Inc., New York, NY. Waligora-Dupriet A. J. Dugay A. Auzeil N. Nicolis I. Rabot S. Huerre M. R. Butel M. J. 2009. Short-chain fatty acids and polyamines in the pathogenesis of necrotizing enterocolitis: Kinetics aspects in gnotobiotic quails. Anaerobe  15: 138– 144. https://doi.org/19233303 Google Scholar CrossRef Search ADS PubMed  Watanabe S. Matsushita K. Stokes J. B. McCray P. B.Jr 1998. Developmental regulation of epithelial sodium channel subunit mRNA expression in rat colon and lung. Am. J. Physiol.  275: G1227– G1235. https://doi.org/9843757 Google Scholar PubMed  Williams A. M. Probert C. S. Stepankova R. Tlaskalova-Hogenova H. Phillips A. Bland P. W. 2006. Effects of microflora on the neonatal development of gut mucosal T cells and myeloid cells in the mouse. Immunology  119: 470– 478. https://doi.org/16995882 Google Scholar CrossRef Search ADS PubMed  Winkler P. Ghadimi D. Schrezenmeir J. Kraehenbuhl J. P. 2007. Molecular and cellular basis of microflora-host interactions. J. Nutr.  137( Suppl. 2): 756S– 772S. https://doi.org/17311973 Google Scholar CrossRef Search ADS PubMed  Wolfs T. G. Derikx J. P. Hodin C. M. Vanderlocht J. Driessen A. de Bruïne A. P. Bevins C. L. Lasitschka F. Gassler N. van Gemert W. G. Buurman W. A. 2010. Localization of the lipopolysaccharide recognition complex in the human healthy and inflamed premature and adult gut. Inflamm. Bowel Dis.  16: 68– 75. https://doi.org/20014022 Google Scholar CrossRef Search ADS PubMed  Wong J. M. de Souza R. Kendall C. W. Emam A. Jenkins D. J. 2006. Colonic health: Fermentation and short chain fatty acids. J. Clin. Gastroenterol.  40: 235– 243. https://doi.org/16633129 Google Scholar CrossRef Search ADS PubMed  Yu V. Y. 2002. Scientific rationale and benefits of nucleotide supplementation of infant formula. J. Paediatr. Child Health  38: 543– 549. https://doi.org/12410863 Google Scholar CrossRef Search ADS PubMed  Zeuthen L. H. Fink L. N. Metzdorff S. B. Kristensen M. B. Licht T. R. Nellemann C. Frøkiaer H. 2010. Lactobacillus acidophilus induces a slow but more sustained chemokine and cytokine response in naïve foetal enterocytes compared to commensal Escherichia coli. BMC Immunol.  11: 2. https://doi.org/20085657 Google Scholar CrossRef Search ADS PubMed  Zocco M. A. Ainora M. E. Gasbarrini G. Gasbarrini A. 2007. Bacteroides thetaiotaomicron in the gut: Molecular aspects of their interaction. Dig. Liver Dis.  39: 707– 712. https://doi.org/17602905 Google Scholar CrossRef Search ADS PubMed  Zoumpopoulou G. Tsakalidou E. Dewulf J. Pot B. Grangette C. 2009. Differential crosstalk between epithelial cells, dendritic cells and bacteria in a co-culture model. Int. J. Food Microbiol.  131: 40– 51. https://doi.org/19264370 Google Scholar CrossRef Search ADS PubMed  Footnotes 1 Based on a presentation at the Companion Animals Symposium titled “Microbes and Health,” at the Joint Annual Meeting, July 11 to 15, 2010, Denver, Colorado. The symposium was sponsored, in part, by Hill's Pet Nutrition Inc. (Topeka, KS) and The Procter & Gamble Company (Cincinnati, OH), with publication sponsored by the Journal of Animal Science and the American Society of Animal Science. American Society of Animal Science http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Animal Science Oxford University Press

COMPANION ANIMALS SYMPOSIUM: Development of the mammalian gastrointestinal tract, the resident microbiota, and the role of diet in early life

Loading next page...
 
/lp/oxford-university-press/companion-animals-symposium-development-of-the-mammalian-3KKTEe2AwX

References (136)

ISSN
0021-8812
eISSN
1525-3163
DOI
10.2527/jas.2010-3705
pmid
21239667
Publisher site
See Article on Publisher Site

Abstract

ABSTRACT Mammalian gastrointestinal (GI) development is guided by genetic determinants established during the evolution of mammals and matched to the natural diet and environment. Coevolution of the host GI tract (GIT) and the resident bacteria has resulted in commensal relationships that are species and even individual specific. The interactions between the host and the GI bacteria are 2-way and of particular importance during the neonatal period, when the GIT needs to adapt rapidly to the external environment, begin processing of oral foods, and acquire the ability to differentiate between and react appropriately to colonizing commensal and potentially pathogenic bacteria. During this crucial period of life, the patterns of gene expression that determine GI structural and functional development are modulated by the bacteria colonizing the previously sterile GIT of fetuses. The types and amounts of dietary inputs after birth influence GI development, species composition, and metabolic characteristics of the resident bacteria, and the interactions that occur between the bacteria and the host. This review provides overviews of the age-related changes in GIT functions, the resident bacteria, and diet, and describes how interactions among these 3 factors influence the health and nutrition of neonates and can have lifelong consequences. Necrotizing enterocolitis is a common GI inflammatory disorder in preterm infants and is provided as an example of interactions that go awry. Other enteric diseases are common in all newborn mammals, and an understanding of the above interactions will enhance efforts to support neonatal health for infants and for farm and companion animals. INTRODUCTION “We must cultivate our garden,” says Candide (from Candide; Voltaire, 1759). When Candide left sheltered castle life and entered into the external world, he faced challenges and hardships, and his survival was dependent on discriminating between good and evil. Similarly, when the fetus emerges from the shelter of the womb, the immature gastrointestinal tract (GIT) must adapt rapidly to oral feeding, the challenges of extrauterine life, and cultivating the garden of colonizing bacteria. Complex interactions have evolved between the mammalian host and the gastrointestinal (GI) microbiota (Ley et al., 2008). Apparently, the extreme costs that would be imposed on the host by trying to maintain a sterile GIT are outweighed by the benefits of instead establishing commensal relationships with bacteria that provide health and nutritional benefits and that pose little or no risk to the host. Hence, the GIT has come to accept the presence of numerous species of bacteria at densities such that shortly after birth, GI bacterial cells outnumber those of the host by about 10-fold. Much like the challenges faced by Candide, after birth the GIT must establish and maintain a delicate balance between the recognition and exclusion of pathogens and the tolerance of commensal bacteria. The GI disorder necrotizing enterocolitis (NEC) is exemplary of the consequences when the balance is disrupted between exclusion and tolerance and when members of the commensal bacteria trigger excessive inflammatory responses, thereby compromising the health of the neonate (Claud, 2009). The interactions among the GIT, the resident microbiota, and diet begin at birth, when the sterile epithelium of the GIT first encounters the colonizing bacteria and begins processing the first meals. During this critical period of life, genetic determinants of immune responses play a central role in the recognition and responses of the developing GIT to the colonizing bacteria. Although dietary inputs influence postnatal development of the GIT, less understood are how dietary inputs have the potential to influence the interactions between the GI epithelium and the colonizing bacteria. The contrasting responses of the neonatal GIT and the resident bacteria among infants fed breast milk and those fed formula (Hanson, 2007; Penders et al., 2007) highlight how interactions among the genetic determinants of GI characteristics, the resident bacteria, and dietary inputs must be considered together to understand postnatal GI development in health and disease. The objective of our review is to acquaint readers with the responses of the neonatal mammalian GIT to the bacteria that colonize and become established, and how diet is an important factor in those interactions. We first provide readers with a general understanding of mammalian GI development, the postnatal changes in the resident bacteria, and shifts in dietary inputs. Although the changes described are shared among different mammalian species, there are differences in the timing and specifics of the developmental events. Next, we describe the interactions that exist among genetic determinants of GI structure and function, the resident bacteria, and diet. A subsequent section uses NEC, often observed in preterm infants, as an example to describe the consequences when the interactions among GI development, the resident bacteria, and diet go awry. We conclude by discussing some dietary strategies to improve mammalian health by optimizing the interactions between the developing GIT and the resident microbiota. DEVELOPMENT OF THE GIT The GIT represents a critical and expansive interface between the external environment and the host. Organogenesis and maturation of the GIT during prenatal life prepare the fetus for the transition at birth from the sterile intrauterine environment and reliance on placental nutrition to the immediate and dramatic changes in the functional demands placed on the GIT by exposure to the contaminated environment, by digesting food, and by other challenges of extrauterine life. The importance of the GIT being functional at the time of birth is evident by the complications of preterm birth and the consequences of immature GI functions. A notable example is the increased risk of NEC among preterm infants, as discussed subsequently. During prenatal development, the GIT acquires the capacities to 1) digest food; 2) defend against pathogens; 3) contribute to osmoregulation; 4) secrete hormones and other signaling molecules that regulate the GIT and other host systems, and 5) detoxify and eliminate toxins produced by metabolism and acquired from the external environment. Some of the GIT capabilities that develop prenatally are vital for the fetus to process the large volumes of amniotic fluid swallowed (up to 750 mL/d by human fetuses; Pritchard 1966). At term, the GIT is able to process milk, respond to bacterial colonization, and tolerate extrauterine environmental conditions. However, the specific structural and functional characteristics of the GIT at birth vary among species. This is exemplified by comparisons of the GIT among newborns of altricial and precocial species with different adult feeding habits and from different environments (Stevens and Hume, 1995). The changes in the GIT associated with weaning can be accelerated by advancing the transition from milk to the adult diet and can be delayed, but not prevented, by extending suckling. This highlights how the patterns and trajectories of GI development are established by genetic determinants (i.e., are “hard wired”), yet the programmed series of events are responsive to dietary inputs (Drozdowski et al., 2010) and environmental conditions (Bailey and Haverson, 2006) and are capable of some flexibility, to allow the developing GIT to adapt to existing conditions (Lebenthal and Lebenthal, 1999). Evidence also exists for “critical period programming” of GI characteristics, whereby dietary inputs early in life can induce epigenetic changes that persist past the period of exposure and can last for the lifetime of an individual (Drozdowski et al., 2010). This includes early programming of the GI immune system by the colonizing bacteria and environmental antigens (Mulder et al., 2009). Digestion At term, the GIT is adapted for and ready to process the first food, which, for most mammals, is colostrum (Drozdowski et al., 2010). The immature digestive functions of preterm infants are considered to contribute to the increased risk of NEC (reviewed by Claud, 2009) and are why total parenteral nutrition (TPN) is used to meet nutrient and energy needs until the GIT develops adequate capacities to process food. Suckling mammals have a minimal capacity to modulate digestive processes adaptively in response to changes in diet composition (Buddington, 1994) and do not acquire the ability to process the adult diet until just before weaning (Drozdowski et al., 2010). When neonates are not fed breast milk, diarrhea can result when the alternate diet includes ingredients such as sucrose, for which there is inadequate expression of sucrase. Defense The GI immune system provides a comprehensive, multilayered defense (Winkler et al., 2007). Much like a gardener, the GI immune system is able to differentiate among the numerous types of GI bacteria that represent a threat and that should be tolerated, and this contributes to the selection of an assemblage of commensal bacteria (Ogra, 2010). This is the culmination of coevolution between the resident bacteria and the innate and adaptive components of the GI immune system, and is dependent on a diversity of extracellular Toll-like receptors (TLR) and intracellular nucleotide-binding oligomerization domain receptors (Shibolet and Podolsky, 2007; Richardson et al., 2010). Aberrant and excessive reactions of the GI immune system to commensal bacteria and other antigens in the GIT causes inflammation and has been associated with several pathologies, including NEC in preterm infants and inflammatory bowel disease, celiac disease, and various food allergies in children and adults. Conversely, inadequate recognition of or responses to pathogens pose obvious health risks. The GI immune functions develop prenatally, and at term, they are capable of recognizing and responding to pathogens, including bacterial DNA motifs and vaccines (Lacroix-Lamandé et al., 2009). Additional development and maturation occur after birth, and the several phases described for the porcine GI immune system (Bailey and Haverson, 2006) are relevant to most mammals. The innate GI defenses include secretions of acid, antimicrobial peptides, lysozyme, and mucus; as well as the tight junctions that link epithelial cells and provide a physical barrier; activated defense cells (e.g., macrophages, neutrophils); and intestinal motility (Eckmann, 2006). These are supplemented at birth by the transient ability of the enterocytes of neonates to absorb antibodies intact and transfer the antibodies present in colostrum to the systemic circuit of newborns (transcytosis), conferring passive immunity. This is dependent on the expression of a receptor (Fc) on the apical membrane that binds the IgG in breast milk (Van de Perre, 2003). The adaptive component of the GI defenses includes the organized lymphoid tissues (e.g., Peyer's patches, mesenteric lymph nodes) that are associated with the GIT, the B and T classes of lymphocytes, and the antigen-presenting dendritic cells (Rumbo and Schiffrin, 2005). A key difference between the adaptive components of the GI and systemic immune systems, despite sharing similar cell types, is the development of oral tolerance, whereby the GI immune system learns to discriminate between bacteria and antigens that pose little or no risk and those that are dangerous (Magalhaes et al. 2007). The learning process has occurred during the coevolution of hosts with their GI bacteria, resulting in receptors and associated signaling pathways and innate defense mechanisms that can discriminate between “the good, the bad, and the ugly.” At birth, the cellular and tissue elements of the adaptive component are less abundant and immature compared with those in the adult, with maturation and learning occurring after birth (Rumbo and Schiffrin, 2005; Mshvildadze and Neu, 2010). The even more immature status of the GI defenses of preterm infants with increased and less regulated nuclear factor-κB signaling contributes to the hyperresponsiveness of the GIT, the increased risk of GI inflammatory disorders such as NEC, and the increased incidence of sepsis (Claud 2009). Osmoregulation The osmoregulatory challenges facing the GI tract differ markedly between fetuses dependent on placental exchange of water and electrolytes and neonates dependent on processing of milk to obtain electrolytes and water. Chloride channels exist in the fetal GI epithelium (Murray et al., 1996), but colonic expression of the sodium channel (also known as ENaC) and absorption of sodium are underdeveloped or are suppressed in fetuses (Watanabe et al., 1998). This may contribute to the osmoregulatory problems, including sodium imbalances, and the special nutritional needs of premature infants. Postnatally, the osmoregulatory functions of the GIT respond to inflammatory cytokines by a combination of decreased ion absorption and increased chloride secretion. The resulting diarrhea and the loss of electrolytes and water are the major cause of morbidity and mortality among newborn animals and infants. Endocrine Secretion Collectively, the regions of the GI tract and the associated organs (e.g., pancreas) represent the largest endocrine system in the vertebrate body. Furthermore, a linkage exists between the GI endocrine and immune functions, leading to the concept of the GI immunoendocrine axis. Specifically, enteroendocrine cells express TLR and respond to luminal antigens by the production of cytokines and defensins (Palazzo et al., 2007; Selleri et al., 2008), and they respond to cytokines and other regulatory molecules originating from GI immune cells. Hence, GI immune responses to colonizing bacteria can alter endocrine secretions by the neonatal GI tract, thereby having GI and systemic implications. The vast diversity of secreted peptides is critical for regulating GI (e.g., gastrin, secretin, cholecystokinin) and systemic functions (e.g., insulin, glucagon, ghrelin). Despite reports of prenatal development of GI endocrine cells (Alumets et al., 1983) and expression of receptors for epidermal growth factor (Chailler and Ménard, 1999), glucagon-like peptide 2 (Burrin et al., 2003), and cholecystokinin (Bourassa et al., 1999), there is only a fragmentary understanding of ontogenetic development of the GI endocrine functions. Detoxification The GIT plays a role in the detoxification and elimination of ingested toxins, including drugs and metabolic wastes from the host and the resident bacteria (Buddington, 2009). This is accomplished by a combination of enzymes that convert and detoxify noxious molecules and export transporters that eliminate the resulting xenobiotic compounds. Although xenobiotic-converting enzymes are expressed in the liver during late gestation, ontogenetic patterns of development for the numerous enzymes and transporters responsible for the detoxification functions of the GIT are not well characterized (Myllynen et al., 2009). THE ASSEMBLAGES OF BACTERIA IN THE GIT The adult GIT is estimated to harbor 400 to 500 species of bacteria, with some estimates of >800 species and >7,000 strains (O'Keefe, 2008). The majority of the GI bacteria have yet to be cultured, and although molecular-based approaches of detection have increased our understanding of the bacterial diversity, these methods have provided few insights into the functional characteristics of the bacteria and their influences on host health (Flint et al., 2007). The GI microbiota also include fungi, protozoa, yeasts, viruses, and bacteriophages (Mackie et al., 1999) that influence host health and nutrition. Of critical interest are the interactions that develop between the microbiome and the GIT of infants (Mshvildadze and Neu, 2010). Regional Distribution The GIT can be considered a small ecosystem (Buddington and Weiher, 1999), with multiple habitats (regions). Within each region, there are dynamic interactions among the resident bacteria, dietary inputs, and the structure and functions of the region that determine the physical, chemical, and biotic characteristics (Kelly et al., 2007). The interactions are even more pronounced during the postnatal period, when the combination of dietary inputs, developing GI functions, and interbacterial interactions play central roles in determining the densities, diversities, and distributions of species that become established within the different regions of the GIT ecosystem. The acidic stomach of adult nonruminant mammals harbors a decreased density (<104 cfu/g) and diversity of bacterial species compared with the small intestine and colon, despite the increased input of nutrients. Bacterial densities and diversity are similarly small in the acid-secreting portion of the ruminant stomach (abomasum), despite the complex and numerically abundant assemblages of bacteria present in the preceding rumen (Nelson et al. 2003). The densities and diversity of bacteria increase distally along the small intestine, with the greatest densities (1011 to 1012 cfu/g) and diversities being in the colon. The declining gradient for oxygen from the proximal small intestine to the colon is paralleled by a reciprocal decline in the aerotolerant bacteria and an increase in the anaerobic species of bacteria. Additional environmental factors that contribute to the proximal-to-distal gradients along the small intestine and colon for the densities and diversities of species include more rapid movement of the digesta proximally and the introduction into the duodenum of bile acids from the gall bladder and antibacterial peptides secreted by the pancreas and the intestine itself (e.g., defensins from Paneth cells). Even within the colon, there is a proximal-to-distal distribution of species and metabolic activities. The proportions of saccharolytic bacteria and short-chain fatty acid (SCFA) production are greater in the proximal colon, whereas proteolytic bacteria and the production of putrefactive metabolites are more prevalent in the distal colon (Macfarlane and Macfarlane, 2003). This distribution corresponds with the greater distal production of ammonia, phenols, indoles, amines, and other toxic and carcinogenic metabolites, which, in adults, contributes to a greater incidence of colorectal cancer in the distal colon. Vertical gradients that extend from the epithelium into the lumen also exist for the distribution of species in the GIT (Kleessen and Blaut, 2005). The populations of bacteria adherent to or immediately adjacent to the epithelium have a profound impact on the GIT and the host, yet they are less understood. Colonization of the Neonatal GIT The sterile GIT of fetuses is rapidly colonized, and within 12 h after delivery, bacteria can be detected throughout the entire GIT and at densities (i.e., cfu/g) that are comparable with those of adults (Mackie et al., 1999). The similar fecal densities of bacteria enumerated in the colons of infants and adults may reflect a maximum density of bacteria that can be supported by the GIT (i.e., “carrying capacity”). Colonization is a stochastic process and results in individual variation in GI bacterial assemblages. This is true even among littermates (Tannock et al., 1990), monozygotic twins (Stewart et al., 2005), and even identical twins (Dicksved et al., 2008). Infants delivered vaginally are colonized by bacteria originating from the maternal GIT, vagina, skin, and surrounding environment (Mackie et al. 1999; Huurre et al., 2008). Infants delivered by caesarian section are not immediately exposed to maternal fecal and vaginal bacteria. Instead, the initial colonizers are nosocomial, originating from medical staff and the hospital environments. Additional bacteria are eventually acquired from the mother (skin, mammary glands) and from outside the hospital environment. Corresponding with the different sources and timing of colonization, the assemblages of GI bacteria differ between infants born vaginally and by caesarian section. The influence of delivery mode on the assemblages is still apparent up to 7 yr after birth (Salminen et al., 2004). Other nondiet factors considered to influence the GI assemblages that colonize and become established are gestational age at delivery, diet, antibiotic use, and the external environment (Penders et al., 2006). Infants with assemblages considered to be beneficial, with fewer pathogens, are typically delivered vaginally outside of hospitals and are exclusively fed breast milk. Which bacteria persist in the GIT is less random, providing supporting evidence for species-specific host-bacteria relations. Notable are the different species of Helicobacter that have been isolated from different vertebrates (Schrenzel et al., 2010). Hence, not all species of bacteria entering the GIT, including probiotic species, are able to persist. Ecological Principles and the GI Bacteria After the initial period of colonization, interbacterial interactions contribute to the changes in species composition and metabolic activities of the resident bacteria (Mackie et al., 1999; Flint et al., 2007). This includes the competitive exclusion of pathogens, probiotics, and other bacteria by commensal bacteria. The mechanisms of exclusion include competition for nutrients and binding sites and the production of metabolites that are toxic to other groups. The process of facilitation, which can be described as cooperative relationships among organisms, leads to further changes in the GI environment, resulting in assemblages with different dominant species. In the GIT, the aerotolerant species that initially dominate reduce the oxygen tension and thereby favor the emergence of anaerobic groups. Another example of interbacterial interactions is a metabolic cross-feeding, whereby one group of bacteria produces metabolites that are used by other groups (Flint et al., 2007). This includes the conversion of lactate produced by bifidobacteria into butyrate and other SCFA by other anaerobic members of the GI bacteria. Recent studies have described quorum sensing among the GI bacteria, triggering adaptive changes in the characteristics of individual bacterial species (Allen and Torres, 2008) and perhaps host cells (Sperandio et al., 2003). The gradual changes in the species composition and distributions of the resident bacteria that occur with increasing age are representative of the ecological principle of succession. Eventually the changes culminate in a “climax community” of species. The composition and productivity of the resident species are also influenced by the stability and extremes of the local environment (Buddington and Weiher, 1999). Environments that are harsh (e.g., stomach) or subject to frequent and large disturbances (e.g., proximal small intestine) have decreased densities and diversities of species. Ecosystems with the greatest densities and diversities of species are characterized by benign conditions and with intermittent disturbances of intermediate magnitude that are sufficient to prevent one or a few species from becoming dominant. In the GIT, the proximal colon provides such an environment and correspondingly has the greatest densities, diversities, and species evenness of bacteria. Among infants, the greatest disturbances to the GI ecosystem are caused by diarrhea and the administration of antibiotics. Both cause dramatic declines in the densities and diversities of the resident bacteria, with a shift in the dominant species (Tanaka et al., 2009). This has the potential to influence GI development (Mshvildadze and Neu, 2010) and actually increase the risk of NEC (Cotten et al., 2009). It is important to note that the disturbances caused by even short-term antibiotic administration may persist for at least 2 yr (Jernberg et al., 2010). DIETARY INPUTS DURING POSTNATAL DEVELOPMENT There is growing appreciation of the influences of diet on the ontogeny of the GIT and the assemblages of bacteria that colonize it and become established (Newburg and Walker, 2007). Neonatal mammals are dependent on breast milk to varying degrees, ranging from the extreme dependency of altricial species, such as marsupials and many laboratory rodents, to the very short periods of suckling for precocial species, such as guinea pigs, which begin to eat the adult diet shortly after birth. Milk composition varies widely among species (Jenness and Sloan, 1970). Notable is the absence of lactose in the milk of pinnipeds, the greater concentration of oligosaccharides in human milk (Newburg, 2009), and the wide species variation in protein, carbohydrate, and fat content. Milk composition is also not consistent during lactation. Colostrum, the first milk produced after birth, has greater protein content because of the increased concentration of immunoglobulins and a diversity of regulatory proteins. Within days after birth, the composition begins to shift from colostrum to mature milk, with the composition typical of the species. Apparently, milk composition has been refined over evolutionary time to match the unique species, age, and individual demands of infants. Manufacturers of formulas for human infants and milk replacers for companion and production animals attempt to mimic the composition of the milk of the target species. The present formulas are relatively simple, with far fewer components than breast milk. There are intense efforts to identify ingredients that can be added to formulas and milk replacers that will promote patterns of GI development and the establishment of commensal assemblages of bacteria that are similar to those when infants are fed breast milk and when neonates of other species are allowed to nurse their dams. For most species and individuals, weaning is a gradual process, with a progressive decline in milk consumption and an increased dependency on the adult diet to provide energy and nutrients. During this period, GI functions and the resident assemblages of bacteria gradually become adult-like. When weaning is sudden or early, diarrhea often results and is accompanied by changes in the species composition and metabolic activities of the GI bacteria (Lallès et al., 2007). Influences of Diet on GI development The rapid postnatal growth and maturation of the GIT are dependent on dietary inputs and are delayed when neonates are provided TPN rather than fed enterally. The importance of luminal nutrients for development of the neonatal GIT has led to the concept of minimal enteral nutrition (atrophic feeding), whereby small amounts of oral nutrients are provided during TPN to encourage GI growth and maturation and reduce the risk of bacterial translocation and sepsis (Bombell and McGuire, 2009). The composition of the food fed to neonates is a determinant of GI growth, maturation, and health. Colostrum includes immunoglobulins that provide passive immunity to the neonate and numerous hormones, cytokines, and other regulatory molecules that stimulate GI growth and maturation, including immune functions (Hanson, 2007). Even coating the mouth of preterm neonates with colostrum may be adequate to stimulate the development of GI and systemic immune functions (Rodriguez et al., 2010). The change in diet composition at weaning triggers changes in enterocyte cytokinetics and patterns of gene expression, coinciding with changes in absorptive and secretory functions (Drozdowski et al., 2010). The secretory characteristics of GI accessory organs, including the pancreas, are also responsive to the diet change at weaning. Influence of Diet on the Developing Assemblages of Bacteria The inputs into ecosystems are key determinants of the abundances, diversity, and production of the resident organisms. Similarly, the assemblages of GI bacteria are responsive to dietary and host inputs (Buddington and Weiher, 1999; Koenig et al., 2010). This is evident from the disturbance to the assemblages of GI bacteria induced by prolonged administration of TPN (Alverdy et al., 2005), causing increases in pathogens and risks of secondary diseases (Harvey et al., 2006). It is not surprising that the amount and composition of the diet fed to infants influence the postnatal changes in the GI bacteria. By doing so, diet indirectly influences postnatal GIT development and disease resistance (Amarri et al., 2006). A central question surrounding neonatal health and nutrition is, “How does breast milk adventitiously influence the developing assemblage of bacteria?” The majority of studies report that infants fed breast milk have less incidence of disease. This corresponds to greater fecal densities of lactic acid-producing bacteria (e.g., bifidobacteria and lactobacilli) compared with infants receiving formula (Penders et al., 2006). Breast milk also reduces the densities of bacteria adherent to the mucosa, and this may contribute to the reduced risk of NEC (Van Haver et al., 2009). It is interesting that providing infants with only a small volume of formula can elicit dramatic changes in the GI bacteria (Mackie et al., 1999). The different patterns of microbial gene expression among piglets fed by the sow or given milk replacer (Poroyko et al., 2010) raises an intriguing possibility that milk has evolved attributes that favor the establishment and dominance of commensal bacteria that provide health and nutritional benefits and that remove undesired species. The discovery of the immune modulation and health benefits of nucleotides (Yu, 2002), which include beneficially modulating the GI bacteria (Singhal et al., 2008), led to the inclusion of nucleotides in infant formulas. Other components of milk reported to provide more than energy and nutrients to infants that can modify the resident bacteria include IgA, human milk oligosaccharides (HMO), lactose, lysozyme, and lactoferrin (Newburg, 2009). A portion of the lactose in milk is not hydrolyzed during transit of the small intestine and is metabolized by colonic bacteria, causing an increase in breath hydrogen. This is particularly true among preterm infants (Kien et al., 1998) and exemplifies how diet influences bacterial metabolism (González et al., 2008). Although lactose fermentation has been interpreted as lactase insufficiency, it may contribute to shifting the luminal environment to be more conducive to commensal bacteria. The multifunctional and diverse HMO are the third most abundant component of human milk, with species and individual differences in the amounts, types, and proportions (Newburg, 2009). The majority of HMO are not digested during transit of the GIT and are considered to encourage the establishment of commensal, health-promoting bacteria by a combination of having prebiotic properties, serving as receptor mimics for pathogens, and modulating mucosal immune functions (Newburg, 2009; Eiwegger et al., 2010). The protein lactoferrin, although abundant in human, but not cow, milk (Coppa et al., 2006), is absent from present infant formulas. Lactoferrin is considered to be immunomodulatory (Suzuki et al., 2005), to have the potential to influence the assemblages of bacteria by being bifidogenic (Coppa et al., 2006), and to have the ability to reduce sepsis among preterm infants (Venkatesh and Abrams, 2010). Collectively, the components of milk highlight a coevolution between milk composition, the developing GIT, and the resident bacteria. Combined, they effectively enhance the ability of the neonate to “cultivate a garden” of health-promoting bacteria. There is also interest in novel ingredients that are not milk based but that may beneficially influence the species composition of the GI bacteria when fed to infants [e.g., prebiotics and probiotics (Sherman et al., 2009)]. The historical emphasis has been on formula ingredients that improve the species composition of the GI microbiota. Less considered, but of critical importance, is the influence of diet on bacterial enzymes (Grönlund et al., 1999), hence metabolism. Bacterial metabolism and the production of SCFA and other metabolites are related to the types and amounts of substrates (Macfarlane and Macfarlane, 2003), such as the responses of the GI bacteria to lactose (Mäkivuokko et al., 2006). Although total concentrations of fecal SCFA are similar for preterm infants fed expressed breast milk or a commercial infant formula (P > 0.9), those fed breast milk have greater concentrations of propionate but relatively less acetate (P < 0.05; R. K. Buddington, unpublished data). It is interesting that the SCFA profiles of the preterm infants fed expressed breast milk are similar to those we have measured for healthy adults. INTERACTIONS BETWEEN THE BACTERIA AND THE INTESTINE The interactions between the resident bacteria and the host GIT involve 2-way communication. This results in gene expression being modulated in the bacteria and the host (Allen and Torres, 2008; Sharma et al., 2010). Moreover, by modulating the expression of host genes, the resident bacteria modify the GI environment, which in turn alters the interactions and balances among the GI bacteria (Mahowald et al., 2009). The complex interactions result in GIT ecosystems that are unique for species, individuals, life history stages, and health states (Dunne 2001), and these can have long-term immune and health implications (Conroy et al., 2009). The interactions between the host and the GI bacteria occur over 3 time scales. There are rapid and reversible interactions that span minutes to hours, other interactions that occur during the life history of individuals, and those that occur over evolutionary time scales. There is ample evidence for the coevolution of the host GIT and the resident bacteria (Ley et al., 2008). This results in commensal and symbiotic relationships that are species specific and that involve genetic adaptations of the bacteria to the host GIT (Schell et al., 2002). The cooperative responses of the GI immune system to the different bacteria have established mutualisms (Slack et al., 2009). The interactions that occur during the life of an individual influence the characteristics of the host and the assemblages of bacteria (densities, diversity, evenness, regional distribution, and functional attributes). These interactions are particularly relevant to neonates and have been the subject of numerous studies and reviews. Specifically, the early responses of the GIT and the resident bacteria can have lifelong health consequences through epigenetic mechanisms. These include the ability of some bacteria to alter the patterns of host gene expression, such as patterns of glycosylation for extracellular proteins (Freitas et al., 2002) in ways that benefit both the commensal bacteria and the host (Bry et al. 1996). Another relevant example is the relationship between early antigen exposure and the risk of allergies and asthma later in life (the “hygiene hypothesis”; Shreiner et al., 2008). Less understood are the rapid and reversible interactions during infancy between the GIT and the bacteria. These transient interactions occur over periods of minutes to hours and allow the GIT and the resident bacteria to adapt to changing conditions, such as those that occur during and between meals of varying size and composition. The interactions between the bacteria and the GIT can be direct, via cell-to-cell contacts. Typically, the adverse influences of pathogenic bacteria require direct contact with epithelial cells and are mediated by surface molecules (Zoumpopoulou et al., 2009). Exemplary is how the attachment of pathogenic Escherichia coli, Salmonella, clostridia, and other pathogens is required to trigger the expression of virulence genes, such as those coding for toxins, invasive mechanisms, or Type III secretion systems that alter the characteristics or cause the death of the attached enterocytes. Members of the commensal bacteria and some probiotic strains are considered to inhibit pathogen adherence and pathogenesis by occupying sites of attachment and by inducing enterocyte expression of the mucin-encoding gene MUC2 and other defense genes that inhibit attachment (Kim et al., 2008) by the production of immunomodulatory molecules (Mazmanian et al., 2005). The influences of the bacteria can also be indirect and mediated by metabolites that alter host gene expression, beneficially or adversely. Some species of bifidobacteria release soluble factors that decrease epithelial cell secretion of inflammatory cytokines (Heuvelin et al., 2009) and chloride (Heuvelin et al., 2010). The SCFA produced by bacterial fermentation of undigested feedstuffs provide up to 10% of the total metabolic energy requirement of humans and even greater percentages among animals with larger hindguts or rumens (Rechkemmer et al., 1988). Corresponding with this, gnotobiotic rodents require 30% more dietary energy and vitamin supplements compared with conventional rodents harboring commensal bacteria capable of fermenting undigested feedstuffs. The SCFA influence colon health (Wong et al., 2006), alter patterns of epithelial cell gene expression (Sanderson, 2004; Vanhoutvin et al., 2009), and stimulate secretion of regulatory peptides that enhance growth and functions of the proximal small intestine (Bartholome et al., 2004). The responses to butyrate are more pronounced than those to acetate and propionate (Basson et al., 2000). However, excessive production of SCFA, including butyrate, has been associated with damage to the GI epithelium and may contribute to NEC (Lin et al., 2005). Often overlooked is the competition between the GIT and the resident bacteria for nutrients. Maintaining reduced densities of bacteria in the proximal small intestine by peristalsis and antibacterial secretions from the pancreas and intestine provides the GIT with the first access to readily available, digestible nutrients. Food not available to the host can and will be metabolized by the bacteria. The Resident Bacteria Influence the Developing GIT Profound differences exist between germ-free and conventional rodents with respect to villus architecture, and enterocyte patterns of proliferation, differentiation, and gene expression (Zocco et al., 2007) and mucosal immune responses (Williams et al., 2006; Hrncir et al., 2008). Bacteria isolated from the GIT of neonates are reported to enhance maturation of the GIT by modulating gene expression (Are et al., 2008). This includes the age-related shifts in the activities of the fucosyl- and sialyltransferases responsible for the weaning-related changes in the glycosylation of enterocyte glycoproteins (Nanthakumar et al., 2005). Even patterns of intestinal motility are responsive to the resident bacteria (Lesniewska et al. 2006). The interactions between the colonizing bacteria and the developing GI immune functions have immediate and long-term consequences on host health (Dimmitt et al., 2010; Mshvildadze and Neu, 2010). The combination of colonizing bacteria, food, and environmental antigens activate the immature GI immune system of the neonate by triggering the rapid maturation, proliferation, and migration of the cellular components of the adaptive immune division. The interactions during infancy are critical for the development of tolerance and to avoid the risk of allergies to food and other environmental antigens later in life (Kukkonen et al. 2008), and are a key factor in the risk of atopic disorders (Penders et al., 2007). The interactions between the bacteria and GI epithelial cells also influence innate immune functions, such as the secretion of mucous and antimicrobial peptides. Additional immunologic challenges at weaning caused by the concurrent shifts in diet and the GI bacteria trigger further changes in GI defense functions. Different species of colonizing bacteria have varying influences on the expression of proinflammatory genes (Zeuthen et al., 2010), the balance between T helper 1 (antibody-mediated) and T helper 2 (cell-mediated) immune responses (Ogra, 2010), including immunoglobulin production (Huurre et al., 2008), the patterns of expression for the TLR and nucleotide-binding oligomerization domain receptors that are critical for antigen discrimination (Lundin et al., 2008), and the development of tolerance to endotoxins (Lotz et al., 2006). These findings have stimulated interest in providing probiotics to infants to modulate the developing immune responses adventitiously. Conversely, changes in the GI bacteria caused by administration of antibiotics during suckling increases the densities and responses of mast cells, apparently predisposing the infant to the development of allergies (Nutten et al., 2007) and potentially altering GI immune development (Schumann et al., 2005). Much less is known about whether and how the assemblages of bacteria influence the postnatal development of other GI functions. Despite the impact of pathogen-induced diarrheas on neonates, the short- and long-term responses of the osmoregulatory functions to the colonizing bacteria have not been described. There is evidence that enteroendocrine cells can respond directly to resident bacteria by the secretion of hormones (Palazzo et al., 2007). The hyperactive immune responses of the neonate, if stimulated, can be expected to influence the other GI functions. For example, inflammatory cytokines secreted in response to pathogenic bacteria are likely to reduce digestive secretions and nutrient absorption and increase the secretion of electrolytes and water. The Developing GIT Influences the Resident Bacteria The GIT functions are key determinants of the chemical characteristics of the luminal environment. Digestive secretions present barriers to the introduction of species, even probiotics, as well as pathogens. Therefore, the changes in the physicochemical environment of the developing GIT (Sanderson, 1999) and the developing innate and adaptive components of the GI immune system have the potential to influence the developing assemblages of bacteria (Salzman et al., 2010). The immature gastric acid production of neonates (Grahnquist et al., 2000) coincides with greater densities of bacteria in the stomach until acid production increases. Postnatal changes in patterns of enterocyte glycosylation of apical membrane glycoproteins (Nanthakumar et al., 2005) influence bacterial metabolism and may represent a coevolved symbiosis between the host and the commensal GI bacteria. NEC: WHEN THE INTERACTIONS GO AWRY The interactions among the resident bacteria, the developing GIT, and the diet are of key importance for the adaptation of neonates to postnatal life (Mshvildadze and Neu, 2010). They are even more important after preterm birth because of the immature state of GI development, the intolerance of many preterm infants to feeding, and the adverse reactions they have to colonizing bacteria. Necrotizing enterocolitis is an inflammatory reaction that is the most common GIT disorder of neonates, particularly those born premature, with the incidence varying from 1 to 8% among neonatal intensive care units (Kosloske, 1994). The NEC disease process is multifactorial, with prematurity, bacterial colonization of the GIT, and feeding recognized as the key contributors. Necrotizing enterocolitis has also been associated with altered GI bacterial assemblages (Hällström et al., 2004), an immature epithelial barrier and immune defenses, and fetal enterocytes that are hyperresponsive (Claud, 2009). This has led to the routine prophylactic administration of antibiotics to preterm, low-birth-weight infants. Unfortunately, this may actually predispose preterm infants to NEC (Cotten et al., 2009) by destabilizing the assemblages of GI bacteria. Additionally, the majority of preterm infants are delivered by caesarian section, which may compromise the normal postnatal spontaneous activation of intestinal epithelial cells (Lotz et al., 2006) and the already impaired recognition of lipopolysaccharide characteristic of preterm birth (Wolfs et al., 2010). Another issue facing preterm infants is the initial dependence many have on parenteral nutrition, which delays GI growth and maturation (Hay, 2008). As a consequence, development of the GI ecosystem is often compromised among preterm infants (Mshvildadze and Neu, 2010). The absence of NEC among germ-free animals demonstrates the essential role of the resident bacteria in the disease process. Moreover, the risk of NEC is increased when formula is fed, whereas infants fed breast milk are protected. This has been corroborated in studies with animal models (newborn mice and rats) that indicate diet is a determinant of NEC risk via effects on both microbiota composition and the response pathways of the host (Sodhi et al., 2008). Because newborn laboratory rodents have limited physiological, anatomical, and developmental relevance to preterm humans, we recently developed a preterm pig model of NEC to better understand the diet-microbiota interactions during early GI development in humans (Sangild et al., 2006). Our studies confirmed that caesarean section and vaginal birth of preterm pigs (at 92% of gestation) resulted in widely different patterns of GI bacterial colonization, yet resulted in similar incidences of NEC (Siggers et al., 2010). When preterm, caesarean-delivered pigs were reared in infant incubators and fed an infant formula, 50% or more spontaneously developed NEC symptoms and the characteristic lesions. The incidence of NEC was about 5% when preterm pigs were instead fed sow or cow colostrum (Bjornvad et al., 2008). This parallels the benefits of providing colostrum to preterm human infants. The protection provided by colostrum vs. the increased risk associated with formula indicates dietary inputs play a central role in NEC. Whether and how diet influences bacterial colonization of the GIT and the role in NEC has been investigated in the pig model in several studies (reviewed by Siggers et al., 2010). Overall, there were few diet-dependent differences in gut colonization, except that certain pathogenic species (e.g., Clostridium perfringens) were consistently associated with intestinal lesions associated with NEC. Moreover, the patterns of bacterial colonization correlated more closely with the degree of intestinal lesions and gestational age at birth (maturity of the epithelium) than with specific diets (colostrum vs. formula). Reviews of clinical trials with human preterm infants that evaluated the efficacy of probiotics as a prophylactic for NEC suggest the NEC risk is reduced (Alfaleh et al., 2010). However, the use of different strains of probiotics and administration regimens confounds interpretations. The administration of probiotics to preterm pigs did not induce notable changes in the GI bacteria, nor did it consistently reduce the incidence of NEC (Siggers et al., 2010). Although the potential benefits of including prebiotics in formula fed to preterm infants have not been adequately investigated and remain uncertain (Sherman et al., 2009), studies with animal models suggest adding prebiotics may reduce the risk of NEC (Butel et al., 2002). However, the addition of prebiotic compounds to the formula fed to preterm pigs failed to improve NEC resistance relative to the formula alone (Møller et al., 2011). Collectively, these studies lead to the conclusion that the presence of bacteria is essential for intestinal inflammatory reactions in newborns. Furthermore, the state of the mucosa is an important determinant of whether the contact with the colonizing bacteria results in severe inflammation and NEC. Controlling the process of bacterial colonization in preterm newborns through diet is difficult. Even so, the species composition of the GI bacteria appears to be less important for NEC risk than the digestive capacity and immune responses of the immature GIT. The detrimental effects of feeding formula may be related to the absence of immunomodulatory factors and nutrients that are present in breast milk and the responses of the preterm GI ecosystem to novel, nonmilk ingredients that are present in formula (e.g., corn syrup solids). Preterm pigs fed formula prepared with corn syrup solids had a greater incidence of NEC compared with when lactose was the predominant source of carbohydrate (Buddington et al., 2008). The beneficial effects of the lactose-based formula were more closely related to improved functions of the intestinal mucosa rather than to improved gut microbiota (Thymann et al., 2009). Even though bacteria colonize the GIT immediately after delivery and are present during the period of TPN, the onset of NEC-related inflammatory reactions in the majority of preterm pigs occurred within hours after the onset of enteral feeding with formula (Oste et al., 2010). The importance of diet is again evident from the overfed, preterm rat pup as a model for NEC (Okada et al., 2010). The importance of diet for inducing NEC in animal models is similar to the development of NEC in preterm human infants after the beginning of enteral feeding. These findings highlight how adverse interactions between the colonizing bacteria and diet in conjunction with immaturity of the GIT are central to the NEC disease process. Despite the role of the GI microbiome in contributing to disease in infants, it is very likely that the metabolic functions of the GI bacteria and the responses to enteral nutrients are more important in triggering NEC. Rectal introduction of SCFA induces mucosal damage (Lin et al., 2005), and introducing a combination of lactose and lactose-fermenting bacteria that generate increased concentrations of SCFA (Waligora-Dupriet et al., 2009) induces mucosal damage and NEC-like characteristics in animal models. Although the etiology of NEC remains uncertain, the interactions between the GI bacteria and diet are key determinants of the sensitivity of the immature GIT to stimuli that elicit detrimental inflammatory reactions. PERSPECTIVES FOR DIETARY MANAGEMENT OF THE DEVELOPING GIT ECOSYSTEM The type (breast milk or formulas with novel ingredients) and amount (full, minimal, or absence) of enteral diet in conjunction with bacterial colonization play significant roles in mediating postnatal development of the GI structure, functions, and resident microbiota. Present infant formulas fail to replicate the important protective effects of breast milk, which can be attributed to the lack of bioactive constituents that modulate GI gene expression, modulate the growth and maturation of GI functions, possess antimicrobial functions and provide the neonate with passive immunity, and others with prebiotic properties that contribute to the selection and dominance of the commensal microbiota. In addition to providing adequate energy and nutrients, the optimal diet for the neonate, term or preterm, needs to include components that reduce or prevent the harmful actions of the resident GI microbiota on the neonatal mucosa. There is understandable interest in increasing the proportion of beneficial bacteria in the GIT of infants to modulate enteric immune functions and thereby improve resistance to GIT pathogens and other health challenges (Dogi et al., 2008). Three principal approaches have been used to date. Although antibiotics remain a mainstay for neonatal care, there is a growing appreciation of and concern about the long-term consequences associated with the disturbances they cause in the developing GI ecosystem (Cotten et al., 2009; Jernberg et al., 2010). Probiotics are of widespread interest, and there are numerous reports of efficacy. However, the benefits are generally transient and do not persist after the probiotic is no longer administered. It has proven possible to provide probiotic bacteria during pregnancy to facilitate colonization of infants born vaginally (Buddington et al., 2010). However, the numerous strains available, the varying responses that can be elicited, and the likely individual-specific responses complicate the selection of strains that provide benefits. The emergence of prebiotics as ingredients in infant formulas mimics the presence of oligosaccharides in breast milk and has shown promise for encouraging the growth of beneficial bacteria already resident in and presumably adapted to the host GIT (Veereman, 2007), thereby providing health benefits (Arslanoglu et al., 2008). Animal models will remain important for investigating the development of the GI ecosystem of human infants, agricultural species, and companion animals and for evaluating the influences of bacteria and diet. The variation in the GI microbiota among species, individuals, ages, and health states will complicate extrapolating results from one species to another. It is not surprising that responses to probiotics and prebiotics vary among species and even individuals (Sullivan and Nord, 2005). A better understanding of how diet influences host-microbiome interactions during the neonatal period will greatly enhance efforts to improve management of the GIT ecosystem, and thereby the health and nutrition of newborns. LITERATURE CITED Alfaleh K. Anabrees J. Bassler D. 2010. Probiotics reduce the risk of necrotizing enterocolitis in preterm infants: A meta-analysis. Neonatology  97: 93– 99. https://doi.org/19707025 Google Scholar CrossRef Search ADS PubMed  Allen C. A. Torres A. G. 2008. Host-microbe communication within the GIT. Adv. Exp. Med. Biol.  635: 93– 101. https://doi.org/18841706 Google Scholar CrossRef Search ADS PubMed  Alumets J. Håkanson R. Sundler F. 1983. Ontogeny of endocrine cells in porcine gut and pancreas. An immunocytochemical study. Gastroenterology  85: 1359– 1372. https://doi.org/6138293 Google Scholar PubMed  Alverdy J. Zaborina O. Wu L. 2005. The impact of stress and nutrition on bacterial-host interactions at the intestinal epithelial surface. Curr. Opin. Clin. Nutr. Metab. Care  8: 205– 209. https://doi.org/15716801 Google Scholar CrossRef Search ADS PubMed  Amarri S. Benatti F. Callegari M. L. Shahkhalili Y. Chauffard F. Rochat F. Acheson K. J. Hager C. Benyacoub J. Galli E. Rebecchi A. Morelli L. 2006. Changes of gut microbiota and immune markers during the complementary feeding period in healthy breast-fed infants. J. Pediatr. Gastroenterol. Nutr.  42: 488– 495. https://doi.org/16707969 Google Scholar CrossRef Search ADS PubMed  Are A. Aronsson L. Wang S. Greicius G. Lee Y. K. Gustafsson J. A. Pettersson S. Arulampalam V. 2008. Enterococcus faecalis from newborn babies regulate endogenous PPARγ activity and IDL10 levels in colonic epithelial cells. Proc. Natl. Acad. Sci. USA  105: 1943– 1948. https://doi.org/18234854 Google Scholar CrossRef Search ADS   Arslanoglu S. Moro G. E. Schmitt J. Tandoi L. Rizzardi S. Boehm G. 2008. Early dietary intervention with a mixture of prebiotic oligosaccharides reduces the incidence of allergic manifestations and infections during the first two years of life. J. Nutr.  138: 1091– 1095. https://doi.org/18492839 Google Scholar CrossRef Search ADS PubMed  Bailey M. Haverson K. 2006. The postnatal development of the mucosal immune system and mucosal tolerance in domestic animals. Vet. Res.  37: 443– 453. https://doi.org/16611557 Google Scholar CrossRef Search ADS PubMed  Bartholome A. L. Albin D. M. Baker D. H. Holst J. J. Tappenden K. A. 2004. Supplementation of total parenteral nutrition with butyrate acutely increases structural aspects of intestinal adaptation after an 80% jejunoileal resection in neonatal piglets. J. Parenter. Enteral Nutr.  28: 210– 222. https://doi.org/15291402 Google Scholar CrossRef Search ADS   Basson M. D. Liu Y. W. Hanly A. M. Emenaker N. J. Shenoy S. G. Gould Rothberg B. E. 2000. Identification and comparative analysis of human colonocyte short-chain fatty acid response genes. J. Gastrointest. Surg.  4: 501– 512. https://doi.org/11077326 Google Scholar CrossRef Search ADS PubMed  Bjornvad C. R. Thymann T. Deutz N. E. Burrin D. G. Jensen S. K. Jensen B. B. Molbak L. Boye M. Larsson L. I. Schmidt M. Michaelsen K. F. Sangild P. T. 2008. Enteral feeding induces diet-dependent mucosal dysfunction, bacterial proliferation, and necrotizing enterocolitis in preterm pigs on parenteral nutrition. Am. J. Physiol. Gastrointest. Liver Physiol.  295: G1092– G1103. https://doi.org/18818317 Google Scholar CrossRef Search ADS PubMed  Bombell S. McGuire W. 2009. Early trophic feeding for very low birth weight infants. Cochrane Database Syst. Rev.  8: CD000504. https://doi.org/19588318 Bourassa J. Lainé J. Kruse M. L. Gagnon M. C. Calvo E. Morisset J. 1999. Ontogeny and species differences in the pancreatic expression and localization of the CCK(A) receptors. Biochem. Biophys. Res. Commun.  260: 820– 828. https://doi.org/10403848 Google Scholar CrossRef Search ADS PubMed  Bry L. Falk P. G. Midtvedt T. Gordon J. L. 1996. A model of host-microbial interactions in an open mammalian ecosystem. Science  273: 1380– 1383. https://doi.org/8703071 Google Scholar CrossRef Search ADS PubMed  Buddington R. K. 1994. Nutrition and ontogenetic development of the intestine. Can. J. Physiol. Pharmacol.  72: 251– 259. https://doi.org/8069771 Google Scholar CrossRef Search ADS PubMed  Buddington, R. K. 2009. Using probiotics and prebiotics to manage the gastrointestinal tract ecosystem. Pages 1– 31 in Prebiotics and Probiotics Science and Technology.  D. Charalampopoulos and R. A. Rastall ed. Springer Science Publishing, New York, NY. Google Scholar CrossRef Search ADS   Buddington R. K. Bering S. B. Thymann T. Sangild P. T. 2008. Aldohexose malabsorption in preterm pigs is directly related to the severity of necrotizing enterocolitis. Pediatr. Res.  63: 382– 387. https://doi.org/18356743 Google Scholar CrossRef Search ADS PubMed  Buddington R. K. Weiher E. 1999. The application of ecological principles and fermentable fibers to manage the gastrointestinal tract ecosystem. J. Nutr.  129( Suppl.): 1446S– 1450S. https://doi.org/10395618 Google Scholar PubMed  Buddington R. K. Williams C. H. Kostek B. M. Buddington K. K. Kullen M. J. 2010. Maternal-to-infant transmission of probiotics: Concept validation in mice, rats, and pigs. Neonatology  97: 250– 256. https://doi.org/19887854 Google Scholar CrossRef Search ADS PubMed  Burrin D. Guan X. Stoll B. Petersen Y. M. Sangild P. T. 2003. Glucagon-like peptide 2: A key link between nutrition and intestinal adaptation in neonates? J. Nutr.  133: 3712– 3716. https://doi.org/14608101 Google Scholar CrossRef Search ADS PubMed  Butel M. J. Waligora-Dupriet A. J. Szylit O. 2002. Oligofructose and experimental model of neonatal necrotising enterocolitis. Br. J. Nutr.  87( Suppl. 2): S213– S219. https://doi.org/12088521 Google Scholar CrossRef Search ADS PubMed  Chailler P. Ménard D. 1999. Ontogeny of EGF receptors in the human gut. Front. Biosci.  4: D87– D101. https://doi.org/9889180 Google Scholar CrossRef Search ADS PubMed  Claud E. C. 2009. Neonatal necrotizing enterocolitis—Inflammation and intestinal immaturity. Antiinflamm. Antiallergy Agents Med. Chem.  8: 248– 259. https://doi.org/20498729 Google Scholar CrossRef Search ADS PubMed  Conroy M. E. Shi H. N. Walker W. A. 2009. The long-term health effects of neonatal microbial flora. Curr. Opin. Allergy Clin. Immunol.  9: 197– 201. https://doi.org/19398905 Google Scholar CrossRef Search ADS PubMed  Coppa G. V. Zampini L. Galeazzi T. Gabrielli O. 2006. Prebiotics in human milk: A review. Dig. Liver Dis.  38( Suppl. 2): S291– S294. https://doi.org/17259094 Google Scholar CrossRef Search ADS PubMed  Cotten, C. M., S. Taylor, B. Stoll, R. N. Goldberg, N. I. Hansen, P. J. Sánchez, N. Ambalavanan, D. K. Benjamin Jr. and NICHD Neonatal Research Network 2009. Prolonged duration of initial empirical antibiotic treatment is associated with increased rates of necrotizing enterocolitis and death for extremely low birth weight infants. Pediatrics  123: 58– 66. Google Scholar CrossRef Search ADS PubMed  Dicksved J. Halfvarson J. Rosenquist M. Järnerot G. Tysk C. Apajalahti J. Engstrand L. Jansson J. K. 2008. Molecular analysis of the gut microbiota of identical twins with Crohn's disease. ISME J.  2: 716– 727. https://doi.org/18401439 Google Scholar CrossRef Search ADS PubMed  Dimmitt R. A. Staley E. M. Chuang G. Tanner S. M. Soltau T. D. Lorenz R. G. 2010. Role of postnatal acquisition of the intestinal microbiome in the early development of immune function. J. Pediatr. Gastroenterol. Nutr.  51: 262– 273. https://doi.org/20639773 Google Scholar PubMed  Dogi C. A. Galdeano C. M. Perdigón G. 2008. Gut immune stimulation by non pathogenic Gram(+) and Gram(−) bacteria. Comparison with a probiotic strain. Cytokine  41: 223– 231. https://doi.org/18248820 Google Scholar CrossRef Search ADS PubMed  Drozdowski L. A. Clandinin T. Thomson A. B. 2010. Ontogeny, growth and development of the small intestine: Understanding pediatric gastroenterology. World J. Gastroenterol.  16: 787– 799. https://doi.org/20143457 Google Scholar PubMed  Dunne C. 2001. Adaptation of bacteria to the intestinal niche: Probiotics and gut disorder. Inflamm. Bowel Dis.  7: 136– 145. https://doi.org/11383587 Google Scholar CrossRef Search ADS PubMed  Eckmann, L. 2006. Innate immunity. Pages 1033– 1066 in Physiology of the Gastrointestinal Tract.  4th ed. L. R. Johnson, K. E. Barrett, F. K. Ghishan, J. L. Merchant, H. M. Said, and J. Wood ed. Elsevier, Amsterdam, the Netherlands. Google Scholar CrossRef Search ADS   Eiwegger T. Stahl B. Haidl P. Schmitt J. Boehm G. Dehlink E. Urbanek R. Szépfalusi Z. 2010. Prebiotic oligosaccharides: In vitro evidence for gastrointestinal epithelial transfer and immunomodulatory properties. Pediatr. Allergy Immunol.  21: 1179– 1188. https://doi.org/20444147 Google Scholar CrossRef Search ADS PubMed  Flint H. J. Duncan S. H. Scott K. P. Louis P. 2007. Interactions and competition within the microbial community of the human colon: Links between diet and health. Environ. Microbiol.  9: 1101– 1111. https://doi.org/17472627 Google Scholar CrossRef Search ADS PubMed  Freitas M. Axelsson L. G. Cayuela C. Midtvedt T. Trugnan G. 2002. Microbial-host interactions specifically control the glycosylation pattern in intestinal mouse mucosa. Histochem. Cell Biol.  118: 149– 161. https://doi.org/12189518 Google Scholar PubMed  González R. Klaassens E. S. Malinen E. de Vos W. M. Vaughan E. E. 2008. Differential transcriptional response of Bifidobacterium longum to human milk, formula milk, and galactooligosaccharide. Appl. Environ. Microbiol.  74: 4686– 4694. https://doi.org/18539808 Google Scholar CrossRef Search ADS PubMed  Grahnquist L. Ruuska T. Finkel Y. 2000. Early development of human gastric H,K-adenosine triphosphatase. J. Pediatr. Gastroenterol. Nutr.  30: 533– 537. https://doi.org/10817284 Google Scholar CrossRef Search ADS PubMed  Grönlund M. M. Salminen S. Mykkänen H. Kero P. Lehtonen O. P. 1999. Development of intestinal bacterial enzymes in infants—Relationship to mode of delivery and type of feeding. APMIS  107: 655– 660. https://doi.org/10440061 Google Scholar CrossRef Search ADS PubMed  Hällström M. Eerola E. Vuento R. Janas M. Tammela O. 2004. Effects of mode of delivery and necrotising enterocolitis on the intestinal microflora in preterm infants. Eur. J. Clin. Microbiol. Infect. Dis.  23: 463– 470. https://doi.org/15168141 Google Scholar CrossRef Search ADS PubMed  Hanson L. A. 2007. Feeding and infant development breast-feeding and immune function. Proc. Nutr. Soc.  66: 384– 396. https://doi.org/17637091 Google Scholar CrossRef Search ADS PubMed  Hay W. W. 2008. Strategies for feeding the preterm infant. Neonatology  94: 245– 254. https://doi.org/18836284 Google Scholar CrossRef Search ADS PubMed  Heuvelin E. Lebreton C. Bichara M. Cerf-Bensussan N. Heyman M. 2010. A Bifidobacterium probiotic strain and its soluble factors alleviate chloride secretion by human intestinal epithelial cells. J. Nutr.  140: 7– 11. https://doi.org/19889806 Google Scholar CrossRef Search ADS PubMed  Heuvelin E. Lebreton C. Grangette C. Pot B. Cerf-Bensussan N. Heyman M. 2009. Mechanisms involved in alleviation of intestinal inflammation by Bifidobacterium breve soluble factors. PLoS ONE  4: e5184. https://doi.org/19381276 Google Scholar CrossRef Search ADS PubMed  Hrncir T. Stepankova R. Kozakova H. Hudcovic T. Tlaskalova-Hogenova H. 2008. Gut microbiota and lipopolysaccharide content of the diet influence development of regulatory T cells: Studies in germ-free mice. BMC Immunol.  9: 65. https://doi.org/18990206 Google Scholar CrossRef Search ADS PubMed  Huurre A. Kalliomäki M. Rautava S. Rinne M. Salminen S. Isolauri E. 2008. Mode of delivery—Effects on gut microbiota and humoral immunity. Neonatology  93: 236– 240. https://doi.org/18025796 Google Scholar CrossRef Search ADS PubMed  Jenness R. Sloan R. E. 1970. The composition of milks of various species: A review. Dairy Sci.  32: 599– 612. Jernberg C. Löfmark S. Edlund C. Jansson J. K. 2010. Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology  156: 3216– 3223. https://doi.org/20705661 Google Scholar CrossRef Search ADS PubMed  Kelly D. King T. Aminov R. 2007. Importance of microbial colonization of the gut in early life to the development of immunity. Mutat. Res.  622: 58– 69. https://doi.org/17612575 Google Scholar CrossRef Search ADS PubMed  Kien C. L. McClead R. E. Cordero L.Jr 1998. Effects of lactose intake on lactose digestion and colonic fermentation in preterm infants. J. Pediatr.  133: 401– 405. https://doi.org/9738725 Google Scholar CrossRef Search ADS PubMed  Kim Y. Kim S. H. Whang K. Y. Kim Y. J. Oh S. 2008. Inhibition of Escherichia coli O157:H7 attachment by interactions between lactic acid bacteria and intestinal epithelial cells. J. Microbiol. Biotechnol.  18: 1278– 1285. https://doi.org/18667857 Google Scholar PubMed  Kleessen B. Blaut M. 2005. Modulation of gut mucosal biofilms. Br. J. Nutr.  93( Suppl. 1): S35– S40. https://doi.org/15877893 Google Scholar CrossRef Search ADS PubMed  Koenig J. E. Spor A. Scalfone N. Fricker A. D. Stombaugh J. Knight R. Angenent L. T. Ley R. E. 2010. Microbes and Health Sackler Colloquium: Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. USA  https://doi.org/10.1073/pnas.1000081107. Kosloske A. M. 1994. Epidemiology of necrotizing enterocolitis. Acta Paediatr.  83:( Suppl. s396): 2– 7. https://doi.org/10.1111/j.1651-2227.1994.tb13232.x. https://doi.org/8086675 Google Scholar CrossRef Search ADS   Kukkonen K. Savilahti E. Haahtela T. Juntunen-Backman K. Korpela R. Poussa T. Tuure T. Kuitunen M. 2008. Long-term safety and impact on infection rates of postnatal probiotic and prebiotic (synbiotic) treatment: Randomized, double-blind, placebo-controlled trial. Pediatrics  122: 8– 12. https://doi.org/18595980 Google Scholar CrossRef Search ADS PubMed  Lacroix-Lamandé S. Rochereau N. Mancassola R. Barrier M. Clauzon A. Laurent F. 2009. Neonate intestinal immune response to CpG oligodeoxynucleotide stimulation. PLoS ONE  4: e8291. https://doi.org/20011519 Google Scholar CrossRef Search ADS PubMed  Lallès J. P. Bosi P. Smidt H. Stokes C. R. 2007. Nutritional management of gut health in pigs around weaning. Proc. Nutr. Soc.  66: 260– 268. https://doi.org/17466106 Google Scholar CrossRef Search ADS PubMed  Lebenthal A. Lebenthal E. 1999. The ontogeny of the small intestinal epithelium. J. Parenter. Enteral. Nutr.  23( Suppl.): S3– S6. Google Scholar CrossRef Search ADS   Lesniewska V. Rowland I. Laerke H. N. Grant G. Naughton P. J. 2006. Relationship between dietary-induced changes in intestinal commensal microflora and duodenojejunal myoelectric activity monitored by radiotelemetry in the rat in vivo. Exp. Physiol.  91: 229– 237. https://doi.org/16263800 Google Scholar CrossRef Search ADS PubMed  Ley R. E. Hamady M. Lozupone C. Turnbaugh P. J. Ramey R. R. Bircher J. S. Schlegel M. L. Tucker T. A. Schrenzel M. D. Knight R. Gordon J. I. 2008. Evolution of mammals and their gut microbes. Science  320: 1647– 1651. https://doi.org/18497261 Google Scholar CrossRef Search ADS PubMed  Lin J. Peng L. Itzkowitz S. Holzman I. R. Babyatsky M. W. 2005. Short-chain fatty acid induces intestinal mucosal injury in newborn rats and down-regulates intestinal trefoil factor gene expression in vivo and in vitro. J. Pediatr. Gastroenterol. Nutr.  41: 607– 611. https://doi.org/16254517 Google Scholar CrossRef Search ADS PubMed  Lotz M. Gütle D. Walther S. Ménard S. Bogdan C. Hornef M. W. 2006. Postnatal acquisition of endotoxin tolerance in intestinal epithelial cells. J. Exp. Med.  203: 973– 984. https://doi.org/16606665 Google Scholar CrossRef Search ADS PubMed  Lundin A. Bok C. M. Aronsson L. Björkholm B. Gustafsson J. A. Pott S. Arulampalam V. Rafter J. Pettersson S. 2008. Gut flora, Toll-like receptors and nuclear receptors: A tripartite communication that tunes innate immunity in large intestine. Cell. Microbiol.  10: 1093– 1103. https://doi.org/18088401 Google Scholar CrossRef Search ADS PubMed  Macfarlane S. Macfarlane G. T. 2003. Regulation of short-chain fatty acid production. Proc. Nutr. Soc.  62: 67– 72. https://doi.org/12740060 Google Scholar CrossRef Search ADS PubMed  Mackie R. I. Sghir A. Gaskins H. R. 1999. Developmental microbial ecology of the neonatal gastrointestinal tract. Am. J. Clin. Nutr.  69: 1035S– 1045S. https://doi.org/10232646 Google Scholar PubMed  Magalhaes J. G. Tattoli I. Girardin S. E. 2007. The intestinal epithelial barrier: How to distinguish between the microbial flora and pathogens. Semin. Immunol.  19: 106– 115. https://doi.org/17324587 Google Scholar CrossRef Search ADS PubMed  Mahowald M. A. Rey F. E. Seedorf H. Turnbaugh P. J. Fulton R. S. Wollam A. Shah N. Wang C. Magrini V. Wilson R. K. Cantarel B. L. Coutinho P. M. Henrissat B. Crock L. W. Russell A. Verberkmoes N. C. Hettich R. L. Gordon J. I. 2009. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc. Natl. Acad. Sci. USA  106: 5859– 5864. https://doi.org/19321416 Google Scholar CrossRef Search ADS   Mäkivuokko H. A. Saarinen M. T. Ouwehand A. C. Rautonen N. E. 2006. Effects of lactose on colon microbial community structure and function in a four-stage semi-continuous culture system. Biosci. Biotechnol. Biochem.  70: 2056– 2063. https://doi.org/16960357 Google Scholar CrossRef Search ADS PubMed  Mazmanian S. K. Liu C. H. Tzianabos A. O. Kasper D. L. 2005. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell  122: 107– 118. https://doi.org/16009137 Google Scholar CrossRef Search ADS PubMed  Møller H. K. Thymann T. Fink L. N. Frokiaer H. Kvistgaard A. S. Sangild P. T. 2011. Bovine colostrum is superior to enriched formulas in stimulating intestinal function and necrotising enterocolitis resistance in preterm pigs. Br. J. Nutr.  105: 44– 53. https://doi.org/20723273 Google Scholar CrossRef Search ADS PubMed  Mshvildadze M. Neu J. 2010. The infant intestinal microbiome: Friend or foe? Early Hum. Dev.  86( Suppl. 1): 67– 71. https://doi.org/20116944 Google Scholar CrossRef Search ADS PubMed  Mulder I. E. Schmidt B. Stokes C. R. Lewis M. Bailey M. Aminov R. I. Prosser J. I. Gill B. P. Pluske J. R. Mayer C. D. Musk C. C. Kelly D. 2009. Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces. BMC Biol.  7: 79. https://doi.org/19930542 Google Scholar CrossRef Search ADS PubMed  Murray C. B. Chu S. Zeitlin P. L. 1996. Gestational and tissue-specific regulation of C1C-2 chloride channel expression. Am. J. Physiol.  271: L829– L837. https://doi.org/8944727 Google Scholar PubMed  Myllynen P. Immonen E. Kummu M. Vähäkangas K. 2009. Developmental expression of drug metabolizing enzymes and transporter proteins in human placenta and fetal tissues. Expert Opin. Drug Metab. Toxicol.  5: 1483– 1499. https://doi.org/19785513 Google Scholar CrossRef Search ADS PubMed  Nanthakumar N. N. Dai D. Meng D. Chaudry N. Newburg D. S. Walker W. A. 2005. Regulation of intestinal ontogeny: Effect of glucocorticoids and luminal microbes on galactosyltransferase and trehalase induction in mice. Glycobiology  15: 221– 232. https://doi.org/15483270 Google Scholar CrossRef Search ADS PubMed  Nelson K. E. Zinder S. H. Hance I. Burr P. Odongo D. Wasawo D. Odenyo A. Bishop R. 2003. Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tract: Insights into an unexplored niche. Environ. Microbiol.  5: 1212– 1220. https://doi.org/14641599 Google Scholar CrossRef Search ADS PubMed  Newburg D. S. 2009. Neonatal protection by an innate immune system of human milk consisting of oligosaccharides and glycans. J. Anim. Sci.  87( Suppl.): 26– 34. https://doi.org/19028867 Google Scholar CrossRef Search ADS PubMed  Newburg D. S. Walker W. A. 2007. Protection of the neonate by the innate immune system of developing gut and of human milk. Pediatr. Res.  61: 2– 8. https://doi.org/17211132 Google Scholar CrossRef Search ADS PubMed  Nutten S. Schumann A. Donnicola D. Mercenier A. Rami S. Garcia-Rodenas C. L. 2007. Antibiotic administration early in life impairs specific humoral responses to an oral antigen and increases intestinal mast cell numbers and mediator concentrations. Clin. Vaccine Immunol.  14: 190– 197. https://doi.org/17151185 Google Scholar CrossRef Search ADS PubMed  O'Keefe S. J. 2008. Nutrition and colonic health: The critical role of the microbiota. Curr. Opin. Gastroenterol.  24: 51– 58. https://doi.org/18043233 Google Scholar CrossRef Search ADS PubMed  Ogra P. L. 2010. Ageing and its possible impact on mucosal immune responses. Ageing Res. Rev.  9: 101– 106. https://doi.org/19664726 Google Scholar CrossRef Search ADS PubMed  Okada K. Fujii T. Ohtsuka Y. Yamakawa Y. Izumi H. Yamashiro Y. Shimizu T. 2010. Overfeeding can cause NEC-like enterocolitis in premature rat pups. Neonatology  97: 218– 224. https://doi.org/19887849 Google Scholar CrossRef Search ADS PubMed  Oste M. Van Haver E. Thymann T. Sangild P. T. Weyns A. Van Ginneken C. J. 2010. Formula induces intestinal apoptosis in preterm pigs within a few hours of feeding. J. Parenter. Enteral. Nutr.  34: 271– 279. Google Scholar CrossRef Search ADS   Palazzo M. Balsari A. Rossini A. Selleri S. Calcaterra C. Gariboldi S. Zanobbio L. Arnaboldi F. Shirai Y. F. Serrao G. Rumio C. 2007. Activation of enteroendocrine cells via TLRs induces hormone, chemokine, and defensin secretion. J. Immunol.  178: 4296– 4303. https://doi.org/17371986 Google Scholar CrossRef Search ADS PubMed  Penders J. Stobberingh E. E. van den Brandt P. A. Thijs C. 2007. The role of the intestinal microbiota in the development of atopic disorders. Allergy  62: 1223– 1236. https://doi.org/17711557 Google Scholar CrossRef Search ADS PubMed  Penders J. Thijs C. Vink C. Stelma F. F. Snijders B. Kummeling I. van den Brandt P. A. Stobberingh E. E. 2006. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics  118: 511– 521. https://doi.org/16882802 Google Scholar CrossRef Search ADS PubMed  Poroyko V. White J. R. Wang M. Donovan S. Alverdy J. Liu D. C. Morowitz M. J. 2010. Gut microbial gene expression in mother-fed and formula-fed piglets. PLoS ONE  5: e12459. https://doi.org/20805981 Google Scholar CrossRef Search ADS PubMed  Pritchard J. A. 1966. Fetal swallowing and amniotic fluid volume. Obstet. Gynecol.  28: 606– 610. https://doi.org/5332288 Google Scholar PubMed  Rechkemmer G. Rönnau K. von Engelhardt W. 1988. Fermentation of polysaccharides and absorption of short chain fatty acids in the mammalian hindgut. Comp. Biochem. Physiol. A  90: 563– 568. https://doi.org/2902962 Google Scholar CrossRef Search ADS   Richardson W. M. Sodhi C. P. Russo A. Siggers R. H. Afrazi A. Gribar S. C. Neal M. D. Dai S. Prindle T. Branca M. Ma C. Ozolek J. Hackam D. J. 2010. Nucleotide-binding oligomerization domain-2 inhibits toll-like receptor-4 signaling in the intestinal epithelium. Gastroenterology  139: 904– 917. https://doi.org/20580721 Google Scholar CrossRef Search ADS PubMed  Rodriguez N. A. Meier P. P. Groer M. W. Zeller J. M. Engstrom J. L. Fogg L. 2010. A pilot study to determine the safety and feasibility of oropharyngeal administration of own mother's colostrum to extremely low-birth-weight infants. Adv. Neonatal Care  10: 206– 212. https://doi.org/20697221 Google Scholar CrossRef Search ADS PubMed  Rumbo M. Schiffrin E. J. 2005. Ontogeny of intestinal epithelium immune functions: Developmental and environmental regulation. Cell. Mol. Life Sci.  62: 1288– 1296. https://doi.org/15971104 Google Scholar CrossRef Search ADS PubMed  Salminen S. Gibson G. R. McCartney A. L. Isolauri E. 2004. Influence of mode of delivery on gut microbiota composition in seven year old children. Gut  53: 1388– 1389. https://doi.org/15306608 Google Scholar CrossRef Search ADS PubMed  Salzman N. H. Hung K. Haribhai D. Chu H. Karlsson-Sjöberg J. Amir E. Teggatz P. Barman M. Hayward M. Eastwood D. Stoel M. Zhou Y. Sodergren E. Weinstock G. M. Bevins C. L. Williams C. B. Bos N. A. 2010. Enteric defensins are essential regulators of intestinal microbial ecology. Nat. Immunol.  11: 76– 83. https://doi.org/19855381 Google Scholar CrossRef Search ADS PubMed  Sanderson I. R. 1999. The physicochemical environment of the neonatal intestine. Am. J. Clin. Nutr.  69: 1028S– 1034S. https://doi.org/10232645 Google Scholar PubMed  Sanderson I. R. 2004. Short chain fatty acid regulation of signaling genes expressed by the intestinal epithelium. J. Nutr.  134: 2450S– 2454S. https://doi.org/15333741 Google Scholar CrossRef Search ADS PubMed  Sangild P. T. Siggers R. H. Schmidt M. Elnif J. Bjornvad C. R. Thymann T. Grondahl M. L. Hansen A. K. Jensen S. K. Boye M. Moelbak L. Buddington R. K. Westrom B. R. Holst J. J. Burrin D. G. 2006. Diet- and colonization-dependent intestinal dysfunction predisposes to necrotizing enterocolitis in preterm pigs. Gastroenterology  130: 1776– 1792. https://doi.org/16697741 Google Scholar CrossRef Search ADS PubMed  Schell M. A. Karmirantzou M. Snel B. Vilanova D. Berger B. Pessi G. Zwahlen M. C. Desiere F. Bork P. Delley M. Pridmore R. D. Arigoni F. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. USA  99: 14422– 14427. https://doi.org/12381787 Google Scholar CrossRef Search ADS   Schrenzel M. D. Witte C. L. Bahl J. Tucker T. A. Fabian N. Greger H. Hollis C. Hsia G. Siltamaki E. Rideout B. A. 2010. Genetic characterization and epidemiology of helicobacters in non-domestic animals. Helicobacter  15: 126– 142. https://doi.org/20402815 Google Scholar CrossRef Search ADS PubMed  Schumann A. Nutten S. Donnicola D. Comelli E. M. Mansourian R. Cherbut C. Corthesy-Theulaz I. Garcia-Rodenas C. 2005. Neonatal antibiotic treatment alters gastrointestinal tract developmental gene expression and intestinal barrier transcriptome. Physiol. Genomics  23: 235– 245. https://doi.org/16131529 Google Scholar CrossRef Search ADS PubMed  Selleri S. Palazzo M. Deola S. Wang E. Balsari A. Marincola F. M. Rumio C. 2008. Induction of pro-inflammatory programs in enteroendocrine cells by the Toll-like receptor agonists flagellin and bacterial LPS. Int. Immunol.  20: 961– 970. https://doi.org/18544573 Google Scholar CrossRef Search ADS PubMed  Sharma R. Young C. Neu J. 2010. Molecular modulation of intestinal epithelial barrier: Contribution of microbiota. J. Biomed. Biotechnol.  2010: 305879. https://doi.org/20150966 Google Scholar PubMed  Sherman P. M. Cabana M. Gibson G. R. Koletzko B. V. Neu J. Veereman-Wauters G. Ziegler E. E. Walker W. A. 2009. Potential roles and clinical utility of prebiotics in newborns, infants, and children: Proceedings from a global prebiotic summit meeting. J. Pediatr.  155: S61– S70. https://doi.org/19840609 Google Scholar CrossRef Search ADS PubMed  Shibolet O. Podolsky D. K. 2007. TLRs in the gut. IV. Negative regulation of Toll-like receptors and intestinal homeostasis: Addition by subtraction. Am. J. Physiol. Gastrointest. Liver Physiol.  292: G1469– G1473. https://doi.org/17554134 Google Scholar CrossRef Search ADS PubMed  Shreiner A. Huffnagle G. B. Noverr M. C. 2008. The “Microflora Hypothesis” of allergic disease. Adv. Exp. Med. Biol.  635: 113– 134. https://doi.org/18841708 Google Scholar CrossRef Search ADS PubMed  Siggers R. H. Siggers J. Thymann T. Boye M. Sangild P. T. 2010. Nutritional modulation of the gut microbiota and immune system in preterm neonates susceptible to necrotizing enterocolitis. J. Nutr. Biochem.  https://doi.org/10.1016/j.jnutbio.2010.08.002. https://doi.org/21193301 Singhal A. Macfarlane G. Macfarlane S. Lanigan J. Kennedy K. Elias-Jones A. Stephenson T. Dudek P. Lucas A. 2008. Dietary nucleotides and fecal microbiota in formula-fed infants: A randomized controlled trial. Am. J. Clin. Nutr.  87: 1785– 1792. https://doi.org/18541569 Google Scholar PubMed  Slack E. Hapfelmeier S. Stecher B. Velykoredko Y. Stoel M. Lawson M. A. Geuking M. B. Beutler B. Tedder T. F. Hardt W. D. Bercik P. Verdu E. F. McCoy K. D. Macpherson A. J. 2009. Innate and adaptive immunity cooperate flexibly to maintain host-microbiota mutualism. Science  325: 617– 620. https://doi.org/19644121 Google Scholar CrossRef Search ADS PubMed  Sodhi C. Richardson W. Gribar S. Hackam D. J. 2008. The development of animal models for the study of necrotizing enterocolitis. Dis. Model. Mech.  1: 94– 98. https://doi.org/19048070 Google Scholar CrossRef Search ADS PubMed  Sperandio V. Torres A. G. Jarvis B. Nataro J. P. Kaper J. B. 2003. Bacteria-host communication: The language of hormones. Proc. Natl. Acad. Sci. USA  100: 8951– 8956. https://doi.org/12847292 Google Scholar CrossRef Search ADS   Stevens, C. E., and I. D. Hume 1995. Comparative Physiology of the Vertebrate Digestive System.  2nd ed. Cambridge Univ. Press, New York, NY. Stewart J. A. Chadwick V. S. Murray A. 2005. Investigations into the influence of host genetics on the predominant eubacteria in the faecal microflora of children. J. Med. Microbiol.  54: 1239– 1242. https://doi.org/16278440 Google Scholar CrossRef Search ADS PubMed  Sullivan A. Nord C. E. 2005. Probiotics and gastrointestinal diseases. J. Intern. Med.  257: 78– 92. https://doi.org/15606379 Google Scholar CrossRef Search ADS PubMed  Suzuki Y. A. Lopez V. Lönnerdal B. 2005. Mammalian lactoferrin receptors: Structure and function. Cell. Mol. Life Sci.  62: 2560– 2575. https://doi.org/16261254 Google Scholar CrossRef Search ADS PubMed  Tanaka S. Kobayashi T. Songjinda P. Tateyama A. Tsubouchi M. Kiyohara C. Shirakawa T. Sonomoto K. Nakayama J. 2009. Influence of antibiotic exposure in the early postnatal period on the development of intestinal microbiota. FEMS Immunol. Med. Microbiol.  56: 80– 87. https://doi.org/19385995 Google Scholar CrossRef Search ADS PubMed  Tannock G. W. Fuller R. Pedersen K. 1990. Lactobacillus succession in the piglet digestive tract demonstrated by plasmid profiling. Appl. Environ. Microbiol.  56: 1310– 1316. https://doi.org/2339885 Google Scholar PubMed  Thymann T. Møller H. K. Stoll B. Støy A. C. Buddington R. K. Bering S. B. Jensen B. B. Olutoye O. O. Siggers R. H. Mølbak L. Sangild P. T. Burrin D. G. 2009. Carbohydrate maldigestion induces necrotizing enterocolitis in preterm pigs. Am. J. Physiol. Gastrointest. Liver Physiol.  297: G1115– G1125. https://doi.org/19808655 Google Scholar CrossRef Search ADS PubMed  Van de Perre P. 2003. Transfer of antibody via mother's milk. Vaccine  21: 3374– 3376. https://doi.org/12850343 Google Scholar CrossRef Search ADS PubMed  Van Haver E. R. Sangild P. T. Oste M. Siggers J. L. Weyns A. L. Van Ginneken C. J. 2009. Diet-dependent mucosal colonization and interleukin-1β responses in preterm pigs susceptible to necrotizing enterocolitis. J. Pediatr. Gastroenterol. Nutr.  49: 90– 98. https://doi.org/19516189 Google Scholar CrossRef Search ADS PubMed  Vanhoutvin S. A. Troost F. J. Hamer H. M. Lindsey P. J. Koek G. H. Jonkers D. M. Kodde A. Venema K. Brummer R. J. 2009. Butyrate-induced transcriptional changes in human colonic mucosa. PLoS ONE  4: e6759. https://doi.org/19707587 Google Scholar CrossRef Search ADS PubMed  Veereman G. 2007. Pediatric applications of inulin and oligofructose. J. Nutr.  137( Suppl.): 2585S– 2589S. https://doi.org/17951508 Google Scholar CrossRef Search ADS PubMed  Venkatesh M. P. Abrams S. A. 2010. Oral lactoferrin for the prevention of sepsis and necrotizing enterocolitis in preterm infants. Cochrane Database Syst. Rev.  12: CD007137. https://doi.org/20464748 Voltaire 1929. Candide.  Random House Inc., New York, NY. Waligora-Dupriet A. J. Dugay A. Auzeil N. Nicolis I. Rabot S. Huerre M. R. Butel M. J. 2009. Short-chain fatty acids and polyamines in the pathogenesis of necrotizing enterocolitis: Kinetics aspects in gnotobiotic quails. Anaerobe  15: 138– 144. https://doi.org/19233303 Google Scholar CrossRef Search ADS PubMed  Watanabe S. Matsushita K. Stokes J. B. McCray P. B.Jr 1998. Developmental regulation of epithelial sodium channel subunit mRNA expression in rat colon and lung. Am. J. Physiol.  275: G1227– G1235. https://doi.org/9843757 Google Scholar PubMed  Williams A. M. Probert C. S. Stepankova R. Tlaskalova-Hogenova H. Phillips A. Bland P. W. 2006. Effects of microflora on the neonatal development of gut mucosal T cells and myeloid cells in the mouse. Immunology  119: 470– 478. https://doi.org/16995882 Google Scholar CrossRef Search ADS PubMed  Winkler P. Ghadimi D. Schrezenmeir J. Kraehenbuhl J. P. 2007. Molecular and cellular basis of microflora-host interactions. J. Nutr.  137( Suppl. 2): 756S– 772S. https://doi.org/17311973 Google Scholar CrossRef Search ADS PubMed  Wolfs T. G. Derikx J. P. Hodin C. M. Vanderlocht J. Driessen A. de Bruïne A. P. Bevins C. L. Lasitschka F. Gassler N. van Gemert W. G. Buurman W. A. 2010. Localization of the lipopolysaccharide recognition complex in the human healthy and inflamed premature and adult gut. Inflamm. Bowel Dis.  16: 68– 75. https://doi.org/20014022 Google Scholar CrossRef Search ADS PubMed  Wong J. M. de Souza R. Kendall C. W. Emam A. Jenkins D. J. 2006. Colonic health: Fermentation and short chain fatty acids. J. Clin. Gastroenterol.  40: 235– 243. https://doi.org/16633129 Google Scholar CrossRef Search ADS PubMed  Yu V. Y. 2002. Scientific rationale and benefits of nucleotide supplementation of infant formula. J. Paediatr. Child Health  38: 543– 549. https://doi.org/12410863 Google Scholar CrossRef Search ADS PubMed  Zeuthen L. H. Fink L. N. Metzdorff S. B. Kristensen M. B. Licht T. R. Nellemann C. Frøkiaer H. 2010. Lactobacillus acidophilus induces a slow but more sustained chemokine and cytokine response in naïve foetal enterocytes compared to commensal Escherichia coli. BMC Immunol.  11: 2. https://doi.org/20085657 Google Scholar CrossRef Search ADS PubMed  Zocco M. A. Ainora M. E. Gasbarrini G. Gasbarrini A. 2007. Bacteroides thetaiotaomicron in the gut: Molecular aspects of their interaction. Dig. Liver Dis.  39: 707– 712. https://doi.org/17602905 Google Scholar CrossRef Search ADS PubMed  Zoumpopoulou G. Tsakalidou E. Dewulf J. Pot B. Grangette C. 2009. Differential crosstalk between epithelial cells, dendritic cells and bacteria in a co-culture model. Int. J. Food Microbiol.  131: 40– 51. https://doi.org/19264370 Google Scholar CrossRef Search ADS PubMed  Footnotes 1 Based on a presentation at the Companion Animals Symposium titled “Microbes and Health,” at the Joint Annual Meeting, July 11 to 15, 2010, Denver, Colorado. The symposium was sponsored, in part, by Hill's Pet Nutrition Inc. (Topeka, KS) and The Procter & Gamble Company (Cincinnati, OH), with publication sponsored by the Journal of Animal Science and the American Society of Animal Science. American Society of Animal Science

Journal

Journal of Animal ScienceOxford University Press

Published: May 1, 2011

There are no references for this article.