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Dynamics of methanogenesis, ruminal fermentation and fiber digestibility in ruminants following elimination of protozoa: a meta-analysis

Dynamics of methanogenesis, ruminal fermentation and fiber digestibility in ruminants following... Background: Ruminal microbes are vital to the conversion of lignocellulose-rich plant materials into nutrients for ruminants. Although protozoa play a key role in linking ruminal microbial networks, the contribution of protozoa to rumen fermentation remains controversial; therefore, this meta-analysis was conducted to quantitatively summarize the temporal dynamics of methanogenesis, ruminal volatile fatty acid (VFA) profiles and dietary fiber digestibility in ruminants following the elimination of protozoa (also termed defaunation). A total of 49 studies from 22 publications were evaluated. Results: The results revealed that defaunation reduced methane production and shifted ruminal VFA profiles to consist of more propionate and less acetate and butyrate, but with a reduced total VFA concentration and decreased dietary fiber digestibility. However, these effects were diminished linearly, at different rates, with time during the first few weeks after defaunation, and eventually reached relative stability. The acetate to propionate ratio and methane production were increased at 7 and 11 wk after defaunation, respectively. Conclusions: Elimination of protozoa initially shifted the rumen fermentation toward the production of more propionate and less methane, but eventually toward the production of less propionate and more methane over time. Keywords: Defaunation, Fiber digestibility, Meta-analysis, Methane production, Rumen fermentation Introduction recovery efficiency is reduced by 38% when the substrate The rumen provides an ideal habitat for protozoa, whose (glucose) is fermented into acetate but increased by 9% 5 6 concentration can reach 10 –10 cells/mL. In return, when fermented into propionate [3, 4]. Protozoa are im- protozoa serve important functions in the rumen micro- portant ruminal hydrogen (H ) producers, and the pro- bial ecosystem, such as predation, competition for nutri- duced H is mostly converted into methane (CH )by 2 4 ents, and involvement in symbiotic relationships with methanogens situated inside protozoa or on their exter- other microorganisms [1, 2]. Protozoa prey on bacteria nal surface [5–7]. The CH emissions from ruminants and fungal spores, but are preferentially retained in the represent 2–12% dietary energy loss [8]. Therefore, the rumen, thus reducing the postruminal microbial protein presence of protozoa seems to adversely affect animals’ supply [3]. Protozoa compete with amylolytic bacteria energy efficiency. for dietary starch, which is mostly fermented into acetate Complete removal of ruminal protozoa, termed defau- by protozoa [2] while mostly into propionate by amylo- nation, has been suggested as an efficient method for re- lytic bacteria [3, 4]. For host animals, the energy ducing CH emissions and enhancing propionate fermentation [9, 10], but these effects have not been consistently observed in studies investigating this * Correspondence: yaojunhu2004@sohu.com 112method [11–13]. Hegarty et al. [12]and Morgavietal. College of Animal Science and Technology, Northwest A&F University, [13] suggested that the duration of defaunation might be Yangling, Shaanxi, China Full list of author information is available at the end of the article © The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 2 of 9 responsible for this inconsistency, but the temporal dynam- variables for extraction. The relevant variables for this ics of methanogenesis and ruminal volatile fatty acid (VFA) meta-analysis included the daily CH production, rumi- profiles after defaunation are difficult to determine experi- nal VFA profiles and dietary fiber total-tract digestibility. mentally because of the difficulties in raising defaunated an- The faunation states of control animals included the imals over a long-term [14]. Meta-analysis is a statistical natural ruminal ecosystem without any treatment or re- method that combines the results from multiple studies to introduction of protozoa after partial defaunation, which achieve a more precise estimate of treatment effects and to appeared to be restored quickly after withdrawal of the explore the potential sources of between-study heterogen- protozoa-inhibiting treatment [18, 19]. The control ani- eity [15, 16]. Two prior meta-analyses [14, 17]havesum- mals into which protozoa were reintroduced after marized the combined responses of rumen fermentation to complete defaunation were excluded from the analysis, defaunation; however, the combined effects on ruminal because preliminary analysis showed that high hetero- VFA profiles were also inconsistent between them, and geneity existed between the faunation and refaunation neither of them explored the time-dependent effects. subgroups (see Additional file 1). Protozoa-free animals Therefore, the current meta-analysis was conducted to were obtained through either the absence of protozoa quantitatively summarize the temporal dynamics of from birth (BF) or artificial removal of protozoa from methanogenesis, ruminal VFA profiles and dietary fiber di- the natural ruminal ecosystem (AF). Artificial defauna- gestibility in ruminants after defaunation, and to explain tion was conducted using chemical agents, such as al- the contribution of the defaunated duration to the kanes and sodium lauryl sulfate, or by applying a rumen between-study heterogeneity. washing technique. The defaunation duration was calcu- lated based on the schedule of experimental activities. Methods The defaunation duration of BF animals was calculated Literature search, screening and data extraction as their age shortened by 4 wk, because ruminal proto- A flowchart detailing the process of literature search, zoa did not appear when newborn calves were fed with screening and data extraction is shown in Fig. 1. The in- milk for 30 d [2], and the concentration of protozoa clusion criteria for the studies were as follows: (1) quickly increased after 5 wk of age [20]. peer-reviewed and published in the English language; (2) The final database included 22 publications, with 49 in complete defaunation in vivo; (3) inclusion of relevant vivo studies that satisfied the inclusion criteria for the 238 papers potentially relevant studies identified from the scientific electronic databases and citations in review papers 169 excluded on the basic of publication type With 45 books, review papers and meeting abstracts With 43 in vitro studies With 81 non-relevant records 47 excluded on the basic of experimental designs With 12 partial defaunation With 20 reintroduced protozoa after complete defaunation With 15 lack of statistical information 22 papers with 49 trials satisfied the inclusion criteria for meta-analysis Data extraction and calculations Preliminary analysis assessment Animal species and number Assessment of Heterogeneity Defaunation methods and duration Publication bias analysis Means and SD of relevant outcomes Meta-analysis and meta-regression analysis Fig. 1 Flow chart of the literature search, screening and data extraction procedures Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 3 of 9 meta-analysis. Summary descriptions of the selected studies homogeneous. When the value of I was over 50%, indi- are provided in Table 1. Briefly, among the 49 selected stud- cating high heterogeneity, studies were combined using a ies, 38 were conducted in sheep, and 11 were conducted in random effects model, based on the assumption that the cattle; 18 measured CH production, 29 measured ruminal expected effect from each study was heterogeneous. VFAs, and 15 measured total-tract fiber digestibility. CH The differences in animal species or ages, daily sampling emissions were measured using the respiration chamber times or dietary forage percentages across the studies caused technique or sulfur hexafluoride tracer technique. Methane that the data of certain relevant variables to vary greatly production was presented in liters per day in most of the acrossthe studies(Table 2). To reduce these potential inter- studies; thus, values presented in grams or kilojoules (kJ) ferences, the effect size in this analysis was estimated via the were converted to liters per day, based on the assumption standardized mean difference (SMD), which was calculated that one mole of CH weighs 16 g or contains 890 kJ of en- as the raw mean difference between the treatment and con- ergy and occupies a volume of 24.5 L (under conditions of trol groups divided by their pooled standard deviations [15]. 25 °C and 1 atmospheric pressure). For example, although cattle CH production in the study by Schönhusen et al. [20] was higher than in other subgroup Data analysis studies involving sheep, it was homogeneous with most of The meta-analysis was performed using Stata 14.1 (Stata them (Additional file 1: Figures S1 and S2). The studies were Corp., Texas, USA). weighted using the inverse of the variance of the differences in means. Details of the calculations used in the Assessment of heterogeneity and effect size meta-analysis are provided by Lean et al. [15]. Between-study variability was quantified via the I statistic, which measures the percentage of variation due to hetero- Meta-regression analysis geneity [15, 21]. When the I value was less than 50%, in- The meta-regression analysis was performed using the dicating low heterogeneity, studies were combined using a Knapp-Hartung restricted maximum likelihood method fixed effects model, which was based on the assumption [22], with the SMD of the individual studies used as the that the expected effect from each study was response variable and the corresponding standard error Table 1 Data sources and characteristics of the studies included in the meta-analysis Source Trials Animal Defaunation duration Outcomes Belanche et al. [44] 2 Sheep 23 wk VFA, digestibility Bird et al. [11] 2 Sheep 11, 26 wk CH , VFA, digestibility Chandramoni et al. [45] 2 Sheep 5, 11 wk CH , digestibility Chaudhary and Srivastava [46] 2 Cattle 18 wk Digestibility Eadie and Gill [47] 2 Sheep 22, 55 wk VFA Eugène et al. [48] 4 Sheep 10, 14, 18, 22 wk Digestibility Frumholtz [38] 3 Sheep 5, 26, 52 wk VFA Hegarty et al. [12] 4 Sheep 12, 22, 24, 33 wk CH , VFA Kasuya et al. [49] 1 Cattle 21 wk Digestibility Kreuzer et al. [50] 3 Sheep 9, 10, 11 wk CH Morgavi et al. [13] 2 Sheep 6 wk, 2 yr CH , VFA Nagaraja et al. [51] 2 Sheep 14 wk VFA Nguyen et al. [33] 2 Sheep 9 wk CH , VFA, digestibility Ozutsumi et al. [35] 1 Cattle 14 wk VFA Santra and Karim [52] 2 Sheep 12 wk Digestibility Santra and Karim [53] 3 Sheep 14 wk Digestibility Santra et al. [54] 2 Sheep 8 wk Digestibility Schönhusen et al. [20] 4 Cattle 4, 5, 6, 7 wk CH , VFA, digestibility Sultana et al. [55] 1 Cattle 14 wk VFA Williams and Dinusson [56] 2 Cattle 30, 56 wk VFA Yáñez-Ruiz et al. [57] 1 Sheep 18 wk VFA Zhou et al. [58] 2 Sheep 5 wk CH , VFA 4 Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 4 of 9 Table 2 Data summary and meta-analysis of relevant variables based on all of the selected studies Variables No. Defaunation group Faunation group Meta-analysis of 2 n Mean SD n Mean SD I , % SMD P-value trials CH , L/d 18 126 20.8 12.4 129 23.4 12.0 71.9 −0.602 0.037 Total VFA, mmol/L 29 211 78.8 29.7 212 87.1 31.3 44.2 −0.549 < 0.001 Individual VFA molar proportion, % Acetate 29 210 67.7 5.6 211 66.3 4.3 67.8 0.358 0.083 Propionate 29 210 21.0 4.8 211 20.6 3.1 73.5 0.150 0.515 Butyrate 27 202 8.2 2.0 203 10.2 2.8 68.3 −1.026 < 0.001 A:P 18 78 3.6 1.6 81 3.5 0.7 77.0 −0.284 0.493 Total-tract fiber digestibility, % NDF 15 109 55.0 11.6 109 58.1 11.8 55.7 −2.063 < 0.001 ADF 11 82 42.8 2.7 82 45.7 3.7 69.8 −3.075 < 0.001 n number of animals, I percentage of heterogeneity across studies, SMD standardized mean difference, A:P acetate: propionate ratio, NDF neutral detergent fiber, ADF acid detergent fiber of the SMD used as the variance. The percentage of 76.8% of the between-study heterogeneity (I = 76.2%) between-study heterogeneity explained by the covariate during the linear phase, and no between-study hetero- (defaunation duration) was quantified via the adjusted geneity (I = 0.0%) was observed after 11 wk (plateau R value. phase), suggesting that little fluctuation occurred during Preliminary analysis showed that the temporal SMD the plateau phase. Interestingly, the defaunated animals dynamics after defaunation included a linear phase during the plateau phase presented higher CH produc- followed by a plateau phase. The durations of the linear tions (SMD = 0.313, P = 0.039) than the control animals. phase and plateau phase for each outcome were dependent on the highest adjusted R of the Ruminal VFA profiles and total-tract fiber digestibility meta-regression analysis and the minimum I of the het- dynamics during adaptation to defaunation erogeneity analysis, respectively; therefore, the two Consistent with the temporal dynamics of CH produc- phases might overlap over a short duration. The prob- tion after defaunation, the ruminal VFA profiles dynam- ability levels were set at P < 0.05 for significance and ics also included a linear phase (≤ 11 wk) and a plateau 0.05 ≤ P < 0.10 for a trend. phase (≥ 7 wk) (Table 3). After defaunation, decreases in the acetate proportion, butyrate proportion and A:P Results (intercept = − 4.086, − 7.059 and − 6.737, respectively), Effect size and heterogeneity across all the studies and an increase in the propionate proportion (intercept The meta-analysis based on all the selected studies = 7.306) were estimated (P < 0.01). These alterations de- showed that elimination of rumen protozoa reduced (P creased linearly (P < 0.01) at different rates over the first < 0.05) CH production, ruminal VFA concentration, 11 wk of defaunation; instead, the ruminal acetate pro- the proportion of butyrate and dietary fiber digestibility, portion (SMD = 0.748, P < 0.001) and A:P (SMD = 0.915, and tended to increase (P = 0.083) the proportion of P = 0.016) were higher, and the propionate proportion acetate (Table 2). However, the heterogeneity across the (SMD = − 0.366, P = 0.033) was lower in defaunated ani- studies was considerable (I > 50%) for most of the re- mals than faunated animals during the plateau phase. sponses to defaunation, except for the ruminal VFA con- Compared with faunated animals, defaunated animals centration (I = 44.2%). exhibited a reduced total VFA concentration (intercept = − 1.883 and P = 0.008), and the reduction decreased Methanogenesis dynamics during adaptation to weekly by 0.132 (P = 0.048) until 12 wk (Table 3). The defaunation duration of defaunation could explain 99.9% of the Compared with that of faunation, the effect size of between-study heterogeneity during the linear phase, al- defaunation on CH emissions presented a linear rela- though the heterogeneity (35.5%) was low. The decrease tionship over time during the first 12 wk (linear phase) in total VFA concentration was still observed (SMD = − after defaunation (Fig. 2 and Table 3): CH production 0.424, P < 0.001) in defaunated animals during the plat- was reduced by defaunation (intercept = − 5.484, P = eau phase (≥ 11 wk). 0.003), and the reduction decreased weekly by 0.486 (P Compared with that of faunation, the effect sizes of = 0.003) until 12 wk. The defaunation duration explained defaunation on total-tract fiber digestibility were linearly Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 5 of 9 ac Fig. 2 Methanogenesis dynamics during adaptation to defaunation. The temporal SMD (standardized mean difference) dynamics (a) after defaunation included a linear phase (≤ 12 wk, yellow portion) followed by a plateau phase (≥ 11 wk, blue portion). The overlap of two phases were the green portion. The linear phase was reanalyzed by meta-regression analysis (b), and the plateau phase was reanalyzed by meta-analysis (c). Circles in the graph represent the estimates from each study, and the size of the circles represents the percentage of weight of each study. The blue diamond represent in panel (c) represents the combined effect and its 95% confidence interval related to defaunation duration (Table 3): total-tract considerable for most of the responses to defaunation. Ex- NDF and ADF digestibility (intercept = − 4.458 and − cess between-study variance increases the risk of incorrect 6.276, respectively) were reduced (P < 0.01) after defau- average effect sizes when combining studies [15]. For ex- nation, and the reductions decreased weekly (P < 0.05) ample, the present meta-analysis based on all the studies by 0.153 and 0.213, respectively, until 23 wk, which was showed that defaunation tended to increase the proportion the longest studied duration in the available data. of ruminal acetate but had no effect on the proportion of propionate. These findings were consistent with a recent Discussion meta-analysis by Newbold et al. [18] but inconsistent with Effect size and heterogeneity across all the studies that of Eugène et al. [14], who reported that defaunation in- Based on all the selected studies, this meta-analysis showed duced a reduction in the ruminal acetate proportion and an that complete elimination of rumen protozoa generated ad- increase in the propionate proportion. Therefore, the po- verse effects on the ruminal VFA concentration, butyrate tential source of heterogeneity among the studies needs to proportion and dietary fiber digestibility; these findings be explored to better understand the responses to treat- were consistent with the results of previous meta-analyses ment, and this additional exploration is also one of most [14, 18]. However, the heterogeneity across the studies was important tasks of meta-analysis [15]. Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 6 of 9 Table 3 Methane emissions, ruminal VFA profiles and total-tract fiber digestibility dynamics during the linear phase and plateau phase Meta-regression analysis for the linear phase Meta-analysis for the plateau phase 2 2 2 Duration, wk No. of trials I , % Intercept P-value Coefficient P-value Adjusted R , % Duration, wk No. of trials I , % Pooled effect size P-value CH ≤ 12 13 76.2 −5.484 0.001 0.486 0.003 76.8 ≥ 11 9 0.0 0.313 0.039 TVFA ≤ 12 12 35.5 −1.883 0.008 0.132 0.048 99.9 ≥ 11 19 46.7 −0.424 < 0.001 Individual VFA molar proportion Acetate ≤ 11 11 76.8 −4.086 0.004 0.563 0.004 76.7 ≥ 7 22 47.5 0.748 < 0.001 Propionate ≤ 11 11 84.5 7.306 < 0.001 −0.898 < 0.001 92.2 ≥ 7 22 51.2 −0.366 0.033 Butyrate ≤ 11 11 80.6 −7.059 < 0.001 0.732 0.001 92.3 ≥ 7 20 54.0 −0.582 0.002 A:P ≤ 11 10 78.6 −6.737 0.001 0.884 0.002 90.8 ≥ 7 10 59.2 0.915 0.016 Total-tract fiber digestibility NDF ≤ 23 15 55.7 −4.458 < 0.001 0.153 0.005 85.0 ADF ≤ 23 11 69.8 −6.276 0.001 0.213 0.030 45.1 2 2 I , percentage of heterogeneity across studies; Intercept, estimate of the effect size after defaunation; Coefficient, estimate of the change in effect size per week following defaunation; Adjusted R , percentage of between-study variance explained by the defaunation duration; TVFA, total VFA Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 7 of 9 The role of protozoa in rumen carbohydrate metabolism pooled analysis, in which the number of replicate ani- Despite the fact that protozoa make up a large portion mals was increased by combining the results of relevant of the rumen biomass, their role in ruminal fermentation individual studies [15, 16]. The CH emissions from ru- and their contribution to the metabolism and nutrition minants contribute to global greenhouse gas emissions of the host are still topics of substantial controversy [2, and represent energy loss for the animals [8, 27, 28]. 14], due to the difficulty of pure cultivation of protozoa Therefore, the potential environmental protection and in vitro. Rumen protozoa are not essential to the animal energy-saving values following defaunation were grad- for survival, and defaunation has therefore been used to ually lost and eventually became negative. estimate the role of ciliate protozoa in rumen function. Acetate production during rumen fermentation is ac- However, the adapted alteration of other microbe after companied by reducing equivalents ([H]) production, defaunation may interfere with such estimations. Hence, whereas propionate production is accompanied by [H] the estimated intercept from the meta-regression ana- consumption [29]; the excess [H] is converted to H . lysis more accurately reflected the role that protozoa The shift in the VFA profiles from propionate to acetate played in rumen fermentation. Reductions in the rumi- following defaunation increased the H available for nal acetate proportion, butyrate proportion and CH methanogenesis, at least partially explaining the production after complete removal of ruminal protozoa time-related changes in CH production observed in this would be expected because protozoa ferment carbohy- study. When glucose is metabolized into acetate, propi- drates into acetate, butyrate and H [2], and the H pro- onate or butyrate, the energy efficiency relative to glu- 2 2 duced is mostly converted to CH by methanogens cose for animal is 62%, 109% and 78%, respectively [3, situated inside protozoa or on their external surface [5– 4]. Propionate fermentation is most energy efficient, due 7]. A strong correlation between CH emissions and to assimilating energy from H and being the main pre- 4 2 protozoa concentration has been reported [23], and cursor of gluconeogenesis in animals [3, 30]. In rumi- protozoa-associated methanogens have been estimated nants, the VFAs produced in the rumen satisfy up to to be responsible for 37% of CH production by rumi- 70% of energy requirements [30]. Shabat et al. [31] and nants [5]. Additionally, ruminal protozoa possess a full Weimer et al. [32] observed that the ruminal total VFA complement of hydrolytic enzymes for fermentation of concentration and propionate proportion were higher in the major components of feedstuffs, and certain ciliates highly efficient cows than in cows with low efficiency. present a wide range of fibrolytic enzyme genes, ingest Therefore, the decreases in the ruminal total VFA concen- small plant particles and use cell wall carbohydrates [18, tration and propionate proportion during the plateau 24]. Moreover, protozoa can indirectly contribute to ru- phase also suggested that the elimination of rumen proto- minal degradation kinetics by maintaining a suitable zoa adversely affected the energy supply of animals in a rumen fermentation environment, for example, by scav- long run. enging oxygen to maintain anaerobiosis and slowing the The time-related variations in CH , VFA profiles and rate of starch fermentation to maintain a proper ruminal dietary fiber digestibility implied a series of complex pH [24], which favors the development and activity of changes in the ruminal ecosystem over the course of bacteria and fungi [25, 26]. Therefore, the reductions in defaunation. Nguyen et al. [33] reported that rumen mi- dietary fiber digestibility and ruminal total VFA concen- crobes had likely not stabilized after 12 wk of defauna- tration observed in this study would be expected after tion, which agrees with our results showing that the the complete removal of ruminal protozoa. linear phase for ruminal VFA profiles and CH emissions lasted 11 wk and 12 wk, respectively. When sudden Temporal dynamics during adaptation to defaunation major changes are made in the diet, it takes approxi- Although protozoa are important ruminal H producers mately 2 wk for the new microbial population balance to and exhibit interspecies H transfer with methanogens, become established [34]; the much longer linear phase as- we found that the effects of short- and long-term defau- sociated with defaunation suggests that protozoa play an nation on CH production were opposite. This finding important role in the ruminal ecosystem. Ruminal metha- supports the conclusion of Morgavi et al. [13], who nogens appear to develop more slowly than bacteria fol- showed that there was not a simple cause-effect relation- lowing defaunation [13]. Hristov et al. [28] noted that ship between rumen protozoa and methanogenesis. Bird reductions in the population of protozoa-associated et al. [11] and Hegarty et al. [12] observed higher CH methanogens might be compensated by an increase in the production (although not significantly so) in long-term population of bacteria- or rumen fluid-associated metha- defaunated ewes (11 and 26 wk) and lambs (12 to 33 nogens, and Mosoni et al. [26] found that long-term wk) than in faunated animals. The significant increasing defaunation (2 yr) increased the abundance of methano- effect of long-term defaunation on CH production de- gens. In addition, ruminal protozoa elimination results in tected in this meta-analysis can be attributed to the increased bacterial abundance and changes in bacterial Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 8 of 9 communities [35, 36]; defaunation has been shown to in- P-value of publication bias is presented. SMD = standardized mean crease the anaerobic fungal population by two fold [37] difference, se = standard error. (DOCX 1373 kb) and the Ruminococcaceae population by six fold [36]. Frumholtz [38] found that long-term defaunation (6 mo) Abbreviations ADF: Acid detergent fiber; AP: Acetate to propionate ratio; NDF: Neutral increased the abundance of cellulolytic bacteria. Similar to detergent fiber; SMD: Standardized mean difference; VFA: Volatile fatty acids protozoa, fungi and cellulolytic bacteria are also the main ruminal cellulolytic and H -producing microbes that gen- Acknowledgments erate acetate, butyrate and/or H as primary end products The authors thank Prof. Chang Xu (Chinese Evidence-Based Medicine Center and Chinese Cochrane Center, West China Hospital, Sichuan University) for [29, 39]. Therefore, it can be concluded that the increase help with data analysis. in the populations of methanogens, fungi and cellulolytic bacteria following defaunation gradually counteracts the Funding This work was supported by the National Key Research and Development defaunation-induced reductions in dietary fiber digestibil- Program of China (grant number: 2017YFD0500500). ity, ruminal A:P and CH production, which may confirm an earlier theory of Weimer [40] indicating that the mul- Availability of data and materials tiple microbial taxa in the ruminal community show func- All the datasets were presented in the main manuscript (reference list in Table 1) and available to readers. tional redundancy (overlap of physiological function) and may therefore be substitutable with little impact on eco- Authors’ contributions system processes [41, 42]. As noted by Taxis et al. [43]re- Conceived and designed the experiments: ZJL, FL and JHY. Performed the experiments: ZJL, QD and YFL. Analyzed the data: ZJL. Contributed to the garding the relationship between ruminal ecosystems and writing of the manuscript: ZJL, TY and YCC. All authors reviewed and function: the players may change but the game remains. approved the manuscript. These observations also suggest that defaunation is not a good model for estimating the role of protozoa in rumen Ethics approval and consent to participate Not applicable. function due to the compensation effects of fungi and bac- teria. Further animal experiments are required to fully Consent for publication understand the succession of rumen bacterial and archaeal Not applicable. community structure and function following defaunation, Competing interests and the metabolic characteristics of rumen protozoa need The authors declare that they have no competing interests. be revealed using their genome and transcriptome data. Author details College of Animal Science and Technology, Northwest A&F University, Conclusions Yangling, Shaanxi, China. State Key Laboratory of Genetic Resources and The present meta-analysis summarized the temporal dy- Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. College of Pastoral Agricultural Science and namics of methanogenesis, ruminal fermentation and Technology, Lanzhou University, Lanzhou, China. dietary fiber digestibility in ruminants after defaunation, and the results showed that defaunation adversely af- Received: 5 July 2018 Accepted: 5 November 2018 fected dietary fiber digestibility and the ruminal VFAs available to the host animals, although the effects were References lessened over time. Furthermore, the energy advantages 1. Ushida K, Jouany JP, Demeyer DI. Effects of presence or absence of rumen of defaunation gained by reducing CH production and protozoa on the efficiency of utilization of concentrate and fibrous feeds. In: Tsuda T, Sasaki Y, Kawashima, editors. Physiological aspects of digestion and shifting ruminal VFA profiles to more propionate were metabolism in ruminants. San Diego: Academic Press. 1991:625–54. gradually lost over time, and the effects eventually be- 2. Williams AG, Coleman GS. The rumen protozoa. 1st ed. New York: Springer- came disadvantageous. Therefore, elimination of rumen Verlag; 1992. 3. Millen DD, Arrigoni MDB, Pacheco RDL. Rumenology. 1st ed. Springer: protozoa adversely affects the energy supply of animals International Publishing; 2016. over the long-term. 4. Ryle M, Ørskov ER. Energy nutrition in ruminants. 1st ed. Netherlands: Springer; 1990. 5. Finlay BJ, Esteban G, Clarke KJ, Williams AG, Embley TM, Hirt RP. Some rumen ciliates have endosymbiotic methanogens. FEMS Microbiol Lett. Additional file 1994;117:157–61. 6. Morgavi DP, Forano E, Martin C, Newbold CJ. Microbial ecosystem and methanogenesis in ruminants. Animal. 2010;4:1024–36. Additional file 1: Figure S1. Forest plot showing the results of the 7. Belanche A, de la Fuente G, Newbold CJ. Study of methanogen subgroup meta-analysis of the anti-methanogenic effect size of defaunation, communities associated with different rumen protozoal populations. FEMS grouped by faunation state and duration of defaunation (11 wk). BF = born Microbiol Ecol. 2014;90:663–77. and reared protozoa free; AF = artificial defaunation; SMD = standardized 8. Johnson KA, Johnson DE. Methane emissions from cattle. J Anim Sci. 1995; mean difference; 95% CI = 95% confidence interval. * I-squared = percentage 73:2483–92. of heterogeneity across studies; P-value of SMD = 0. Figure S2. Funnel plot 9. Whitelaw FG, Eadie JM, Bruce LA, Shand WJ. Methane formation in faunated for the effect size of defaunation on CH production in (A) all studies, (B) and ciliate-free cattle and its relationship with rumen volatile fatty acid short-term defaunation, (C) long-term defaunation, and (D) refaunation. The proportions. Br J Nutr. 1984;52:261–75. Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 9 of 9 10. Faichney GJ, Graham NM, Walker DM. Rumen characteristics, methane 37. Newbold CJ, Hillman K. The effect of ciliate protozoa on the turnover of emissions, and digestion in weaned lambs reared in isolation. Aust J Agric bacterial and fungal protien in the rumen of sheep. Lett Appl Microbiol. Res. 1999;50:1083–90. 1990;11:100–2. 11. Bird SH, Hegarty RS, Woodgate R. Persistence of defaunation effects on 38. Frumholtz PP. Manipulation of the rumen fermentation and its effects on digestion and methane production in ewes. Aust J Exp Agric. 2008;48:152–5. digestive physiology: University of Aberdeen; 1991. 12. Hegarty RS, Bird SH, Vanselow BA, Woodgate R. Effects of the absence of 39. Morvan B, Rieu-Lesme F, Fonty G, Gouet P. In vitro interactions between protozoa from birth or from weaning on the growth and methane rumen H -producing cellulolytic microorganisms and H -utilizing 2 2 production of lambs. Br J Nutr. 2008;100:1220–7. acetogenic and sulfate-reducing bacteria. Anaerobe. 1996;2:175–80. 40. Weimer PJ. Redundancy, resilience, and host specificity of the ruminal 13. Morgavi DP, Martin C, Jouany JP, Ranilla MJ. Rumen protozoa and microbiota: implications for engineering improved ruminal fermentations. methanogenesis: not a simple cause–effect relationship. Br J Nutr. 2012;107:388–97. Front Microbiol. 2015;6:296. 14. Eugène M, Archimède H, Sauvant D. Quantitative meta-analysis on the 41. Lawton JH, Brown VK. Redundancy in ecosystems. In: Schulze ED, Mooney effects of defaunation of the rumen on growth, intake and digestion in HA, editors. Biodiversity and ecosystem function. Berlin: Springer; 1994. p. ruminants. Livest Prod Sci. 2004;85:81–97. 255–70. 15. Lean IJ, Rabiee AR, Duffield TF, Dohoo IR. Invited review: use of meta- 42. Rosenfeld JS. Functional redundancy in ecology and conservation. Oikos. analysis in animal health and reproduction: methods and applications. J 2002;98:156–62. Dairy Sci. 2009;92:3545–65. 43. Taxis TM, Wolff S, Gregg SJ, Minton NO, Zhang C, Dai J, et al. The players 16. Viechtbauer W. Learning from the past: refining the way we study may change but the game remains: network analyses of ruminal treatments. J Clin Epidemiol. 2010;63:980–2. microbiomes suggest taxonomic differences mask functional similarity. 17. Newbold CJ, de la Fuente G, Belanche A, Ramos-Morales E, McEwan NR. The Nucleic Acids Res. 2015. https://doi.org/10.1093/nar/gkv973. role of ciliate protozoa in the rumen. Front Microbiol. 2015;6:1313. 44. Belanche A, Abecia L, Holtrop G, Guada JA, Castrillo C, de la Fuente G, et al. 18. Sauer FD, Fellner V, Kinsman R, Kramer JK, Jackson HA, Lee AJ, et al. Study of the effect of presence or absence of protozoa on rumen Methane output and lactation response in Holstein cattle with monensin or fermentation and microbial protein contribution to the chyme. J Anim Sci. unsaturated fat added to the diet. J Anim Sci. 1998;76:906–14. 2011;89:4163–74. 19. Guan H, Wittenberg KM, Ominski KH, Krause DO. Efficacy of ionophores in 45. Chandramoni JSB, Tiwari CM, Haque N, Murarilal KMY. Energy metabolism cattle diets for mitigation of enteric methane. J Anim Sci. 2006;84:1896–906. and methane production in faunated and defaunated sheep fed two diets 20. Schönhusen U, Zitnan R, Kuhla S, Jentsch W, Derno M, Voigt J. Effects of with same concentrate to roughage ratio (70:30) but varying in protozoa on methane production in rumen and hindgut of calves around composition. Asian-Australas J Anim Sci. 2001;14:1238–44. time of weaning. Arch Anim Nutr. 2003;57:279–95. 46. Chaudhary LC, Srivastava A. Performance of growing Murrah buffalo calves 21. Higgins JPT, Thompson SG, Deeks JJ, Altman DG. Measuring inconsistency as affected by treatment with Manoxol and the presence of ciliate protozoa in meta-analyses. BMJ. 2003;327:557–60. in the rumen. Anim Feed Sci Technol. 1995;51:281–6. 22. Knapp G, Hartung J. Improved tests for a random effects meta-regression 47. Eadie JM, Gill JC. The effect of the absence of rumen ciliate protozoa on with a single covariate. Stat Med. 2003;22:2693–710. growing lambs fed on a roughage–concentrate diet. Br J Nutr. 1971;26:155–67. 23. Guyader J, Eugène M, Nozière P, Morgavi DP, Doreau M, Martin C. Influence 48. Eugène M, Sauvant D, Weisbecker JL, Archimède H. Effects of defaunation of rumen protozoa on methane emission in ruminants: a meta-analysis on digestion of fresh Digitaria decumbens grass and growth of lambs. approach. Animal. 2014;8:1816–25. Animal. 2010;4:439–45. 24. Nagaraja TG. Microbiology of the rumen. In: Millen DD, Arrigoni MDB, 49. Kasuya N, Wada I, Shimada M, Kawai H, Itabashi H. Effect of presence of Pacheco RDL, editors. Rumenology. Cham: Springer; 2016. p. 39–61. rumen protozoa on degradation of cell wall constituents in gastrointestinal 25. Jouany JP, Demeyer DI, Grain J. Effect of defaunating the rumen. Anim Feed tract of cattle. Anim Sci J. 2007;78:275–80. Sci Technol. 1988;21:229–65. 50. Kreuzer M, Kirchgessner M, Müller HL. Effect of defaunation on the loss of 26. Mosoni P, Martin C, Forano E, Morgavi DP. Long-term defaunation increases energy in wethers fed different quantities of cellulose and normal or the abundance of cellulolytic ruminococci and methanogens but does not steamflaked maize starch. Anim Feed Sci Technol. 1986;16:233–41. affect the bacterial and methanogen diversity in the rumen of sheep. J 51. Nagaraja TG, Godfrey SI, Winslow SW, Rowe JB, Kemp KE. Effect of Anim Sci. 2011;89:783–91. virginiamycin on ruminal fermentation in faunated or ciliate-free sheep 27. Karakurt I, Aydin G, Aydiner K. Sources and mitigation of methane emissions overfed with barley grain. Small Rumin Res. 1995;17:1–8. by sectors: a critical review. Renew Energy. 2012;39:40–8. 52. Santra A, Karim SA. Growth performance of faunated and defaunated 28. Hristov AN, Oh J, Lee C, Meinen R. Mitigation of greenhouse gas emissions in Malpura weaner lambs. Anim Feed Sci Technol. 2000;86:251–60. livestock production: a review of technical options for non-CO emissions. 53. Santra A, Karim SA. Nutrient utilization and growth performance of defaunated Food and Agriculture Organization of the United Nations: Rome; 2013. and faunated lambs maintained on complete diets containing varying proportion 29. Janssen PH. Influence of hydrogen on rumen methane formation and of roughage and concentrate. Anim Feed Sci Technol. 2002;101:87–99. fermentation balances through microbial growth kinetics and fermentation 54. Santra A, Karim SA, Chaturvedi OH. Rumen enzyme profile and fermentation thermodynamics. Anim Feed Sci Technol. 2010;160:1–22. characteristics in sheep as affected by treatment with sodium lauryl sulfate 30. Bergman EN. Energy contributions of volatile fatty acids from the as defaunating agent and presence of ciliate protozoa. Small Rumin Res. gastrointestinal tract in various species. Physiol Rev. 1990;70:567–90. 2007;67:126–37. 31. Shabat SKB, Sasson G, Doron-Faigenboim A, Durman T, Yaacoby S, Berg Miller ME, 55. Sultana H, Miyazawa K, Kanda S, Itabashi H. Fatty acid composition of et al. Specific microbiome-dependent mechanisms underlie the energy harvest ruminal bacteria and protozoa, and effect of defaunation on fatty acid efficiency of ruminants. ISME J. 2016. https://doi.org/10.1038/ismej.2016.62. profile in the rumen with special reference to conjugated linoleic acid in 32. Weimer PJ, Cox MS, de Paula TV, Lin M, Hall MB, Suen G. Transient changes cattle. Anim Sci J. 2011;82:434–40. in milk production efficiency and bacterial community composition 56. Williams PP, Dinusson WE. Ruminal volatile fatty acid concentrations and resulting from near-total exchange of ruminal contents between high- and weight gains of calves reared with and without ruminal ciliated protozoa. J low-efficiency Holstein cows. J Dairy Sci. 2017;100:7165–82. Anim Sci. 1973;36:588–91. 33. Nguyen SH, Bremner G, Cameron M, Hegarty RS. Methane emissions, 57. Yáñez-Ruiz DR, Williams S, Newbold CJ. The effect of absence of protozoa ruminal characteristics and nitrogen utilisation changes after refaunation of on rumen biohydrogenation and the fatty acid composition of lamb protozoa-free sheep. Small Rumin Res. 2016;144:48–55. muscle. Br J Nutr. 2007;97:938–48. 34. Reece WO. Dukes’ physiology of domestic animals. 12th ed. Comstock Pub. 58. Zhou YY, Mao HL, Jiang F, Wang JK, Liu JX, McSweeney CS. Inhibition of Associates: Ithaca; 2004. rumen methanogenesis by tea saponins with reference to fermentation 35. Ozutsumi Y, Tajima K, Takenaka A, Itabashi H. The effect of protozoa on the pattern and microbial communities in Hu sheep. Anim Feed Sci Technol. composition of rumen bacteria in cattle using 16S rRNA gene clone 2011;166–167:93–100. libraries. Biosci Biotechnol Biochem. 2005;69:499–506. 36. Morgavi DP, Rathahao-Paris E, Popova M, Boccard J, Nielsen KF, Boudra H. Rumen microbial communities influence metabolic phenotypes in lambs. Front Microbiol. 2015;6:1060. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Animal Science and Biotechnology Springer Journals

Dynamics of methanogenesis, ruminal fermentation and fiber digestibility in ruminants following elimination of protozoa: a meta-analysis

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Life Sciences; Agriculture; Biotechnology; Food Science; Animal Genetics and Genomics; Animal Physiology
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Abstract

Background: Ruminal microbes are vital to the conversion of lignocellulose-rich plant materials into nutrients for ruminants. Although protozoa play a key role in linking ruminal microbial networks, the contribution of protozoa to rumen fermentation remains controversial; therefore, this meta-analysis was conducted to quantitatively summarize the temporal dynamics of methanogenesis, ruminal volatile fatty acid (VFA) profiles and dietary fiber digestibility in ruminants following the elimination of protozoa (also termed defaunation). A total of 49 studies from 22 publications were evaluated. Results: The results revealed that defaunation reduced methane production and shifted ruminal VFA profiles to consist of more propionate and less acetate and butyrate, but with a reduced total VFA concentration and decreased dietary fiber digestibility. However, these effects were diminished linearly, at different rates, with time during the first few weeks after defaunation, and eventually reached relative stability. The acetate to propionate ratio and methane production were increased at 7 and 11 wk after defaunation, respectively. Conclusions: Elimination of protozoa initially shifted the rumen fermentation toward the production of more propionate and less methane, but eventually toward the production of less propionate and more methane over time. Keywords: Defaunation, Fiber digestibility, Meta-analysis, Methane production, Rumen fermentation Introduction recovery efficiency is reduced by 38% when the substrate The rumen provides an ideal habitat for protozoa, whose (glucose) is fermented into acetate but increased by 9% 5 6 concentration can reach 10 –10 cells/mL. In return, when fermented into propionate [3, 4]. Protozoa are im- protozoa serve important functions in the rumen micro- portant ruminal hydrogen (H ) producers, and the pro- bial ecosystem, such as predation, competition for nutri- duced H is mostly converted into methane (CH )by 2 4 ents, and involvement in symbiotic relationships with methanogens situated inside protozoa or on their exter- other microorganisms [1, 2]. Protozoa prey on bacteria nal surface [5–7]. The CH emissions from ruminants and fungal spores, but are preferentially retained in the represent 2–12% dietary energy loss [8]. Therefore, the rumen, thus reducing the postruminal microbial protein presence of protozoa seems to adversely affect animals’ supply [3]. Protozoa compete with amylolytic bacteria energy efficiency. for dietary starch, which is mostly fermented into acetate Complete removal of ruminal protozoa, termed defau- by protozoa [2] while mostly into propionate by amylo- nation, has been suggested as an efficient method for re- lytic bacteria [3, 4]. For host animals, the energy ducing CH emissions and enhancing propionate fermentation [9, 10], but these effects have not been consistently observed in studies investigating this * Correspondence: yaojunhu2004@sohu.com 112method [11–13]. Hegarty et al. [12]and Morgavietal. College of Animal Science and Technology, Northwest A&F University, [13] suggested that the duration of defaunation might be Yangling, Shaanxi, China Full list of author information is available at the end of the article © The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 2 of 9 responsible for this inconsistency, but the temporal dynam- variables for extraction. The relevant variables for this ics of methanogenesis and ruminal volatile fatty acid (VFA) meta-analysis included the daily CH production, rumi- profiles after defaunation are difficult to determine experi- nal VFA profiles and dietary fiber total-tract digestibility. mentally because of the difficulties in raising defaunated an- The faunation states of control animals included the imals over a long-term [14]. Meta-analysis is a statistical natural ruminal ecosystem without any treatment or re- method that combines the results from multiple studies to introduction of protozoa after partial defaunation, which achieve a more precise estimate of treatment effects and to appeared to be restored quickly after withdrawal of the explore the potential sources of between-study heterogen- protozoa-inhibiting treatment [18, 19]. The control ani- eity [15, 16]. Two prior meta-analyses [14, 17]havesum- mals into which protozoa were reintroduced after marized the combined responses of rumen fermentation to complete defaunation were excluded from the analysis, defaunation; however, the combined effects on ruminal because preliminary analysis showed that high hetero- VFA profiles were also inconsistent between them, and geneity existed between the faunation and refaunation neither of them explored the time-dependent effects. subgroups (see Additional file 1). Protozoa-free animals Therefore, the current meta-analysis was conducted to were obtained through either the absence of protozoa quantitatively summarize the temporal dynamics of from birth (BF) or artificial removal of protozoa from methanogenesis, ruminal VFA profiles and dietary fiber di- the natural ruminal ecosystem (AF). Artificial defauna- gestibility in ruminants after defaunation, and to explain tion was conducted using chemical agents, such as al- the contribution of the defaunated duration to the kanes and sodium lauryl sulfate, or by applying a rumen between-study heterogeneity. washing technique. The defaunation duration was calcu- lated based on the schedule of experimental activities. Methods The defaunation duration of BF animals was calculated Literature search, screening and data extraction as their age shortened by 4 wk, because ruminal proto- A flowchart detailing the process of literature search, zoa did not appear when newborn calves were fed with screening and data extraction is shown in Fig. 1. The in- milk for 30 d [2], and the concentration of protozoa clusion criteria for the studies were as follows: (1) quickly increased after 5 wk of age [20]. peer-reviewed and published in the English language; (2) The final database included 22 publications, with 49 in complete defaunation in vivo; (3) inclusion of relevant vivo studies that satisfied the inclusion criteria for the 238 papers potentially relevant studies identified from the scientific electronic databases and citations in review papers 169 excluded on the basic of publication type With 45 books, review papers and meeting abstracts With 43 in vitro studies With 81 non-relevant records 47 excluded on the basic of experimental designs With 12 partial defaunation With 20 reintroduced protozoa after complete defaunation With 15 lack of statistical information 22 papers with 49 trials satisfied the inclusion criteria for meta-analysis Data extraction and calculations Preliminary analysis assessment Animal species and number Assessment of Heterogeneity Defaunation methods and duration Publication bias analysis Means and SD of relevant outcomes Meta-analysis and meta-regression analysis Fig. 1 Flow chart of the literature search, screening and data extraction procedures Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 3 of 9 meta-analysis. Summary descriptions of the selected studies homogeneous. When the value of I was over 50%, indi- are provided in Table 1. Briefly, among the 49 selected stud- cating high heterogeneity, studies were combined using a ies, 38 were conducted in sheep, and 11 were conducted in random effects model, based on the assumption that the cattle; 18 measured CH production, 29 measured ruminal expected effect from each study was heterogeneous. VFAs, and 15 measured total-tract fiber digestibility. CH The differences in animal species or ages, daily sampling emissions were measured using the respiration chamber times or dietary forage percentages across the studies caused technique or sulfur hexafluoride tracer technique. Methane that the data of certain relevant variables to vary greatly production was presented in liters per day in most of the acrossthe studies(Table 2). To reduce these potential inter- studies; thus, values presented in grams or kilojoules (kJ) ferences, the effect size in this analysis was estimated via the were converted to liters per day, based on the assumption standardized mean difference (SMD), which was calculated that one mole of CH weighs 16 g or contains 890 kJ of en- as the raw mean difference between the treatment and con- ergy and occupies a volume of 24.5 L (under conditions of trol groups divided by their pooled standard deviations [15]. 25 °C and 1 atmospheric pressure). For example, although cattle CH production in the study by Schönhusen et al. [20] was higher than in other subgroup Data analysis studies involving sheep, it was homogeneous with most of The meta-analysis was performed using Stata 14.1 (Stata them (Additional file 1: Figures S1 and S2). The studies were Corp., Texas, USA). weighted using the inverse of the variance of the differences in means. Details of the calculations used in the Assessment of heterogeneity and effect size meta-analysis are provided by Lean et al. [15]. Between-study variability was quantified via the I statistic, which measures the percentage of variation due to hetero- Meta-regression analysis geneity [15, 21]. When the I value was less than 50%, in- The meta-regression analysis was performed using the dicating low heterogeneity, studies were combined using a Knapp-Hartung restricted maximum likelihood method fixed effects model, which was based on the assumption [22], with the SMD of the individual studies used as the that the expected effect from each study was response variable and the corresponding standard error Table 1 Data sources and characteristics of the studies included in the meta-analysis Source Trials Animal Defaunation duration Outcomes Belanche et al. [44] 2 Sheep 23 wk VFA, digestibility Bird et al. [11] 2 Sheep 11, 26 wk CH , VFA, digestibility Chandramoni et al. [45] 2 Sheep 5, 11 wk CH , digestibility Chaudhary and Srivastava [46] 2 Cattle 18 wk Digestibility Eadie and Gill [47] 2 Sheep 22, 55 wk VFA Eugène et al. [48] 4 Sheep 10, 14, 18, 22 wk Digestibility Frumholtz [38] 3 Sheep 5, 26, 52 wk VFA Hegarty et al. [12] 4 Sheep 12, 22, 24, 33 wk CH , VFA Kasuya et al. [49] 1 Cattle 21 wk Digestibility Kreuzer et al. [50] 3 Sheep 9, 10, 11 wk CH Morgavi et al. [13] 2 Sheep 6 wk, 2 yr CH , VFA Nagaraja et al. [51] 2 Sheep 14 wk VFA Nguyen et al. [33] 2 Sheep 9 wk CH , VFA, digestibility Ozutsumi et al. [35] 1 Cattle 14 wk VFA Santra and Karim [52] 2 Sheep 12 wk Digestibility Santra and Karim [53] 3 Sheep 14 wk Digestibility Santra et al. [54] 2 Sheep 8 wk Digestibility Schönhusen et al. [20] 4 Cattle 4, 5, 6, 7 wk CH , VFA, digestibility Sultana et al. [55] 1 Cattle 14 wk VFA Williams and Dinusson [56] 2 Cattle 30, 56 wk VFA Yáñez-Ruiz et al. [57] 1 Sheep 18 wk VFA Zhou et al. [58] 2 Sheep 5 wk CH , VFA 4 Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 4 of 9 Table 2 Data summary and meta-analysis of relevant variables based on all of the selected studies Variables No. Defaunation group Faunation group Meta-analysis of 2 n Mean SD n Mean SD I , % SMD P-value trials CH , L/d 18 126 20.8 12.4 129 23.4 12.0 71.9 −0.602 0.037 Total VFA, mmol/L 29 211 78.8 29.7 212 87.1 31.3 44.2 −0.549 < 0.001 Individual VFA molar proportion, % Acetate 29 210 67.7 5.6 211 66.3 4.3 67.8 0.358 0.083 Propionate 29 210 21.0 4.8 211 20.6 3.1 73.5 0.150 0.515 Butyrate 27 202 8.2 2.0 203 10.2 2.8 68.3 −1.026 < 0.001 A:P 18 78 3.6 1.6 81 3.5 0.7 77.0 −0.284 0.493 Total-tract fiber digestibility, % NDF 15 109 55.0 11.6 109 58.1 11.8 55.7 −2.063 < 0.001 ADF 11 82 42.8 2.7 82 45.7 3.7 69.8 −3.075 < 0.001 n number of animals, I percentage of heterogeneity across studies, SMD standardized mean difference, A:P acetate: propionate ratio, NDF neutral detergent fiber, ADF acid detergent fiber of the SMD used as the variance. The percentage of 76.8% of the between-study heterogeneity (I = 76.2%) between-study heterogeneity explained by the covariate during the linear phase, and no between-study hetero- (defaunation duration) was quantified via the adjusted geneity (I = 0.0%) was observed after 11 wk (plateau R value. phase), suggesting that little fluctuation occurred during Preliminary analysis showed that the temporal SMD the plateau phase. Interestingly, the defaunated animals dynamics after defaunation included a linear phase during the plateau phase presented higher CH produc- followed by a plateau phase. The durations of the linear tions (SMD = 0.313, P = 0.039) than the control animals. phase and plateau phase for each outcome were dependent on the highest adjusted R of the Ruminal VFA profiles and total-tract fiber digestibility meta-regression analysis and the minimum I of the het- dynamics during adaptation to defaunation erogeneity analysis, respectively; therefore, the two Consistent with the temporal dynamics of CH produc- phases might overlap over a short duration. The prob- tion after defaunation, the ruminal VFA profiles dynam- ability levels were set at P < 0.05 for significance and ics also included a linear phase (≤ 11 wk) and a plateau 0.05 ≤ P < 0.10 for a trend. phase (≥ 7 wk) (Table 3). After defaunation, decreases in the acetate proportion, butyrate proportion and A:P Results (intercept = − 4.086, − 7.059 and − 6.737, respectively), Effect size and heterogeneity across all the studies and an increase in the propionate proportion (intercept The meta-analysis based on all the selected studies = 7.306) were estimated (P < 0.01). These alterations de- showed that elimination of rumen protozoa reduced (P creased linearly (P < 0.01) at different rates over the first < 0.05) CH production, ruminal VFA concentration, 11 wk of defaunation; instead, the ruminal acetate pro- the proportion of butyrate and dietary fiber digestibility, portion (SMD = 0.748, P < 0.001) and A:P (SMD = 0.915, and tended to increase (P = 0.083) the proportion of P = 0.016) were higher, and the propionate proportion acetate (Table 2). However, the heterogeneity across the (SMD = − 0.366, P = 0.033) was lower in defaunated ani- studies was considerable (I > 50%) for most of the re- mals than faunated animals during the plateau phase. sponses to defaunation, except for the ruminal VFA con- Compared with faunated animals, defaunated animals centration (I = 44.2%). exhibited a reduced total VFA concentration (intercept = − 1.883 and P = 0.008), and the reduction decreased Methanogenesis dynamics during adaptation to weekly by 0.132 (P = 0.048) until 12 wk (Table 3). The defaunation duration of defaunation could explain 99.9% of the Compared with that of faunation, the effect size of between-study heterogeneity during the linear phase, al- defaunation on CH emissions presented a linear rela- though the heterogeneity (35.5%) was low. The decrease tionship over time during the first 12 wk (linear phase) in total VFA concentration was still observed (SMD = − after defaunation (Fig. 2 and Table 3): CH production 0.424, P < 0.001) in defaunated animals during the plat- was reduced by defaunation (intercept = − 5.484, P = eau phase (≥ 11 wk). 0.003), and the reduction decreased weekly by 0.486 (P Compared with that of faunation, the effect sizes of = 0.003) until 12 wk. The defaunation duration explained defaunation on total-tract fiber digestibility were linearly Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 5 of 9 ac Fig. 2 Methanogenesis dynamics during adaptation to defaunation. The temporal SMD (standardized mean difference) dynamics (a) after defaunation included a linear phase (≤ 12 wk, yellow portion) followed by a plateau phase (≥ 11 wk, blue portion). The overlap of two phases were the green portion. The linear phase was reanalyzed by meta-regression analysis (b), and the plateau phase was reanalyzed by meta-analysis (c). Circles in the graph represent the estimates from each study, and the size of the circles represents the percentage of weight of each study. The blue diamond represent in panel (c) represents the combined effect and its 95% confidence interval related to defaunation duration (Table 3): total-tract considerable for most of the responses to defaunation. Ex- NDF and ADF digestibility (intercept = − 4.458 and − cess between-study variance increases the risk of incorrect 6.276, respectively) were reduced (P < 0.01) after defau- average effect sizes when combining studies [15]. For ex- nation, and the reductions decreased weekly (P < 0.05) ample, the present meta-analysis based on all the studies by 0.153 and 0.213, respectively, until 23 wk, which was showed that defaunation tended to increase the proportion the longest studied duration in the available data. of ruminal acetate but had no effect on the proportion of propionate. These findings were consistent with a recent Discussion meta-analysis by Newbold et al. [18] but inconsistent with Effect size and heterogeneity across all the studies that of Eugène et al. [14], who reported that defaunation in- Based on all the selected studies, this meta-analysis showed duced a reduction in the ruminal acetate proportion and an that complete elimination of rumen protozoa generated ad- increase in the propionate proportion. Therefore, the po- verse effects on the ruminal VFA concentration, butyrate tential source of heterogeneity among the studies needs to proportion and dietary fiber digestibility; these findings be explored to better understand the responses to treat- were consistent with the results of previous meta-analyses ment, and this additional exploration is also one of most [14, 18]. However, the heterogeneity across the studies was important tasks of meta-analysis [15]. Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 6 of 9 Table 3 Methane emissions, ruminal VFA profiles and total-tract fiber digestibility dynamics during the linear phase and plateau phase Meta-regression analysis for the linear phase Meta-analysis for the plateau phase 2 2 2 Duration, wk No. of trials I , % Intercept P-value Coefficient P-value Adjusted R , % Duration, wk No. of trials I , % Pooled effect size P-value CH ≤ 12 13 76.2 −5.484 0.001 0.486 0.003 76.8 ≥ 11 9 0.0 0.313 0.039 TVFA ≤ 12 12 35.5 −1.883 0.008 0.132 0.048 99.9 ≥ 11 19 46.7 −0.424 < 0.001 Individual VFA molar proportion Acetate ≤ 11 11 76.8 −4.086 0.004 0.563 0.004 76.7 ≥ 7 22 47.5 0.748 < 0.001 Propionate ≤ 11 11 84.5 7.306 < 0.001 −0.898 < 0.001 92.2 ≥ 7 22 51.2 −0.366 0.033 Butyrate ≤ 11 11 80.6 −7.059 < 0.001 0.732 0.001 92.3 ≥ 7 20 54.0 −0.582 0.002 A:P ≤ 11 10 78.6 −6.737 0.001 0.884 0.002 90.8 ≥ 7 10 59.2 0.915 0.016 Total-tract fiber digestibility NDF ≤ 23 15 55.7 −4.458 < 0.001 0.153 0.005 85.0 ADF ≤ 23 11 69.8 −6.276 0.001 0.213 0.030 45.1 2 2 I , percentage of heterogeneity across studies; Intercept, estimate of the effect size after defaunation; Coefficient, estimate of the change in effect size per week following defaunation; Adjusted R , percentage of between-study variance explained by the defaunation duration; TVFA, total VFA Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 7 of 9 The role of protozoa in rumen carbohydrate metabolism pooled analysis, in which the number of replicate ani- Despite the fact that protozoa make up a large portion mals was increased by combining the results of relevant of the rumen biomass, their role in ruminal fermentation individual studies [15, 16]. The CH emissions from ru- and their contribution to the metabolism and nutrition minants contribute to global greenhouse gas emissions of the host are still topics of substantial controversy [2, and represent energy loss for the animals [8, 27, 28]. 14], due to the difficulty of pure cultivation of protozoa Therefore, the potential environmental protection and in vitro. Rumen protozoa are not essential to the animal energy-saving values following defaunation were grad- for survival, and defaunation has therefore been used to ually lost and eventually became negative. estimate the role of ciliate protozoa in rumen function. Acetate production during rumen fermentation is ac- However, the adapted alteration of other microbe after companied by reducing equivalents ([H]) production, defaunation may interfere with such estimations. Hence, whereas propionate production is accompanied by [H] the estimated intercept from the meta-regression ana- consumption [29]; the excess [H] is converted to H . lysis more accurately reflected the role that protozoa The shift in the VFA profiles from propionate to acetate played in rumen fermentation. Reductions in the rumi- following defaunation increased the H available for nal acetate proportion, butyrate proportion and CH methanogenesis, at least partially explaining the production after complete removal of ruminal protozoa time-related changes in CH production observed in this would be expected because protozoa ferment carbohy- study. When glucose is metabolized into acetate, propi- drates into acetate, butyrate and H [2], and the H pro- onate or butyrate, the energy efficiency relative to glu- 2 2 duced is mostly converted to CH by methanogens cose for animal is 62%, 109% and 78%, respectively [3, situated inside protozoa or on their external surface [5– 4]. Propionate fermentation is most energy efficient, due 7]. A strong correlation between CH emissions and to assimilating energy from H and being the main pre- 4 2 protozoa concentration has been reported [23], and cursor of gluconeogenesis in animals [3, 30]. In rumi- protozoa-associated methanogens have been estimated nants, the VFAs produced in the rumen satisfy up to to be responsible for 37% of CH production by rumi- 70% of energy requirements [30]. Shabat et al. [31] and nants [5]. Additionally, ruminal protozoa possess a full Weimer et al. [32] observed that the ruminal total VFA complement of hydrolytic enzymes for fermentation of concentration and propionate proportion were higher in the major components of feedstuffs, and certain ciliates highly efficient cows than in cows with low efficiency. present a wide range of fibrolytic enzyme genes, ingest Therefore, the decreases in the ruminal total VFA concen- small plant particles and use cell wall carbohydrates [18, tration and propionate proportion during the plateau 24]. Moreover, protozoa can indirectly contribute to ru- phase also suggested that the elimination of rumen proto- minal degradation kinetics by maintaining a suitable zoa adversely affected the energy supply of animals in a rumen fermentation environment, for example, by scav- long run. enging oxygen to maintain anaerobiosis and slowing the The time-related variations in CH , VFA profiles and rate of starch fermentation to maintain a proper ruminal dietary fiber digestibility implied a series of complex pH [24], which favors the development and activity of changes in the ruminal ecosystem over the course of bacteria and fungi [25, 26]. Therefore, the reductions in defaunation. Nguyen et al. [33] reported that rumen mi- dietary fiber digestibility and ruminal total VFA concen- crobes had likely not stabilized after 12 wk of defauna- tration observed in this study would be expected after tion, which agrees with our results showing that the the complete removal of ruminal protozoa. linear phase for ruminal VFA profiles and CH emissions lasted 11 wk and 12 wk, respectively. When sudden Temporal dynamics during adaptation to defaunation major changes are made in the diet, it takes approxi- Although protozoa are important ruminal H producers mately 2 wk for the new microbial population balance to and exhibit interspecies H transfer with methanogens, become established [34]; the much longer linear phase as- we found that the effects of short- and long-term defau- sociated with defaunation suggests that protozoa play an nation on CH production were opposite. This finding important role in the ruminal ecosystem. Ruminal metha- supports the conclusion of Morgavi et al. [13], who nogens appear to develop more slowly than bacteria fol- showed that there was not a simple cause-effect relation- lowing defaunation [13]. Hristov et al. [28] noted that ship between rumen protozoa and methanogenesis. Bird reductions in the population of protozoa-associated et al. [11] and Hegarty et al. [12] observed higher CH methanogens might be compensated by an increase in the production (although not significantly so) in long-term population of bacteria- or rumen fluid-associated metha- defaunated ewes (11 and 26 wk) and lambs (12 to 33 nogens, and Mosoni et al. [26] found that long-term wk) than in faunated animals. The significant increasing defaunation (2 yr) increased the abundance of methano- effect of long-term defaunation on CH production de- gens. In addition, ruminal protozoa elimination results in tected in this meta-analysis can be attributed to the increased bacterial abundance and changes in bacterial Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 8 of 9 communities [35, 36]; defaunation has been shown to in- P-value of publication bias is presented. SMD = standardized mean crease the anaerobic fungal population by two fold [37] difference, se = standard error. (DOCX 1373 kb) and the Ruminococcaceae population by six fold [36]. Frumholtz [38] found that long-term defaunation (6 mo) Abbreviations ADF: Acid detergent fiber; AP: Acetate to propionate ratio; NDF: Neutral increased the abundance of cellulolytic bacteria. Similar to detergent fiber; SMD: Standardized mean difference; VFA: Volatile fatty acids protozoa, fungi and cellulolytic bacteria are also the main ruminal cellulolytic and H -producing microbes that gen- Acknowledgments erate acetate, butyrate and/or H as primary end products The authors thank Prof. Chang Xu (Chinese Evidence-Based Medicine Center and Chinese Cochrane Center, West China Hospital, Sichuan University) for [29, 39]. Therefore, it can be concluded that the increase help with data analysis. in the populations of methanogens, fungi and cellulolytic bacteria following defaunation gradually counteracts the Funding This work was supported by the National Key Research and Development defaunation-induced reductions in dietary fiber digestibil- Program of China (grant number: 2017YFD0500500). ity, ruminal A:P and CH production, which may confirm an earlier theory of Weimer [40] indicating that the mul- Availability of data and materials tiple microbial taxa in the ruminal community show func- All the datasets were presented in the main manuscript (reference list in Table 1) and available to readers. tional redundancy (overlap of physiological function) and may therefore be substitutable with little impact on eco- Authors’ contributions system processes [41, 42]. As noted by Taxis et al. [43]re- Conceived and designed the experiments: ZJL, FL and JHY. Performed the experiments: ZJL, QD and YFL. Analyzed the data: ZJL. Contributed to the garding the relationship between ruminal ecosystems and writing of the manuscript: ZJL, TY and YCC. All authors reviewed and function: the players may change but the game remains. approved the manuscript. These observations also suggest that defaunation is not a good model for estimating the role of protozoa in rumen Ethics approval and consent to participate Not applicable. function due to the compensation effects of fungi and bac- teria. Further animal experiments are required to fully Consent for publication understand the succession of rumen bacterial and archaeal Not applicable. community structure and function following defaunation, Competing interests and the metabolic characteristics of rumen protozoa need The authors declare that they have no competing interests. be revealed using their genome and transcriptome data. Author details College of Animal Science and Technology, Northwest A&F University, Conclusions Yangling, Shaanxi, China. State Key Laboratory of Genetic Resources and The present meta-analysis summarized the temporal dy- Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. College of Pastoral Agricultural Science and namics of methanogenesis, ruminal fermentation and Technology, Lanzhou University, Lanzhou, China. dietary fiber digestibility in ruminants after defaunation, and the results showed that defaunation adversely af- Received: 5 July 2018 Accepted: 5 November 2018 fected dietary fiber digestibility and the ruminal VFAs available to the host animals, although the effects were References lessened over time. Furthermore, the energy advantages 1. Ushida K, Jouany JP, Demeyer DI. Effects of presence or absence of rumen of defaunation gained by reducing CH production and protozoa on the efficiency of utilization of concentrate and fibrous feeds. In: Tsuda T, Sasaki Y, Kawashima, editors. Physiological aspects of digestion and shifting ruminal VFA profiles to more propionate were metabolism in ruminants. San Diego: Academic Press. 1991:625–54. gradually lost over time, and the effects eventually be- 2. Williams AG, Coleman GS. The rumen protozoa. 1st ed. New York: Springer- came disadvantageous. Therefore, elimination of rumen Verlag; 1992. 3. Millen DD, Arrigoni MDB, Pacheco RDL. Rumenology. 1st ed. Springer: protozoa adversely affects the energy supply of animals International Publishing; 2016. over the long-term. 4. Ryle M, Ørskov ER. Energy nutrition in ruminants. 1st ed. Netherlands: Springer; 1990. 5. Finlay BJ, Esteban G, Clarke KJ, Williams AG, Embley TM, Hirt RP. Some rumen ciliates have endosymbiotic methanogens. FEMS Microbiol Lett. Additional file 1994;117:157–61. 6. Morgavi DP, Forano E, Martin C, Newbold CJ. Microbial ecosystem and methanogenesis in ruminants. Animal. 2010;4:1024–36. Additional file 1: Figure S1. Forest plot showing the results of the 7. Belanche A, de la Fuente G, Newbold CJ. Study of methanogen subgroup meta-analysis of the anti-methanogenic effect size of defaunation, communities associated with different rumen protozoal populations. FEMS grouped by faunation state and duration of defaunation (11 wk). BF = born Microbiol Ecol. 2014;90:663–77. and reared protozoa free; AF = artificial defaunation; SMD = standardized 8. Johnson KA, Johnson DE. Methane emissions from cattle. J Anim Sci. 1995; mean difference; 95% CI = 95% confidence interval. * I-squared = percentage 73:2483–92. of heterogeneity across studies; P-value of SMD = 0. Figure S2. Funnel plot 9. Whitelaw FG, Eadie JM, Bruce LA, Shand WJ. Methane formation in faunated for the effect size of defaunation on CH production in (A) all studies, (B) and ciliate-free cattle and its relationship with rumen volatile fatty acid short-term defaunation, (C) long-term defaunation, and (D) refaunation. The proportions. Br J Nutr. 1984;52:261–75. Li et al. Journal of Animal Science and Biotechnology (2018) 9:89 Page 9 of 9 10. Faichney GJ, Graham NM, Walker DM. Rumen characteristics, methane 37. Newbold CJ, Hillman K. The effect of ciliate protozoa on the turnover of emissions, and digestion in weaned lambs reared in isolation. Aust J Agric bacterial and fungal protien in the rumen of sheep. Lett Appl Microbiol. Res. 1999;50:1083–90. 1990;11:100–2. 11. Bird SH, Hegarty RS, Woodgate R. Persistence of defaunation effects on 38. Frumholtz PP. Manipulation of the rumen fermentation and its effects on digestion and methane production in ewes. Aust J Exp Agric. 2008;48:152–5. digestive physiology: University of Aberdeen; 1991. 12. Hegarty RS, Bird SH, Vanselow BA, Woodgate R. Effects of the absence of 39. Morvan B, Rieu-Lesme F, Fonty G, Gouet P. In vitro interactions between protozoa from birth or from weaning on the growth and methane rumen H -producing cellulolytic microorganisms and H -utilizing 2 2 production of lambs. Br J Nutr. 2008;100:1220–7. acetogenic and sulfate-reducing bacteria. Anaerobe. 1996;2:175–80. 40. Weimer PJ. Redundancy, resilience, and host specificity of the ruminal 13. Morgavi DP, Martin C, Jouany JP, Ranilla MJ. Rumen protozoa and microbiota: implications for engineering improved ruminal fermentations. methanogenesis: not a simple cause–effect relationship. Br J Nutr. 2012;107:388–97. Front Microbiol. 2015;6:296. 14. Eugène M, Archimède H, Sauvant D. Quantitative meta-analysis on the 41. Lawton JH, Brown VK. Redundancy in ecosystems. In: Schulze ED, Mooney effects of defaunation of the rumen on growth, intake and digestion in HA, editors. Biodiversity and ecosystem function. Berlin: Springer; 1994. p. ruminants. Livest Prod Sci. 2004;85:81–97. 255–70. 15. Lean IJ, Rabiee AR, Duffield TF, Dohoo IR. Invited review: use of meta- 42. Rosenfeld JS. Functional redundancy in ecology and conservation. Oikos. analysis in animal health and reproduction: methods and applications. J 2002;98:156–62. Dairy Sci. 2009;92:3545–65. 43. Taxis TM, Wolff S, Gregg SJ, Minton NO, Zhang C, Dai J, et al. The players 16. Viechtbauer W. Learning from the past: refining the way we study may change but the game remains: network analyses of ruminal treatments. J Clin Epidemiol. 2010;63:980–2. microbiomes suggest taxonomic differences mask functional similarity. 17. Newbold CJ, de la Fuente G, Belanche A, Ramos-Morales E, McEwan NR. The Nucleic Acids Res. 2015. https://doi.org/10.1093/nar/gkv973. role of ciliate protozoa in the rumen. Front Microbiol. 2015;6:1313. 44. Belanche A, Abecia L, Holtrop G, Guada JA, Castrillo C, de la Fuente G, et al. 18. Sauer FD, Fellner V, Kinsman R, Kramer JK, Jackson HA, Lee AJ, et al. Study of the effect of presence or absence of protozoa on rumen Methane output and lactation response in Holstein cattle with monensin or fermentation and microbial protein contribution to the chyme. J Anim Sci. unsaturated fat added to the diet. J Anim Sci. 1998;76:906–14. 2011;89:4163–74. 19. Guan H, Wittenberg KM, Ominski KH, Krause DO. Efficacy of ionophores in 45. Chandramoni JSB, Tiwari CM, Haque N, Murarilal KMY. Energy metabolism cattle diets for mitigation of enteric methane. J Anim Sci. 2006;84:1896–906. and methane production in faunated and defaunated sheep fed two diets 20. Schönhusen U, Zitnan R, Kuhla S, Jentsch W, Derno M, Voigt J. Effects of with same concentrate to roughage ratio (70:30) but varying in protozoa on methane production in rumen and hindgut of calves around composition. Asian-Australas J Anim Sci. 2001;14:1238–44. time of weaning. Arch Anim Nutr. 2003;57:279–95. 46. Chaudhary LC, Srivastava A. Performance of growing Murrah buffalo calves 21. Higgins JPT, Thompson SG, Deeks JJ, Altman DG. Measuring inconsistency as affected by treatment with Manoxol and the presence of ciliate protozoa in meta-analyses. BMJ. 2003;327:557–60. in the rumen. Anim Feed Sci Technol. 1995;51:281–6. 22. Knapp G, Hartung J. Improved tests for a random effects meta-regression 47. Eadie JM, Gill JC. The effect of the absence of rumen ciliate protozoa on with a single covariate. Stat Med. 2003;22:2693–710. growing lambs fed on a roughage–concentrate diet. Br J Nutr. 1971;26:155–67. 23. Guyader J, Eugène M, Nozière P, Morgavi DP, Doreau M, Martin C. Influence 48. Eugène M, Sauvant D, Weisbecker JL, Archimède H. Effects of defaunation of rumen protozoa on methane emission in ruminants: a meta-analysis on digestion of fresh Digitaria decumbens grass and growth of lambs. approach. Animal. 2014;8:1816–25. Animal. 2010;4:439–45. 24. Nagaraja TG. Microbiology of the rumen. In: Millen DD, Arrigoni MDB, 49. Kasuya N, Wada I, Shimada M, Kawai H, Itabashi H. Effect of presence of Pacheco RDL, editors. Rumenology. Cham: Springer; 2016. p. 39–61. rumen protozoa on degradation of cell wall constituents in gastrointestinal 25. Jouany JP, Demeyer DI, Grain J. Effect of defaunating the rumen. Anim Feed tract of cattle. Anim Sci J. 2007;78:275–80. Sci Technol. 1988;21:229–65. 50. Kreuzer M, Kirchgessner M, Müller HL. Effect of defaunation on the loss of 26. Mosoni P, Martin C, Forano E, Morgavi DP. Long-term defaunation increases energy in wethers fed different quantities of cellulose and normal or the abundance of cellulolytic ruminococci and methanogens but does not steamflaked maize starch. Anim Feed Sci Technol. 1986;16:233–41. affect the bacterial and methanogen diversity in the rumen of sheep. J 51. Nagaraja TG, Godfrey SI, Winslow SW, Rowe JB, Kemp KE. Effect of Anim Sci. 2011;89:783–91. virginiamycin on ruminal fermentation in faunated or ciliate-free sheep 27. Karakurt I, Aydin G, Aydiner K. Sources and mitigation of methane emissions overfed with barley grain. Small Rumin Res. 1995;17:1–8. by sectors: a critical review. Renew Energy. 2012;39:40–8. 52. Santra A, Karim SA. Growth performance of faunated and defaunated 28. Hristov AN, Oh J, Lee C, Meinen R. Mitigation of greenhouse gas emissions in Malpura weaner lambs. Anim Feed Sci Technol. 2000;86:251–60. livestock production: a review of technical options for non-CO emissions. 53. Santra A, Karim SA. Nutrient utilization and growth performance of defaunated Food and Agriculture Organization of the United Nations: Rome; 2013. and faunated lambs maintained on complete diets containing varying proportion 29. Janssen PH. Influence of hydrogen on rumen methane formation and of roughage and concentrate. Anim Feed Sci Technol. 2002;101:87–99. fermentation balances through microbial growth kinetics and fermentation 54. Santra A, Karim SA, Chaturvedi OH. Rumen enzyme profile and fermentation thermodynamics. Anim Feed Sci Technol. 2010;160:1–22. characteristics in sheep as affected by treatment with sodium lauryl sulfate 30. Bergman EN. Energy contributions of volatile fatty acids from the as defaunating agent and presence of ciliate protozoa. Small Rumin Res. gastrointestinal tract in various species. Physiol Rev. 1990;70:567–90. 2007;67:126–37. 31. Shabat SKB, Sasson G, Doron-Faigenboim A, Durman T, Yaacoby S, Berg Miller ME, 55. Sultana H, Miyazawa K, Kanda S, Itabashi H. Fatty acid composition of et al. Specific microbiome-dependent mechanisms underlie the energy harvest ruminal bacteria and protozoa, and effect of defaunation on fatty acid efficiency of ruminants. ISME J. 2016. https://doi.org/10.1038/ismej.2016.62. profile in the rumen with special reference to conjugated linoleic acid in 32. Weimer PJ, Cox MS, de Paula TV, Lin M, Hall MB, Suen G. Transient changes cattle. Anim Sci J. 2011;82:434–40. in milk production efficiency and bacterial community composition 56. Williams PP, Dinusson WE. Ruminal volatile fatty acid concentrations and resulting from near-total exchange of ruminal contents between high- and weight gains of calves reared with and without ruminal ciliated protozoa. J low-efficiency Holstein cows. J Dairy Sci. 2017;100:7165–82. Anim Sci. 1973;36:588–91. 33. Nguyen SH, Bremner G, Cameron M, Hegarty RS. Methane emissions, 57. Yáñez-Ruiz DR, Williams S, Newbold CJ. The effect of absence of protozoa ruminal characteristics and nitrogen utilisation changes after refaunation of on rumen biohydrogenation and the fatty acid composition of lamb protozoa-free sheep. Small Rumin Res. 2016;144:48–55. muscle. Br J Nutr. 2007;97:938–48. 34. Reece WO. Dukes’ physiology of domestic animals. 12th ed. Comstock Pub. 58. Zhou YY, Mao HL, Jiang F, Wang JK, Liu JX, McSweeney CS. Inhibition of Associates: Ithaca; 2004. rumen methanogenesis by tea saponins with reference to fermentation 35. Ozutsumi Y, Tajima K, Takenaka A, Itabashi H. The effect of protozoa on the pattern and microbial communities in Hu sheep. Anim Feed Sci Technol. composition of rumen bacteria in cattle using 16S rRNA gene clone 2011;166–167:93–100. libraries. Biosci Biotechnol Biochem. 2005;69:499–506. 36. Morgavi DP, Rathahao-Paris E, Popova M, Boccard J, Nielsen KF, Boudra H. Rumen microbial communities influence metabolic phenotypes in lambs. Front Microbiol. 2015;6:1060.

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Published: Dec 18, 2018

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