Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield.

Ruminants are essential for global food security, but these are major sources of the greenhouse gas methane. Methane yield is controlled by the cycling of molecular hydrogen (H2), which is produced during carbohydrate fermentation and is consumed by methanogenic, acetogenic, and respiratory microorganisms. However, we lack a holistic understanding of the mediators and pathways of H2 metabolism and how this varies between ruminants with different methane-emitting phenotypes. Here, we used metagenomic, metatranscriptomic, metabolomics, and biochemical approaches to compare H2 cycling and reductant disposal pathways between low-methane-emitting Holstein and high-methane-emitting Jersey dairy cattle. The Holstein rumen microbiota had a greater capacity for reductant disposal via electron transfer for amino acid synthesis and propionate production, catalyzed by enzymes such as glutamate synthase and lactate dehydrogenase, and expressed uptake [NiFe]-hydrogenases to use H2 to support sulfate and nitrate respiration, leading to enhanced coupling of H2 cycling with less expelled methane. The Jersey rumen microbiome had a greater proportion of reductant disposal via H2 production catalyzed by fermentative hydrogenases encoded by Clostridia, with H2 mainly taken up through methanogenesis via methanogenic [NiFe]-hydrogenases and acetogenesis via [FeFe]-hydrogenases, resulting in enhanced methane and acetate production. Such enhancement of electron incorporation for metabolite synthesis with reduced methanogenesis was further supported by two in vitro measurements of microbiome activities, metabolites, and public global microbiome data of low- and high-methane-emitting beef cattle and sheep. Overall, this study highlights the importance of promoting alternative H2 consumption and reductant disposal pathways for synthesizing host-beneficial metabolites and reducing methane production in ruminants.

Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids.

Goats are globally invaluable ruminants that balance food security and environmental impacts, and their commensal microbiome residing in the gastrointestinal tract (GIT) is associated with animal health and productivity. However, the reference genomes and functional repertoires of GIT microbes in goat kids have not been fully elucidated. Herein, we performed a comprehensive landscape survey of the GIT microbiome of goat kids using metagenomic sequencing and binning, spanning a dense sampling regime covering three gastrointestinal compartments spatially and five developmental ages temporally. We recovered 1002 high-quality metagenome-assembled genomes (termed the goat kid GIT microbial catalog [GKGMC]), 618 of which were novel. They encode more than 2.3 million nonredundant proteins, and represent a variety of carbohydrate-degrading enzymes and metabolic gene clusters. The GKGMC-enriched microbial taxa, particularly Sodaliphilus, expanded the microbial tree of life in goat kids. Using this GKGMC, we first deciphered the prevalence of fiber-degrading bacteria for carbohydrate decomposition in the rumen and colon, while the ileal microbiota specialized in the uptake and conversion of simple sugars. Moreover, GIT microorganisms were rapidly assembled after birth, and their carbohydrate metabolic adaptation occurred in three phases of progression. Finally, phytobiotics modified the metabolic cascades of the ileal microbiome, underpinned by the enrichment of Sharpea azabuensis and Olsenella spp. implicated in lactate formation and utilization. This GKGMC reference provides novel insights into the early-life microbial developmental dynamics in distinct compartments, and offers expanded resources for GIT microbiota-related research in goat kids.

Microbiome-transcriptome analysis reveals that dietary supplementation with macleaya cordata extract alters multiple immune pathways with minimal impact on microbial structure.

Background: As a potential antibiotic alternative, macleaya cordata extract (MCE) has anti-inflammatory, antioxidant, and antimicrobial properties. This study was conducted to assess the impact of MCE supplementation on the gut microbiota and its interplay with the host in young goats. Thirty female black goats with similar body weight (5.63 ± 0.30 kg) were selected and randomly allotted into one of three diets: a control diet (Control), a control diet with antibiotics (Antibiotics, 21 mg/kg/day vancomycin and 42 mg/kg/day neomycin), and a control diet with MCE (MCE, 3.75% w/w premix). Results: Principal coordinate analysis of the microbial community showed that samples of Antibiotic clustered separately from both Control and MCE (p < 0.001). The random forest analysis revealed that, in comparison to the Control group, the impact of Antibiotics on the microbiota structure was more pronounced than that of MCE (number of featured microbiota, 13 in Antibiotics and >6 in MCE). In addition, the pathways of significant enrichment either from DEGs between Antibiotics and Control or from DEGs between MCE and Control were almost identical, including Th17 cell differentiation, butanoate metabolism, T-cell receptor signaling pathway, intestinal immune network for IgA production, antigen processing and presentation, and ABC transporters. Furthermore, an integrative analysis indicated that significant positive correlations (p < 0.05) were observed between HEPHL1 and the featured biomarkers Atopostipes, Syntrophococcus, Romboutsia, and Acinetobacter in the MCE group. Conversely, several significant negative correlations (p < 0.05) were identified between HEPHL1 and the featured biomarkers Clostridium_XlVa, Phascolarctobacterium, Desulfovibrio, Cloacibacillus, Barnesiella, Succinatimonas, Alistipes, Oscillibacter, Ruminococcus2, and Megasphaera in the Antibiotics group. Conclusion: Collectively, the analysis of microbiome-transcriptome data revealed that dietary supplementation with MCE produced significant alterations in multiple immune pathways, while having minimal impact on the microbial structure.

The epithelial transcriptome and mucosal microbiota are altered for goats fed with a low-protein diet.

Introduction: Feeding low protein (LP) diet to animals impose severe challenge to animals' immune homeostasis. However, limited knowledge about the underlying adaption mechanism of host and ruminal microbiota responding to LP diet were well understood. Herein, this study was performed to examine the changes in relative abundance of ruminal microbiota and host ruminal mucosal transcriptome profiles in response to a LP diet. Methods: A total of twenty-four female Xiangdong balck goats with similar weight (20.64 ± 2.40 kg) and age (8 ± 0.3 months) were randomly assigned into two groups, LP (5.52% crude protein containing diet) and CON (10.77% crude protein containing diet) groups. Upon completion of the trial, all goats were slaughtered after a 16-hour fasting period in LiuYang city (N 28°15', E 113°63') in China. HE staining, free amino acids measurement, transcriptome analysis and microbiome analysis were applied to detect the morphology alterations, free amino acids profile alterations and the shift in host ruminal mucosal transcriptome and ruminal microbiota communities. Results: Firstly, the results showed that feeding LP diet to goats decreased the rumen papilla width (P = 0.043), surface area (P = 0.013) and total ruminal free amino acids concentration (P = 0.016). Secondly, microbiome analysis indicated that 9 microbial genera, including Eubacterium and Prevotella, were enriched in LP group while 11 microbial genera, including Butyrivibrio and Ruminococcus, were enriched in CON group. Finally, in terms of immune-related genes, the expression levels of genes involved in tight junction categories (e.g., MYH11, PPP2R2C, and MYL9) and acquired immunity (e.g., PCP4 and CXCL13) were observed to be upregulated in the LP group when compared to the CON group. Conclusion: Under the LP diet, the rumen exhibited increased relative abundance of pathogenic microbiota and VFA-degrading microbiota, leading to disruptions in immune homeostasis within the host's ruminal mucosa. These findings indicate that the ruminal microbiota interacts with host results in the disruption in animals' immune homeostasis under LP diet challenge.

Compared to antibiotic, feeding peony byproducts can improve growth performance, rumen fermentation, slaughter parameters, and meat quality of lambs.

Our objective was to determine effects of feeding lamb's peony byproducts, including stem and leaves (PSL), root (PR), and seeds meal (PSM), on growth, rumen fermentation, slaughter parameters, and meat quality. Sixty-four lambs (14.0 ± 2.1 kg) were allocated into eight treatments based on BW: no additives (CON), 0.15% aureomycin (CONA), low/high levels of PSL (5%/10% PSL replaced 5%/10% Chinese hay), PR (basal diet with 0.5%/1.0% PR), PSM (5%/10% PSM replaced 5%/10% soybean meal). Growth, digestibility, and rumen fermentation had dose responses whereas slaughter parameters, meat quality, or amino acids indexes were not. Peony byproducts increased DMI (p < 0.001) compared to CON, but higher levels were more advantageous (p = 0.003). However, low levels of peony byproducts decreased the NH3 -N concentration, but increased total volatile fatty acids mole percent more than high levels of that (p < 0.001). All peony byproducts increased dressing percentage (p < 0.05), increased pH and tenderness than CON (p < 0.05). In addition, PSL and PSM improved amino acid profiles of meat compared to CON, and were even better than CONA (p < 0.05). Therefore, peony byproducts not only improved animal growth but also reduced the frequency of antibiotic use in animal feeding.

Temporal changes in muscle characteristics during growth in the goat.

This study aimed to explore the temporal accumulative process of functional components and take insight into their dynamic regulatory metabolic pathways in the longissimus during growth in goats. Results showed that the intermuscular fat content, cross-sectional area and fast- to slow-switch fiber ratio of the longissimus were synchronously increased from d1 to d90. The dynamic profiles of functional components and transcriptomic pathways of the longissimus both exhibited two distinct phases during animal development. Expression of genes involved in de novo lipogenesis was increased from birth to weaning, leading to the accumulation of palmitic acid in the first phase. Accumulation of functional oleic acid, linoleic acid and linolenic acid in the second phase was dominatingly driven by enhancement in expression of genes related to fatty acid elongation and desaturation after weaning. A shift from serine to glycine production was observed after weaning, which was linked to the expression profile of genes involved in their interconversion. Our findings systematically reported the key window and pivotal targets of the functional components' accumulation process in the chevon.

The expression of nutrient chemosensing gate molecules in the ileum and colon is altered for goats fed on a high-grain diet.

Limited knowledge is clarified about alterations in the related expression of nutrient chemosensors in the distal small intestine and hindgut under a high-grain (HG) diet in small ruminants. Herein, this study was performed to investigate the expression changes related to nutrient sensing and transport in the ileal and colonic epithelium of goats in response to feeding an HG diet. Twelve Liuyang black goats (similar age and weight) were randomly assigned into two groups: an HG diet (concentrate: hay = 90:10) and a CON diet (concentrate: hay = 55:45). Immunohistochemistry was applied to detect morphological changes in the gut epithelium together with altered expression of chemosensors in the ileum and colon. The results showed that feeding an HG diet increased ileal villus height and depth and induced mucosal sloughing in the colon. The expressions of the nutrient transporters GLUT2, GLUT5, SGLT2, CD36, rBAT, EAAT3, and LAT2 and sensing receptors GPR43 and T1R1 were promoted in the ileum under HG conditions. Moreover, feeding an HG diet also enhanced the expression of GLUT2, SGLT2, CD36, and GPR43 in the colon. These findings indicate that adaptation of the gastrointestinal tract to the HG diet promoted the absorption of glucose, fatty acids, and amino acids in goats.

Enhancing Metabolic Efficiency through Optimizing Metabolizable Protein Profile in a Time Progressive Manner with Weaned Goats as a Model: Involvement of Gut Microbiota.

Feeding a growing global population and lowering environmental pollution are the two biggest challenges facing ruminant livestock. Considering the significance of nitrogen metabolism in these challenges, a dietary intervention regarding metabolizable protein profiles with different rumen-undegradable protein (RUP) ratios (high RUP [HRUP] versus low RUP [LRUP]) was conducted in young ruminants with weaned goats as a model. Fecal samples were collected longitudinally for nine consecutive weeks to dissect the timing and duration of intervention, as well as its mechanism of action involving the gut microbiota. Results showed that at least 6 weeks of intervention were needed to distinguish the beneficial effects of HRUP, and HRUP intervention improved the metabolic efficiency of goats as evidenced by enhanced growth performance and nutrient-apparent digestibility at week 6 and week 8 after weaning. Integrated analysis of bacterial diversity, metabolites, and inferred function indicated that HRUP intervention promoted Eubacterium abundance, several pathways related to bacterial chemotaxis pathway, ABC transporters, and butanoate metabolism and thereafter elicited a shift from acetate production toward butyrate and branched-chain amino acid (BCAA) production. Meanwhile, three distinct phases of microbial progression were noted irrespective of dietary treatments, including the enrichment of fiber-degrading Ruminococcus, the enhancement of microbial cell motility, and the shift of fermentation type as weaned goats aged. The current report provides novel insights into early-life diet-microbiota axis triggered by metabolic protein intervention and puts high emphasis on the time window and duration of dietary intervention in modulating lifelong performance of ruminants. IMPORTANCE Precise dietary intervention in early-life gastrointestinal microbiota has significant implications in the long-life productivity and health of young ruminants, as well as in lowering their environmental footprint. Here, using weaned goats as a model, we report that animals adapted to high rumen-undegradable protein diet in a dynamic manner by enriching fecal community that could effectively move toward and scavenge nutrients such as glucose and amino acids and, thereafter, elicit butyrate and BCAA production. Meanwhile, the three dynamic assembly trajectories in fecal microbiota highlight the importance of taking microbiota dynamics into account. Our findings systematically reported when, which, and how the fecal microbiome responded to metabolizable protein profile intervention in young ruminants and laid a foundation for improving the productivity and health of livestock due to the host-microbiota interplay.

Distribution of free amino acids and mRNA expression of their corresponding transporters in the intestinal mucosa of goats feeding on a corn grain versus corn gluten diet.

BACKGROUND: Intestinal amino acid (AA) chemosensing has been implicated in the regulation of AA absorption, nitrogen metabolism and hormone release, thereby playing an indispensable role in maintaining metabolic homeostasis in mammals. The objective of this experiment was to study the distribution of free AA and the expression of AA transporting related genes along the small and large intestines of Liuyang black goats, together with the effects of dietary corn grain replaced by dietary corn gluten feed (CGF). RESULTS: The CGF replacement did not alter (P > 0.05) AA profiles and the expression of AA transporting related genes in the intestinal mucosa. Intriguingly, in terms of gut regions, the concentrations of aspartic acid and glutamic acid in the mucosa of ileum were remarkably less (P < 0.001) than those in the large intestine. Moreover, the concentrations of most cationic and neutral AAs shared the same distribution pattern, with the jejunum and ileum holding the greatest and least levels (P < 0.05), respectively. It was notable that the expression of both anionic and cationic AA transporters in the small intestine was exceedingly greater (P < 0.001) than those in the large intestine. As for transporters of neutral AA, system ASC, L, and A showed an extremely distinctive expression pattern. CONCLUSION: The jejunum would be the primary site of transporting AA, while CGF substitution does not exert a disadvantageous influence on the AA chemosensing systems of the first-pass metabolism. © 2021 Society of Chemical Industry.

Dietary amylose:amylopectin ratio influences the expression of amino acid transporters and enzyme activities for amino acid metabolism in the gastrointestinal tract of goats.

This study was designed to investigate the effects of dietary starch structure on muscle protein synthesis and gastrointestinal amino acid (AA) transport and metabolism of goats. Twenty-seven Xiangdong black female goats (average body weight = 9·00 ± 1·12 kg) were randomly assigned to three treatments, i.e., fed a T1 (normal maize 100 %, high amylose maize 0 %), T2 (normal maize 50 %, high amylose maize 50 %) and T3 (normal maize 0 %, high amylose maize 100 %) diet for 35 d. All AA in the ileal mucosa were decreased linearly as amylose:amylopectin increased in diets (P < 0·05). The plasma valine (linear, P = 0·03), leucine (linear, P = 0·04) and total AA content (linear, P = 0·03) increased linearly with the increase in the ratio of amylose in the diet. The relative mRNA levels of solute carrier family 38 member 1 (linear, P = 0·01), solute carrier family 3 member 2 (linear, P = 0·02) and solute carrier family 38 member 9 (linear, P = 0·02) in the ileum increased linearly with the increase in the ratio of amylose in the diet. With the increase in the ratio of amylose:amylopectin in the diet, the mRNA levels of acetyl-CoA dehydrogenase B (linear, P = 0·04), branched-chain amino acid transferase 1 (linear, P = 0·02) and branched-chain α-keto acid dehydrogenase complex B (linear, P = 0·01) in the ileum decreased linearly. Our results revealed that the protein abundances of phosphorylated mammalian target of rapamycin (p-mTOR) (P < 0·001), phosphorylated 4E-binding protein 1 (P < 0·001) and phosphorylated ribosomal protein S6 kinases 1 (P < 0·001) of T2 and T3 were significantly higher than that of T1. In general, a diet with a high amylose ratio could reduce the consumption of AA in the intestine, allowing more AA to enter the blood to maintain higher muscle protein synthesis through the mTOR pathway.

Rumen-protected glucose supplementation in transition dairy cows shifts fermentation patterns and enhances mucosal immunity.

Manipulation of perinatal diets, such as supplementing feed with rumen-protected glucose (RPG), has been positively regarded as a strategy to improve milking performance. This study was conducted to assess the effects of RPG on the fermentation profiles, resident microbiota and mucosal immunity in the cecum. Ten Holstein dairy cows were randomly assigned to either a 25 g/kg RPG diet (DM basis) or a 11 g/kg coating fat diet (control, CON). Compared with the CON group, the acetate-to-propionate ratio was lower in the RPG group. Gene expression analysis indicated that RPG supplementation tended to upregulate the expression of Na+/H+ hydrogen exchanger 3 (NHE3) (P = 0.076). RPG supplementation downregulated the expression of genes involved in self-rehabilitation such as matrix metalloproteinase 1 (MMP1), MMP3, MMP9 and MMP13. Additionally, the mRNA expression of genes involved in immunity including Toll-like receptors (TLR4, TLR6 and TLR7) and proinflammatory cytokines (immune interferon gamma [IFNG] and interleukins interleukin 17A [IL17F], IL17A, IL22), was downregulated by RPG supplementation. Nonetheless, no differences existed in the bacterial copy number and beta diversity between the 2 groups. Overall, supplementation with RPG would probably cause a shift towards propionate production in the cecal digesta, and promote the immune homeostasis of the cecal mucosa in transition dairy cows. Our results extended the basic understanding of RPG supplementation and utilization in transition dairy cows in terms of host microbe interplay in the cecum.

Substitution of ramie (Boehmeria nivea) for alfalfa in improving the carcass and meat quality of Liuyang Black goats.

Ramie (Boehmeria nivea) is noted for the production of a large biomass that has a high protein content and is rich in antioxidants. It may thus serve as a high-quality forage material to replace alfalfa and improve the meat quality of farmed animals. In this study, we evaluated the carcass characteristics and meat quality of goats when 0, 35%, 75%, and 100% of dietary alfalfa was replaced with ramie. Crude protein content (linear, P < 0.0001) and key muscle color values at 24 h after slaughter decreased with increasing ramie levels. The content of most individual amino acids, non-essential amino acids (NEAA), total amino acids (TAA), branched chain amino acids (BCAA), functional amino acids (FAA), and flavor amino acids (DAA) decreased (P < 0.05) with increasing dietary ramie. The diet in which 35% of alfalfa was replaced with ramie yielded meat with the highest amino acid content, whereas the fatty acid profile was unaffected by the inclusion of ramie. These results indicate that ramie could be used as a potential dietary forage resource for goats, and that substituting 35% of alfalfa with ramie, which is equivalent to 126 g/kg DM content, would be optimal in terms of goat meat quality.

Correction: Martinez-Fernandez et al. Seasonal and Nutrient Supplement Responses in Rumen Microbiota Structure and Metabolites of Tropical Rangeland Cattle. Microorganisms 2020, 8, 1550.

We have found one inadvertent error in our paper published in Microorganisms [...].

Seasonal and Nutrient Supplement Responses in Rumen Microbiota Structure and Metabolites of Tropical Rangeland Cattle.

This study aimed to characterize the rumen microbiota structure of cattle grazing in tropical rangelands throughout seasons and their responses in rumen ecology and productivity to a N-based supplement during the dry season. Twenty pregnant heifers grazing during the dry season of northern Australia were allocated to either N-supplemented or un-supplemented diets and monitored through the seasons. Rumen fluid, blood, and feces were analyzed before supplementation (mid-dry season), after two months supplementation (late-dry season), and post supplementation (wet season). Supplementation increased average daily weight gain (ADWG), rumen NH3-N, branched fatty acids, butyrate and acetic:propionic ratio, and decreased plasma δ15N. The supplement promoted bacterial populations involved in hemicellulose and pectin degradation and ammonia assimilation: Bacteroidales BS11, Cyanobacteria, and Prevotella spp. During the dry season, fibrolytic populations were promoted: the bacteria Fibrobacter, Cyanobacteria and Kiritimatiellaeota groups; the fungi Cyllamyces; and the protozoa Ostracodinium. The wet season increased the abundances of rumen protozoa and fungi populations, with increases of bacterial families Lachnospiraceae, Ruminococcaceae, and Muribaculaceae; the protozoa Entodinium and Eudiplodinium; the fungi Pecoramyces; and the archaea Methanosphera. In conclusion, the rumen microbiota of cattle grazing in a tropical grassland is distinctive from published studies that mainly describe ruminants consuming better quality diets.

Diet with a High Proportion of Rice Alters Profiles and Potential Function of Digesta-Associated Microbiota in the Ileum of Goats.

Effects of a high proportion of concentrate in the diet on the ileal microbiota and metabolites in small ruminants are rarely reported. This study was designed to investigate the ileal microbiota and its relationship with host metabolic function in goats and aimed to elucidate the mechanisms involving in the ileal adaptation to a diet containing a high proportion of rice. Sixteen goats were equally divided into two groups and fed a diet with a normal concentrate proportion (NC, 55% concentrate) or a high-concentrate diet (HC, 90% concentrate). Results showed that the HC diet decreased bacterial diversity and elevated the abundance of five genera (Clostridium_sensu_stricto_1, Eubacterium_nodatum_group, Ruminococcus_gauvreauii_group, Eubacterium_coprostanoligenes_group and Ruminococcus 1), but reduced the number of Anaerotruncus. Microbial functional potentials indicated that the HC diet activated the pathways related to metabolism of carbohydrate, glycan, lipid and vitamins, but inhibited the pathways associated with cell motility and signal transduction. The activities of amylase and alkaline phosphatase were greater (p < 0.05) in the intestinal digesta of the HC-fed goats. However, there were no differences in the villus height, crypt depth and the ratio of villus height to crypt depth in the ileum between the two groups. These results indicate that the HC diet alters the bacterial community and pathways related to the metabolism of dietary nutrients and cell motility and signal transduction of bacteria in the ileum of goats.

Integrative plasma proteomic and microRNA analysis of Jersey cattle in response to high-altitude hypoxia.

Blood has been widely collected and analyzed for diagnosing and monitoring diseases in humans and animals; a range of plasma proteins and peptide can be used as biomarkers to describe pathological or physiological status. Changes in the environment such as high-altitude hypoxia (HAH) can lead to adaptive changes in the blood system of mammals. However, the adaptation mechanism induced by HAH remains unclear. In this study, we used 12 multiparous Jersey cattle (400 ± 35 kg, average 3 yr old, dry period). We applied an iTRAQ (isobaric tags for relative and absolute quantitation) proteomics approach and microRNA (miRNA) microarray to explore differences in the plasma proteomic and miRNA profiles of Jersey cattle exposed to HAH conditions in Nyingchi, Tibet (altitude 3,000 m) and HAH-free conditions in Shenyang, China (altitude 50 m). Such quantitative proteomic strategies are suitable for accurate and comprehensive prediction of miRNA targets. In total, 264 differentially expressed proteins (127 upregulated, fold-change >1.2; 137 downregulated, fold-change <0.8) and 47 differential miRNAs (25 upregulated, fold-change >2; 22 downregulated, fold-change <0.5) were observed in the HAH-stressed group compared with the HAH-free group. Integrative analysis of proteomic and miRNA profiles demonstrated that the biological processes associated with differentially expressed proteins were immune response, complement system, and conjugation system. Integrative analysis of canonical pathways showed that most were associated with acute phase response signaling (z-score = -0.125), liver X receptor/retinoid X receptor (LXR/RXR) activation pathway (z-score = 1.134), coagulation system (z-score = -0.943), and complement system (z-score = -0.632). The current results indicated that Jersey cattle exposed to HAH could adapt to that condition through regulation of inflammatory homeostasis by inhibiting the acute phase response, coagulation system, and complement system and promoting LXR/RXR activation.

Linkages between Epithelial Microbiota and Host Transcriptome in the Ileum during High-Grain Challenges: Implications for Gut Homeostasis in Goats.

A high-grain (HG) diet can result in ruminal subacute acidosis, which is detrimental to gut health and can lead to decreased productivity. This study investigated the ileal epithelial microbiota and its relationship with host epithelial function in goats fed a HG diet (concentrate/hay, 90:10) and a control diet (concentrate/hay, 55:45), aiming to elucidate the mechanisms involved in ileal adaptation to subacute acidosis. The HG challenge increased the ileal volatile fatty acid concentration ( p = 0.030) and altered the ileal epithelial microbiota by increasing (FDR < 0.05) relative abundances of active carbohydrate and protein degraders Synergistetes, Prevotella, Fibrobacter, Clostridium, Treponema, and unclassified Ruminococcaceae by 20.1-, 6.3-, 16.8-, 8.5-, 19.9-, and 7.1-fold, respectively. However, the HG diet tended to reduce (FDR < 0.10) the relative abundance of Candidatus Arthromitus (38.8 ± 36.1 versus 2.1 ± 3.1). Microbial functional potentials inferred using PICRUSt indicated that the HG challenge elevated abundances of pathways associated with metabolism of amino acid, glycan, cofactors, and vitamins, whereras it decreased pathways associated with signal transduction, xenobiotic biodegradation, and metabolism. Additionally, in the ileal epithelium of HG goats, transcriptome analysis identified the increment (FDR < 0.10) of candidate genes involved in metabolism of carbohydrates, lipids, proteins, vitamins, and the proinflammatory cytokine pathway, while downregulating genes encoding antimicrobials and complements (FDR < 0.05). Collectively, the HG challenge shifted the structure and functional potentials of the ileal microbial community and affected the host responses in the ileum of goats toward increased metabolic activities of macro- and micronutrients, together with an increased risk of gut inflammation.

Rhubarb Supplementation Promotes Intestinal Mucosal Innate Immune Homeostasis through Modulating Intestinal Epithelial Microbiota in Goat Kids.

The abuse and misuse of antibiotics in livestock production pose a potential health risk globally. Rhubarb can serve as a potential alternative to antibiotics, and several studies have looked into its anticancer, antitumor, and anti-inflammatory properties. The aim of this study was to test the effects of rhubarb supplementation to the diet of young ruminants on innate immune function and epithelial microbiota in the small intestine. Goat kids were fed with a control diet supplemented with or without rhubarb (1.25% DM) and were slaughtered at days 50 and 60 of age. Results showed that the supplementation of rhubarb increased ileal villus height (P = 0.036), increased jejujal and ileal anti-inflammatory IL-10 production (P < 0.05), increased jejunal and ileal Claudin-1 expression at both mRNA and protein levels (P < 0.05), and decreased ileal pro-inflammatory IL-1ß production (P < 0.05). These changes in innate immune function were accompanied by shifts in ileal epithelial bacterial ecosystem in favor of Blautia, Clostridium, Lactobacillus, and Pseudomonas, and with a decline in the relative abundance of Staphylococcus (P < 0.001) when rhubarb was supplemented. Additionally, age also affected (P < 0.05) crypt depth, cytokine production, Claudin-1 expression and relative abundances of specific genera in epithelial bacteria. Collectively, the supplementation of rhubarb could enhance host mucosal innate immune homeostasis by modulating intestinal epithelial microbiota during the early stages of animal development.

Molecular hydrogen generated by elemental magnesium supplementation alters rumen fermentation and microbiota in goats.

We tested the hypotheses that supplementation of a diet with elemental Mg increases ruminal dissolved H2 (dH2) in rumen fluid, which in turn alters rumen fermentation and microbial community in goats. In a randomised block design, twenty growing goats were allocated to two treatments fed the same basal diet with 1·45 % Mg(OH)2 or 0·6 % elemental Mg. After 28 d of adaptation, we collected total faeces to measure total tract digestibility, rumen contents to analyse fermentation end products and microbial groups, and measured methane (CH4) emission using respiration chambers. Ruminal Mg2+ concentration was similar in both treatments. Elemental Mg supplementation increased dH2 at 2·5 h post morning feeding (+180 %, P<0·001). Elemental Mg supplementation decreased total volatile fatty acid concentration (-8·6 %, P<0·001), the acetate:propionate ratio (-11·8 %, P<0·03) and fungal copy numbers (-63·6 %, P=0·006), and increased propionate molar percentage (+11·6 %, P<0·001), methanogen copy numbers (+47·9 %, P<0·001), dissolved CH4 (+35·6 %, P<0·001) and CH4 emissions (+11·7 %, P=0·03), compared with Mg(OH)2 supplementation. The bacterial community composition in both treatments was overall similar. Ruminal dH2 was negatively correlated with acetate molar percentage and fungal copy numbers (P<0·05), and positively correlated with propionate molar percentage and methanogen copy numbers (P<0·05). In summary, elemental Mg supplementation increased ruminal dH2 concentration, which inhibited rumen fermentation, enhanced methanogenesis and seemed to shift fermentation pathways from acetate to propionate, and altered microbiota by decreasing fungi and increasing methanogens.

Shifts in Host Mucosal Innate Immune Function Are Associated with Ruminal Microbial Succession in Supplemental Feeding and Grazing Goats at Different Ages.

Gastrointestinal microbiota may play an important role in regulating host mucosal innate immune function. This study was conducted to test the hypothesis that age (non-rumination, transition and rumination) and feeding type [Supplemental feeding (S) vs. Grazing (G)] could alter ruminal microbial diversity and maturation of host mucosal innate immune system in goat kids. MiSeq sequencing was applied to investigate ruminal microbial composition and diversity, and RT-PCR was used to test expression of immune-related genes in ruminal mucosa. Results showed that higher (P < 0.05) relative abundances of Prevotella, Butyrivibrio, Pseudobutyrivibrio, Methanobrevibacter.gottschalkii, Neocallimastix, Anoplodinium-Diplodinium, and Polyplastron, and lower relative abundance of Methanosphaera (P = 0.042) were detected in the rumen of S kids when compared to those in G kids. The expression of genes encoding TLRs, IL1α, IL1ß and TICAM2 was down-regulated (P < 0.01), while expression of genes encoding tight junction proteins was up-regulated (P < 0.05) in the ruminal mucosa of S kids when compared to that in G kids. Moreover, irrespective of feeding type, relative abundances of ruminal Prevotella, Fibrobacter, Ruminococcus, Butyrivibrio, Methanobrevibacter, Neocallimastix, and Entodinium increased with age. The expression of most genes encoding TLRs and cytokines increased (P < 0.05) from day 0 to 7, while expression of genes encoding tight junction proteins declined with age (P < 0.05). This study revealed that the composition of each microbial domain changed as animals grew, and these changes might be associated with variations in host mucosal innate immune function. Moreover, supplementing goat kids with concentrate could modulate ruminal microbial composition, enhance barrier function and decrease local inflammation. The findings provide useful information in interpreting microbiota and host interactions, and developing nutritional strategies to improve the productivity and health of rumen during early life.