Rumen Microbiome and Metabolome of Tibetan Sheep (Ovis aries) Reflect Animal Age and Nutritional Requirement.
ABSTRACT: The rumen microbiota plays an important role in animal functional attributes. These microbes are indispensable for the normal physiological development of the rumen, and may also convert the plant polysaccharides from grass into available milk and meat, making it highly valuable to humans. Exploring the microbial composition and metabolites of rumen across developmental stages is important for understanding ruminant nutrition and metabolism. However, relatively few reports have investigated the microbiome and metabolites across developmental stages in ruminants. Using 16S rRNA gene sequnecing, metabolomics and high-performance liquid chromatography techniques, we compared the rumen microbiota, metabolites and short chain fatty acids (SCFAs) between lambs and sub-adult Tibetan sheep (Ovis aries) from Qinghai-Tibetan Plateau. Bacteroidetes and Spirochaetae were enriched in sub-adult sheep, while Firmicutes and Tenericutes were more abundant in young individuals. The sub-adult individuals had higher alpha diversity values than those in young sheep. Metabolomics analysis showed that the content of essential amino acids and related gene functional pathways in rumen were different between the lambs and sub-adult population. L-Leucine that participates in valine, leucine and isoleucine biosynthesis was more abundant in the lambs, while phenylethylamine that takes part in phenylalanine metabolism was more enriched in the sub-adults. Both rumen microbial community structures and metabolite profiles were impacted by age, but rumen SCFA concentration was relatively stable between different age stages. Some specific microbes (e.g., Clostridium and Ruminococcaceae) were positively associated with L-Leucine but negatively correlated with phenylethylamine, implying that rumen microbes may play different roles for metabolite production at different ages. Mantel test analysis showed that rumen microbiota was significantly correlated with metabolomics and SCFA profiles. Our results indicates the close relationship between microbial composition and metabolites, and also reveal different nutritional requirement for different ages in ruminants, thus having important significance for regulating animal nutrition and metabolism by microbiome intervention.
Project description:The rumen microbiota is an essential part of ruminants shaping their nutrition and health. Despite its importance, it is not fully understood how various groups of rumen microbes affect host-microbe relationships and functions. The aim of the study was to simultaneously explore the rumen microbiota and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted) that differentially restricted the acquisition of microbes. Rumen microbiota, fermentation parameters, digestibility and growth were monitored for up to 31 weeks of age. Microbiota assembled in isolation from other ruminants lacked protozoa and had low bacterial and archaeal diversity whereas digestibility was not affected. Exposure to adult sheep microbiota increased bacterial and archaeal diversity independently of protozoa presence. For archaea, Methanomassiliicoccales displaced Methanosphaera. Notwithstanding, protozoa induced differences in functional traits such as digestibility and significantly shaped bacterial community structure, notably Ruminococcaceae and Lachnospiraceae lower up to 6 folds, Prevotellaceae lower by ~40%, and Clostridiaceae and Veillonellaceae higher up to 10 folds compared to microbiota without protozoa. An orthogonal partial least squares-discriminant analysis of urinary metabolome matched differences in microbiota structure. Discriminant metabolites were mainly involved in amino acids and protein metabolic pathways while a negative interaction was observed between methylotrophic methanogens Methanomassiliicoccales and trimethylamine N-oxide. These results stress the influence of gut microbes on animal phenotype and show the potential of metabolomics for monitoring rumen microbial functions.
Project description:BACKGROUND:Meat quality is a complex trait affected by genotypic and environmental factors. In a previous study, it was found that feedstuffs have various effects on the growth rate and meat quality of lambs. However, the underlying mechanisms are still not entirely clear. RESULTS:In this study, to investigate the mechanisms that impact meat quality in twin sheep fed either with high fiber low protein (HFLP) forage (Ceratoides) or low fiber high protein (LFHP) forage (alfalfa) diets, multi omics techniques were utilized for integration analysis based on the feed nutritional value and the sheep microbiome, transcriptome, metabolome, and fatty acid profile. Results showed that the production performance and the muscle components of lambs were significantly affected by feeds. The essential fatty acid (linoleic acid and arachidonic acid) content of the muscle, based on gas chromatography-mass spectrometry analysis, was increased when lambs were fed with HFLP. The microbes in the lambs' rumen fed a HFLP diet were more diverse than those of the LFHP fed group. Besides, the ratio of Bacteroidetes and Firmicutes in the rumen of the sheep fed a LFHP diet was 2.6 times higher than that of the HFLP fed group. Transcriptome analysis of the muscle revealed that the genes related to glucose metabolic processes and fatty acid biosynthesis were significantly differentially expressed between the two groups. Potential cross talk was found between the sfour omics data layers, which helps to understand the mechanism by which feedstuffs affect meat quality of lambs. CONCLUSION:Feed systems may affect the epigenetic regulation of genes involved in the glucose metabolic pathway. HFLP feeds could induce gluconeogenesis to maintain glucose levels in blood, resulting in decreased fat content in muscle. The multiple omics analysis showed that the microbiota structure is significantly correlated with the metabolome and gene expression in muscle. This study laid a theoretical foundation for controlling the nutrient intake of sheep; it suggested that its fatty acid spectrum modifications and the removal of meat quality detrimental material could guide sheep feeding for functional mutton.
Project description:Modulating the assembly of the ruminal microbiota might have practical implications in production. We tested how an early-life dietary intervention in lambs influences the diversity and function of the ruminal microbiota during and after the intervention. Microbiota resilience during a repeated dietary intervention was also tested. The treatment, aiming to mitigate enteric methane emissions, combined garlic essential oil and linseed oil. Fifty-six lambs and their dams were allocated to two groups and treatment (T1) or placebo (C1) was drenched from birth until 10 weeks of life. Lambs were weaned at 8 weeks. From 16 to 20 weeks, lambs in each group were divided in two subgroups that received (T1-T2 and C1-T2) or not (T1-C2 and C1-C2) the same treatment. Measurements were done at 8, 14, and 20 weeks. Average daily gain was similar between groups. Methane production was reduced by treatment at 8 and 20 weeks but at 14 weeks it was similar between C1 and T1. Interestingly, early-life treated lambs displayed a numerical increase (P = 0.12) in methane emissions at 20 weeks compared with non-treated lambs. Concentration of VFA was not affected by the intervention at 8 or 14 weeks but a lower concentration was observed in T2 lambs compared with C2 at week 20. Metataxonomics (rRNA gene) revealed differences in archaeal communities between groups of lambs when treatment was applied (weeks 8 and 20); whereas, in accord with methane emissions, these differences disappeared when treatment was discontinued (week 14). Protozoal community structure was not affected by treatment. In contrast, bacterial community structure differed between treated and non-treated lambs during and after the intervention. Rumen and urine LC-MS and NMR metabolomics at week 20 separated C2 from T2 lambs and correlation analysis highlighted interactions between microbes and metabolites, notably that of methylated compounds and Methanomassiliicocceae methanogens. This study demonstrates that a long-term early-life intervention induced modifications in the composition of the rumen bacterial community that persisted after the intervention ceased with little or no effect on archaeal and protozoal communities. However, there was no persistency of the early-life intervention on methanogenesis indicating resilience for this function.
Project description:Early consumption of starter feed promotes rumen development in lambs. We examined rumen development in lambs fed starter feed for 5 weeks using histological and biochemical analyses and by performing high-throughput sequencing in rumen tissues. Additionally, rumen contents of starter feed-fed lambs were compared to those of breast milk-fed controls. Our physiological and biochemical findings revealed that early starter consumption facilitated rumen development, changed the pattern of ruminal fermentation, and increased the amylase and carboxymethylcellulase activities of rumen micro-organisms. RNA-seq analysis revealed 225 differentially expressed genes between the rumens of breast milk- and starter feed-fed lambs. These DEGs were involved in many metabolic pathways, particularly lipid and carbohydrate metabolism, and included HMGCL and HMGCS2. Sequencing analysis of 16S rRNA genes revealed that ruminal bacterial communities were more diverse in breast milk-than in starter feed-fed lambs, and each group had a distinct microbiota. We conclude that early starter feeding is beneficial to rumen development and physiological function in lambs. The underlying mechanism may involve the stimulation of ruminal ketogenesis and butanoate metabolism via HMGCL and HMGCS2 combined with changes in the fermentation type induced by ruminal microbiota. Overall, this study provides insights into the molecular mechanisms of rumen development in sheep.
Project description:Prickly pear cactus peels (Opuntia ficus-indica, PPCP) are sustainable byproducts available in arid regions and a rich source of antioxidants. Fifteen multiparous Barki ewes (2-3 years old, 46.94 ± 0.59 kg body weight, BW) at postpartum were individually distributed in three equal groups and fed diets supplemented with PPCP at doses of 0, 5 and 10 g/head/day. Lambs were individually distributed into three equal groups according to their mothers' groups to investigate the maternal effect on lambs' growth performance, hematology and serum metabolites. This trial lasted for 56 days from birth to weaning. Moreover, nine adult male Barki sheep with a live BW of 65.76 ± 0.54 kg were randomly allocated into three equal groups to determine the effect of PPCP on the nutrient digestibility of the experimental diets. The results indicate that supplementing PPCP at low levels (5 g/head/day) increased milk yield (p = 0.050), fat-corrected milk (p = 0.022), energy-corrected milk (p = 0.015) and the yield of milk constituents compared to 10 g PPCP and the control group. In addition, lambs suckling from ewes fed the diet supplemented with 5 g PPCP had a higher (p = 0.001) weaning BW compared to other groups. Serum total protein, globulin, superoxide dismutase, glutathione peroxidase enzyme activities and the triiodothyronine hormone improved significantly in lambs suckling from ewes fed diets supplemented with 5 g PPCP compared to the control group. Serum cholesterol profile and kidney activities were enhanced significantly in lambs suckling from ewes fed diets supplemented with 5 and 10 g of PPCP compared to the control group. The dietary supplementation of 5 g PPCP improved the crude protein digestibility, digestible crude protein value, nitrogen balance and rumen fermentation characteristics of male sheep compared to the control group. In conclusion, supplementation with 5 g PPCP improved ewes' milk production, offspring growth and physiological status. Furthermore, it improved the crude protein digestibility and rumen fermentation characteristics of Barki sheep.
Project description:Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not. We conducted shotgun sequencing of microbial DNA from the rumen contents of 16 sheep that differed in their residual feed intake (RFI), a measure of feed efficiency. Metagenomic reads from each sheep were mapped onto a database-derived microbial metabolic network, which was linked to the sheep metabolic network by interface metabolites (metabolites transferred from microbes to host). No single enzyme was identified as being significantly different in abundance between the low and high RFI animals (P > 0.05, Wilcoxon test). However, when we analyzed the metabolic network as a whole, we found several differences between efficient and inefficient animals. Microbes from low RFI (efficient) animals use a suite of enzymes closer in network space to the host's reactions than those of the high RFI (inefficient) animals. Similarly, low RFI animals have microbial metabolic networks that, on average, contain reactions using shorter carbon chains than do those of high RFI animals, potentially allowing the host animals to extract metabolites more efficiently. Finally, the efficient animals possess community networks with greater Shannon diversity among their enzymes than do inefficient ones. Thus, our system approach to the ruminal microbiome identified differences attributable to feed efficiency in the structure of the microbes' community metabolic network that were undetected at the level of individual microbial taxa or reactions.
Project description:In this study, we studied the fibrolytic potential of the rumen microbiota in the rumen of 6 lambs separated from their dams from 12h of age and artificially fed with milk replacer (MR) and starter feed from d8, in absence (3 lambs) or presence (3 lambs) of a combination of the live yeast Saccharomyces cerevisiae CNCM I-1077 and selected yeast metabolites. The fibrolytic potential of the rumen microbiota of the lambs at 56 days of age was analyzed with a DNA microarray (FibroChip) targeting genes coding for 8 glycoside hydrolase (GH) families. Overall design: We analysed two groups of lambs, with or without the feed supplement. These represented six samples (3 control and 3 supplemented lambs).
Project description:Rumen microbiome composition and functionality is linked to animal feed efficiency, particularly for bovine ruminants. To investigate this in sheep, we compared rumen bacterial and archaeal populations (and predicted metabolic processes) of sheep divergent for the feed efficiency trait feed conversion ratio (FCR). In our study 50 Texel cross Scottish Blackface (TXSB) ram lambs were selected from an original cohort of 200 lambs. From these, 26 were further selected for experimentation based on their extreme FCR (High Feed Efficiency, HFE = 13; Low Feed Efficiency, LFE = 13). Animals were fed a 95% concentrate diet ad libitum over 36 days. 16S rRNA amplicon sequencing was used to investigate the rumen bacterial and archaeal communities in the liquid and solid rumen fractions of sheep divergent for FCR. Weighted UniFrac distances separated HFE and LFE archaea communities from the liquid rumen fraction (Permanova, P < 0.05), with greater variation observed for the LFE cohort (Permdisp, P < 0.05). LFE animals exhibited greater Shannon and Simpson diversity indices, which was significant for the liquid rumen fraction (P < 0.05). Methanobrevibacter olleyae (in liquid and solid fractions) and Methanobrevibacter millerae (liquid fraction) were differentially abundant, and increased in the LFE cohort (P.adj < 0.05), while Methanobrevibacter wolinii (liquid fraction) was increased in the HFE cohort (P.adj < 0.05). This suggests that methanogenic archaea may be responsible for a potential loss of energy for the LFE cohort. Bacterial community composition (Permanova, P > 0.1) and diversity (P > 0.1) was not affected by the FCR phenotype. Only the genus Prevotella 1 was differentially abundant between HFE and LFE cohorts. Although no major compositional shifts of bacterial populations were identified amongst the feed efficient cohorts (FDR > 0.05), correlation analysis identified putative drivers of feed efficiency with Ruminococcaceae UCG-014 (liquid, rho = -0.53; solid, rho = -0.56) and Olsenella (solid, rho = -0.40) exhibiting significant negative association with FCR (P < 0.05). Bifidobacterium and Megasphaera showed significant positive correlations with ADG. Major cellulolytic bacteria Fibrobacter (liquid, rho = 0.43) and Ruminococcus 1 (liquid, rho = 0.41; solid, rho = 41) correlated positively with FCR (P < 0.05). Our study provides evidence that feed efficiency in sheep is likely influenced by compositional changes to the archaeal community, and abundance changes of specific bacteria, rather than major overall shifts within the rumen microbiome.
Project description:The objective of this study was to evaluate the effects of dietary supplementation with live yeast (Saccharomyces cerevisiae), mannan-oligosaccharides and the combination of these additives on the inflammatory response, ruminal parameters and rumen morphology of sheep fed a high grain-based diet. Thirty-Two Dorper x Santa Ines crossbred lambs with an average weight of 24±2 kg were distributed in a completely randomized design. The animals were housed in individual stalls and fed ad libitum. Diet treatments were: Control (without additive); LY (2 g/kg DM of live yeast, Saccharomyces cerevisiae), MOS (2 g/kg DM of mannan-oligosaccharides) and LY+MOS (2 g/kg DM of LY + 2 g/kg DM of MOS). The experiment lasted 42 days. The supplementation with MOS alone and the additives combination resulted in increased ruminal pH (P<0.01), while the total concentrations of short chain fatty acids (SCFA) in the rumen were higher (P<0.05) only in the diets with LY and MOS. Ammonia (NH3) concentration in the rumen decreased (P<0.04) with the additives usage. Diets with LY, MOS and with additives combination reduced (P<0.01) the levels of lipopolysaccharides (LPS) in the plasma with values of 0.46; 0.44 and 0.04 EU/mL, respectively when compared to the control (0.93 EU/mL). MOS and LY+MOS treatments had reduced stratum corneum thickness (P<0.01) in comparison to the control treatment. The total thickness of ruminal epithelium was lower with the addition of MOS in the diet (P<0.03) than with LY additive. The incidence and severity of hepatic abscesses in animals whose diet was supplemented with LY and LY+MOS was lower (P<0.05) than in animals fed the control diet. The use of LY, MOS and LY+MOS in the high-concentrate diets for sheep reduced NH3 concentrations and LPS translocation into the bloodstream. Diets containing MOS and LY+MOS enhanced the health of the ruminal epithelium by reducing the thickness of the stratum corneum, and diets containing LY and LY+MOS decreased the incidence and severity of hepatic abscesses.
Project description:BACKGROUND:Postbiotics have been established as potential feed additive to be used in monogastric such as poultry and swine to enhance health and growth performance. However, information on the postbiotics as feed additive in ruminants is very limited. The aim of this study was to elucidate the effects of supplementation of postbiotics in newly-weaned lambs on growth performance, digestibility, rumen fermentation characteristics and microbial population, blood metabolite and expression of genes related to growth and volatile fatty acid transport across the rumen epithelium. RESULTS:Postbiotic supplementation increased weight gain, feed intake, nutrient intake and nutrient digestibility of the lambs. No effect on ruminal pH and total VFA, whereas butyrate and ruminal ammonia-N concentration were improved. The lambs fed with postbiotics had higher blood total protein, urea nitrogen and glucose. However, no difference was observed in blood triglycerides and cholesterol levels. Postbiotics increased the population of fibre degrading bacteria but decreased total protozoa and methanogens in rumen. Postbiotics increased the mRNA expression of hepatic IGF-1 and ruminal MCT-1. CONCLUSIONS:The inclusion of postbiotics from L. plantarum RG14 in newly-weaned lambs improved growth performance, nutrient intake and nutrient digestibility reflected from better rumen fermentation and microbial parameters, blood metabolites and upregulation of growth and nutrient intake genes in the post-weaning lambs.