Dataset Information

Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages.

ABSTRACT: A cattle-yak, which is a hybrid between a yak (Bos grunniens) and cattle (Bos taurus), is an important livestock animal, but basic questions regarding its physiology and environmental adaptation remain unanswered. To address this issue, the present study examined the species composition and functional characteristics of rumen microorganisms in the cattle-yak of different ages (2 and 3 years old) by metagenomic analysis. We found that rumen microbial community composition was similar at the two ages. Firmicutes, Fibrobacteres, Euryarchaeota, Bacteroidetes, and Proteobacteria were the predominant phyla, with Firmicutes accounting for the highest percentage of bacteria in 2-year-old (48%) and 3-year-old (46%) animals. Bacterial species involved in lignocellulose degradation were detected in the rumen of adult cattle-yaks including Ruminococcus flavefaciens, Ruminococcus albus, Fibrobacter succinogenes, and Prevotella ruminicola, with F. succinogenes being the most abundant. A total of 145,489 genes were annotated according to the Carbohydrate-active Enzyme database, which identified glycoside hydrolases as the most highly represented enzyme family. Further functional annotation revealed specific microflora and genes in the adult rumen that are potentially related to plateau adaptability. These results could explain the heterosis of the cattle-yak and provide insight into mechanisms of physiologic adaptation in plateau animals.

SUBMITTER: Sha Y

PROVIDER: S-EPMC7073488 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages.

Sha Yuzhu Y Hu Jiang J Shi Bingang B Dingkao Renqing R Wang Jiqing J Li Shaobin S Zhang Wei W Luo Yuzhu Y Liu Xiu X

BioMed research international 20200303

A cattle-yak, which is a hybrid between a yak (<i>Bos grunniens</i>) and cattle (<i>Bos taurus</i>), is an important livestock animal, but basic questions regarding its physiology and environmental adaptation remain unanswered. To address this issue, the present study examined the species composition and functional characteristics of rumen microorganisms in the cattle-yak of different ages (2 and 3 years old) by metagenomic analysis. We found that rumen microbial community composition was simila ...[more]

PMID: 32190661

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Project description:Current knowledge about the relationships between ruminal bacterial communities and metabolite profiles in the yak rumen is limited. This is due to differences in the nutritional and metabolic features between yak and other ordinary cattle combined with difficulties associated with farm-based research and a lack of technical guidance. A comprehensive analysis of the composition and alterations in ruminal metabolites is required to advance the development of modern yak husbandry. In the current study, we characterized the effect of feed type on the ruminal fluid microbiota and metabolites in yak using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS). Bacteroidetes and Firmicutes were the predominant bacterial phyla in the yak rumen. At the genus level, the relative abundance of Bacteroidales BS11 gut group, Prevotellaceae UCG-003, Ruminococcaceae UCG-011, Bacteroidales RF16 group and Ruminococcaceae UCG-010 was significantly (P < 0.01) higher in the forage group compared to that in the concentrate group, while the concentrate group harbored higher proportions of Bacteroidales S24-7 group, Ruminococcaceae NK4A214, Succiniclasticum and Ruminococcus 2. Yak rumen metabolomics analysis combined with enrichment analysis revealed that feed type altered the concentrations of ruminal metabolites as well as the metabolic pattern, and significantly (P < 0.01) affected the concentrations of ruminal metabolites involved in protein digestion and absorption (e.g., L-arginine, ornithine, L-threonine, L-proline and β-alanine), purine metabolism (e.g., xanthine, hypoxanthine, deoxyadenosine and deoxyadenosine monophosphate) and fatty acid biosynthesis (e.g., stearic acid, myristic acid and arachidonic acid). Correlation analysis of the association of microorganisms with metabolite features provides us with a comprehensive understanding of the composition and function of microbial communities. Associations between utilization or production were widely identified between affected microbiota and certain metabolites, and these findings will contribute to the direction of future research in yak.

Project description:Our aim was to simultaneously investigate the gut bacteria typical characteristic and conduct rumen metabolites profiling of high production dairy cows when compared to low-production dairy cows. The bacterial differences in rumen fluid and feces were identified by 16S rDNA gene sequencing. The metabolite differences were identified by metabolomics profiling with liquid chromatography mass spectrometry (LC-MS). The results indicated that the high-production dairy cows presented a lower rumen bacterial richness and species evenness when compared to low-production dairy cows. At the phylum level, the high-production cows increased the abundance of Proteobacteria and decreased the abundance of Bacteroidetes, SR1, Verrucomicrobia, Euryarchaeota, Planctomycetes, Synergistetes, and Chloroflexi significantly (p < 0.05). At the genus level, the rumen fluid of the high-production group was significantly enriched for Butyrivibrio, Lachnospira, and Dialister (p < 0.05). Meanwhile, rumen fluid of high-production group was depleted for Prevotella, Succiniclasticum, Ruminococcu, Coprococcus,YRC22, CF231, 02d06, Anaeroplasma, Selenomonas, and Ruminobacter significantly (p < 0.05). A total of 92 discriminant metabolites were identified between high-production cows and low-production cows. Compared to rumen fluid of low-production dairy cows, 10 differential metabolites were found up-regulated in rumen fluid of high-production dairy cows, including 6alpha-Fluoropregn-4-ene-3,20-dione, 3-Octaprenyl-4-hydroxybenzoate, disopyramide, compound III(S), 1,2-Dimyristyl-sn-glycerol, 7,10,13,16-Docosatetraenoic acid, ferrous lactate, 6-Deoxyerythronolide B, vitamin D2, L-Olivosyl-oleandolide. The remaining differential metabolites were found down-regulated obviously in high-production cows. Metabolic pathway analyses indicated that most increased abundances of rumen fluid metabolites of high-yield cows were related to metabolic pathways involving biosynthesis of unsaturated fatty acids, steroid biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis. Most down-regulated metabolic pathways were relevant to nucleotide metabolism, energy metabolism, lipid metabolism and biosynthesis of some antibiotics.

Project description:The rumen microbiota of ruminants plays a vital role in fiber digestion, and environmental factors affect its community structure. The yak (Bos grunniens) is the main livestock species that inhabits the Qinghai-Tibet Plateau (QTP) at regions located at high-altitude of 3,000-5,000 m. This work investigated the rumen bacterial community of yak that grazed on the QTP during the whole year to evaluate the relationship between the rumen bacterial community and the nutrient composition of forage plant at three stages. In this study, the diversity of the rumen prokaryotic community composition was monitored in 10 full-grazing yak in an alpine meadow of the QTP. The nutrient composition of three forage growth stages was determined: re-green stage (REGY), grassy stage (GY), and withered stage (WGY). High-throughput sequencing of bacterial 16S rRNA gene was used. The results showed that the nutritive composition of the alpine meadow changed with the seasons: crude protein (CP) (13.22%) was high in forage during REGY (spring), while neutral detergent fiber (NDF) (59.00%) was high during WGY (winter). Microbial diversity and richness were highest during REGY and the average number of operational taxonomic units from 30 samples was 4,470. The microbial composition was dominated by members of Bacteroidetes (51.82%), followed by Firmicutes (34.08%), and the relative microbial abundance changed in the three forage growth stages. Unweighted UniFrac distance PcoA showed that the bacterial community structure differed between REGY, GY, and WGY. Furthermore, taxonomic groups did not present differences regarding gender in these three stages. The rumen microbiota was enriched with functional potentials that were related to ABC transporters, the two-component system, Aminoacyl-tRNA biosynthesis, and metabolism of Purine, Pyrimidine, Starch and sucrose metabolism. Significant differences were found in the composition, diversity, and function of yak ruminal microorganisms during different forage growth stages. This indicates that microbial changes in the rumen depend on changes in the forage nutritional composition. These findings provide evidence on the rumen microbial diversity of yaks in the QTP.

Project description:Management of metabolic hydrogen ([H]) in the rumen has been identified as an important consideration when reducing ruminant CH4 emissions. However, little is known about hydrogen flux and microbial rumen population responses to CH4 inhibition when animals are fed with slowly degradable diets. The effects of the anti-methanogenic compound, chloroform, on rumen fermentation, microbial ecology, and H2/CH4 production were investigated in vivo. Eight rumen fistulated Brahman steers were fed a roughage hay diet (Rhode grass hay) or roughage hay:concentrate diet (60:40) with increasing levels (low, mid, and high) of chloroform in a cyclodextrin matrix. The increasing levels of chloroform resulted in an increase in H2 expelled as CH4 production decreased with no effect on dry matter intakes. The amount of expelled H2 per mole of decreased methane, was lower for the hay diet suggesting a more efficient redirection of hydrogen into other microbial products compared with hay:concentrate diet. A shift in rumen fermentation toward propionate and branched-chain fatty acids was observed for both diets. Animals fed with the hay:concentrate diet had both higher formate concentration and H2 expelled than those fed only roughage hay. Metabolomic analyses revealed an increase in the concentration of amino acids, organic, and nucleic acids in the fluid phase for both diets when methanogenesis was inhibited. These changes in the rumen metabolism were accompanied by a shift in the microbiota with an increase in Bacteroidetes:Firmicutes ratio and a decrease in Archaea and Synergistetes for both diets. Within the Bacteroidetes family, some OTUs assigned to Prevotella were promoted under chloroform treatment. These bacteria may be partly responsible for the increase in amino acids and propionate in the rumen. No significant changes were observed for abundance of fibrolytic bacteria, protozoa, and fungi, which suggests that fiber degradation was not impaired. The observed 30% decrease in methanogenesis did not adversely affect rumen metabolism and the rumen microbiota was able to adapt and redirect [H] into other microbial end-products for both diets. However, it is also required dietary supplements or microbial treatments to capture the additional H2 expelled by the animal to further improve rumen digestive efficiency.

Project description:The gut microbiota is closely associated with the health and production performance of livestock. Partial studies on ruminant microbiota are already in progress in the Qinghai-Tibetan Plateau Area (QTPA) in China, but large-scale and representative profiles for the QTPA are still lacking. Here, 16S rRNA sequencing was used to analyze 340 samples from yak, cattle, yak-cattle hybrids, and Tibetan sheep, which lived in a shared environment from 4 eco-regions of the QTPA during the same season, and aimed to investigate the fecal microbiota community composition, diversity, and potential function. All samples were clustered into 2 enterotypes, which were derived from the genera Ruminococcaceae UCG-005 and Acinetobacter, respectively. Environment, human activity, species, and parasitization all affected the fecal microbiota. By assessing the relationship between the fecal microbiota and the above variables, we identified a scattered pattern of fecal microbiota dissimilarity based more significantly on diet over other factors. Additionally, gastrointestinal nematode infection could reduce the capacity of the bacterial community for biosynthesis of other secondary metabolites, carbohydrate metabolism, and nucleotide metabolism. Ultimately, this study provided a fecal microbiota profile for ruminants living in 4 eco-regions of the QTPA and its potential future applications in developing animal husbandry regimes. IMPORTANCE Cattle, yak, and sheep reside as the main ruminants distributed throughout most regions of Qinghai-Tibetan Plateau Area (QTPA) in China. However, there is a lack of large-scale research in the QTPA on their fecal microbiota, which can regulate and reflect host health as an internalized "microbial organ." Our study depicted the fecal microbiota community composition and diversity of yak, cattle, yak-cattle hybrids, and Tibetan sheep from 4 eco-regions of the QTPA. Additionally, our results demonstrated here that the ruminant samples could be clustered into 2 enterotypes and that diet outweighed other factors in shaping fecal microbiota in the QTPA. This study provided a basis for understanding the microbiota characteristic of ruminants and its possible applications for livestock production in the QTPA.

Project description:BackgroundThe major greenhouse gas from ruminants is enteric methane (CH4) which in 2010, was estimated at 2.1 Gt of CO2 equivalent, accounting for 4.3% of global anthropogenic greenhouse gas emissions. There are extensive efforts being made around the world to develop CH4 mitigating inhibitors that specifically target rumen methanogens with the ultimate goal of reducing the environmental footprint of ruminant livestock production. This study examined the individual and combined effects of supplementing a high-forage diet (90% barley silage) fed to beef cattle with the investigational CH4 inhibitor 3-nitrooxypropanol (3-NOP) and canola oil (OIL) on the rumen microbial community in relation to enteric CH4 emissions and ruminal fermentation.Results3-NOP and OIL individually reduced enteric CH4 yield (g/kg dry matter intake) by 28.2% and 24.0%, respectively, and the effects were additive when used in combination (51.3% reduction). 3-NOP increased H2 emissions 37-fold, while co-administering 3-NOP and OIL increased H2 in the rumen 20-fold relative to the control diet. The inclusion of 3-NOP or OIL significantly reduced the diversity of the rumen microbiome. 3-NOP resulted in targeted changes in the microbiome decreasing the relative abundance of Methanobrevibacter and increasing the relative abundance of Bacteroidetes. The inclusion of OIL resulted in substantial changes to the microbial community that were associated with changes in ruminal volatile fatty acid concentration and gas production. OIL significantly reduced the abundance of protozoa and fiber-degrading microbes in the rumen but it did not selectively alter the abundance of rumen methanogens.ConclusionsOur data provide a mechanistic understanding of CH4 inhibition by 3-NOP and OIL when offered alone and in combination to cattle fed a high forage diet. 3-NOP specifically targeted rumen methanogens and partly inhibited the hydrogenotrophic methanogenesis pathway, which increased H2 emissions and propionate molar proportion in rumen fluid. In contrast, OIL caused substantial changes in the rumen microbial community by indiscriminately altering the abundance of a range of rumen microbes, reducing the abundance of fibrolytic bacteria and protozoa, resulting in altered rumen fermentation. Importantly, our data suggest that co-administering CH4 inhibitors with distinct mechanisms of action can both enhance CH4 inhibition and provide alternative sinks to prevent excessive accumulation of ruminal H2.

Dataset Information

Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages.

Publications

Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages.

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