Multi-Omics Analysis Reveals a Dependent Relationship Between Rumen Bacteria and Diet of Grass- and Grain-Fed Yaks

Xu, Chenchen; Liu, Wenwen; Sun, Baozhong; Zhang, Songshan; Zhang, Shou; Yang, Yuanli; Lei, Yuanhua; Chang, Lan; Xie, Peng; Suo, Huayi

doi:10.3389/fmicb.2021.642959

Cited by 14 publications

(21 citation statements)

References 37 publications

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“…This may be because there is much less crude fiber in grain than in forage. Similar results were reported by Xu et al (11) in a study exploring the differences in rumen bacteria between grass-fed and grain-fed yaks. A comprehensive analysis of the composition of the yak rumen microbiota would provide important insights into microbially mediated metabolic processes.…”

Section: Introductionsupporting

confidence: 90%

“…There is increasing evidence that animal phenotypic characteristics are closely related to rumen microbes, and that the concentrations of metabolites in the rumen affect rumen bacterial function ( 10 , 11 , 63 ). Overall, the relative changes of rumen microbes and metabolites and their associations may be the main factors affecting yak production performance.…”

Section: Discussionmentioning

confidence: 99%

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Dietary Concentrate-to-Forage Ratio Affects Rumen Bacterial Community Composition and Metabolome of Yaks

Dai

et al. 2022

Front. Nutr.

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Changes in dietary composition affect the rumen microbiota in ruminants. However, information on the effects of dietary concentrate-to-forage ratio changes on yak rumen bacteria and metabolites is limited. This study characterized the effect of three different dietary concentrate-to-forage ratios (50:50, C50 group; 65:35, C65 group; 80:20, C80 group) on yak rumen fluid microbiota and metabolites using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS) analyses. Rumen fermentation parameters and the abundance of rumen bacteria were affected by changes in the dietary concentrate-to-forage ratio, and there was a strong correlation between them. At the genus level, higher relative abundances of norank_f__F082, NK4A214_group, Lachnospiraceae_NK3A20_group, Acetitomaculum, and norank_f__norank_o__Clostridia_UCG-014 were observed with a high dietary concentrate-to-forage ratio (P < 0.05). Combined metabolomic and enrichment analyses showed that changes in the dietary concentrate-to-forage ratio significantly affected rumen metabolites related to amino acid metabolism, protein digestion and absorption, carbohydrate metabolism, lipid metabolism, and purine metabolism. Compared with the C50 group, 3-methylindole, pantothenic acid, D-pantothenic acid, and 20-hydroxy-leukotriene E4 were downregulated in the C65 group, while spermine and ribose 1-phosphate were upregulated. Compared to the C50 group, Xanthurenic acid, tyramine, ascorbic acid, D-glucuronic acid, 6-keto-prostaglandin F1a, lipoxin B4, and deoxyadenosine monophosphate were upregulated in the C80 group, while 3-methylindole and 20-hydroxy-leukotriene E4 were downregulated. All metabolites (Xanthurenic acid, L-Valine, N-Acetyl-L-glutamate 5-semialdehyde, N-Acetyl-L-glutamic acid, Tyramine, 6-Keto-prostaglandin F1a, Lipoxin B4, Xanthosine, Thymine, Deoxyinosine, and Uric acid) were upregulated in the C80 group compared with the C65 group. Correlation analysis of microorganisms and metabolites provided new insights into the function of rumen bacteria, as well as a theoretical basis for formulating more scientifically appropriate feeding strategies for yak.

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Section: Introductionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Dietary Concentrate-to-Forage Ratio Affects Rumen Bacterial Community Composition and Metabolome of Yaks

Dai

et al. 2022

Front. Nutr.

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“…These results suggest that LA and SA systems differ not only in the relative abundance of species but also in the taxonomic composition with distinctive species in both systems. At the phylum level, Bacteroidetes and Firmicutes were the two most abundant classifications in both systems, which agrees with the previous ruminant studies (Xu et al, 2021 ; Zhang et al, 2021 ). Bacteroidetes as one of the most abundant phyla in the rumen has a wide range of sugar degradation and protein hydrolysis potential, which is significant for the digestion and utilization of non-fibrous polysaccharides and proteins (Woodmansey, 2007 ; De Mulder et al, 2016 ).…”

Section: Discussionsupporting

confidence: 92%

“…Diet is one of the important factors affecting rumen microbial diversity, due to microbial preferences for specific substrates. Previous studies have shown that high forage diet significantly increased the relative abundance of fibrobacterota (Pandit et al, 2018 ; Xu et al, 2021 ). Forages with different nutritional quality can also affect rumen microorganisms.…”

Section: Discussionmentioning

confidence: 94%

Metagenomic Analysis Revealed Differences in Composition and Function Between Liquid-Associated and Solid-Associated Microorganisms of Sheep Rumen

Hao

Shi

et al. 2022

Front. Microbiol.

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The rumen microbiota plays a key role in the utilization of plant materials by ruminants, yet little is known about the key taxa and their genetic functions of the rumen sub-environment involved in the ruminal degradation process. Understanding the differences in the composition and function of ruminal microbiota in the liquid-associated (LA) and solid-associated (SA) systems is needed to further study and regulate rumen function and health. In this study, rumen contents of nine sheep were collected to separate LA and SA systems with elution and centrifugal precipitation. Metagenome sequencing was used to investigate the differences in microbial composition and genetic functions of LA and SA systems, with special emphasis on their degradational potential toward carbohydrates. Results showed that the dominant species composition was similar between the two systems, but SA microorganisms had a higher relative abundance than LA microorganisms in all taxa. The concentration of fiber-degrading bacteria, such as Ruminococcus, Treponema, and Fibrobacter, was higher and Prevotella was lower in the SA vs. LA system. Additionally, SA microorganisms dominated in cellulose degradation, while LA microorganisms were more important in starch utilization based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO)'s functional categories and Carbohydrate-Active Enzymes (CAZymes). In general, SA microorganisms are more abundant and important in metabolic functions than LA, such as carbohydrate and amino acid metabolisms. In summary, the key differential biomarkers between LA and SA systems were Prevotella, Ruminococcus, Treponema, and Fibrobacter. Ruminal microbes degraded carbohydrates synergistically with SA, thus, more focusing on cellulose and hemicellulose, while LA is more important to starch.

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“…Previous studies indicate that the species diversity and abundance of rumen microorganisms play a critical role in maintaining host physiology (Xu et al, 2021). While Chao1 and ACE indices are primarily used to measure species richness, the Simpson and Shannon indices combine the richness and evenness of a species.…”

Section: Discussionmentioning

confidence: 99%

Effect of Saccharomyces cerevisiae culture mitigates heat stress-related dame in dairy cows by multi-omics

Jiang²,

Feng³

et al. 2022

Front. Microbiol.

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The effect of heat stress on ruminants is an important issue. In recent years, the growth of the Chinese dairy industry has rapidly increased, generating RMB 468,738 million revenue in 2021. A decreased milk yield is the most recognized impact of heat stress on dairy cows and results in significant economic loss to dairy producers. Heat stress also lowers immunity and antioxidant capacity and changes the bacterial composition and metabolites of the rumen. The purpose of this study was to investigate the effect of addition Saccharomyces cerevisiae culture on heat-stressed cows. The impact of S. cerevisiae culture on microbiota composition, functional profiles, and metabolomics was assessed in heat-stressed cows. A total of 45 Holstein cows in mid-lactation were selected and randomly divided into three groups (15 cows per group). Groups D-C, D-A, and D-B were fed with the basal diet, the basal diet + first S. cerevisiae culture 100 g/day, and the basal diet + second S. cerevisiae culture 30 g/day, respectively. The trial lasted 60 days. There was an increased abundance of the Phylum Firmicutes in the rumen of heat-stressed dairy cows fed with S. cerevisiae, of which four genera had significantly higher abundance, Ruminococcus_gauvreauii_group, Butyrivibrio_2, Moryella, and Ruminiclostridium_6. At the functional level, ten pathways differed significantly between the three groups (P < 0.05), with an increase in fatty acid biosynthesis, fatty acid metabolism, PPAR signaling pathway, ferroptosis, and biotin metabolism in the treatment groups. More differential metabolites were found in the D-C and D-A groups than in the D-C and D-B groups. These results indicate that S. cerevisiae cultures can influence the health status of heat-stressed cows by modulating rumen microbial composition, function, and metabolites, thereby improving rumen cellulolytic capacity. This study can provide or offer suggestions or recommendations for the development and utilization of feed additives.

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Multi-Omics Analysis Reveals a Dependent Relationship Between Rumen Bacteria and Diet of Grass- and Grain-Fed Yaks

Cited by 14 publications

References 37 publications

Dietary Concentrate-to-Forage Ratio Affects Rumen Bacterial Community Composition and Metabolome of Yaks

Dietary Concentrate-to-Forage Ratio Affects Rumen Bacterial Community Composition and Metabolome of Yaks

Metagenomic Analysis Revealed Differences in Composition and Function Between Liquid-Associated and Solid-Associated Microorganisms of Sheep Rumen

Effect of Saccharomyces cerevisiae culture mitigates heat stress-related dame in dairy cows by multi-omics

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