Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants

Gruninger, Robert J.; Ribeiro, Gabriel de Oliveira; Cameron, Andrew; McAllister, Tim A.

doi:10.1017/s1751731119000752

Cited by 76 publications

(51 citation statements)

References 102 publications

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“…In ruminants, protein from the diet is generally degraded quickly and converted into microbial protein in the rumen, and then microbial protein flows into the small intestine ( Gruninger et al, 2019 ). Therefore, it was believed that peptide absorption occurred mostly in the small intestine.…”

Section: Resultsmentioning

confidence: 99%

Expression of the Tas1r3 and Pept1 genes in the digestive tract of wagyu cattle

Fan

Saito

Matsumura

2020

Translational Animal Science

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Animals have precise recognition systems for amino acids and peptides that regulate their feeding behavior as well as metabolic responses. Because of their particular gastrointestinal structure, ruminants are expected to have unique mechanisms of amino acid regulation in the digestive tract. To better understand these mechanisms in the ruminant digestive tract, the expression of Tas1r3 and Pept1 was studied along the gastrointestinal tract of Japanese Black cattle through quantitative RT-PCR and immunohistochemistry. Tas1r3 mRNA was detected ubiquitously along the gastrointestinal tract, and the most predominant expression was observed in the reticulum. In addition, the presence of Tas1r3 receptor was confirmed in the rumen through immunohistochemistry. The expression level of Pept1 mRNA was higher in the forestomach (rumen, reticulum, and omasum) and small intestine (duodenum) than that in the tongue, and predominant expression was observed in the rumen. By contrast, a negligible amount of Pept1 mRNA was detected in the abomasum and large intestine. Further studies on the roles of Tas1r3 and Pept1 in the digestive tract, in particular, in the four components of the stomach, will help us to understand the mechanisms of amino acids regulation in ruminants and provide the basis for formulating cattle diets to improve the health and productivity of cattle.

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Section: Resultsmentioning

confidence: 99%

Expression of the Tas1r3 and Pept1 genes in the digestive tract of wagyu cattle

Fan

Saito

Matsumura

2020

Translational Animal Science

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“…The BCAA were primarily converted to BCVFA, but the latter was more extensively assimilated into bacterial branched-chain fatty acids. The BCVFA are required growth factors for numerous strains of cellulolytic bacteria (Stewart et al, 1997), which are key to initiating colonization and optimizing degradability of fiber in the rumen (Gruninger et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. II: Relation with solid passage rate and pH on neutral detergent fiber degradation and microbial function in continuous culture

Roman-Garcia

Mitchell

Denton

et al. 2021

Journal of Dairy Science

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To support improving genetic potential for increased milk production, intake of digestible carbohydrate must also increase to provide digestible energy and microbial protein synthesis. We hypothesized that the provision of exogenous branched-chain volatile fatty acids (BCVFA) would improve both neutral detergent fiber (NDF) degradability and efficiency of microbial protein synthesis. However, BCVFA should be more beneficial with increasing efficiency of bacterial protein synthesis associated with increasing passage rate (k p ). We also hypothesized that decreasing pH would increase the need for isobutyrate over 2-methylbutyrate. To study these effects independent from other sources of variation in vivo, we evaluated continuous cultures without (control) versus with BCVFA (0 vs. 2 mmol/d each of isobutyrate, isovalerate, and 2-methylbutyrate), low versus high k p of the particulate phase (2.5 vs. 5.0%/h), and high versus low pH (ranging from 6.3 to 6.8 diurnally vs. 5.7 to 6.2) in a 2 × 2 × 2 factorial arrangement of treatments. Diets were 50% forage pellets and 50% grain pellets administered twice daily. Without an interaction, NDF degradability tended to increase from 29.7 to 35.0% for main effects of control compared with BCVFA treatments. Provision of BCVFA increased methanogenesis, presumably resulting from improved NDF degradability. Decreasing pH decreased methane production. Total volatile fatty acid (VFA) and acetate production were decreased with increasing k p , even though true organic matter degradability and bacterial nitrogen flow were not affected by treatments. Decreas-ing pH decreased acetate but increased propionate and valerate production, probably resulting from a shift in bacterial taxa and associated VFA stoichiometry. Decreasing pH decreased isobutyrate and isovalerate production while increasing 2-methylbutyrate production on a net basis (subtracting doses). Supplementing BCVFA improved NDF degradability in continuous cultures administered moderate (15.4%) crude protein diets (excluding urea in buffer) without major interactions with culture pH and k p .

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“…The composition of rumen microbiota is affected by several factors, such as diet [3][4][5], age and health [6,7], breed [8], diet and age [9], environment, and host genetics [10]. Diet composition is found to have a major influence on the community structure and fermentation patterns of rumen microbes [11], which in turn affect methane production, host health, and productivity [12].…”

Section: Introductionmentioning

confidence: 99%

Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages

et al. 2021

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Seven Italian Simmental cows were monitored during three different physiological stages, namely late lactation (LL), dry period (DP), and postpartum (PP), to evaluate modifications in their metabolically-active rumen bacterial and protozoal communities using the RNA-based amplicon sequencing method. The bacterial community was dominated by seven phyla: Proteobacteria, Bacteroidetes, Firmicutes, Spirochaetes, Fibrobacteres, Verrucomicrobia, and Tenericutes. The relative abundance of the phylum Proteobacteria decreased from 47.60 to 28.15% from LL to DP and then increased to 33.24% in PP. An opposite pattern in LL, DP, and PP stages was observed for phyla Verrucomicrobia (from 0.96 to 4.30 to 1.69%), Elusimicrobia (from 0.32 to 2.84 to 0.25%), and SR1 (from 0.50 to 2.08 to 0.79%). The relative abundance of families Succinivibrionaceae and Prevotellaceae decreased in the DP, while Ruminococcaceae increased. Bacterial genera Prevotella and Treponema were least abundant in the DP as compared to LL and PP, while Ruminobacter and Succinimonas were most abundant in the DP. The rumen eukaryotic community was dominated by protozoal phylum Ciliophora, which showed a significant decrease in relative abundance from 97.6 to 93.9 to 92.6 in LL, DP, and PP, respectively. In conclusion, the physiological stage-dependent dietary changes resulted in a clear shift in metabolically-active rumen microbial communities.

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Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants

Cited by 76 publications

References 102 publications

Expression of the Tas1r3 and Pept1 genes in the digestive tract of wagyu cattle

Expression of the Tas1r3 and Pept1 genes in the digestive tract of wagyu cattle

Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. II: Relation with solid passage rate and pH on neutral detergent fiber degradation and microbial function in continuous culture

Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages

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