- Invited Review - Understanding the Functionality of the Rumen Microbiota: Searching for Better Opportunities for Rumen Microbial Manipulation

Overview

Journal Anim Biosci

Specialty Veterinary Medicine

Date 2024 Jan 8

PMID 38186256

Authors

Wenlingli Qi

Ming-Yuan Xue

Ming-Hui Jia

Shuxian Zhang

Qiongxian Yan

Hui-Zeng Sun

Affiliations

Soon will be listed here.

Abstract

Rumen microbiota play a central role in the digestive process of ruminants. Their remarkable ability to break down complex plant fibers and proteins, converting them into essential organic compounds that provide animals with energy and nutrition. Research on rumen microbiota not only contributes to improving animal production performance and enhancing feed utilization efficiency but also holds the potential to reduce methane emissions and environmental impact. Nevertheless, studies on rumen microbiota face numerous challenges, including complexity, difficulties in cultivation, and obstacles in functional analysis. This review provides an overview of microbial species involved in the degradation of macromolecules, the fermentation processes, and methane production in the rumen, all based on cultivation methods. Additionally, the review introduces the applications, advantages, and limitations of emerging omics technologies such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics, in investigating the functionality of rumen microbiota. Finally, the article offers a forward-looking perspective on the new horizons and technologies in the field of rumen microbiota functional research. These emerging technologies, with continuous refinement and mutual complementation, have deepened our understanding of rumen microbiota functionality, thereby enabling effective manipulation of the rumen microbial community.

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References

Lin L, Lai Z, Yang H, Zhang J, Qi W, Xie F . Genome-centric investigation of bile acid metabolizing microbiota of dairy cows and associated diet-induced functional implications. ISME J. 2022; 17(1):172-184. PMC: 9750977. DOI: 10.1038/s41396-022-01333-5. View

Chen L, Anantharaman K, Shaiber A, Eren A, Banfield J . Accurate and complete genomes from metagenomes. Genome Res. 2020; 30(3):315-333. PMC: 7111523. DOI: 10.1101/gr.258640.119. View

Stevenson D, Weimer P . Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR. Appl Microbiol Biotechnol. 2007; 75(1):165-74. DOI: 10.1007/s00253-006-0802-y. View

Tan P, Liu H, Zhao J, Gu X, Wei X, Zhang X . Amino acids metabolism by rumen microorganisms: Nutrition and ecology strategies to reduce nitrogen emissions from the inside to the outside. Sci Total Environ. 2021; 800:149596. DOI: 10.1016/j.scitotenv.2021.149596. View

Schiebenhoefer H, Van Den Bossche T, Fuchs S, Renard B, Muth T, Martens L . Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis. Expert Rev Proteomics. 2019; 16(5):375-390. DOI: 10.1080/14789450.2019.1609944. View

Jiang Q, Lin L, Xie F, Jin W, Zhu W, Wang M . Metagenomic insights into the microbe-mediated B and K vitamin biosynthesis in the gastrointestinal microbiome of ruminants. Microbiome. 2022; 10(1):109. PMC: 9306216. DOI: 10.1186/s40168-022-01298-9. View

Li F, Li C, Chen Y, Liu J, Zhang C, Irving B . Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle. Microbiome. 2019; 7(1):92. PMC: 6567441. DOI: 10.1186/s40168-019-0699-1. View

Ross E, Moate P, Marett L, Cocks B, Hayes B . Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing. J Dairy Sci. 2013; 96(9):6030-46. DOI: 10.3168/jds.2013-6766. View

Belanche A, Doreau M, Edwards J, Moorby J, Pinloche E, Newbold C . Shifts in the rumen microbiota due to the type of carbohydrate and level of protein ingested by dairy cattle are associated with changes in rumen fermentation. J Nutr. 2012; 142(9):1684-92. DOI: 10.3945/jn.112.159574. View

10.

Solden L, Hoyt D, Collins W, Plank J, Daly R, Hildebrand E . New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11. ISME J. 2016; 11(3):691-703. PMC: 5322302. DOI: 10.1038/ismej.2016.150. View

11.

Auffret M, Dewhurst R, Duthie C, Rooke J, Wallace R, Freeman T . The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle. Microbiome. 2017; 5(1):159. PMC: 5725880. DOI: 10.1186/s40168-017-0378-z. View

12.

Shabat S, Sasson G, Doron-Faigenboim A, Durman T, Yaacoby S, Miller M . Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants. ISME J. 2016; 10(12):2958-2972. PMC: 5148187. DOI: 10.1038/ismej.2016.62. View

13.

Kim C, Ma J, Lee I . HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota. Nat Commun. 2022; 13(1):6367. PMC: 9606305. DOI: 10.1038/s41467-022-34149-0. View

14.

Deusch S, Seifert J . Catching the tip of the iceberg - evaluation of sample preparation protocols for metaproteomic studies of the rumen microbiota. Proteomics. 2015; 15(20):3590-5. DOI: 10.1002/pmic.201400556. View

15.

Shinkai T, Mitsumori M, Sofyan A, Kanamori H, Sasaki H, Katayose Y . Comprehensive detection of bacterial carbohydrate-active enzyme coding genes expressed in cow rumen. Anim Sci J. 2016; 87(11):1363-1370. DOI: 10.1111/asj.12585. View

16.

Morais S, Mizrahi I . The Road Not Taken: The Rumen Microbiome, Functional Groups, and Community States. Trends Microbiol. 2019; 27(6):538-549. DOI: 10.1016/j.tim.2018.12.011. View

17.

von Meijenfeldt F, Arkhipova K, Cambuy D, Coutinho F, Dutilh B . Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome Biol. 2019; 20(1):217. PMC: 6805573. DOI: 10.1186/s13059-019-1817-x. View

18.

Cai S, Li J, Hu F, Zhang K, Luo Y, Janto B . Cellulosilyticum ruminicola, a newly described rumen bacterium that possesses redundant fibrolytic-protein-encoding genes and degrades lignocellulose with multiple carbohydrate- borne fibrolytic enzymes. Appl Environ Microbiol. 2010; 76(12):3818-24. PMC: 2893506. DOI: 10.1128/AEM.03124-09. View

19.

Hess M, Sczyrba A, Egan R, Kim T, Chokhawala H, Schroth G . Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011; 331(6016):463-7. DOI: 10.1126/science.1200387. View

20.

Sasson G, Morais S, Kokou F, Plate K, Trautwein-Schult A, Jami E . Metaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits. ISME J. 2022; 16(11):2610-2621. PMC: 9563048. DOI: 10.1038/s41396-022-01295-8. View