The gastrointestinal tract (GIT) microbiota of production animals are firmly established as key features that underpin animal health, development, and productivity. The earliest microbes to colonize the gut are especially important and affect GIT morphology, and biochemistry (local and systemic), and immunology of the animal with critical impacts on nutrition, production efficiency, and resistance to disease. Although disruptions of an animal’s GIT microbiota can occur at any age with profound consequences, disruptions during early GIT development can be particularly severe and have significant and long-lasting impacts.
With that in mind our group has set out to determine where these earliest microbes are obtained, what factors significantly influence their acquisition, and their relationships with health, immune development and efficacy, and nutritional efficiency. We have shown that ~44% of GIT microbes are acquired maternally from the skin of the udder, microbes in the colostrum/milk, and from the dam’s vagina (Yeoman et al. 2018). Each of these regions contributes to differing populations of microbes found in the differing regions of the GIT (Yeoman et al. 2018). Each region of the GIT (rumen, small intestine, and colon/large intestine) collectively affects the efficient use of feed (Perea et al. 2017). Our ultimate goal is to develop smart strategies based on basic science to optimize the GIT microbiome to benefit the health and performance of agricultural livestock species.
Contact Dr Yeoman for more information on this project.
Overview of the Ruminant Gastrointestinal Tract (GIT) Microbiome
Yeoman, C.J., White, B.A. 2014. Gastrointestinal tract microbiota and probiotics in production animals. In: Annual Reviews of Animal Biosciences (book chapter). Eds: Lewin HA, Roberts RM, Berens M. Ann. Rev. Anim. Biosci. 2: 469 – 486., Palo Alto CA, USA.
Kadriu H, Yeoman CJ. 2021. The unseen minority: Biogeographical investigations of the ruminant gastrointestinal microbiome highlight the importance of frequently ignored regions. In: Kogut MH & Zhang G. (Eds.), Gut Microbiota, Immunity, and Health in Production Animals. In press. Springer Nature.
Successional Development of the Ruminant GIT Microbiome
Yeoman CJ, Ishaq SL, Bichi E, Olivo SK, Lowe JL, Aldridge BM. 2018. Biogeographical differences in the influence of maternal microbial sources on the early successional development of the bovine neonatal gastrointestinal tract. Scientific Reports. 8: 3197. doi:10.1038/s41598-018-21440-8
Swartz JD, Lachman M, Westveer K, O’Neill T, Geary T, Kott RW, Berardinelli JG, Hatfield PG, Thomson JM, Roberts A, Yeoman CJ. 2014. Characterization of the vaginal microbiota of ewes and cows reveals a unique microbiota with low levels of lactobacilli and near-neutral pH. Front. Vet. Sci. 1: 19.
Xie G, Duff GC, Hall LW, Allen JD, Burrows CD, Bernal-Rigoli JC, Dowd SE, Guerriero V, Yeoman CJ. 2013. Alteration of digestive tract microbiome in neonatal Holstein bull calves by bacitracin methylene diasalicylate treatment and scours. J. Animal Sci. 91: 4984-90. doi: 10.2527/jas.2013-6304
Ecology of the Ruminant GIT Microbiome
Henderson G, Cox F, Ganesh S, Jonker A, Young W, et al. 2015. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Scientific Reports 5: 14567. doi:10.1038/srep14567
Yeoman CJ, Fields C, Lepercq P, Ruiz P, Forano E, White BA, Mosoni P. 2021. In vivo competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens and Ruminoccus albus in a gnotobiotic sheep model revealed by multi-omic analyses. mBio. In press.
Grinberg I.R., Yin G., Borovok I., Miller M.E., Yeoman C.J., Dassa B., Yu Z., Mizrahi I., Flint H.J., Bayer E.A., White B.A., Lamed R. 2015. Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome. Microbiol. Lett. 362: 1 – 10.
Brulc JM, Yeoman CJ, Wilson MK, Berg Miller ME, Jeraldo P, Jindou S, Goldenfeld N, Flint HJ, Lamed R, Borovok I, Vodovnik M, Nelson KE, Bayer EA, White BA. (2011) Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen. PLoS One 6(10) e25329
Yeoman CJ, Chia N, Yildirim S, Berg Miller ME, Kent A, Stumpf R, Leigh SR, Nelson KE, White BA, Wilson BA. (2011) Towards an Evolutionary Model of Animal-Associated Microbiomes. Entropy 13(3) 570 – 594
Nutritional Ecology of the Ruminant GIT
Perea K, Perz K, Olivo SK, Williams A, Lachman M, Ishaq SL, Thomson J, Yeoman CJ. 2017. Feed efficiency phenotypes in lambs involve changes in ruminal, colonic, and small intestine-located microbiota. Journal of Animal Sciences. 95(6):2585-2592. doi: 10.2527/jas.2016.1222
Piao, H., Lachman, M., Malfatti, S., Sczybra, A., Knierim, B., Auer, M., Tringe, S.G., Mackie, R.I., Yeoman, C.J., Hess. M. 2014. Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling. Front. Microbiol. 5: 307
Dassa B, Borovok I, V. Ruimy-Israeli, R. Lamed, H.J. Flint, S. Duncan, B. Henrissat, P. Coutinho, M. Morrison, P. Masoni, C.J. Yeoman, B.A. White, E.A. Bayer. 2014. Rumen cellulomics: Divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains. PLoS One 9: e99221.
Ishaq SL, Lachman MM, Wenner BA, Baeza A, Butler M, Gates E, Olivo S, Geddes JB, Hatfield P, Yeoman CJ. 2019. Pelleted-hay alfalfa feed increases sheep wether weight gain and rumen bacterial richness over loose-hay alfalfa feed. PLoS One 14: e0215797. DOI: 10.1371/journal.pone.0215797
Ishaq SL, Page CM, Yeoman CJ, Murphy TW, Van Emon ML, Stewart WC. 2019. Zinc-amino-acid supplementation alters yearling ram rumen bacterial communities but zinc sulfate supplementation does not. Journal of Animal Sciences. 97: 687 – 697. DOI: 10.1093/jas/sky456.
Kabel MA, Yeoman CJ, Han Y, Dodd D, Abbas CA, de Bont JA, Morrison M, Cann IK, Mackie RI. (2011) Biochemical characterization and relative expression levels of multiple carbohydrate esterases by the xylanolytic rumen bacterium Prevotella ruminicola 23 grown on an ester-enriched substrate. Applied and Environmental Microbiology 77(16) 5671-5681
Kelly WJ, Leahy SC, Altermann E, Yeoman CJ, Dunne JC, Kong Z, Pacheco DM, Li D, Noel SJ, Moon CD, Cookson AL, Attwood GT. (2010) The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment. PLoS One 5( 8 ): e11942
Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, Li D, Kong Z, McTavish S, Sang C, Lambie SC, Janssen PH, Dey D, Attwood GT. (2010) The genome of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One 5(1): e8926
Microbial Modulation of Host Immune Function
Schachtschneider KM, Yeoman CJ, Isaacson RE, White BA, Schook LB, Pieters M. 2013. Modulation of systemic immune responses through commensal gastrointestinal microbiota. PLoS One 8:e53969.