Understanding the Interactions Among the Early Successional Development of the Ruminant Gut Microbiome, Immune System, and Animal Health

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.

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Related Publications

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.

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

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

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

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.

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.

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.

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.

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

Yeoman CJ, Chia N, Jeraldo P, Sipos M, Goldenfeld ND, White BA. (2012) The microbiome of the chicken gastrointestinal tract. Animal Health Research Reviews 13(1): 89-99

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

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

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

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