Montana State University

Department of Animal & Range Sciences

P.O. Box 172900
Bozeman, MT 59717-2900

Tel: (406) 994-3722
Fax: (406) 994-5589
Location: 103 Animal Bioscience Building

Department Head:

Dr. Glenn Duff

Dr. Carl Yeoman

Assistant Professor, Rumen/Gastrointestinal Microbiology
321 Animal Bioscience Building
Montana State University
P.O. Box 172900
Bozeman, MT 59717-2900
Phone: (406) 994-7440
Fax: (406) 994-5589

Visit the Yeoman Lab webpage


B.S.  Massey University, Microbiology and Genetics, 2003
Ph.D.  Massey University, Palmerston North, Microbial Genomics, 2009


ARNR 520  (F)  Advanced Ruminant Nutrition  ‹ Syllabus
ARNR 507  (S)  Research Methods
BIOM 405  (F)  Host-associated Microbial Ecosystems

Research Interests

My research exploits molecular techniques to examine the microbial ecology associated with animal systems.  My specific focus is on the microbial ecosystems of the gut and their role in health, nutrition and performance, and those occupying the vaginal tract and their relation to reproductive performance and neonatal health.  I believe that microbial ecosystems have an evolved ecology principally governed by their symbioses, as is evident in many systems.  Obtaining a system-wide understanding of these relationships is fundamental to improving human health, livestock systems, the interactions of each with the environment.


  • NIH-NIAID  (R21)  Microbial Polyamine-Mediated Reductions in Vaginal Acidity; A Mechanistic Understanding of Vaginal Dysbiosis.  (PI Yeoman)

  • USDA-NIFA  (Climate Change Program)  Development Of Dietary Interventions To Mitigate Climate-Induced Alterations Of Rainbow Trout (Oncorhynchus mykiss) Gut Microbial Populations and Protein Metabolism.  (PI Yeoman)

  • USDA-NIFA  (Tribal Colleges Program)  Undergraduate Student Research Experience:  Building Student Education Attainment by Developing Scientific Research Abilities.  (PI Schumacher)

  • NIH  (NHGRI R25)  Guiding Indigenous Students in Next-generation Genomic Studies with the Summer Internship for Native Americans with an Interest in Genomics.  (PI Malhi)

  • Montana Wheat and Barley Committee  Determining the Potential of Wheat Stem Sawfly Endosymbiotic Microbiota for Exploitation in Developing Unique Management Strategies.  (PI Yeoman)

  • Land ‘O’ Lakes  Supply of Milk Replacer for Neonatal Lamb Studies.

Recent Publications


  • Swartz, J. D., Lachman, M., Westveer, K., O’Neill, T., Geary, T., Kott, R. W., Berardinelli, J. G., Hatfield, P. G., Thomson, J. M., Roberts, A., and Yeoman, C. J.  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.  (In press)
  • Amato, K. R., Leigh, S. R., Kent, A., Mackie, R. I., Yeoman, C. J., Stumpf, R. M., Wilson, B. A., Nelson, K. E., White, B. A., and Garber, P. A.  2014.  The role of gut microbes in satisfying the nutritional demands of adult and juvenile wild, black howler monkeys (Alouatta pigra).  Am. J. Phys. Anthropol.  (In press)
  • Yildirim, S., Yeoman, C. J.,, Janga, S. C, Thomas, S. M, Ho, M., Leigh, S. R, Consortium, P. M, White, B. A, Wilson, B. A, and Stumpf, R. M.  2014.  Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance.  ISME J.  (In press)
  • Piao, H., Lachman, M., Malfatti, S., Sczybra, A., Knierim, B., Auer, M., Tringe, S. G., Mackie, R. I., Yeoman, C. J., and 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., Ruimy-Israeli, V., Lamed, R., Flint, H. J., Duncan, S. H., Henrissat, B., Coutinho, P., Morrison, M., Mosoni, P., Yeoman, C. J., White, B. A, and Bayer, E. A.  2014.  Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains.  PLoS One  9:e99221.
  • Yeoman, C. J., and White, B. A.  2014.  Gastrointestinal tract microbiota and probiotics in production animals.  Annu. Rev. Anim. Biosci.  2:469–486.
  • Walther-António, M. R., Jeraldo, P., Berg Miller, M. E., Yeoman, C. J., Nelson, K. E., Wilson, B. A., White, B. A., Chia, N., and Creedon, D. J.  2014.  Pregnancy’s stronghold on the vaginal microbiome.  PLoS One  9:e98514.
  • 2013

  • Marietta, E. V., Gomez, A., Yeoman, C. J., Tilahun, A., Clark, C. R., Luckey, D., Murray, J. A., White, B. A., Kudva, Y. C., and Rajagopalan, G.  2013.  Low incidence of type I diabetes in non-obese diabetic mice raised on a gluten-free diet is associated with changes in the intestinal microbiota.  PLoS One  8:78687.
  • Stumpf, R. M., Wilson, B. A., Rivera, A., Yildirim, S., Yeoman, C. J., White, B. A., Polk, J. D., and Leigh, S. R.  2013.  Primate vaginal microbial ecology:  Comparative context and implications for human health and disease.  Am. J. Phys. Anthropol.  57:119–134.
  • Amato, K. R., Yeoman, C. J., Kent, A., Righini, N., Carbonero, F., Estrada, A., Gaskins, H. R., Stumpf, R. M., Yildirim, S., Torralba, M., Gillis, M., Wilson, B. A., Nelson, K. E., White, B. A., and Leigh, S. R.  2013.  Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes.  ISME J.  7:1344-1353.  (Manuscript was Editors Choice in April 12, 2013 edition of Science)
  • Yeoman, C. J., Thomas, S. M., Miller, M. E., Ulanov, A. V., Torralba, M., Lucas, S., Gillis, M., Cregger, M., Gomez, A., Ho, M., Leigh, S. R., Stumpf, R., Creedon, D. J., Smith, M. A., Weisbaum, J. S., Nelson, K. E., Wilson, B. A., and White, B. A.  2013.  A multi-omic systems-based approach reveals metabolic markers of bacterial vaginosis and insight into the disease.  PLoS One 8:e56111.
  • Schachtschneider, K. M., Yeoman, C. J., Isaacson, R. E., White, B. A., Schook, L. B., and Pieters, M.  2013.  Modulation of systemic immune responses through commensal gastrointestinal microbiota.  PLoS One 8:e53969.
  • Vodovnik, M., Duncan, S. H., Reid, M. D., Cantlay, L., Turner, K., Parkhill, J., Lamed, R., Yeoman, C. J., Miller, M. E., White, B. A., Bayer, E. A., Marinšek-Logar, R., and Flint, H. J.  2013.  Expression of cellulosome components and type IV pili within the extracellular proteome of Ruminococcus flavefaciens 007.  PLoS One 8:e65333.
  • Xie, G., Duff, G. C., Hall, L. W., Allen, J. D., Burrows, C. D., Bernal-Rigoli, J. C., Dowd, S. E., Guerriero, V., Yeoman, C. J.  2013.  Alteration of digestive tract microbiome in neonatal Holstein bull calves by bacitracin methylene diasalicylate treatment and scours.  J. Animal Sci.  (In press.)
  • 2012

  • Yeoman, C. J., Chia, N., Jeraldo, P., Sipos, M., Goldenfeld, N. D., and White, B. A.  2012.  The microbiome of the chicken gastrointestinal tract.  Animal Health Research Reviews  13(1):89-99.
  • Yeoman, C. J., Stumpf, R. M., White, B. A., Wilson, B. A., Nelson, K. E., Torralba, M., Gillis, M., Mugisha, L., and Leigh, S. R.  2012.  Metagenomic comparisons of gastrointestinal microbial function in hominoids. American Journal of Physical Anthropology  147(s54):308.
  • Gomez, A. M., Luckey, D., Yeoman, C. J., Marietta, E. V., Berg Miller, M. E., Murray, J. A., White, B. A., and Taneja, V.  2012.  Loss of sex and age driven differences in the gut microbiome characterize arthritis-susceptible *401 mice but not arthritis-resistant *402 mice.  PLoS One  7(4):e36095.
  • Yeoman, C. J.  2012.  Simian Metagenomics.  In, Encyclopedia of Metagenomics, Animals.  Ed. Karen E Nelson (Editor in Chief), Bryan A. White, Sarah Highlander, Francisco Rodriguez-Valera (Volume editors).  Springer.
  • Berg Miller, M. E., Yeoman, C. J., Chia, N., Tringe, S. G., Edwards, R. A., Flint, H. J., Lamed, R., Bayer, E. A., and White, B. A.  2012.  Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.  Environmental Microbiology  14(1):207-227.
  • 2011

  • White, B. A., Gomez, A. M., Ho, M., Berg Miller, M., Thomas, S., Yeoman, C. J., Yildirim, S., Creedon, D. J., Goldberg, T., Leigh, S. R., Nelson, K. E., Stumpf, R. M., and Wilson, B. A.  2011.  Comparative analysis of the vaginal microbiome in health and disease.  Genome Biology  11:S14.
  • Brulc, J. M., Yeoman, C. J., Wilson, M. K., Berg Miller, M. E., Jeraldo, P., Jindou, S., Goldenfeld, N., Flint, H. J., Lamed, R., Borovok, I., Vodovnik, M., Nelson, K. E., Bayer, E. A., and White, B. A.  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, M. A., Yeoman, C. J., Han, Y., Dodd, D., Abbas, C. A., de Bont, J. A., Morrison, M., Cann, I. K., and Mackie, R. I.  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.
  • Amato, K., Yeoman, C. J., Righini, N., Kent, A., Estrada, A., Munoz, D., Stumpf, R. M., White, B. A., Nelson, K. E., Torralba, M., Gillis, M., and Leigh, S. R.  2011.  Gastrointestinal microbial community composition and habitat structure in howler monkeys (Alouatta pigra).  American Journal of Physical Anthropology  144(S52):75.
  • Yildirim, S., Rivera, A. J., Leigh, S. R., Yeoman, C. J., White, B. A., Goldberg, T. L., Wilson, B. A., Stumpf, R. M.  2011.  Vaginal microbial community structure and maternal ecology in primates.  American Journal of Physical Anthropology  144(S52):315-316.
  • Yeoman, C. J., Kelly, W. J., Rakonjac, J., Leahy, S. C., Altermann, E., and Attwood, G. T.  2011.  The large episomes of Butyrivibrio proteoclasticus B316(T) have arisen through intragenomic gene shuttling from the chromosome to smaller Butyrivibrio-specific plasmids.  Plasmid  66(2):67-78.
  • Yeoman, C. J., Chia, N., Yildirim, S., Berg Miller, M. E., Kent, A., Stumpf, R., Leigh, S. R., Nelson, K. E., White, B. A., and Wilson, B. A.  2011.  Towards an Evolutionary Model of Animal-Associated Microbiomes.  Entropy  13(3):570-594.
  • 2010

  • Yildirim, S., Yeoman, C. J., Sipos, M., Torralba, M., Wilson, B. A., Goldberg, T. L., Stumpf, R. M., Leigh, S. R., White, B. A., and Nelson, K. E.  2010.  Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities.  PLoS One  5(11):e13963.
  • Yeoman, C. J., Yildirim, S., Thomas, S. M., Durkin, A. S., Torralba, M., Sutton, G., Buhay, C. J., Ding, Y., Dugan-Rocha, S. P., Muzny, D. M., Qin, X., Gibbs, R. A., Leigh, S. R., Stumpf, R., White, B. A., Highlander, S. K., Nelson, K. E., and Wilson, B. A.  2010.  Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential.  PLoS One  5(8):e12411. Research applauded here.
  • Kelly, W. J., Leahy, S. C., Altermann, E., Yeoman, C. J., Dunne, J. C., Kong, Z., Pacheco, D. M., Li, D., Noel, S. J., Moon, C. D., Cookson, A. L., and Attwood, G. T.  2010.  The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment.  PLoS One  5(8):e11942.
  • Leahy, S. C., Kelly, W. J., Altermann, E., Ronimus, R. S., Yeoman, C. J., Pacheco, D. M., Li, D., Kong, Z., McTavish, S., Sang, C., Lambie, S. C., Janssen, P. H., Dey, D., and Attwood, G. T.  2010.  The genome of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions.  PLoS One  5(1):e8926.
  • Yeoman, C. J., Han, Y., Dodd, D., Schroeder, C. M., Mackie, R. I., and Cann, I. K.  2010.  Thermostable enzymes as biocatalysts in the biofuel industry.  Advances in Applied Microbiology  70:1-55.
  • Brulc, J. M., Yeoman, C. J., Nelson, K. E., and White, B. A.  2010.  Emerging methods in rumen microbiology.  Proc. Graz. Livestock Nutr. Conf.  Hess, B. W., DelCurto, T., Bowman, J.G.P., and Waterman, R. C. (eds)  Proceedings of the Western Section of the American Society of Animal Science.