Publications

2017

(55.) Nelson TM, Borgogna JC, Michalek, RD, Roberts DW, Rath JM, Glover ED, Ravel J, Shardell MD, Yeoman CJ, Brotman RM. 2017. Cigarette smoking is associated with an altered vaginal tract metabolomic profile. Scientific Reports. In press.

(54.) Borgogna JC, Yeoman CJ. 2017. The Application of Molecular Methods to Improving Our Understanding of the Vaginal Microbiomes Role in Health and Disease. In: Methods in Microbiology (book chapter). Ed. Colin Harwood. Elsevier. 44: In press. https://doi.org/10.1016/bs.mim.2017.08.003

(53.) Betiku OC, Yeoman CJ, Gaylord TG, Duff GC, Hamerly T, Bothner B, Block SS, Sealey WM. 2017. Differences in Amino Acid Catabolism by Gut Microbes with/without Prebiotics Inclusion in GDDY-based Diet Affect Feed Utilization in Rainbow Trout. Aquaculture. In press

(52.) Ishaq SL, Yeoman CJ, Whitney TR. 2017. Ground redberry juniper and urea in supplements fed to Rambouillet ewe lambs. Part 2: Ewe lamb rumen microbial communities. Journal of Animal Sciences. In press

(51.) 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

(50.) Ishaq SL, Johnson SP, Miller ZJ, Lehnhoff EA, Olivo S, Yeoman CJ, Menalled FD. 2017. Impact of cropping systems, soil inoculum, and plant species identity on soil bacterial community structure. Microbial Ecology 73(2): 417-434. doi: 10.1007/s00248-016-0861-2.


2016

 (49.)  Feng W, Minor D, Liu M, Li J, Ishaq SL, Yeoman CJ, Lei B. 2016. Null mutations of group A Streptococcus orphan kinase RocA: Selection in mouse infection and comparison with CovS mutations in alteration of in vitro and in vivo protease SpeB expression and virulence. Infection and Immunity 85: e00790-16. doi: 10.1128/IAI.00790-16

(48.)  Stumpf RM, Gomez A, Amato KR, Yeoman CJ, Polk JD, Wilson BA, Nelson KE, White BA, Leigh SR. 2016. Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications. Biological Conservation 199: 56 – 66. http://dx.doi.org/10.1016/j.biocon.2016.03.035

(47.) Despres J, Forano E, Lepercq P, Comtet-Marre S, Jubelin G, Chambon C, Yeoman CJ, Berg Miller ME, Fields CJ, Martens E, Terrapon N, Henrissat B, White BA, Mosoni P. 2016. Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level. BMC Genomics. 17(1):326. doi: 10.1186/s12864-016-2680-8

(46.) Vlčkováa K, Gomez A, Petrželkovád KJ, Whittierg CA, Toddi AF, Yeoman CJ, Nelson KE, Wilson BA, Stumpf RM, Modrýa D, White BA, Leigh SR. 2016. Effect of antibiotic treatment on the gastrointestinal microbiome of free-ranging western lowland gorillas (Gorilla g. gorilla). Microbial Ecology. 72(4):943-954. doi:10.1007/s00248-016-0745-5

(45.) Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, Modry D, Todd A, Jost Robinson CA, Remis MJ, Torralba MG, Morton E, Umaña JD, Carbonero F, Gaskins HR, Nelson KE, Wilson BA, Stumpf RM, White BA, Leigh SR, Blekhman R. 2016. Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep. 14(9):2142-53. doi: 10.1016/j.celrep.2016.02.013.

(44.) Despres J, Forano E, Lepercq P, Comtet-Marre S, Jubelin G, Yeoman CJ, Miller ME, Fields CJ, Terrapon N, Le Bourvellec C, Renard CM, Henrissat B, White BA, Mosoni P. 2016. Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics. 17(1):147. doi: 10.1186/s12864-016-2472-1

(43.)  Gomez A, Rothman JM, Petrzelkova K, Yeoman CJ, Vickova K, Umana JD, Carr M, Modry D, Todd A, Torralba M, Nelson KE, Stumpf RM, Wilson BA, White BA, Leigh SR. 2016. Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp. ISME J. 10(2):532. doi: 10.1038/ismej.2015.146


2015

(42.) Amato KR, Yeoman CJ, Cerda G, Schmitt C, Danzy Cramer J, Berg Miller ME, Gomez A, Turner T, Wilson BA, Stumpf RM, Nelson KE, White BA, Knight R, Leigh SR. Variable responses of human and non-human primate gut microbiomes to a Western diet. Microbiome. 3: 53. doi: 10.1186/s40168-015-0120-7

(41.) 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

(40.) Nelson, T. M., J. L. Borgogna, R. M. Brotman, J. Ravel, S. T. Walk, C. J. Yeoman. 2015. Vaginal biogenic amines: Biomarkers of bacterial vaginosis or precursors to vaginal dysbiosis? Front. Physiol. 6:253. doi: 10.3389/fphys.2015.00253

(39.) Kapheim K. M., V. D. Rao, C. J. Yeoman, B. A. Wilson, B. A. White, N. Goldenfeld, and G. E. Robinson.  2015.  Caste-specific differences in hindgut microbial communities of honey bees (Apis Mellifera).  PLoS One  10(4): e0123911

(38.) Ham, B. R., Myrick, C. A., Barrows, F. T., Yeoman, C.J, Duff, G., Maskill, M. G., Sealey, W. M. 2015. Feed characteristics alter growth efficiency of cutthroat trout. J. Fish Wildlife Mgmt 6: e1944-687

(37.) Gomez A, Petrzelkova K, Yeoman CJ, Vickova K, Mrazek J, Koppova I, Carbonero F, Ulanov A, Modry D, Todd A, Torralba M, Nelson KE, Gaskins HR, Wilson B, Stumpf RM, White BA, Leigh SR. 2015. Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology. Mol. Ecol. 24: 2551 – 65

(36.) 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.

(35.) Ham, B. R., F. T. Barrows, A. Huttinger, G. C. Duff, C. J. Yeoman, M. Maskill, and W. M. Sealey.  2015.  Evaluation of dietary soy sensitivity in Snake River Cutthroat trout.  N. Am. J. Aquaculture.  77: 195-205

(34.) 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., Garber, P. A. 2015. The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra). Microbial Ecology. 69: 434 – 443


2014

(33.)  Yildirim S, Yeoman CJ, Janga SC, Thomas SM, Ho M, Leigh SR, Consortium PM, White BA, Wilson BA, Stumpf RM. 2014. Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance. ISME J. 8: 2431 – 2444.

(32.) 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.

(31.) Amato KR, Leigh SR, Kent A, Mackie RI, Yeoman CJ, Stumpf RM, Wilson BA, Nelson KE, White BA. 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. 155: 652 – 654.

(30.) Yeoman, C.J. 2014. Simian Metagenomics. In, Encyclopedia of Metagenomics, , – Animals (2nd Edition). Eds. Karen E Nelson (Editor in Chief), Bryan A White, Sarah Highlander, Francisco Rodriguez-Valera (Volume editors). Springer.

(29.) 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

(28.) 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.

(27.) Walther-António, M.R., Jeraldo, P., Berg Miller, M.E., Yeoman, C.J., Nelson, K.E., Wilson, B.A., White, B.A., Chia, N., Creedon, D.J. 2014. Pregnancy’s stronghold on the vaginal microbiome. PLoS One 9: e98514.

(26.) 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.


2013

(25.) Amato KR, Yeoman CJ, Kent A, Righini N, Carbonero F, Estrada A, Gaskins HR, Stumpf RM, Yildirim S, Torralba M, Gillis M, Wilson BA, Nelson KE, White BA, Leigh SR. 2013. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME J. 7: 1344-1353. doi: 10.1038/ismej.2013.16. Manuscript was Editors Choice in April 12, 2013 edition of Science

(24.) Yeoman CJThomas SM, Miller ME, Ulanov AV, Torralba M, Lucas S, Gillis M, Cregger M, Gomez A, Ho M, Leigh SR, Stumpf R, Creedon DJ, Smith MA, Weisbaum JS, Nelson KE, Wilson BA, White BA. 2013. A multi-omic systems-based approach reveals metabolic markers of bacterial vaginosis and insight into the disease. PLoS One 8: e56111. doi: 10.1371/journal.pone.0056111.

(23.) Schachtschneider KM, Yeoman CJIsaacson RE, White BA, Schook LB, Pieters M. 2013. Modulation of systemic immune responses through commensal gastrointestinal microbiota. PLoS One 8:e53969.

(22.) Stumpf RM, Wilson BA, Rivera A, Yildirim S, Yeoman CJ, White BA, Polk JD, Leigh SR. 2013. Primate vaginal microbial ecology: Comparative context and implications for human health and disease. Am. J. Phys. Anthropol. 152 (S57):119-34. doi: 10.1002/ajpa.22395.

(21.) Marietta, E.V., Gomez, A.M., Yeoman, C.J., Tilahun, A.Y., Clark, C.R., Luckey, D.H., Murray, J.A., White, B.A., Kudva, Y.C., Rajagopalan, G. 2013. Low incidence of spontaneous type 1 diabetes in non-obese diabetic mice raised on gluten-free diets is associated with changes in the intestinal microbiome. PLoS One 8: e78687

(20.) Xie G, Duff GC, Hall LW, Allen JD, Burrows CD, Bernal-Rigoli JC, Dowd SE, Guerriero V, Yeoman CJ2013. 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


2012

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

(17.) Yeoman CJ, Stumpf RM, White BA, Wilson BA, Nelson KE, Torralba M, Gillis M, Mugisha L, Leigh SR. (2012) Metagenomic comparisons of gastrointestinal microbial function in hominoids. American Journal of Physical Anthropology 147(s54): 308

(16.) Gomez AM, Luckey D, Yeoman CJMarietta EV, Berg Miller ME, Murray JA, White BA, Taneja V. (2012) Loss of sex and age driven differences in the gut microbiome characterize arthritis-susceptible *401 mice but not arthritis-resistant *402 micePLoS One 7(4): e36095

(15.) Yeoman CJ(2012) Terrestrial vertebrate animal metagenomics, non-domesticated primates, simiansIn, Encyclopedia of Metagenomics, Animals. Ed. Karen E Nelson (Editor in Chief), Bryan A White, Sarah Highlander, Francisco Rodriguez-Valera (Volume editors). Springer; refworks.springer.com/mrw/index.php?id=3638.

(14.) Berg Miller ME, Yeoman CJ, Chia N, Tringe SG, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA. (2012) Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiomeEnvironmental Microbiology 14(1) 207-227


2011

(13.) White BA, Gomez AM, Ho M, Berg Miller M, Thomas S, Yeoman CJ, Yildirim S, Creedon DJ, Goldberg T, Leigh SR, Nelson KE, Stumpf RM, WilsonBA. (2011) Comparative analysis of the vaginal microbiome in health and diseaseGenome Biology 11: S1  4

(12.) 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 rumenPLoS One 6(10) e25329

(11.) 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 substrateApplied and Environmental Microbiology 77(16) 5671-5681. doi: 10.1128/AEM.05321-11

(10.) Amato K, Yeoman CJ, Righini N, Kent A, Estrada A, Munoz D, Stumpf RM, White BA, Nelson KE, Torralba M, Gillis M, Leigh SR. (2011) Gastrointestinal microbial community composition and habitat structure in howler monkeys (Alouatta pigra).  American Journal of Physical Anthropology 144(S52): 75.

(9.) Yildirim S, Rivera AJ, Leigh SR, Yeoman CJ, White BA, Goldberg TL, Wilson BA, Stumpf RM. (2011) Vaginal microbial community structure and maternal ecology in primates. American Journal of Physical Anthropology 144(S52): 315-316.

(8.) Yeoman CJ, Kelly WJ, Rakonjac J, Leahy SC, Altermann E, Attwood GT. (2011) The large episomes of Butyrivibrio proteoclasticus B316(T) have arisen through intragenomic gene shuttling from the chromosome to smaller Butyrivibrio-specific plasmidsPlasmid 66(2) 67-78. doi: 10.1016/j.plasmid.2011.05.002

(7.) 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 MicrobiomesEntropy 13(3) 570 – 594


2010

(6.) Yildirim S, Yeoman CJ, Sipos M, Torralba M, Wilson BA, Goldberg TL, Stumpf RM, Leigh SR, White BA, Nelson KE. (2010) Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communitiesPLoS One 5(11) e13963

(5.) Yeoman CJ, Yildirim S, Thomas SM, Durkin AS, Torralba M, Sutton G, Buhay CJ, Ding Y, Dugan-Rocha SP, Muzny DM, Qin X, Gibbs RA, Leigh SR, Stumpf R, White BA, Highlander SK, Nelson KE, Wilson BA. (2010) Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potentialPLoS One 5( 8 ): e12411. doi: 10.1371/journal.pone.0012411 [research applauded by Faculty of 1000]

(4.) 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 environmentPLoS One 5( 8 ): e11942

(3.) 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 emissionsPLoS One 5(1): e8926. doi: 10.1371/journal.pone.0008926.

(2.) Yeoman CJ, Han Y, Dodd D, Schroeder CM, Mackie RI, Cann IK. (2010) Thermostable enzymes as biocatalysts in the biofuel industryAdvances in Applied Microbiology 70: 1 – 55

(1.) Brulc JM, Yeoman CJNelson KE, White BA. (2010) Emerging methods in rumen microbiology. Proc. Graz. Livestock Nutr. Conf. Hess BW, DelCurto T, Bowman JGP, Waterman RC. (eds) Proceedings of the Western Section of the American Society of Animal Science.