Community characterization and functional analysis of microbiomes of farm animals

The microbiota of mammals contributes significantly to various fundamental aspects of productivity and health. Whereas the human microbiome has been studied in great detail and depth, the microbiomes of farm animals are much less well known. Our research focuses on analyzing the variation in the microbiota in farm animals in response to different nutrition, reproduction and disease conditions. One focus of our research are bacteria attached to the rumen wall (also called “epimural” bacteria), as the rumen wall is the central interface between the host and its ruminal microbiota. Another main research area is the microbiota of the reproductive tract of different livestock species.

Most of the current research on microbiota describes communities at different times and conditions (i.e. “who is there”). While this is an important first step, we are applying functional analyses by using metagenome shotgun and metatranscriptome sequencing as tools to analyze the functional capacity (“what can they do”) function and activity of microbiota in situ (“what are they doing”). Both descriptive and functional methods are thus essential for our research. One of our main aims is to understand the interactions between bacteria and farm animals focusing on basic research questions, such as e.g. nutrition, reproduction and disease. Interdisciplinary research is essential in order to understand the complex interaction between animals and their microbiota, and to improve animal production without compromising animal health.

Selected Publications:

  • Rahic-Seggerman FM, Iske C, Graham J, Fuerst N, Schmitz-Esser S, Kohles MR. 2025. Effect of rabbit gastrointestinal stasis (RGIS) on the fecal microbiota of pet rabbits (Oryctolagus cuniculus). PLoS One. 20(2):e0318810. doi: 10.1371/journal.pone.0318810.
  • Jonas LC, Youngs CR, Schmitz-Esser S. 2025. Combined analysis of 16S rRNA gene sequencing data reveals core vaginal bacteria across livestock species. Front Microbiol. 16:1524000. doi: 10.3389/fmicb.2025.1524000
  • Altendorf BJ, Anderson CJ, von Seggern I, Wiersema ML, Schmitz-Esser S, Koltes DA. 2024. Impacts of excreta exposure and age on ileal microbial communities, intestinal permeability, and corticosterone in hens housed in enriched colonies and cage-free housing systems. Poultry 3(3), 267-283
  • Kiefer ZE, Koester LR, Studer JM, Schmitz-Esser S, Ross JW. 2024. Evaluation of fecal microbiota of late gestation sows in relation to pelvic organ prolapse risk. Front Microbiol. 15:1384583. doi: 10.3389/fmicb.2024.1384583
  • Fries-Craft K, Anderson CJ, Schmitz-Esser S, Bobeck EA. 2024. Sequencing approaches to identify distal jejunum microbial community composition and function in broiler chickens fed anti-interleukin-10 during coccidiosis and necrotic enteritis challenge. Poult Sci. 103(9):104001. doi: 10.1016/j.psj.2024.104001
  • Cassas MS, Jonas LC, Anderson CJ, Schmitz-Esser S, Youngs CR. 2024. Temporal changes in ewe vaginal microbiota throughout gestation. Front Microbiol. 15:1359678. doi: 10.3389/fmicb.2024.1359678.
  • Koester LR, Hayman K, Anderson CJ, Tibbs-Cortes BW, Daniels KM, Seggerman FM, Gorden PJ, Lyte M, Schmitz-Esser S. 2023. Influence of a sodium-saccharin sweetener on the rumen content and rumen epithelium microbiota in dairy cattle during heat stress. J Anim Sci. 101:skac403. doi: 10.1093/jas/skac403.
  • Wickramasinghe J, Anderson CJ, Kaya CA, Gorden PJ, Ribeiro FRB, Dohms J, Rigert S, Schmitz-Esser S, Appuhamy R. 2022. Evaluating Ruminal and Small Intestinal Morphology and Microbiota Composition of Calves Fed a Macleaya cordata Extract Preparation. Animals (Basel). 13(1):54. doi: 10.3390/ani13010054.
  • Koester LR, Petry AL, Youngs CR, Schmitz-Esser S. 2021. Ewe Vaginal Microbiota: Associations With Pregnancy Outcome and Changes During Gestation. Front Microbiol. 12:745884. doi: 10.3389/fmicb.2021.745884.
  • Kiefer ZE, Koester LR, Studer JM, Chipman AL, Mainquist-Whigham C, Keating AF, Schmitz-Esser S, Ross JW. 2021. Vaginal microbiota differences associated with pelvic organ prolapse risk during late gestation in commercial sows. Biol Reprod. 105(6):1545-1561. doi: 10.1093/biolre/ioab178
  • Petry AL, Patience JF, Huntley NF, Koester LR, Bedford MR, Schmitz-Esser S. 2021. Xylanase Supplementation Modulates the Microbiota of the Large Intestine of Pigs Fed Corn-Based Fiber by Means of a Stimbiotic Mechanism of Action. Front Microbiol. 12:619970
  • Kiefer ZE, Koester LR, Showman L, Studer JM, Chipman AL, Keating AF, Schmitz-Esser S, Ross JW. 2021. Vaginal microbiome and serum metabolite differences in late gestation commercial sows at risk for pelvic organ prolapse. Sci Rep. 11(1):6189.
  • Anderson CJ, Koester LR, Schmitz-Esser S. 2021. Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets. Front Microbiol. 12:625400
  • Wiersema ML, Koester LR, Schmitz-Esser S, Koltes DA. 2021. Comparison of intestinal permeability, morphology, and ileal microbial communities of commercial hens housed in conventional cages and cage-free housing systems. Poult Sci. 100(2):1178-1191.
  • Petry AL, Patience JF, Koester LR, Huntley NF, Bedford MR, Schmitz-Esser S. 2021. Xylanase modulates the microbiota of ileal mucosa and digesta of pigs fed corn-based arabinoxylans likely through both a stimbiotic and prebiotic mechanism. PLoS One. 16(1):e0246144. doi: 10.1371/journal.pone.0246144
  • Kilburn LR, Koester LR, Schmitz-Esser S, Serão NVL, Rossoni Serão MC. 2020. High-Fat Diets Led to OTU-Level Shifts in Fecal Samples of Healthy Adult Dogs. Front Microbiol; 11:564160. doi: 10.3389/fmicb.2020.564160
  • Koester LR, Poole DH, Serão NVL, Schmitz-Esser S. 2020. Beef cattle that respond differently to fescue toxicosis have distinct gastrointestinal tract microbiota. PLoS One. 15(7):e0229192.
  • Wickramasinghe HKJP, Anast JM, Schmitz-Esser S, Serão NVL, Appuhamy JADRN. 2020. Beginning to offer drinking water at birth increases the species richness and the abundance of Faecalibacterium and Bifidobacterium in the gut of preweaned dairy calves. J Dairy Sci. 103(5):4262-4274.
  • Sanglard LP, Schmitz-Esser S, Gray KA, Linhares DCL, Yeoman CJ, Dekkers JCM, Niederwerder MC, Serão NVL. 2020. Vaginal microbiota diverges in sows with low and high reproductive performance after porcine reproductive and respiratory syndrome vaccination. Sci Rep. 10(1):3046.
  • Sanglard LP, Schmitz-Esser S, Gray KA, Linhares DCL, Yeoman CJ, Dekkers JCM, Niederwerder MC, Serão NVL. 2020. Investigating the Relationship Between Vaginal Microbiota and Host Genetics and Their Impact on Immune Response and Farrowing Traits in Commercial Gilts. J Anim Breed Genet. 137 (1), 84-102
  • Klein-Jöbstl D, Quijada NM, Dzieciol M, Feldbacher B, Wagner M, Drillich M, Schmitz-Esser S, Mann E. 2019. Microbiota of newborn calves and their mothers reveals possible transfer routes for newborn calves' gastrointestinal microbiota. PLoS One. 14(8):e0220554.
  • Zwirzitz B, Pinior B, Metzler-Zebeli B, Handler M, Gense K, Knecht C, Ladinig A, Dzieciol M, Wetzels SU, Wagner M, Schmitz-Esser S, Mann E. 2019. Microbiota of the Gut-Lymph Node Axis: Depletion of Mucosa-Associated Segmented Filamentous Bacteria and Enrichment of Methanobrevibacter by Colistin Sulfate and Linco-Spectin in Pigs. Front Microbiol. 10:599.
  • Lyte M, Daniels KM, Schmitz-Esser S. 2019. Fluoxetine-induced alteration of murine gut microbial community structure: evidence for a microbial endocrinology-based mechanism of action responsible for fluoxetine-induced side effects. PeerJ. 7:e6199. doi: 10.7717/peerj.6199.
  • Zhang W, Liu W, Hou R, Zhang L, Schmitz-Esser S, Sun H, Xie J, Zhang Y, Wang C, Li L, Yue B, Huang H, Wang H, Shen F, Zhang Z. 2018. Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose. ISME J. (5):1319-1328
  • Mann E, Wetzels SU, Wagner M, Zebeli Q, Schmitz-Esser S. 2018. Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria. Front Microbiol. 9:43.
  • Wetzels SU, Mann E, Pourazad P, Qumar M, Pinior B, Metzler-Zebeli BU, Wagner M, Schmitz-Esser S, Zebeli Q. 2017. Epimural bacterial community structure in the rumen of Holstein cows with different responses to a long-term subacute ruminal acidosis diet challenge. J. Dairy Sci. 100:1829–1844
  • Wetzels SU, Mann E, Metzler-Zebeli BU, Pourazad P, Qumar M, Klevenhusen F, Pinior B, Wagner M, Zebeli Q, Schmitz-Esser S. 2016. Epimural indicator phylotypes of transiently-induced subacute ruminal acidosis in dairy cattle. Front. Microbiol. 7:274
  • Mann E, Wetzels SU, Pinior B, Metzler-Zebeli BU, Wagner M, Schmitz-Esser S. 2016. Psychrophile spoilers dominate the bacterial microbiome in musculature samples of slaughter pigs. Meat Sci. 117:36-40.
  • Mann E, Pinior B, Wetzels SU, Metzler-Zebeli BU, Wagner M, Schmitz-Esser S. 2015. The metabolically active bacterial microbiome of tonsils and mandibular lymph nodes of slaughter pigs. Front. Microbiol. 6:1362. doi: 10.3389/fmicb.2015.01362
  • Mann E, Dzieciol M, Pinior B, Neubauer V, Metzler-Zebeli BU, Wagner M, Schmitz-Esser S. High diversity of viable bacteria isolated from lymph nodes of slaughter pigs and its possible impacts for food safety. 2015. J Appl Microbiol. 119(5):1420-1432
  • Wetzels S. U., Mann E, Metzler-Zebeli B. U., Wagner M., Klevenhusen F., Zebeli Q., Schmitz-Esser S. Pyrosequencing reveals shifts in the bacterial epimural community relative to dietary concentrate amount in goats. 2015. J. Dairy Sci. 98(8):5572-87.
  • Klein-Jöbstl D, Schornsteiner E, Mann E, Wagner M, Drillich M, Schmitz-Esser S. 2014. Pyrosequencing reveals diverse fecal microbiota in Simmental calves during early development. Front. Microbiol. 17;5:622.
  • Mann E., Dzieciol M., Metzler-Zebeli B. U., Wagner M., Schmitz-Esser S. 2014. Microbiomes of unreactive and pathologically altered ileocecal lymph nodes of slaughter pigs. Appl. Environ. Microbiol. 80:193-203.