Stephan Schmitz-Esser

Areas of Research

• Food safety: Listeria monocytogenes
• Animal microbiota
• Livestock reproductive tract microbiota

Publications

1. Shelkamy M.M.S., Hashish A., Srednik M.E., Chaves M., Macedo N.R., Gadu E., Schmitz-Esser S., Zhang Q., Wang C., Sato Y., El-Gazzar M. 2025. Prevalence of Nonpathogenic Avibacterium paragallinarum in Naïve-Healthy Layer Flocks Across Multiple States in the United States. Transboundary and Emerging Diseases 2025:9994679. DOI: 10.1155/tbed/9994679
2. Rahic-Seggerman F.M., Iske C., Graham J., Fuerst N., Schmitz-Esser S., Kohles M.R. 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
3. Jonas L.C., Youngs C.R., Schmitz-Esser S. 2025. Combined analysis of 16S rRNA gene sequencing data reveals core vaginal bacteria across livestock species. Frontiers in Microbiology. 16:1524000. DOI: 10.3389/fmicb.2025.1524000
4. Shelkamy M.M.S., Hashish A., Chaves M., Srednik M.E., Macedo N.R., Gadu E., Sato Y., Schmitz-Esser S., Zhang Q., El-Gazzar M. 2024 Development and Validation of PCR Assays for Improved Diagnosis of Infectious Coryza by Differentiating Pathogenic and Nonpathogenic Avibacterium paragallinarum. Avian Diseases Journal. DOI: 10.1637/aviandiseases-D-24-00041
5. Studer J.M,. Kiefer Z.E., Koester L.R., Johnson E.M., Schmitz-Esser S., Farkas A., Galina Pantoja L., Vonnahme K.A., Greiner L.L., Keating A.F., Baumgard L.H., Ross J.W. 2024. Evaluation of circulating immune cells, analytes and inflammatory markers in sows affected with postpartum dysgalactia syndrome. Journal of Animal Science. 102:skae270. DOI: 10.1093/jas/skae270
6. Altendorf B.J., Anderson C.J.*, von Seggern I., Wiersema M.L., Schmitz-Esser S., Koltes D.A. 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; DOI: 10.3390/poultry3030020
7. Kiefer Z.E., Koester L.R.*, Studer J.M., Schmitz-Esser S., Ross J.W. 2024. Evaluation of fecal microbiota of late gestation sows in relation to pelvic organ prolapse risk. Frontiers in Microbiology. 15:1384583. DOI: 10.3389/fmicb.2024.1384583
8. Fries-Craft K., Schmitz-Esser S., Bobeck E.A. 2024. Broiler chicken distal jejunum microbial communities are more responsive to coccidiosis or necrotic enteritis challenge than dietary anti-interleukin-10 in a model using Salmonella Typhimurium- Eimeria maxima- Clostridium perfringens coinfection. Poultry Science. 2024 June 22; 103(9):104000. DOI: 10.1016/j.psj.2024.104000
9. Fries-Craft K., Anderson C.J., Schmitz-Esser S., Bobeck E.A. 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. Poultry Science. 103(9):104001. DOI: 10.1016/j.psj.2024.104001
10. Zhang W., Zheng L., Xie J., Su X., Zhang M., Huang H., Schmitz-Esser S., Du S., Yang Y., Xie J., Zhang Q., Yu S., Guo Q., Wang H., Zhang L., Yang K., Hou R. 2024. The giant panda gut harbors a high diversity of lactic acid bacteria revealed by a novel culturomics pipeline. mSystems. 9(7):e0052024. DOI: 10.1128/msystems.00520-24
11. Cassas M.S., Jonas L.C., Anderson C.J., Schmitz-Esser S., Youngs C.R. 2024. Temporal changes in ewe vaginal microbiota throughout gestation. Frontiers in Microbiology. 15:1359678. DOI: 10.3389/fmicb.2024.1359678
12. Tibbs-Cortes B.W., Rahic-Seggerman F.M., Schmitz-Esser S., Boggiatto P.M., Olsen S., Putz E.J. 2024. Fecal and vaginal microbiota of vaccinated and nonvaccinated pregnant elk challenged with Brucella abortus. Frontiers in Veterinary Science. 11:1334858. DOI: 10.3389/fvets.2024.1334858
13. Rahic-Seggerman F.M., Rosenthal K., Miller C., Iske C., Graham J., Schmitz-Esser S., Kohles M.R. 2024. Effects of diet on the bacterial and eukaryotic microbiota across the gastrointestinal tract of healthy rabbits (Oryctolagus cuniculus). American Journal of Veterinary Research. 85(4):1-11. DOI: 10.2460/ajvr.23.10.0234
14. Fries-Craft K., Schmitz-Esser S., Bobeck E.A. 2023. Dietary peptide-specific antibodies against interleukin-4 differentially alter systemic immune cell responses during Eimeria challenge with minimal impacts on the cecal microbiota. Poultry Science. 102(12):103134. DOI: 10.1016/j.psj.2023.103134
15. Fries-Craft K., Schmitz-Esser S., Bobeck E.A. 2023. Dietary alfalfa hay or lipid-soluble alfalfa extract may improve broiler growth, but fiber presence may be detrimental during Eimeria vaccine challenge. Poultry Science. 102(11):103019. DOI: 10.1016/j.psj.2023.103019
16. Anderson C.J., Altendorf B.J., Schmitz-Esser S., Koltes D.A. 2023. Characterization of the eukaryotic microbial communities in the chicken ileum in cage-free and conventional commercial housing systems. Poultry Science. 102(5):102621. DOI: 10.1016/j.psj.2023.102621
17. Tibbs-Cortes B.W., Schultz D.L., Tibbs-Cortes L.E., Schmitz-Esser S. 2023. FISHing for Rickettsia in tardigrades: additional evidence for tardigrade endosymbionts. Zoological Journal of the Linnean Society, 200(1), 230–238. DOI: 10.1093/zoolinnean/zlad081
18. Koester L.R., Hayman K., Anderson C.J., Tibbs-Cortes B.W., Daniels K.M., Seggerman F.M., Gorden P.J., 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. Journal of Animal Science. 101:skac403. DOI: 10.1093/jas/skac403
19. Zhang W., Xie J., Xia S., Fan X., Schmitz-Esser S., Zeng B., Zheng L., Huang H., Wang H., Zhong J., Zhang Z., Zhang L., Jiang M., Hou R. Evaluating a potential model to analyze the function of the gut microbiota of the giant panda. 2022. Frontiers in Microbiology. 13:1086058. DOI: 10.3389/fmicb.2022.1086058
20. Wickramasinghe J., Anderson C.J., Kaya C.A., Gorden P.J., Ribeiro F.R.B., 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
21. Wasendorf C., Schmitz-Esser S., Eischeid C.J., Leyhe M.J., Nelson E.N., Rahic-Seggerman F.M.*, Sullivan K.E., Peters N.T. 2022. Genome analysis of Erwinia persicina reveals implications for soft rot pathogenicity in plants. Frontiers in Microbiology. 13:1001139. DOI: 10.3389/fmicb.2022.1001139
22. Anast J.M., Etter A.J., Schmitz-Esser S. 2022. Comparative analysis of Listeria monocytogenes plasmid transcriptomes reveals common and plasmid-specific gene expression patterns and high expression of noncoding RNAs. MicrobiologyOpen. (5):e1315. DOI: 10.1002/mbo3.1315
23. Schultz D.L., Selberherr M., Stouthamer C.M., Doremus M.R., Kelly S.E., Hunter M.S., Schmitz-Esser S. 2022. Sex-based de novo transcriptome assemblies of the parasitoid wasp Encarsia suzannae, a host of the manipulative heritable symbiont Cardinium hertigii. Gigabyte. DOI: 10.46471/gigabyte.68
24. Tibbs-Cortes L.E., Tibbs-Cortes B.W., Schmitz-Esser S. 2022. Tardigrade community microbiomes in North American orchards include putative endosymbionts and plant pathogens. Frontiers in Microbiology. 13:866930. DOI: 10.3389/fmicb.2022.866930
25. Greiner L.L., Humphrey D.C., Holland S.N., Anderson C.J., Schmitz-Esser S. 2022. The validation of the existence of the entero-mammary pathway and the assessment of the differences of the pathway between first and third parity sows. Translational Animal Science. 6(2):txac047. DOI: 10.1093/tas/txac047
26. Quijada N.M., Dzieciol M., Schmitz-Esser S., Wagner M., Selberherr E. 2022. Metatranscriptomic analyses unravel dynamic changes in the microbial and metabolic transcriptional profiles in artisanal Austrian hard-cheeses during ripening. Frontiers in Microbiology. 13:813480. DOI: 10.3389/fmicb.2022.813480
27. Doremus M.R., Stouthamer C.M., Kelly S.E., Schmitz-Esser S., Hunter M.S. 2022. Quality over quantity: unraveling the contributions to cytoplasmic incompatibility caused by two coinfecting Cardinium symbionts. Heredity (Edinb). 128(3):187-195. DOI: 10.1038/s41437-022-00507-3
28. Selberherr E., Penz T., König L., Conrady B., Siegl A., Horn M., Schmitz-Esser S. 2022. The life cycle-dependent transcriptional profile of the obligate intracellular amoeba symbiont Amoebophilus asiaticus. FEMS Microbiology Ecology. 98(1):fiac001. DOI: 10.1093/femsec/fiac001
29. Koester L.R., Petry A.L., Youngs C.R., Schmitz-Esser S. 2021. Ewe vaginal microbiota: associations with pregnancy outcome and changes during gestation. Frontiers in Microbiology. 12:745884. DOI: 10.3389/fmicb.2021.745884
30. Kiefer Z.E., Koester L.R., Studer J.M., Chipman A.L., Mainquist-Whigham C., Keating A.F., Schmitz-Esser S., Ross J.W. 2021. Vaginal microbiota differences associated with pelvic organ prolapse risk during late gestation in commercial sows. Biology of Reproduction. 105(6):1545-1561. DOI: 10.1093/biolre/ioab178
31. Anast J.M., Schmitz-Esser S. 2021. Certain Listeria monocytogenes plasmids contribute to increased UVC ultraviolet light stress. FEMS Microbiology Letters. 368(17):fnab123. DOI: 10.1093/femsle/fnab123
32. Wagner M., Slaghuis J., Göbel W., Vázquez-Boland J.A., Rychli K., Schmitz-Esser S. 2021. Virulence pattern analysis of three Listeria monocytogenes lineage I epidemic strains with distinct outbreak histories. Microorganisms 9(8):1745. DOI: 10.3390/microorganisms9081745
33. Yan Z., Xu Q., Hsu W.H., Schmitz-Esser S., Ayala J., Hou R., Yao Y., Jiang D., Yuan S., Wang H. 2021. Consuming different structural parts of bamboo induce gut microbiome changes in captive Giant Pandas. Current Microbiology. 78(8):2998-3009. DOI: 10.1007/s00284-021-02503-y
34. Petry A.L., Patience J.F., Huntley N.F., Koester L.R., Bedford M.R., 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. Frontiers in Microbiology. 12:619970. DOI: 10.3389/fmicb.2021.619970
35. Anderson C.J., Koester L.R., Schmitz-Esser S. 2021. Rumen epithelial communities share a core bacterial microbiota: A meta-analysis of 16S rRNA gene Illumina MiSeq sequencing datasets. Frontiers in Microbiology. 12:625400. DOI: 10.3389/fmicb.2021.625400
36. Kiefer Z.E., Koester L.R.*, Showman L., Studer J.M., Chipman A.L., Keating A.F., Schmitz-Esser S., Ross J.W. 2021. Vaginal microbiome and serum metabolite differences in late gestation commercial sows at risk for pelvic organ prolapse. Scientific Reports 11(1):6189. DOI: 10.1038/s41598-021-85367-3
37. Schmitz-Esser S., Anast J.M., Cortes B.W. 2021. A large-scale sequencing-based survey of plasmids in Listeria monocytogenes reveals global dissemination of plasmids. Frontiers in Microbiology. 12:653155. DOI: 10.3389/fmicb.2021.653155
38. Schmitz-Esser S. 2021. The rumen epithelial microbiota: Possible gatekeepers of the rumen epithelium and its potential contributions to epithelial barrier function and animal health and performance. Meat and Muscle Biology 4 (2) p.19, 1–11. DOI: 10.22175/mmb.11672
39. Wiersema M.L., Koester L.R., Schmitz-Esser S., Koltes D.A. 2021. Comparison of intestinal permeability, morphology and ileal microbial communities of commercial hens housed in conventional cages and cage-free housing systems. Poultry Science 100(2):1178-1191. DOI: 10.1016/j.psj.2020.10.052
40. Petry A.L., Patience J.F., Koester L.R.*, Huntley N.F., Bedford M.R., 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
41. Doremus M.R., Stouthamer C.M., Kelly S.E., Schmitz-Esser S., Hunter M.S. 2020. Cardinium localization during its parasitoid wasp host's development provides insights into cytoplasmic incompatibility. Frontiers in Microbiology. 11:606399. DOI: 10.3389/fmicb.2020.606399
42. Kilburn L.R., Koester L.R., Schmitz-Esser S., Serão N.V.L., Rossoni Serão M.C. 2020. High-fat diets led to OTU-level shifts in fecal samples of healthy adult dogs. Frontiers in Microbiology. 11:564160. DOI: 10.3389/fmicb.2020.564160
43. Quijada N.M., Schmitz-Esser S., Zwirzitz B., Guse C., Strachan C.R., Wagner M., Wetzels S.U., Selberherr E., Dzieciol M. 2020. Austrian raw-milk hard-cheese ripening involves successional dynamics of non-inoculated bacteria and fungi. Foods; 9(12):1851. DOI: 10.3390/foods9121851
44. Wagner E., Zaiser A., Leitner R., Quijada N.M., Pracser N., Pietzka A., Ruppitsch W., Schmitz-Esser S., Wagner M., Rychli K. 2020. Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains. BMC Genomics; 21(1):847. DOI: 10.1186/s12864-020-07263-w
45. Anast J.M., Bobik T.A., Schmitz-Esser S. 2020. The cobalamin-dependent gene cluster of Listeria monocytogenes: Implications for virulence, stress response and food safety. Frontiers in Microbiology. 11:601816. DOI: 10.3389/fmicb.2020.601816
46. Quijada N.M., Bodas R., Lorenzo J.M., Schmitz-Esser S., Rodríguez-Lázaro D., Hernández M. 2020. Dietary supplementation with sugar beet fructooligosaccharides and garlic residues promotes growth of beneficial bacteria and increases weight gain in neonatal lambs. Biomolecules; 10(8):1179. DOI: 10.3390/biom10081179
47. Koester L.R., Poole D.H., Serão N.V.L., Schmitz-Esser S. 2020. Beef cattle that respond differently to fescue toxicosis have distinct gastrointestinal tract microbiota. PLoS One. 15(7):e0229192. DOI: 10.1371/journal.pone.0229192
48. Anast J.M., Schmitz-Esser S. 2020. The transcriptome of Listeria monocytogenes during co-cultivation with cheese rind bacteria suggests adaptation by induction of ethanolamine and 1,2-propanediol catabolism pathway genes. PLoS One. 15(7):e0233945. DOI: 10.3389/fmicb.2019.03110
49. Fries-Craft K., Anast J.M., Schmitz-Esser S., Bobeck E.A. 2020. Host immunity and the colon microbiota of mice infected with Citrobacter rodentium are beneficially modulated by lipid-soluble extract from late-cutting alfalfa in the early stages of infection. PLoS One. 15(7):e0236106. DOI: 10.1371/journal.pone.0236106
50. Wickramasinghe H.K.J.P., Anast J.M., Schmitz-Esser S., Serão N.V.L., Appuhamy J.A.D.R.N. 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. Journal of Dairy Science 103(5):4262-4274. DOI: 10.3168/jds.2019-17258
51. Sanglard L.P., Schmitz-Esser S., Gray K.A., Linhares D.C.L., Yeoman C.J., Dekkers J.C.M., Niederwerder M.C., Serão N.V.L. 2020. Vaginal microbiota diverges in sows with low and high reproductive performance after porcine reproductive and respiratory syndrome vaccination. Scientific Reports 10(1):3046. DOI: 10.1038/s41598-020-59955-8
52. Cortes B.W., Naditz A.L., Anast J.M., Schmitz-Esser S. 2020. Transcriptome sequencing of Listeria monocytogenes reveals major gene expression changes in response to lactic acid stress exposure but a less pronounced response to oxidative stress. Frontiers in Microbiology. 10:3110. DOI: 10.3389/fmicb.2019.03110
53. Sanglard L.P., Schmitz-Esser S., Gray K.A., Linhares D.C.L., Yeoman C.J., Dekkers J.C.M., Niederwerder M.C., Serão N.V.L. 2020. Investigating the relationship between vaginal microbiota and host genetics and their impact on immune response and farrowing traits in commercial gilts. Journal of Animal Breeding and Genetics 137 (1), 84-102. DOI: 10.1111/jbg.12456