Colonic microbiota assembly and interactions
Our research in this area works to characterize factors that shape assembly and disruption of colonic microbial communities, investigate mucin-microbiota interactions, and better understand how microbial interactions contribute to colonization resistance.
Huang X, Johnson AE, Brehm, JN, Do, TVT, Auchtung TA, McCullough HC, Lerma, AI, Haidacher SJ, Hoch KM, Horvath TD, Sorg JA, Haag AM, Auchtung JM*. 2025. Clostridioides difficile colonization is not mediated by bile salts and utilizes Stickland fermentation of proline in an in vitro model. mSphere 10:e0104924. PMCID: PMC11852769.
McCullough HC, Song H-S*, Auchtung JM*. 2025. Diversity in chemical subunits and linkages: A key molecular determinant of microbial richness, community structure, microbiota interactions, and substrate utilization. Microbiol Spect 13:e0261824. PMCID: PMC11970232
Auchtung TA, Lerma AI, Schuchart K, Auchtung JM*. 2025. Evaluating effects of antibiotics across preclinical models of the human gastrointestinal microbiota. bioRxiv doi: https://doi.org/10/1101/2025.01.23.634623. [PREPRINT]
Biswas B, Do TVT, Auchtung J*, Piepenbrink KH. 2025. Dissecting the role of flagellar subunits in C. difficile mucosal colonization. bioRxiv doi: https://doi.org/10.1101/2025.01.02.631138. [PREPRINT]
Sidner B, Lerma A, Biswas B, Do TVT, Yu Y, Ronish LA, McCullough H, Auchtung JM, Piepenbrink KH. 2023. Flagellin is essential for initial attachment to mucosal surfaces by Clostridioides difficile. Microbiol Spectr. 11:e0212023. PMCID: PMC10714722
Motta-Romero HA, Perez-Donado CE, Auchtung JM, Rose DJ. 2023. Toxicity of cadmium on dynamic human gut microbiome cultures and the protective effect of cadmium-tolerant bacteria autochthonous to the gut. Chemosphere 338:139581. PMID: 37474038
Engevik MA, Engevik AC, Engevik KA, Auchtung JM, Chang-Graham AL, Ruan W, Luna RA, Hyser JM, Spinler JK, Versalovic J. Mucin-Degrading Microbes Release Monosaccharides That Chemoattract Clostridioides difficile and Facilitate Colonization of the Human Intestinal Mucus Layer. 2021. ACS Infect Dis 7:1126-1142. PMCID: PMC8110611.
Kessel AK, McCullough HC, Auchtung JM, Bernstein HC, Song H-S. 2020. Predictive interactome modeling for precision microbiome engineering. Curr Opin Chem Eng 30:77-85. doi.org/10.1016/jcoche.2020.08.003.
Engevik M, Danhof HA, Auchtung J, Endres BT, Ruan W, Bassères E, Engevik AC, Wu Q, Nicholson M, Luna RA, Garey KW, Crawford SE, Estes MK, Lux R, Yacyshyn MB, Yacyshyn B, Savidge T, Britton RA, Versalovic J. 2020. Fusobacterium nucleatum adheres to Clostridioides difficile via the RadD adhesin to enhance biofilm formation in intestinal mucus. Gastroenterology 160:1301-1314. PMCID: PMC7956072.
Auchtung JM, Preisner EC, Collins J, Lerma AI, Britton RA. 2020. Identification of Simplified Microbial Communities That Inhibit Clostridioides difficile Infection through Dilution/Extinction. mSphere 5:e00387-20. PMCID: PMC7392540.
Collins J, Robinson C, Danhof H, Knetsch CW, van Leeuwen HC, Lawley TD, Auchtung JM, Britton RA. 2018. Dietary trehalose enhances virulence of epidemic Clostridium difficile. Nature. 553:291-294. PMCID: PMC5984069.
Collins J, Auchtung JM*. 2017. Control of Clostridium difficile Infection by Defined Microbial Communities. Microbiol Spectr. 5:10.1128/microbiolspec.BAD-0009-2016. PMCID: PMC5736378.
Spinler JK, Auchtung J, Brown A, Boonma P, Oezguen N, Ross CL, Luna RA, Runge J, Versalovic J, Peniche A, Dann SM, Britton RA, Haag A, Savidge TC. 2017. Next-Generation Probiotics Targeting Clostridium difficile through Precursor-Directed Antimicrobial Biosynthesis. Infect Immun. 85: e00303-17. PMCID: PMC5607411.
Robinson CD#, Auchtung JM#, Collins J, Britton RA. 2014. Epidemic Clostridium difficile strains demonstrate increased competitive fitness compared to nonepidemic isolates. Infect Immun. 82:2815-25. PMCID: PMC4097
Colonic microbiota interactions with dietary bioactive compounds
Research in this area involves collaborative projects to understand how dietary bioactive compounds influences health and disease.
Christensen C, Kok CR, Harris CL, Moore N, Wampler HL, Zhuang W, Wu SS, Hutkins R, Izard J*, Auchtung JM*. 2024. Microbiota, metabolic profiles and immune biomarkers in infants receiving formula with added bovine milk fat globule membrane: a randomized, controlled trial. Front Nutr 11:1465174. PMCID:PMC11497130
Mahnic A, Auchtung JM, Poklar Ulrih N, Britton RA, Rupnik M. 2020. Microbiota in vitro modulated with polyphenols shows decreased colonization resistance against Clostridioides difficile but can neutralize cytotoxicity. Sci Rep. 10:8358. PMCID: PMC7239955.
Microbiota interactions of fermented foods
Research in this area involves collaborative projects to understand how fermented food microbes interact to produce products with potential human health benefits.
Auchtung JM*, Hallen-Adams HE, Hutkins R*. 2025. Microbial interactions and ecology in fermented food ecosystems. Nat Rev Microbiol doi:10.138/s41579-025-01191-2. PMID:40410356.
Mendelson C, Sparkes S, Merenstein DJ, Christensen C, Sharma V, Desale S, Auchtung JM, Kok CR, Hallen-Adams HE, Hutkins R. 2023. Kombucha tea as an anti-hyperglycemic agent in humans with diabetes - a randomized controlled pilot investigation. Front Nutr. 10:1190248. PMCID: PMC10426908
Christensen CM, Kok CR, Auchtung JM*, Hutkins R*. 2022. Prebiotics enhance persistence of fermented-food associated bacteria in in vitro cultivated fecal microbial communities. Front Microbiol. 13:908506. PMCID: PMC9479011
Method and model development
Our collaborative studies have also led to improved method and model development for studying the colonic microbiota and its metabolites.
Fofanova TY, Karandikar UC, Auchtung JM, Wilson RL, Valentin, AJ, Grande-Allen KJ, Estes MK, Hoffman K, Ramani S, Stewart CJ, Petrosino JF. 2024. A novel system to culture human intestinal organoids under physiological oxygen content to study microbial-host interaction. PLoS ONE 19(7):e0300666. PMCID: PMC11271918
Masi AC, Fofanova TY, Lamb CA, Auchtung JM, Britton RA, Estes MK, Ramani S, Cockell SJ, Coxhead J, Embleton ND, Berrington JE, Petrosino JF, Stewart CJ. 2022. Distinct gene expression profiles between human preterm-derived and adult-derived intestinal organoids exposed to Enterococcus faecalis: a pilot study. Gut 71:2141-2143. PMCID: PMC9231289
Horvath TD, Haidacher SJ, Oezguen N, Hoch KM, Auchtung JM, Haag AM. 2020. Ruggedness testing of liquid chromatography-tandem mass spectrometry system components using microbiome-relevant methods and matrices. J Microbiol Methods. 177:106020. PMID: 32795635.
Horvath TD, Haidacher SJ, Hoch KM, Auchtung JM, Haag AM. 2020. A high-throughput LC-MS/MS method for the measurement of the bile acid/salt content in microbiome-derived sample sets. MethodsX 7:100951. PMCID: PMC7327831.
Auchtung JM, Robinson CD, Farrell K, Britton RA. 2016. MiniBioReactor Arrays (MBRAs) as a Tool for Studying C. difficile Physiology in the Presence of a Complex Community. Methods Mol Biol. 1476:235-58. doi: 10.1007/978-1-4939-6361-4_18. PDF available upon request.
Auchtung JM, Robinson CD, Britton RA. 2015. Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs). Microbiome 3:42. PMCID: PMC4588258.
Collins J, Auchtung JM, Schaefer L, Eaton KA, Britton RA. 2015. Humanized microbiota mice as a model of recurrent Clostridium difficile disease. Microbiome. 3:35. PMCID: PMC4546040.
Persistence of fungi in the human digestive tract
Research led by a former lab member, Tommy Auchtung, also contributed to a better understanding of fungal colonization of the human gastrointestinal tract.
Auchtung TA, Stewart CJ, Smith DP, Triplett EW, Agardh D, Hagopian WA, Ziegler AG, Rewers MJ, She JX, Toppari J, Lernmark Å, Akolkar B, Krischer JP, Vehik K, Auchtung JM, Ajami NJ, Petrosino JF. 2022. Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study. Nat Commun. 13:3151. PMCID: PMC9174155
Auchtung TA, Fofanova TY, Stewart CJ, Nash AK, Wong MC, Gesell JR, Auchtung JM, Ajami NJ, Petrosino JF. Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi. mSphere 3: e00092-18. PMCID: PMC5874442.
* Indicates corresponding author
# Indicates equal contribution