Skip to content


Contact Information

P: 864-656-2328

Campus Location

132 Long Hall, Clemson, SC 29634


Monday - Friday:
8 a.m. - 4:30 p.m.


Profile Photo

Anna Seekatz

Biological Sciences

Assistant Professor

Life Sciences Building 157A [Office]
Life Sciences Building 160F [Lab]
Life Sciences Building 172 [Research Laboratory Service]

Educational Background

PhD, Molecular Microbiology and Immunology, University of Maryland School of Medicine, 2013
BS, Cellular and Molecular Biology, Western Washington University, 2006

Profile/About Me

I'm a microbiologist at Clemson University interested in the gut microbiome. I received my PhD at the University of Maryland School of Medicine, where I first learned about the importance of your gut microbes. After a postdoc position at the University of Michigan, I joined Clemson's Department of Biological Sciences as an Assistant Professor. When I am not thinking about the gut, I like to cook, embroider, and sing karaoke.

Research Interests

My lab is interested in studying interactions within the gut microbiota, the indigenous microbes that live in our gastrointestinal tract. We use a combination of bioinformatics, animal models of disease, and traditional microbiology to understand how beneficial microbes function during health and disease states.

One focus of the lab is Clostridioides (Clostridium) difficile infection (CDI), a serious nosocomial infection that affects half a million individuals per year in the United States. The majority of CDI cases occur after antibiotic use, and we know that a healthy gut microbiome is important in resistance to C. difficile. Fecal microbiota transplantation (FMT) has become a common and effective treatment method for combatting recurrence of infection, which impacts 20-30% of individuals with CDI. While it is known that a diverse community of microbes is necessary for clearance of C. difficile, the functional contribution of these communities remains unknown. We study how microbial communities interact with the host to clear C. difficile in a mouse model of recurrent disease. We aim to understand: 1) which microbes are involved, 2) what metabolites are important, and 3) how the host responds during C. difficile clearance and disease recovery.

A developing research focus of our lab includes investigating interactions between commensal bacteria in the gut. A diversity of commensal Clostridia inhabit the mammalian gut, yet there is a dearth of information available for many species commonly associated with health. We aim to 1) develop targeted isolation pipelines for specific commensals (i.e., species within the Lachnospiraceae family), 2) characterize strain heterogeneity within prevalent species in the gut, and 3) identify the functional dependence of Clostridial species on the mammalian gut environment.

Research Group (Lab)

Sophie Millard, PhD Candidate
Clara Flores, PhD Student
Christine Woelfel-Monsivais, PhD Student
Disha Bhattacharjee, PhD, Postdoctoral Fellow

Courses Taught

Pathogenic Bacteriology (MICR4110)
Creative inquiry (BIOL4941): Characterization of commensal Clostridia in the gastrointestinal tract

Selected Publications

Bhattacharjee D, Flores C, Woelfel-Monsivais C, and Seekatz AM. Diversity and prevalence of Clostridium innocuum in the human gut microbiota. BioRxiv, 2022; Jun 30. (preprint; submitted to mSphere, under revision).

Monaghan TM, Seekatz AM, Mullish BH, Moore-Gillon CCER, Dawson LF, Ahmed A, Kao D, Chan WC. Clostridioides difficile: innovations in target discovery and potential for therapeutic success. Expert Opin Ther Targets, 2021; 25(11):949. doi: 10.1080/14728222.2021.2008907. PMID: 34793686.

Monaghan TM, Biswas RN, Nashine RR, Joshi SS, Mullish BH, Seekatz AM, Blanco JM, McDonald JAK, Marchesi JR, Yau TO, Christodoulou N, Hatziapostolou M, Pucic-Bakovic M, Vuckovic F, Klicek F, Lauc G, Xue N, Dottorini T, Ambalkar S, Satav A, Polytarchou C, Acharjee A, and Kashyap RS. Multiomics profiling reveals signatures of dysmetabolism in urban populations in central India. Microorganisms, 2021; 9(7):1485. PMID: 34361920.

Monaghan TM, Seekatz AM, Markham NO, Yau TO, Hatziapostolou M, Jilani T, Christodoulou N, Toach B, Birli E, Pomenya O, Louie T, Lacy DB, Kim P, Lee C, Kao D, and Polytarchou C. Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection Associates With Functional Alterations in Circulating microRNAs. Gastroenterology, 2021; S0016-5058(21)00577-1. PMID: 33844988.

Bhattacharjee D, Seekatz AM. Dilution as a solution: targeting microbial populations with a simplified dilution strategy. mSphere, 2020; 5:e00701-20. PMID: 32727864.

Rao K, Seekatz AM, Bassis CM, Sun Y, Mantlo E, and Bachman MA. Enterobacterales Infection after Intestinal Dominance in Hospitalized Patients. mSphere 2020; 5(4):e004560-20. PMID: 32699120.

Seekatz AM. mSphere of Influence: Translating Gut Microbiome Studies To Benefit Human Health. mSphere, 2020; 5e00592-20. PMID: 32641428. Shimasaki T, Seekatz A, Bassis C, Rhee Y, Yelin RD, Fogg L, Dangana T, Cisneros EC, Weinstein RA, Okamoto K, Lolans K, Schoeny M, Lin MY, Moore NM, Young VB, Hayden MK; Centers for Disease Control and Prevention Epicenters Program. Increased relative abundance of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae within the gut microbiota is associated with risk of bloodstream infection in long-term acute care hospital patients. Clin Infect Dis 2018; Sep 18 . PMID: 30239622.

Seekatz AM, Bassis CM, Fogg L, Moore NM, Rhee Y, Lolans K, Weinstein RA, Lin MY, Young VB, and Hayden MK. Gut microbiota and clinical features distinguish colonization with Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae at the time of admission to a long-term acute care hospital. Open Forum Infect Dis 2018; July 31, 5(8):ofy190. PMID: 30151415.

Seekatz AM, Wolfrum E, DeWald CM, Putler RKB, Vendrov KC, Rao K, and Young VB. Presence of multiple Clostridium difficile strains at primary infection is associated with development of recurrent disease. Anaerobe 2018; May 31 (epub ahead of print). PMID: 29859301.

Seekatz AM, Rao K, Chang YM, Freeman AE, Kao JY, and Young VB. Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection. Anaerobe 2018; April 12.

Daquigan N, Seekatz AM, Greathouse KL, Young VB, and White JR. High-resolution profiling of the gut microbiome reveals the extent of Clostridium difficile burden. NPJ Biofilms Microbiomes 2017 5(3):35. PMID: 29214047.

Bassis CM, Moore NM, Lolans K, Seekatz AM, Weinstein RA, Young VB, and Hayden MK. Comparison of stool versus rectal swab samples and storage conditions on bacterial community profiles. BMC Microbiol 2017 17(1):78. PMID: 28359329.

Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, Young VB, Henrissat B, Wilmes P, Stappenbeck TS, Núñez G, and Martens EC. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 2016 Nov 17;167(5):1339-1353.e21. PMID: 27863247.

Seekatz AM, Rao K, Santhosh K, Young VB. Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection. Genome Med. 2016 Apr 27;8(1):47. PMID: 27121861.

Seekatz AM, Theriot CM, Molloy CT, Wozniak KL, Bergin IL, Young VB. Fecal Microbiota Transplantation Eliminates Clostridium difficile in a Murine Model of Relapsing Disease. Infect Immun. 2015 Oct;83(10):3838-46. Epub 2015 Jul 13. PMID: 26169276.

Seekatz AM, Young VB. Clostridium difficile and the microbiota. J Clin Invest. 2014 Oct;124(10):4182-9. Epub 2014 Jul 18 PMID: 25036699.

Seekatz AM, Aas J, Gessert CE, Rubin TA, Saman DM, Bakken JS, Young VB. Recovery of the gut microbiome following fecal microbiota transplantation. MBio. 2014 Jun 17;5(3):e00893-14. PMID: 24939885.

Full list of citations available at:


Github: ASeekatz
Github: Seekatz Lab

Contact Information

P: 864-656-2328

Campus Location

132 Long Hall, Clemson, SC 29634


Monday - Friday:
8 a.m. - 4:30 p.m.