Gautam Dantas, PhD

Pathology and Immunology
Laboratory and Genomic Medicine
Molecular Microbiology
Biomedical Engineering

Molecular Microbiology and Microbial Pathogenesis Program
Computational and Systems Biology Program
Molecular Genetics and Genomics Program
Evolution, Ecology and Population Biology Program

  • 314-362-7238

  • 314-286-0867

  • 314-362-2156

  • 8510

  • Couch Biomedical Research Building, 4515 McKinley Ave, 5th Floor, Rm 5314




  • anibiotic resistance, synthetic biology, bioenergy, human microbiome, metagenomics, microbial ecology and biodiversity

  • (1) Dynamics, ecology, and evolution of antibiotic resistance, (2) Engineering enhanced probiotics to treat GI disorders, (3) Engineering microbial biofuel catalysts

Research Abstract:

Our research group develops novel technologies to understand, harness, and engineer the biochemical processing potential of microbial communities. We work at the interface of microbial genomics, quantitative ecology, synthetic biology, systems biology, and computational biology to study problems with biotechnological and biomedical relevance. Our current projects are focused on three major themes: (1) understanding and predicting how diverse microbiomes respond to chemical and biological perturbations, (2) harnessing these insights to rationally design therapeutic strategies to curtail antibiotic resistant pathogens and remedy pathological microbiome states, and (3) engineering microbial catalysts to convert renewable biomass into value chemicals such as biofuels and pharmaceuticals. More details at

Mentorship and Commitment to Diversity Statement:
I lead an interdisciplinary research and training group of basic scientists, engineers, and clinicians, spanning formal expertise in microbiology, biochemistry, genomics, pathology, infectious diseases, pediatrics, ecology and evolution, systems biology, biomedical engineering, chemical engineering, and computational biology. In addition to my research efforts, I am deeply committed to education, mentoring, and training. I am the co-Chief of Research for the Division of Laboratory and Genomic Medicine. I am also the co-Director of the Computational & Systems Biology (CSB) graduate program, have served on the steering committee for both the CSB and Molecular Microbiology & Microbial Pathogenesis graduate programs, regularly teach in 3 graduate-level courses, and have served on over 100 qualifying exam and thesis committees. In November 2019, I participated in the “Maximizing Research Mentoring Relationships Workshop” led by an NRMN-trained facilitator, and I will continue to regularly participate in formal mentor training. Over the past 13 years, I have mentored 17 postdoctoral fellows (12 PhD, 4 MD/PhD, 1 MD), 33 graduate students (including 2 MSTP), 2 medical students, 9 research technicians, and over 100 undergraduate interns. I have graduated 17 PhD, 1 MD/PhD, and 1 MSc students; three are independent faculty, six are in post-doctoral training, one is a K-12 teacher, and eight work in biotech. Six of my postdoctoral mentees have earned faculty positions, and four work in the biotech industry. I am committed to providing a nurturing, well-supported, and actively mentored environment for my team to collaboratively tackle basic science and translational research problems.

Selected Publications:

1. Thänert R, Choi J8, Reske KA, Hink T, Thänert A, Wallace MA, Wang B, Seiler S, Cass C, Bost MH, Struttmann EL, Iqbal ZH, Sax SR, Fraser VJ, Baker AW, Foy KR, Williams B, Xu B, Capocci-Tolomeo P, Lautenbach E, Burnham CD, Dubberke ER, Kwon JH, Dantas G; CDC Prevention Epicenters Program. Persisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements. Cell Host Microbe. 2022 May 9:S1931-3128(22)00214-1. doi: 10.1016/j.chom.2022.04.008. PMID: 35545083.

2. Fishbein SR, Robinson JI, Hink T, Reske KA, Newcomer EP, Burnham CD, Henderson JP, Dubberke ER, Dantas G. Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis. ELife. 2022. doi: 10.7554/eLife.72801. PMID: 35083969.

3. Rottinghaus AG, Ferreiro A, Fishbein SRS, Dantas G, Moon TS. Genetically stable CRISPR-based kill switches for engineered microbes. Nature Communications. 2022. doi: 10.1038/s41467-022-28163-5. PMID: 35115506.

4. Kwak S, Mahmud B, Dantas G. A Tunable and Expandable Transactivation System in Probiotic Yeast Saccharomyces boulardii. ACS Synth Biol. 2021. doi: 10.1021/acssynbio.1c00384. PMID: 34939781.

5. Langdon A, Schwartz DJ, Bulow C, Sun X, Hink T, Reske KA, Jones C, Burnham CD, Dubberke ER, Dantas G. Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study. Genome Medicine. 2021. doi: 10.1186/s13073-021-00843-9. PMID: 33593430.

6. Gasparrini AJ, Wang B, Sun X, Kennedy EA, Hernandez-Leyva A, Ndao IM, Tarr PI, Warner BB, Dantas G. Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome. Nature Microbiology. 2019 Dec;4(12):2285-2297. doi: 10.1038/s41564-019-0550-2. PMCID: PMC6879825.

7. D'Souza AW, Potter RF, Wallace M, Shupe A, Patel S, Sun X, Gul D, Kwon JH, Andleeb S, Burnham CD, Dantas G. Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces. Nature Commun. 2019 Oct 8;10(1):4569. doi: 10.1038/s41467-019-12563-1. PMCID: PMC6783542.

8. Crook N, Ferreiro A, Gasparrini AJ, Pesesky MW, Gibson MK, Wang B, Sun X, Condiotte Z, Dobrowolski S, Peterson D, Dantas G. Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut. Cell Host Microbe. 2019 Apr 10. doi: 10.1016/j.chom.2019.02.005. PMCID: PMC6487504.

9. Boolchandani M, D'Souza AW, Dantas G. Sequencing-based methods and resources to study antimicrobial resistance. Nature Rev. Genetics. 2019 Mar 18. doi: 10.1038/s41576-019-0108-4. PMCID: PMC6525649.

10. Ferreiro A, Crook N, Gasparrini AJ, Dantas G. Multiscale Evolutionary Dynamics of Host-Associated Microbiomes. Cell. 2018 Mar 8;172(6):1216-1227. doi: 10.1016/j.cell.2018.02.015. PMCID: PMC5846202.

11. Baumann-Dudenhoeffer AM, D'Souza AW, Tarr PI, Warner BB, Dantas G. Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes. Nature Medicine. 2018 doi: 10.1038/s41591-018-0216-2. PMCID: PMC6294307.

12. Crofts TS, Gasparrini AJ, Dantas G. Next-generation approaches to understand and combat the antibiotic resistome. Nature Rev. Microbiology. 2017 Apr 10. doi: 10.1038/nrmicro.2017.28. PMCID: PMC5681478.

13. Park J, Gasparrini AJ, Reck MR, Symister CT, Elliott JL, Vogel JP, Wencewicz TA, Dantas G, Tolia NH. Plasticity, dynamics, and inhibition of emerging tetracycline resistance enzymes. Nature Chemical Biology. 2017 May 8. doi: 10.1038/nchembio.2376. PMCID: PMC5478473.

14. Langdon A, Crook N, Dantas G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med. 2016 Apr 13;8(1):39. doi: 10.1186/s13073-016-0294-z. PMID: 27074706; PMCID: PMC4831151.

15. Gibson MK, Wang B, Ahmadi S, Burnham CAD, Tarr PI, Warner BB, Dantas G. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nature Microbiology. 2016. doi: 10.1038/nmicrobiol.2016.24. PMCID: PMC5031140.

16. Pehrsson EC, Tsukayama P, Patel S, Mejía M, Sosa-Soto G, Navarrete KM, Calderon M, Cabrera L, Hoyos W, Bertoli MT, Berg DE, Gilman RH, Dantas G. Interconnected microbiomes and resistomes in low-income human habitats. Nature. 2016. doi: 10.1038/nature17672. PMCID: PMC4869995.

17. Forsberg KJ, Patel S, Gibson MK, Lauber CL, Knight R, Fierer N, Dantas G. Bacterial phylogeny structures soil resistomes across habitats. Nature 2014; 509: 612. doi: 10.1038/nature13377. PMCID: PMC4079543.

18. Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MO, Dantas G. The shared antibiotic resistome of soil bacteria and human pathogens. Science. 2012 Aug 31;337(6098):1107-11. doi: 10.1126/science.1220761. PMCID: PMC4070369.

19. Dantas G, Sommer MO, Oluwasegun RD, Church GM. Bacteria subsisting on antibiotics. Science. 2008 Apr 4;320(5872):100-3. doi: 10.1126/science.1155157. PMID: 18388292.

20. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science. 2003 Nov 21;302(5649):1364-8. PMID: 14631033.

Last Updated: 11/15/2022 9:04:57 AM

In the Dantas Lab we are interested in defining fundamental mechanisms of microbiome stability, resilience, and remediation, and translating these insights into personalized, microbiome-directed therapeutics. We leverage extensive clinical collaborations alongside cutting-edge molecular, multi-omic, and engineering approaches to systematically 1) understand the functional effects of host-microbiome disruption in defined cohorts relevant to human health, 2) predict key molecular features indicative of microbiome-specific responses to disruption using computational, statistical, and mechanistic animal models, and 3) remediate host-microbiome disruptions using engineered probiotic platforms for targeted interventions.
Back To Top

Follow us: