Faculty > Faculty By Appointment > Gautam Dantas, PhD

Associate Professor, Pathology and Immunology
Associate Professor, Biomedical Engineering
Associate Professor, Molecular Microbiology
4515 McKinley Building, Rm 5314
Office: (314) 362-7238
Lab: (314) 362-0867
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The Dantas Lab works at the interface of microbial genomics, ecology, synthetic biology, and systems biology, to understand, harness, and engineer the biochemical processing potential of microbial communities. Our research projects are broadly organized under four themes, described briefly below: Microbial Ecology, Translational Microbiology, Microbial Engineering, and Technology Development. More information can be found at: Dantas Lab Research

Microbes are the most ubiquitous lifeforms on Earth. They are found across all habitats studied to date, including the bodies of every living thing (including humans), as well terrestrial, subterranean, and aquatic environments. Microbes collectively represent one of the largest reservoirs of biomass, estimated to account for 350-550 Petagrams (1 Pg = 10^15 grams = 1 billion tons) of carbon, 85-130 Pg of nitrogen, and 9-14 Pg of phosphorous. Their diverse biochemical and metabolic activities impact and control nearly all aspects of biotic and abiotic processes on the planet. In virtually all cases, microbes live and work in complex ecosystems composed of incredibly diverse taxonomic lineages. We take a quantitative ecological perspective in our study of diverse microbial communities, with a focus on human associated microbiota and interconnected environmental habitats. Accordingly, one of our major goals is to understand and quantitatively predict the effects of anthropogenic interventions (e.g. antibiotics) on microbial community composition and function. More information about our recent and ongoing efforts in this area can be found at: Dantas Lab - Microbial Ecology

While a majority of microbes on our planet are beneficial (or at least benign) to humans, a small minority are pathogenic, and contribute to human suffering and mortality. Antibiotics are our primary therapeutics against the infectious diseases caused by these pathogens. Unfortunately, resistance to these life-saving drugs has steadily increased in pathogens since the first wide-scale discovery and deployment of these drugs in the 1930s, while the pipeline of new antibiotics coming to market has dramatically decreased over the past few decades. Some pathogens are now resistant to almost all of our current antibiotics, raising the dark prospect of a post-antibiotic era where we begin to succumb to common infectious agents. Drug resistant infections currently claim hundreds of thousands of lives worldwide, and are estimated to add over 35 billion dollars in healthcare costs annually in the US alone. We urgently require novel therapies to combat these threats, as well as an improved understanding of ways to detect and curb the evolution of new resistance. A parallel motivation for novel microbial therapeutics is the maintenance of healthy states of the human microbiota, and rescue from perturbed states (for instance, those caused by overuse of antibiotics in agriculture and the clinic). The thousands of years of co-evolution of humans and their resident microbiota has resulted in a delicate ecological balance which provides benefits to both the host and the trillions of microbes that live in and on the body. Disruption of this balance has been hypothesized to lead to a number of human pathologies which may parallel the burden of infectious diseases, including aberrant immune responses (e.g. asthma and allergies), gastrointestinal disorders (e.g. inflammatory bowel disease), and cancer. Accordingly, one of our major goals is to evaluate and design novel diagnostics and therapies for maintaining healthy human commensal microbial communities and defeating pathogenic microbes. More information about our recent and ongoing efforts in this area can be found at: Dantas Lab - Translational Microbiology

As a complement to our ecological and translational focus on understanding microbial community functions, we aim to bioprospect for novel industrial and therapeutic applications. One of the reasons that microbes are ubiquitous on our planet is their ability to metabolize and biochemically modify virtually all available organic substrates. Their capacity to exist in complex communities, often in association with other living hosts, is enabled by the incredible diversity of small molecules which they produce for modulating their intracellular interactions, both cooperative and offensive. Indeed, most antibiotics currently used in the clinic are natural products (or their semi-synthetic derivatives) of soil-dwelling bacteria. In addition to a source of therapeutic molecules, microbes also have the capacity to produce high-value industrial compounds (e.g. bioplastics, biofuels etc.) from renewable substrates, raising the prospect of biologically-derived alternatives to non-renewable, environmentally-unsustainable, fossil-based compounds (e.g. petroleum, plastics etc.). Accordingly, one of our major goals is to bioprospect and genetically engineer novel beneficial functions in microbes for biomedical and industrial applications. More information about our recent and ongoing efforts in this area can be found at: Dantas Lab - Microbial Engineering

Central to our diverse biological goals to understand and harness microbial community functions is a strong focus on technology development. We are particularly interested in technologies for microbial systems-level analyses and engineering, requiring the development and application of meta-omics methods and complementary computational tools to both analyze multi-scale data and build predictive models. Our published efforts have focused on methods for studying (meta)genomes and (meta)transcriptomes, and we are currently expanding our capacities in lipidomics, metabolic analyses, mechanistic protein biochemical and structural analyses, and conventional and gnotobiotic mouse husbandry and manipulation. One of our major goals is to develop novel high-throughput experimental and computational tools to study and modulate microbial communities. More information about our recent and ongoing efforts in this area can be found at: Dantas Lab - Technology Development

Selected Publications:

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

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.

Yoneda A*, Henson WR*, Goldner NK, Park KJ, Forsberg KJ, Kim SJ, Pesesky MW, Foston M, Dantas G, Moon TS. Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630. Nucleic Acids Research. 2016. PMID: 26837573.

Gonzales PR, Pesesky MW, Bouley R, Ballard A, Biddy BA, Suckow MA, Wolter WR, Schroeder VA, Burnham CD, Mobashery S, Chang M, Dantas G. Synergistic, collaterally sensitive β-lactam combinations suppress resistance in MRSA. Nature Chemical Biology. 2015 Sep 14. doi: 10.1038/nchembio.1911. PMID: 26368589.

Pesesky MW*, Hussain T*, Wallace M, Wang B, Andleeb S, Burnham CAD, Dantas G. KPC and NDM-1 are harbored by related Enterobacteriaceae strains and plasmid backbones from distinct geographies. Emerging Infectious Diseases. 2015 Jun. doi: 10.3201/eid2106.141504.

Gibson MK, Forsberg KJ, Dantas G. Improved annotation of antibiotic resistance functions reveals microbial resistomes cluster by ecology. ISME J. 2014; doi: ISMEJ.2014.106. PMID: 25003965.

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. PMID: 24847883. PMCID: PMC4079543.

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. PMID: 22936781. PMCID: PMC4070369.

Sommer MO*, Dantas G*, Church GM. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science. 2009 Aug 28;325(5944):1128-31. doi: 10.1126/science.1176950. PMID: 19713526.

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.

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.

DBBS Graduate Program Affiliation

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