Distinguished Scientist and Systems Genetics Group Leader
ORNL
Research
Research in my laboratory combines experimental and computational approaches to study microbial evolution (with emphasis on Archaea), interspecies interaction, adaptation to various environments and the composition and dynamics of microbial communities. Specific groups of organisms and communities include uncultured taxa from the human microbiota (TM7, SR1, Chloroflexi and others), human microbiota dynamics in health and disease, symbiotic/parasitic Nanoarchaeota from high temperature environments, communities, taxa and genes involved in bioremediation, bioenergy, biogeochemical cycles.
Experimental and computational microbial genomics
The exponential increase in microbial genomic and metagenomic data provides new opportunities to understanding functional diversification in gene families and evolution of genome size/composition as part of organism adaptation to specific niches. Analyzing large genomic datasets and especially metagenomic data presents however computational challenges in terms of gene identification, functional inferences and taxonomical assignments. We are integrating computational genomics and phylogenetic approaches to correlate genomic and metagenomic data with the ecology and evolution of individual microbes and communities. Microbial systems under study include species relevant to bioremediation and bioenergy, the mammalian gut microbiota, species and communities from extreme environments and oceanic niches. We are also using targeted genomics of single cells and specific populations to sequence the genomes of uncultured bacteria and archaea. This approach bridges the gap between characterization of cultured organisms, which represent a minute fraction of the microbial diversity and metagenomics, which provides only a glimpse of the genomic information of complex communities. We are developing experimental and computational tools necessary to achieve reliable isolation and genomic sequencing of any specific microbes, rare or abundant, from any type of community.
Uncultured members of the human microbiota
Using single cell genomics and metagenomics we are studying bacterial and archaeal components of the human microbiota and their potential role in health and disease. We have determined the sequence of individual cells representing selected uncultured taxa at different phylogenetic levels (TM7, SR1, Chloroflexi, Deltaproteobacteria, Synergistes). Aside from providing insight into adaptation to the human host and potential role in disease, the genomic data is being used to design approaches for isolation, cultivation and study of these bacteria in the laboratory.
Nanoarchaeota
Several research projects in that lab focus on the study of Nanoarchaeota, a group of hyperthemophilic archaea. Until recently, the only cultivated representative of this group was Nanoarchaeaum equitans, an ectoparasite/symbiont on the archaeon Ignicoccus hospitalis. We integrate transcriptomic, proteomic and comparative genomic approaches to study this system and understand mechanisms of interspecies communication, exchange as well as genomic co-evolution. We are characterizing the diversity of Nanoarchaeota in many marine and terrestrial high temperature environments and using single cell genomics we have recently characterized the first terrestrial symbiotic nanoarchaeal system fro Yellowstone National Park. Ongoing microbial cultivation and physiology, metagenomics, single cell genomic sequencing and comparative genomics are aimed at isolating and characterizing such nanoarchaeal systems from various high temperature environments and understanding the evolution of archaeal symbiosis and parasitism.
Education
- Ph.D.: Genetics and Development-University of Texas Southwestern Medical Center at Dallas (1997)
- B.S.: Biology-Babes Bolyai University, Cluj-Napoca Romania (1988)
Publications
Podar M, Makarova KS, Graham DE, Wolf YI, Koonin EV, Reysenbach AL. Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park. Biol Direct. 2013 Apr 22;8(1):9.
Campbell AG, Campbell JH, Schwientek P, Woyke T, Sczyrba A, Allman S, Beall CJ, Griffen A, Leys E, Podar M. Multiple single-cell genomes provide insight into functions of uncultured deltaproteobacteria in the human oral cavity. PLoS One. 2013;8(3).
Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Söll D, Podar M. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5540-5.
Parks JM, Johs A, Podar M, Bridou R, Hurt RA Jr, Smith SD, Tomanicek SJ, Qian Y, Brown SD, Brandt CC, Palumbo AV, Smith JC, Wall JD, Elias DA, Liang L. The genetic basis for bacterial mercury methylation. Science. 2013 Mar 15;339(6125):1332-5.
Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ Microbiol. 2013 15(6), 1882-1899
Zhou Y, Gao H, Mihindukulasuriya KA, Rosa PS, Wylie KM, Vishnivetskaya T, Podar M, Warner B, Tarr PI, Nelson DE, Fortenberry JD, Holland MJ, Burr SE, Shannon WD, Sodergren E, Weinstock GM. Biogeography of the ecosystems of the healthy human body. Genome Biol. 2013 Jan 14;14(1):R1.
Human Microbiome Project Consortium. A framework for human microbiome research. Nature. 2012 Jun 13;486(7402):215-21
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012 Jun 13;486(7402):207-14
Campbell JH, Foster CM, Vishnivetskaya T, Campbell AG, Yang ZK, Wymore A, Palumbo AV, Chesler EJ, Podar M. Host genetic and environmental effects on mouse intestinal microbiota. ISME J. 2012 Nov;6(11):2033-44.
Griffen AL, Beall CJ, Campbell JH, Firestone ND, Kumar PS, Yang ZK, Podar M, Leys EJ. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J. 2012 Jun;6(6):1176-85
Giannone RJ, Huber H, Karpinets T, Heimerl T, Küper U, Rachel R, Keller M, Hettich RL, Podar M. Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans--Ignicoccus hospitalis relationship. PLoS One. 2011;6(8):e22942. doi: 10.1371/journal.pone.0022942.
Podar, M., Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall M, Lykidis A, Mavrommatis K, Sun H, Hudson ME, Chen W, Deciu C, Hutchison D, Eads JR, Anderson A, Fernandes F, Szeto E, Lapidus A, Kyrpides NC, Saier MH Jr, Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, Stetter KO. (2008). A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol. 10;9(11):R158.