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Ongoing Projects

1. Comparative genomics to better understand microbial speciation and evolution

We perform comparative analyses of genomes of isolates to evaluate how bacteria adapt to environmental perturbations and what is the relative importance of the genetic mechanisms of genome evolution and plasticity. This work has also important implications for the bacterial species definition. We study several important groups including, but not limited to, E. coli, Campylobacter jejuni, Shewanella spp, Burkholderia spp, and Synechococcus spp. In addition, we are developing novel whole-genome-based bioinformatics approaches for cataloguing and studying the total bacterial diversity, such as the Average Nucleotide Identity (ANI). For instance, see our recent PNAS paper on E. coli:

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species.





2.Time-series metagenomics of Lake Lanier, Atlanta, GA

Lake Lanier is an important freshwater lake for the South East US as it represents the main source of drinking water for the Atlanta metropolitan area and is extremely popular with boaters, houseboats, jet skiers and others. To better characterize the microbial communities associated with human-impacted freshwater ecosystems, we have begun the systematic sampling of the lake Lanier microbial communities, in-situ and over time, using cutting-edge metagenomics and metatranscriptomics techniques. This work was recently funded by the NSF "Dimensions of Biodiversity" program. For further details, see:





3. Bioinformatics tools for microbial genomes and metagenomes

With support from the NSF "Advances in Biological Informatics" program, we are developing novel bioinformatics tools for specialized tasks in the analysis of microbial genomes and metagenomes such as how to determine the level of the coverage of a microbial community obtained by sequencing (Nonpareil), how to determine the taxonomic identity of a metagenomic read or contig, including those representing previously un-described taxa (MyTaxa), how to detect metagenomic reads encoding a target gene of interest (ROCker tool), and an ANI/AAI calculatorFor further details, see our "Tools" webpage from the menu above and link below:


4. Microbial adaptations to anthropogenic increase of CO2

With support from the US Department of Energy and in collaboration with researchers at the University of Oklahoma, Michigan State University and University of Florida, we perform comparative metagenomic analyses of microbial communities from Alaskan soils and soils of temperate regions to investigate how the corresponding microbial ommunities respond to increased atmospheric CO2 and temperature, especially with respect to release or sequestration of carbon.






5. Species interactions within dechlorinating communities

With support from the NSF and in collaboration with Drs. Loeffler and Ritalahti (University of Tennessee), we employ a combination of microbial physiology, biochemistry and bioinformatic approaches to explore the symbiotic interactions between microbial organisms responsible for the bioremediation of important contaminants such as chlorinated hydrocarbons. For further details, see:







6. Controlling antibiotic resistance in engineered systems

With support from the NSF and in collaboration with Dr. Pavlostathis (Georgia Tech), we explore the role of disinfectants such as quaternary ammonia compounds in proliferating (microbial) antibiotic resistance in engineered systems, such as bioreactors of wastewater treatment plants. For further details, see:


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