The Microbial Genome Atlas (MiGA) project
THIS SEMINAR HAS BEEN CANCELLED
Dr. Kostas Konstantinidis
September 13 at 12:20pm in the Fralin Auditorium, 102 Fralin Hall
Hosted by Dr. B. Vinatzer
Dr. Kostas Konstantinidis joined the School of Civil and Environmental Engineering at Georgia Institute of Technology as an Assistant Professor in November 2007, and holds the Maulding Faculty Fellow Chair in Environmental Engineering since July 2018. His education and research interests are at the interface of environmental microbiology with engineering, genomics and computational biology. The overarching goal of his research is to broaden our understanding of the genetic and metabolic diversity of the smallest organisms on the planet, the bacteria and archaea, and the role of this diversity for ecosystem function and resilience to natural as well as anthropogenic perturbations. He is also interested in the biotechnological applications of microbial diversity in the bioremediation of environmental pollutants and the assessment of water quality. Dr. Konstantinidis has published >100 peer-reviewed articles, ten in PNAS alone, and six book chapters in these research areas, which have received >10,000 citations (Google Scholar). He received several national and international distinctions for his work, including the 2010 Skerman Award from the World Federation for Culture Collections (www.wfcc.info) for the ANI work, the 2012 Sigma Xi Young Faculty Research Award, and a 2014 Kavli Frontiers of Science Fellowship.
The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of microbial species and their communities to date as exemplified by the Ribosomal Database Project (RDP; https://rdp.cme.msu.edu). Nonetheless, several aspects of rRNA gene-based studies remain problematic. Most importantly, how to better resolve microbial communities at levels at which the 16S rRNA gene provides inadequate resolution, namely the species and finer levels, and how to best catalogue whole-genome diversity and fluidity. To bridge this gap, we have developed the "genome-equivalent" of RDP called the MiGA project (available at: www.microbial-genomes.org). MiGA allows the classification and gene-content diversity study of query genome(s) or assembled contig(s) against a reference database of microbial genomes using the ANI/AAI concept (currently using the ~13,000 isolate genomes available in NCBI's Genome database). Examples of using MiGA to perform high-resolution microbial source tracking in riverine ecosystems as well as micro-diversity and epidemiological studies of bacterial pathogens will be presented. The new insights emerging from these studies for the prokaryotic species concept will be also discussed. Our more recently developed computational solutions that will allow MiGA to scale-up with the increasing volume of genomic and metagenomic sequence data that are becoming available, and encompass the "uncultivated majority" of microbes, will be highlighted.