Genomic Diversity of Escherichia Isolates from Diverse Habitats

Konstantinidis KT (2012) Genomic Diversity of Escherichia Isolates from Diverse Habitats. PLoS ONE 7(10): e47005. doi:10.1371/journal.pone.0047005 Genomic Diversity of Escherichia Isolates from Diverse Habitats Seungdae Oh 0 1 Sarah Buddenborg 0 1 Deborah R. Yoder-Himes 0 1 James M. Tiedje 0 1 Konstantinos T. Konstantinidis 0 1 Matthias Horn, University of Vienna, Austria 0 a Current address: Department of Biology, University of New Mexico , Albuquerque , New Mexico, United States of America b Current address: Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts , United States of America 1 1 School of Civil and Environmental Engineering, Georgia Institute of Technology , Atlanta , Georgia , United States of America, 2 Center for Microbial Ecology, Michigan State University , East Lansing, Michigan , United States of America, 3 School of Biology, Georgia Institute of Technology , Atlanta , Georgia , United States of America, 4 Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology , Atlanta, Georgia , United States of America Our understanding of the Escherichia genus is heavily biased toward pathogenic or commensal isolates from human or animal hosts. Recent studies have recovered Escherichia isolates that persist, and even grow, outside these hosts. Although the environmental isolates are typically phylogenetically distinct, they are highly related to and phenotypically indistinguishable from their human counterparts, including for the coliform test. To gain insights into the genomic diversity of Escherichia isolates from diverse habitats, including freshwater, soil, animal, and human sources, we carried out comparative DNA-DNA hybridizations using a multi-genome E. coli DNA microarray. The microarray was validated based on hybridizations with selected strains whose genome sequences were available and used to assess the frequency of microarray false positive and negative signals. Our results showed that human fecal isolates share two sets of genes (n.90) that are rarely found among environmental isolates, including genes presumably important for evading host immune mechanisms (e.g., a multi-drug transporter for acids and antimicrobials) and adhering to epithelial cells (e.g., hemolysin E and fimbrial-like adhesin protein). These results imply that environmental isolates are characterized by decreased ability to colonize host cells relative to human isolates. Our study also provides gene markers that can distinguish human isolates from those of warm-blooded animal and environmental origins, and thus can be used to more reliably assess fecal contamination in natural ecosystems. - Funding: This work was supported by the NSF (award DEB-0516252, http://www.nsf.gov/, to J.M.T. and K.T.K.) and the U.S. Department of Energy (award DEFG02-07ER64389, http://energy.gov/, to J.M.T. and K.T.K.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. Escherichia coli is believed to have the gastrointestinal tract of human and/or animal hosts as its preferred habitat. Accordingly, it has been traditionally thought that E. coli does not reproduce well outside its hosts [13], and thus, can serve as an indicator organism of fecal contamination of natural ecosystems (coliform test) [2,46]. However, recent studies suggest that certain populations of the Escherichia genus, including populations conventionally classified as E. coli, may reproduce outside their hosts and, in fact, persist better in natural environments such as soil and water [79]. Further, the ecological and metabolic versatility of the species, reflected in the open pan-genome structure (.15,000 unique genes in the pan-genome of 61 genomes) and the high intra-species genome plasticity (i.e., ninetenths of the pan-genome represent accessory or strain-specific genes) [10], emphasizes the functional potential of the species for adapting to a broad range of habitats and environmental perturbations, including possibly non-host associated habitats. These findings have revolutionized the traditional view of the ecology of E. coli. Walk and colleagues described several clades of environmentally-adapted strains that are clearly members of the Escherichia genus; yet phylogenetically distinct compared to other Escherichia representatives (e.g., E. fergusoni, E. albertii, and E. coli) based on multi-locus sequence analysis (MLSA) [11]. Despite the phylogenetic differentiation, traditional phenotypic profiling based on the ability to utilize 31 carbon substrates or providing positive signal for the coliform test revealed no significant differences between the former environmental strains and human Escherichia representatives. Further, Ihssen and colleagues showed that environmental E. coli isolates, originating from raw drinking water sources, share genetic and physiological features in major important functions such as carbon utilization and stress defense with E. coli isolates from human and animal feces [12]. These findings have important implications for assessing contamination of natural reservoirs, which is frequently based on counting E. coli cells using phenotypic- and culture-based approaches [2,4,5]. In contrast to these previous studies, our recent study based on whole genome sequence analysis of Escherichia isolates from human and environmental sources identified several genes and pathways specific to each of the two sets of isolates [13]. For example, the environmental-specific genes were associated with acquisition of resources important for survival in the environment (e.g., diol utilization and lysozyme production), whereas human-specific functions were related to transport and utilization of nutrients abundant in the gut (e.g., N-acetylglucosamine and gluconate). In this study, we aimed to identify new niche-specific genes for Escherichia isolates recovered from diverse habitats based on the analysis of twenty-seven strains, including fifteen previously uncharacterized isolates whose genomes have not been sequenced yet. We performed whole genome DNA-DNA hybridizations among isolates collected from freshwater, soil, animal, and human sources using a multi-genome E. coli microarray. Our comparative study revealed new gene signatures that are shared among strains recovered from human feces (enteric) and that rarely occur in environmental strains. The gene products may be needed for life in the human gastrointestinal (GI) tract, but dispensable for survival in the environment. These findings not only advance the understanding of the genetic footprint of ecological specialization in the Escherichia genus but also provide molecular biomarkers that can distinguish closely related, phenotypically indistinguishable enteric and environmental strains (...truncated)