Genomic Diversity of Escherichia Isolates from Diverse Habitats
Abstract
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 thosemore »
- Authors:
-
- Georgia Institute of Technology, Atlanta, GA (United States); Michigan State University, East Lansing, MI (United States)
- Michigan State University, East Lansing, MI (United States)
- Georgia Institute of Technology, Atlanta, GA (United States)
- Publication Date:
- Research Org.:
- Michigan State Univ., East Lansing, MI (United States); Georgia Institute of Technology, Atlanta, GA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Science Foundation (NSF)
- OSTI Identifier:
- 1904625
- Grant/Contract Number:
- FG02-07ER64389; DEB-0516252
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 7; Journal Issue: 10; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; microarrays; Escherichia; genomics; Escherichia coli; genomic signal processing; animal phylogenetics; evolutionary genetics; human genomics
Citation Formats
Oh, Seungdae, Buddenborg, Sarah, Yoder-Himes, Deborah R., Tiedje, James M., and Konstantinidis, Konstantinos T. Genomic Diversity of Escherichia Isolates from Diverse Habitats. United States: N. p., 2012.
Web. doi:10.1371/journal.pone.0047005.
Oh, Seungdae, Buddenborg, Sarah, Yoder-Himes, Deborah R., Tiedje, James M., & Konstantinidis, Konstantinos T. Genomic Diversity of Escherichia Isolates from Diverse Habitats. United States. https://doi.org/10.1371/journal.pone.0047005
Oh, Seungdae, Buddenborg, Sarah, Yoder-Himes, Deborah R., Tiedje, James M., and Konstantinidis, Konstantinos T. Mon .
"Genomic Diversity of Escherichia Isolates from Diverse Habitats". United States. https://doi.org/10.1371/journal.pone.0047005. https://www.osti.gov/servlets/purl/1904625.
@article{osti_1904625,
title = {Genomic Diversity of Escherichia Isolates from Diverse Habitats},
author = {Oh, Seungdae and Buddenborg, Sarah and Yoder-Himes, Deborah R. and Tiedje, James M. and Konstantinidis, Konstantinos T.},
abstractNote = {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.},
doi = {10.1371/journal.pone.0047005},
journal = {PLoS ONE},
number = 10,
volume = 7,
place = {United States},
year = {Mon Oct 08 00:00:00 EDT 2012},
month = {Mon Oct 08 00:00:00 EDT 2012}
}
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