Genomic and Physiological Characteristics of Novel Escherichia Strains Isolated from Freshwater Sources

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Dr. Aaron Best, Biology, Chelsea Payne

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Escherichia coli is primarily viewed as a commensal of the mammalian gut, but this view is changing with the recognition of “naturalized” populations of Escherichia found in non-host associated, secondary environments. The majority of Escherichia genome sequences comes from studies of host-associated isolates. While these strains are important to health and agriculture, they do not adequately address the potential diversity of strains found in secondary environments (e.g., freshwater streams and lakes, beach sands, soils). These sources may serve as reservoirs in which diverse strains of Escherichia exchange genetic information. We produced genome sequences of Escherichia isolates from freshwater sources as part of a longitudinal survey of microbial communities in Lake Macatawa Watershed. Relationships of isolates with publicly available sequenced Escherichia strains were determined using core genome phylogenetic inference. Approximately 98% of watershed strains are related to traditional E. coli; 2% of strains are related to non-traditional environmental clades. Members of Phylogroup B1, often isolated from freshwater environments in previous studies, make up 46% of the strains within the E. coli lineage. We used in silico methods to screen watershed strains for antibiotic resistance genes and virulence factors. Most watershed strains contain ≤30 antibiotic resistance genes, consistent with strains isolated from host sources, but more than the number of genes found within the non-traditional environmental clades. We conducted comparisons to determine protein families that distinguish among watershed isolates and reference Escherichia strains within established phylogroups. While there are protein families that clearly distinguish between different phylogroups, few differences were observed between watershed and related reference E. coli strains. Physiological experiments testing metabolic activity of watershed strains at 2-11°C revealed that many metabolize glucose at 8°C. These data expand our knowledge of potentially naturalized E. coli strains, allowing better water quality monitoring techniques that quantify E. coli as fecal indicator bacteria.


This research was supported by the National Science Foundation under grant No. MCB-11616737 and the Herbert H. and Grace A. Dow Foundation.

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