Escherichia coli isolates (collectively termed UNISED) repeatedly harvested from marine sediment are identified as distinctly environmental-specific, showing the ability to survive outside the gastrointestinal tracts of warm-blooded animals. This discovery leads to the hypothesis that UNISED E. coli may gain certain functions that allow them to persist in the external environment and challenges the use of E. coli as a fecal indicative bacteria (FIB) for water pollution detection.

LC-MS-based shotgun proteomics was performed on E. coli monocultures, and co-cultures of two or more UNISED isolates in nutritional-limited (M9) media and in the presence of mitomycin C (DNA damaging compound) to explore stress responses. Label-free quantification is performed to overlay differentially...[ Read more ]

Escherichia coli isolates (collectively termed UNISED) repeatedly harvested from marine sediment are identified as distinctly environmental-specific, showing the ability to survive outside the gastrointestinal tracts of warm-blooded animals. This discovery leads to the hypothesis that UNISED E. coli may gain certain functions that allow them to persist in the external environment and challenges the use of E. coli as a fecal indicative bacteria (FIB) for water pollution detection.

LC-MS-based shotgun proteomics was performed on E. coli monocultures, and co-cultures of two or more UNISED isolates in nutritional-limited (M9) media and in the presence of mitomycin C (DNA damaging compound) to explore stress responses. Label-free quantification is performed to overlay differentially changed proteins with known protein-protein interaction networks to provide insights of bacterial interactions and survival as shown in our results. Hypothetical and unannotated proteins discovered to be differentially expressed between strains and between mono-culture and co-culture conditions might be future targets for follow-up studies in environmental E. coli and in bacterial communities’ research.

Using the protein database from UniProt E. coli K12 (a commonly used lab strain), around 900 – 1000 proteins were identified on average at a false discovery rate of 0.01 by the search engine Comet, indicating a large degree of sequence overlaps among the strains. Notably, using our custom-generated protein sequence databases from the whole genome sequences of the strains, we could identify around 100-200 more unique proteins, compared to the highly curated K12 database. This result implied that there exist substantial number of strain-specific protein sequences not found in the K12 genome, and these proteins are expressed under the conditions examined. By comparing the observed proteomes of different strains quantitatively, hundreds of proteins, some clustered in known pathways, were identified to be differentially expressed in UNISED strains compared to K12, offering biological insights regarding the physiology and ecology of these E. coli strains.