Transcriptomic and rRNA:rDNA signatures of environmental versus enteric enterococcus faecalis isolates under oligotrophic freshwater conditions

Brittany Suttner, Minjae Kim, Eric R. Johnston, Luis H. Orellana, Carlos A. Ruiz-Perez, Luis M. Rodriguez-R, Janet K. Hatt, Joe Brown, Jorge W. Santo Domingo, Konstantinos T. Konstantinidis

Research output: Contribution to journalArticlepeer-review


The use of enterococci as a fecal indicator bacterial group for public health risk assessment has been brought into question by recent studies showing that "naturalized" populations of Enterococcus faecalis exist in the extraenteric environment. The extent to which these naturalized E. faecalis organisms can confound water quality monitoring is unclear. To determine if strains isolated from different habitats display different survival strategies and responses, we compared the decay patterns of three E. faecalis isolates from the natural environment (environmental strains) against three human gut isolates (enteric strains) in laboratory mesocosms that simulate an oligotrophic, aerobic freshwater environment. Our results showed similar overall decay rates between enteric and environmental isolates based on viable plate and quantitative PCR (qPCR) counts. However, the enteric isolates exhibited a spike in copy number ratios of 16S rRNA gene transcripts to 16S rRNA gene DNA copies (rRNA:rDNA ratios) between days 1 and 3 of the mesocosm incubations that was not observed in environmental isolates, which could indicate a different stress response. Nevertheless, there was no strong evidence of differential gene expression between environmental and enteric isolates related to habitat adaptation in the accompanying mesocosm metatranscriptomes. Overall, our results provide novel information on how rRNA levels may vary over different growth conditions (e.g., standard lab versus oligotrophic) for this important indicator bacteria. We also observed some evidence for habitat adaptation in E. faecalis; however, this adaptation may not be substantial or consistent enough for integration in water quality monitoring.

Original languageEnglish
Article numbere00817-21
JournalMicrobiology spectrum
Issue number2
StatePublished - Oct 2021

Bibliographical note

Publisher Copyright:
© 2021 American Society for Microbiology. All rights reserved.


  • Bioinformatics
  • Environmental microbiology
  • Fecal organisms
  • Metatranscriptomics
  • Public health
  • RRNA
  • Water quality

ASJC Scopus subject areas

  • Physiology
  • Ecology
  • General Immunology and Microbiology
  • Genetics
  • Microbiology (medical)
  • Cell Biology
  • Infectious Diseases


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