Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems

Joanne B. Emerson, Rachel I. Adams, Clarisse M.Betancourt Román, Brandon Brooks, David A. Coil, Katherine Dahlhausen, Holly H. Ganz, Erica M. Hartmann, Tiffany Hsu, Nicholas B. Justice, Ivan G. Paulino-Lima, Julia C. Luongo, Despoina S. Lymperopoulou, Cinta Gomez-Silvan, Brooke Rothschild-Mancinelli, Melike Balk, Curtis Huttenhower, Andreas Nocker, Parag Vaishampayan, Lynn J. Rothschild

Research output: Contribution to journalReview article

99 Scopus citations

Abstract

While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.

Original languageEnglish (US)
Number of pages1
JournalMicrobiome
Volume5
Issue number1
DOIs
StatePublished - Aug 16 2017

Keywords

  • DNA sequencing
  • Flow cytometry
  • Infectivity
  • Live/dead
  • Low biomass
  • Metagenomics
  • Microbial ecology
  • PMA
  • RNA
  • Viability
  • qPCR

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

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    Emerson, J. B., Adams, R. I., Román, C. M. B., Brooks, B., Coil, D. A., Dahlhausen, K., Ganz, H. H., Hartmann, E. M., Hsu, T., Justice, N. B., Paulino-Lima, I. G., Luongo, J. C., Lymperopoulou, D. S., Gomez-Silvan, C., Rothschild-Mancinelli, B., Balk, M., Huttenhower, C., Nocker, A., Vaishampayan, P., & Rothschild, L. J. (2017). Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome, 5(1). https://doi.org/10.1186/s40168-017-0285-3