Evidence map›Paper›PMID 28810907›Full record

ReviewMicrobiome2017

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 and 10 more

Open access · goldAbstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Microbiome, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 225 papers, 3 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
225citing papers in PubMed, 3 pooled it
33.1field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

225 citing papers in PubMed, 3 syntheses or guidelines pooled it, 484 citations in OpenAlex.

  1. AI-Enabled Imaging for Pathogen Detection Under Stress Conditions: A Systematic Review.Comprehensive reviews in food science and food safety · 2026
    Pooled it
  2. Pooled it
  3. The Human Respiratory Microbiome: Current Understandings and Future Directions.American journal of respiratory cell and molecular biology · 2023
    Pooled it
  4. Article
  5. Article
  6. Article
  7. Review
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Review
  15. Review
  16. Review
  17. Article
  18. Article
  19. Article
  20. Article

165 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

20 authors at 12 institutions in 4 countries.

Joanne B EmersonDepartment of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA. jbemerson@ucdavis.edu.
Rachel I AdamsDepartment of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA, 94720, USA.
Clarisse M Betancourt RománBiology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA.
Brandon BrooksDepartment of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA, 94720, USA.
David A CoilGenome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA.
Katherine DahlhausenGenome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA.
Holly H GanzGenome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA.
Erica M HartmannBiology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA.
Tiffany HsuDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA, 02115, USA.
Nicholas B JusticeLawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA, 94720, USA.
Ivan G Paulino-LimaUniversities Space Research Association, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 377, Moffett Field, CA, 94035-1000, USA.
Julia C LuongoDepartment of Mechanical Engineering, University of Colorado at Boulder, 1111 Engineering Drive, 427 UCB, Boulder, CO, 80309, USA.
Despoina S LymperopoulouDepartment of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA, 94720, USA.
Cinta Gomez-SilvanLawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA, 94720, USA.
Brooke Rothschild-MancinelliDivision of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JH, UK.
Melike BalkDepartment of Earth Sciences - Petrology, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands.
Curtis HuttenhowerDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA, 02115, USA.
Andreas NockerIWW Water Centre, Moritzstrasse 26, 45476, Mülheim an der Ruhr, Germany.
Parag VaishampayanBiotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
Lynn J RothschildPlanetary Sciences and Astrobiology, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 361, Moffett Field, CA, 94035-1000, USA. Lynn.J.Rothschild@nasa.gov.
University of California, Berkeley · USUniversity of California, Davis · USAmes Research Center · USHarvard University · USLawrence Berkeley National Laboratory · USUniversity of Oregon · USIWW Water Centre · DEJet Propulsion Laboratory · USThe Ohio State University · USUniversity of Colorado Boulder · USUniversity of Edinburgh · GBUtrecht University · NL

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Bacterial Physiological PhenomenaEcosystemMicrobial ViabilityBacteriaBiomassHigh-Throughput Nucleotide SequencingHumansMetagenomicsMicrobial ConsortiaReal-Time Polymerase Chain ReactionSequence Analysis, DNADNA sequencingFlow cytometryInfectivityLive/deadLow biomassMetagenomicsMicrobial ecologyPMAqPCRRNAViability

Identifiers

PMID28810907
PMCPMC5558654
OpenAlexW2740951628

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.