Evidence map›Paper›PMID 41120764›Full record

ArticleNature microbiology2025

Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism.

Skyler Friedline, Elizabeth A McDaniel, Matthew Scarborough, Maxwell Madill, Kate Waring, Vivian S Lin, Rex R Malmstrom, Danielle Goudeau, William Chrisler, Morten K D Dueholm and 13 more

Abstract read
PubMed Publisher
In one paragraph

Article in Nature microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
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

23 authors.

Skyler FriedlineDepartment of Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0000-0002-1027-7631
Elizabeth A McDanielDepartment of Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0000-0003-4692-0913
Matthew ScarboroughDepartment of Civil and Environmental Engineering, University of Vermont, Burlington, VT, USA.
Maxwell MadillDepartment of Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
Kate WaringDepartment of Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
Vivian S LinBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
Rex R MalmstromDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-4758-7369
Danielle GoudeauDOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-3785-032X
William ChrislerEnvironmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
Morten K D DueholmCenter for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
Leo J GorhamBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
Chathuri J KombalaBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.ORCID http://orcid.org/0000-0002-3847-8769
Lydia H GriggsBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
Heather M OlsonBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.ORCID http://orcid.org/0000-0002-4501-9587
Sophie B LehmannEnvironmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
Nathalie MunozEnvironmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.ORCID http://orcid.org/0000-0002-2723-3512
Jesse TrejoBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
Nikola TolicEnvironmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
Ljiljana Pasa-TolicEnvironmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.ORCID http://orcid.org/0000-0001-9853-5457
Sarah M WilliamsEnvironmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
Mary LiptonEnvironmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
Steven J HallamGenome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0000-0002-4889-6876
Ryan M ZielsDepartment of Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada. ziels@mail.ubc.ca.ORCID http://orcid.org/0000-0003-3705-6078

Funding

Genome British Columbia SIP027Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada) CRDPJ 543962-19Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada) RGPIN-2018-04585
6 · The paper itself

Abstract

Syntrophic microbial consortia can contribute substantially to the activity of anoxic ecosystems but are often too rare to allow the study of their in situ physiologies using traditional molecular methods. Here we combined bioorthogonal non-canonical amino acid tagging (BONCAT), stable isotope probing and metaproteomics to improve the recovery of proteins from active members and track isotope incorporation in an anaerobic digestion community. Click-chemistry-enabled cell sorting and direct protein pull-down coupled to metaproteomics improved recovery of isotopically labelled proteins during anaerobic acetate oxidation. BONCAT-enabled protein profiles revealed elevated activity and labelling of a rare and so-far uncharacterized syntrophic bacterium belonging to the family Natronincolaceae that expressed a previously hypothesized oxidative glycine pathway for syntrophic acetate oxidation. Stable-isotope-probing-informed metabolic modelling predicted that this organism accounted for a majority of acetate flux, suggesting that the oxidative glycine pathway is an important route for anaerobic carbon transformation and is probably central to community metabolism in natural and engineered ecosystems.

Indexed as

BacteriaMicrobial ConsortiaProteomicsAcetatesAnaerobiosisBacterial ProteinsGlycineIsotope LabelingOxidation-ReductionProteomeAcetatesBacterial ProteinsGlycineProteome

Identifiers

PMID41120764

What OpenQuestion holds

Textmetadata
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.