Evidence map›Paper›PMID 29088705›Full record

SynthesisNature2017

A communal catalogue reveals Earth's multiscale microbial diversity.

Luke R Thompson, Jon G Sanders, Daniel McDonald, Amnon Amir, Joshua Ladau, Kenneth J Locey, Robert J Prill, Anupriya Tripathi, Sean M Gibbons, Gail Ackermann and 33 more

Open access · hybridAbstract readMeta-Analysis
PubMed Full text at PMC Publisher
In one paragraph

Synthesis in Nature, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,259 papers, 3 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
1,259citing papers in PubMed, 3 pooled it
185.6field-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

1,259 citing papers in PubMed, 3 syntheses or guidelines pooled it, 2,810 citations in OpenAlex.

  1. Pooled it
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  18. Rainfall Shapes the Diversity of Soil Nitrogen-Fixing Microorganisms Worldwide.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
  19. Article
  20. Article

1,199 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

43 authors at 20 institutions in 30 countries.

Luke R ThompsonDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Jon G SandersDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Daniel McDonaldDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Amnon AmirDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Joshua LadauThe Gladstone Institutes and University of California San Francisco, San Francisco, California, USA.
Kenneth J LoceyDepartment of Biology, Indiana University, Bloomington, Indiana, USA.
Robert J PrillIndustrial and Applied Genomics, IBM Almaden Research Center, San Jose, California, USA.
Anupriya TripathiDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Sean M GibbonsDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Gail AckermannDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Jose A Navas-MolinaDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Stefan JanssenDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Evguenia KopylovaDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Yoshiki Vázquez-BaezaDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Antonio GonzálezDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
James T MortonDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Siavash MirarabDepartment of Electrical and Computer Engineering, University of California San Diego, La Jolla, California, USA.
Zhenjiang Zech XuDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Lingjing JiangDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Mohamed F HaroonDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
Jad KanbarDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Qiyun ZhuDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Se Jin SongDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Tomasz KosciolekDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Nicholas A BokulichPathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA.
Joshua LeflerDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Colin J BrislawnEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Gregory HumphreyDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Sarah M OwensBiosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.
Jarrad Hampton-MarcellBiosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.
Donna Berg-LyonsBioFrontiers Institute, University of Colorado, Boulder, Colorado, USA.
Valerie McKenzieDepartment of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.
Noah FiererDepartment of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.
Jed A FuhrmanDepartment of Biological Sciences, University of Southern California, Los Angeles, California, USA.
Aaron ClausetBioFrontiers Institute, University of Colorado, Boulder, Colorado, USA.
Rick L StevensComputing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA.
Ashley ShadeDepartment of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA.
Katherine S PollardThe Gladstone Institutes and University of California San Francisco, San Francisco, California, USA.
Kelly D GoodwinOcean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA.
Janet K JanssonEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Jack A GilbertBiosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.
Rob KnightDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.
Earth Microbiome Project Consortium
University of California San Diego · USUniversity of Chicago · USUniversity of Colorado Boulder · USUNSW Sydney · AUArgonne National Laboratory · USBangor University · GBThe University of Melbourne · AUUniversity of Puerto Rico System · PRInstituto Venezolano de Investigaciones Científicas · VEOregon State University · USPlymouth Marine Laboratory · GBUniversidad de Granada · ESUniversity of California, Davis · USUniversity of Illinois Chicago · USUniversity of Naples Federico II · ITUniversity of Pennsylvania · USColorado State University · USCornell University · USLawrence Berkeley National Laboratory · USMichigan State University · US

Funding

Culturing of the uncultured: reverse genomics and multispecies consortia in oralR01DE024463 · NIDCR · UT-BATTELLE, LLC-OAK RIDGE NATIONAL LAB · PI JOULINE, IGOR B., LEYS, EUGENE J · 2014 to 2018
$8.2M
Continued Development and Maintenance of the MG-RAST Metagenomics PipelineR01AI123037 · NIAID · PURDUE UNIVERSITY · PI GRAMA, ANANTH, MEYER, FOLKER · 2016 to 2020
$3.7M
NIAID NIH HHS R01 AI123037NIDCR NIH HHS R01 DE024463
6 · The paper itself

Abstract

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Indexed as

BiodiversityEarth, PlanetAnimalsArchaeaBacteriaEcologyGene DosageGeographic MappingHumansMicrobiotaPlantsRNA, Ribosomal, 16SRNA, Ribosomal, 16S

Identifiers

PMID29088705
PMCPMC6192678
OpenAlexW2766358903

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.