ArticleNature biotechnology2024
Greengenes2 unifies microbial data in a single reference tree.
Erratum issuedAbstract read
In one paragraph
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 402 papers, 2 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
402citing papers in PubMed, 2 pooled it
–field-weighted citation impact
What it found
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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.
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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.
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Who cites it
402 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Standardized 16S Meta-Analysis Reveals Consistent Host-Associated Patterns in Laminariales Epiphytic Microbiomes.MicrobiologyOpen · 2026Pooled it
- The Indoor Microbiome: Sampling, Analysis and Emerging Trends.Environmental microbiology reports · 2026Pooled it
- Effects of Heat-KilledNutrients · 2026Trial
- Trial
- Latent tuberculosis infection shapes gut microbiome and immune-metabolic interactions in people living with HIV.Gut microbes · 2026Article
- Perinatal ampicillin exposure alters murine maternal fecal bile acid and acylcarnitine profiles.Gut microbes · 2026Article
- Multi-omic modelling of body mass index response to a dietary weight loss intervention.Gut microbes · 2026Article
- Article
- Population scale analysis reveals gut microbiome diversity and functional shifts linked to obesity.iScience · 2026Article
- Diversification of biofilm architecture among freshwaterApplied and environmental microbiology · 2026Article
- From trees to graphs: rethinking phylogeny in microbiome prediction.Applied and environmental microbiology · 2026Article
- Ecological Patterns of Gut Microbiota During Elexacaftor/Tezacaftor/Ivacaftor Therapy in Cystic Fibrosis.Microorganisms · 2026Article
- Safety Assessment on Probiotic Mixture "Prohep" and Longitudinal Evaluation on its Gut Microbial Modulation Ability in Mice.Probiotics and antimicrobial proteins · 2026Article
- Integrated Multi-Omics Reveals Complementary Luminal and Mucosal Host-Microbiome Interactions Associated with Disease Activity and Phenotype in Paediatric Inflammatory Bowel Disease.Microorganisms · 2026Article
- Lycopene mitigates T-2 toxin-induced systemic inflammation and oxidative stress in association with gut microbiota and SCFAs regulation in mice.Stress biology · 2026Article
- Effects of ResB supplementation on gut microbiome composition in elderly pneumonia: a randomized pilot trial.European journal of clinical nutrition · 2026Article
- The Combination of Phytogenic in High-Starch Diets for Growing Cattle and Its Effects on Immunomodulation, Fermentation, Microbiota, and Performance.Animals : an open access journal from MDPI · 2026Article
- Gut microbiome changes in a captive giant panda with cardiovascular disease.The Journal of veterinary medical science · 2026Article
- Megascale microbiome analysis with DartUniFrac.Nature biotechnology · 2026Article
- Sex-specific gut microbial and metabolic responses to inhaled diesel exhaust particle exposure are modified by probiotic treatment in C57BL/6 mice.Research square · 2026Article
342 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
25 authors.
Daniel McDonaldDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.
Yueyu JiangDepartment of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA.
Metin BalabanBioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
Kalen CantrellDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
Qiyun ZhuSchool of Life Sciences, Arizona State University, Tempe, AZ, USA.ORCID http://orcid.org/0000-0002-3568-6271
Antonio GonzalezDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.
James T MortonBiostatistics & Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
Giorgia NicolaouHalicioglu Data Science Institute, University of California San Diego, La Jolla, CA, USA.
Donovan H ParksAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.ORCID http://orcid.org/0000-0001-6662-9010
Søren M KarstDepartment of Obstetrics and Gynecology, Columbia University, New York, NY, USA.
Mads AlbertsenDepartment of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.ORCID http://orcid.org/0000-0002-6151-190X
Philip HugenholtzAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.ORCID http://orcid.org/0000-0001-5386-7925
Todd DeSantisDepartment of Informatics, Second Genome, Brisbane, CA, USA.
Se Jin SongCenter for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
Andrew BartkoCenter for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-1237-2747
Aki S HavulinnaFinnish Institute for Health and Welfare, Helsinki, Finland.ORCID http://orcid.org/0000-0002-4787-8959
Pekka JousilahtiFinnish Institute for Health and Welfare, Helsinki, Finland.
Susan ChengDivision of Cardiology, Brigham and Women's Hospital, Boston, MA, USA.
Michael InouyeCambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
Teemu NiiranenFinnish Institute for Health and Welfare, Helsinki, Finland.
Mohit JainSapient Bioanalytics, LLC, San Diego, CA, USA.
Veikko SalomaaFinnish Institute for Health and Welfare, Helsinki, Finland.ORCID http://orcid.org/0000-0001-7563-5324
Leo LahtiDepartment of Computing, University of Turku, Turku, Finland.
Siavash MirarabDepartment of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-5410-1518
Rob KnightDepartment of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA. robknight@eng.ucsd.edu.ORCID http://orcid.org/0000-0002-0975-9019
Funding
National Centralized Repository for Alzheimer's Disease and Related Dementias (NCRAD)U24AG021886 · NIA · INDIANA UNIV-PURDUE UNIV AT INDIANAPOLIS · PI TATIANA M. FOROUD · 2002 to 2026
$119.8MProject 4 - Mechanistic studies on the role of the gut microbiome in models for Alzheimer's diseaseU19AG063744 · NIA · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI Rima F Kaddurah-Daouk · 2019 to 2026
$54.1MThe UCSD Microbiome and Metagenomics Center (Summit Supplement)U24DK131617 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Jack Anthony Gilbert, ROB KNIGHT · 2022 to 2026
$15.3MMapping host-microbe-metabolite interactions in 3D to find diet-derived enhancers of immunityDP1AT010885 · NCCIH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI KNIGHT, ROB · 2019 to 2023
$5.5MBiology-aware machine learning methods for characterizing microbiome genotype and phenotypeR35GM142725 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MIR ARABBAYGI, SIAVASH · 2021 to 2025
$1.9MNational Science Foundation (NSF) RAPID 20385.09National Science Foundation (NSF) XSEDE BIO210103NCCIH NIH HHS DP1 AT010885NIA NIH HHS U19 AG063744NIA NIH HHS U24 AG021886NIDDK NIH HHS U24 DK131617NIGMS NIH HHS R35 GM142725U.S. Department of Health & Human Services | National Institutes of Health (NIH) 1R35GM142725U.S. Department of Health & Human Services | National Institutes of Health (NIH) DP1-AT010885U.S. Department of Health & Human Services | National Institutes of Health (NIH) U19AG063744U.S. Department of Health & Human Services | National Institutes of Health (NIH) U24DK131617
Abstract
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.
Indexed as
MetagenomicsPhylogenyRNA, Ribosomal, 16SBacteriaDatabases, GeneticMetagenomeRNA, Ribosomal, 16S
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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.