ArticlebioRxiv : the preprint server for biology2026
Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data.
Abstract readPreprint
In one paragraph
Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
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.
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.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
75 authors.
Helena Mannochio-RussoSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-4961-2353
Wilhan D Gonçalves NunesSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-0609-6678
Shipei XingSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-6227-6959
Fernanda de OliveiraSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-9441-4113
Andrés Mauricio Caraballo-RodríguezSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-5499-2728
Paulo Wender Portal GomesSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Vincent Charron-LamoureuxSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Julius AgongoSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Nicole E AvalonDepartment of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.ORCID 0000-0003-3588-892X
Tammy BuiSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Lucia CanceladaScripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.ORCID 0000-0002-7438-9587
Marc G ChevretteDepartment of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA.ORCID 0000-0002-7209-0717
Andrés CumsilleDepartment of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA.ORCID 0000-0003-2087-7435
Moysés B de AraújoGrupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, 69065-001 Manaus-AM, Brazil.ORCID 0000-0003-3837-1440
Marilyn De GraeveSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-6916-401X
Victoria DeleraySkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0009-0002-3201-2578
Mohamed S DoniaDepartment of Molecular Biology, Princeton University, Princeton, NJ, USA.ORCID 0000-0002-9604-2912
Mutsawashe B DzvetaResearch Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
Yasin El AbieadSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-4392-7706
Ronald J EllisDepartment of Neurosciences, University of California San Diego, San Diego, CA 92093, USA.
Donald FranklinDepartment of Psychiatry, University of California San Diego, San Diego, CA 92093, USA.
Neha GargSchool of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.ORCID 0000-0002-2760-7123
Harsha GoudaSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-4511-5875
Claude Y Hamany DjandeResearch Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.ORCID 0000-0003-2077-8699
Anastasia HiskiaInstitute of Nanoscience & Nanotechnology, NCSR Demokritos, Athens, Greece.ORCID 0000-0002-3674-3223
Benjamin N HoSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Chambers C HughesDepartment of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, 72076 Tübingen, Germany.
Sunghoon HwangDepartment of Molecular Biology, Princeton University, Princeton, NJ, USA.
Sofia IliakopoulouAquOmixLab, Department of Water Quality Control, Athens Water Supply & Sewerage Company (EYDAP SA), Athens, Greece.
Jennifer E IudicelloDepartment of Psychiatry, University of California San Diego, San Diego, CA 92093, USA.ORCID 0000-0003-2854-7684
Alan K JarmuschSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-2228-6308
Triantafyllos KaloudisAquOmixLab, Department of Water Quality Control, Athens Water Supply & Sewerage Company (EYDAP SA), Athens, Greece.ORCID 0000-0003-1909-0256
Irina KoesterScripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.ORCID 0000-0002-1571-882X
Robert KonkelDepartment of Marine Biology and Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Gdynia, Poland.
Hector H F KoolenGrupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, 69065-001 Manaus-AM, Brazil.
Kine Eide KvitneSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-8118-7660
Sabina Leanti La RosaFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway.ORCID 0000-0003-3527-8101
Anny LamSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Santosh LamichhaneInstitute of Biomedicine, Faculty of Medicine, & Turku Clinical Microbiome Bank, Clinical Microbiology & Microbe Centre, Turku University Hospital and University of Turku and Wellbeing Services County of Southwest Finland,Turku, Finland.
Motseoa LephatsiResearch Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
Scott LetendreHIV Neurobehavioral Research Program, University of California San Diego, San Diego, CA 92093, USA.ORCID 0000-0003-3490-4975
Sarolt MagyariSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-4573-0915
Hanna Mazur-MarzecDepartment of Marine Biology and Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Gdynia, Poland.
Daniel McDonaldDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-0876-9060
Ipsita MohantySkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-5311-6443
Mónica Monge-LoríaSchool of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.ORCID 0009-0006-8544-0196
David J MooreDepartment of Psychiatry, University of California San Diego, San Diego, CA 92093, USA.ORCID 0000-0001-9699-318X
Thiago André Moura VeigaInstitute of Environmental, Chemical and Pharmaceutical Sciences, Department of Chemistry, Federal University of São Paulo, Diadema, 09972-270, Brazil.ORCID 0000-0002-1377-158X
Musiwalo S MulaudziResearch Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
Lerato NephaliDepartment of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
Griffith NguyenSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Martin OrsághInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.ORCID 0000-0003-1145-6137
Abubaker PatanSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-1415-7829
Tomáš PluskalInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.ORCID 0000-0002-6940-3006
Phillip B PopeFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway.ORCID 0000-0002-2067-4059
Lívia Soman de MedeirosInstitute of Environmental, Chemical and Pharmaceutical Sciences, Department of Chemistry, Federal University of São Paulo, Diadema, 09972-270, Brazil.ORCID 0000-0001-8743-3340
Paolo StinconeUniversity of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany.ORCID 0000-0002-2214-6655
Andrej TekelInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.ORCID 0009-0005-7523-149X
Sydney ThomasSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Ralph R TorresScripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.ORCID 0000-0002-5816-6068
Shirley M TsunodaSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-3974-8038
Fidele TugizimanaResearch Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.ORCID 0000-0001-8172-6599
Martijn van FaassenDepartment of Laboratory Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands.
Felipe Vasquez-CastroSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-2591-7117
Giovanni A VitaleUniversity of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany.ORCID 0000-0002-7143-6317
Berenike C WagnerUniversity of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany.ORCID 0000-0002-7691-7531
Crystal X WangDepartment of Psychiatry, University of California San Diego, San Diego, CA 92093, USA.ORCID 0000-0002-0525-809X
Sevasti-Kiriaki ZervouInstitute of Nanoscience & Nanotechnology, NCSR Demokritos, Athens, Greece.ORCID 0000-0003-3049-9351
Haoqi Nina ZhaoSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-3908-630X
Simone ZuffaSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-7237-3402
Daniel PetrasUniversity of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany.
Laura-Isobel McCallDepartment of Chemistry and Biochemistry, San Diego State University, San Diego, California, USA.ORCID 0000-0002-1243-8953
Rob KnightDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-0975-9019
Mingxun WangDepartment of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA.
Pieter C DorresteinSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Funding
STRUCTURAL NEUROIMAGING COREP30MH062512 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Jessica Lynette Montoya · 2001 to 2026
$50.4MMass Spectrometry-based Untargeted MetabolomicsZICES103363 · NIEHS · NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES · PI JARMUSCH, ALAN · 2021 to 2025
$6.5MBiopsychosocial Phenotypes and Potential Mechanisms in CHARTERR01MH125720 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ELLIS, RONALD J., LETENDRE, SCOTT L · 2021 to 2025
$3.7MCollaborative Microbial Metabolite CenterU24DK133658 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PIETER C DORRESTEIN · 2022 to 2026
$2.9MA Genomic Approach to Discovering Novel Cathepsin Inhibitors from CyanobacteriaF32AT011475 · NCCIH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI AVALON, NICOLE ELIZABETH · 2022 to 2024
$218kCNS HIV ANTI-RETROVIRAL THERAPY EFFECTS RESEARCH /CHARTER/ -278022005-278022005N01MH022005 · NIMH · UNIVERSITY OF CA -SAN DIEGO · PI GRANT, IGOR · 2003 to 2006
–Intramural NIH HHS ZIC ES103363NCCIH NIH HHS F32 AT011475NIDDK NIH HHS U24 DK133658NIMH NIH HHS N01 MH022005NIMH NIH HHS P30 MH062512NIMH NIH HHS R01 MH125720
Abstract
Microbial metabolites play a critical role in regulating ecosystems, including the human body and its microbiota. However, understanding the physiologically relevant role of these molecules, especially through liquid chromatography tandem mass spectrometry (LC-MS/MS)-based untargeted metabolomics, poses significant challenges and often requires manual parsing of a large amount of literature, databases, and webpages. To address this gap, we established the Collaborative Microbial Metabolite Center knowledgebase (CMMC-KB), a platform that fosters collaborative efforts within the scientific community to curate knowledge about microbial metabolites. The CMMC-KB aims to collect comprehensive information about microbial molecules originating from microbial biosynthesis, drug metabolism, exposure-related molecules, food, host-derived molecules, and, whenever available, their known activities. Molecules from other sources, including host-produced, dietary, and pharmaceutical compounds, are also included. By enabling direct integration of this knowledgebase with downstream analytical tools, including molecular networking, we can deepen insights into microbiota and their metabolites, ultimately advancing our understanding of microbial ecosystems.
Identifiers
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.