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[Preprint]. 2026 Jan 26:2026.01.24.701521.

doi: 10.64898/2026.01.24.701521.

Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data

Helena Mannochio-Russo¹, Wilhan D Gonçalves Nunes¹, Shipei Xing¹, Fernanda de Oliveira^{1

2}, Andrés Mauricio Caraballo-Rodríguez¹, Paulo Wender Portal Gomes^{1

3}, Vincent Charron-Lamoureux¹, Julius Agongo¹, Nicole E Avalon^{4

5

6}, Tammy Bui¹, Lucia Cancelada^{7

8}, Marc G Chevrette^{9

10}, Andrés Cumsille^{9

10}, Moysés B de Araújo^{11

12}, Marilyn De Graeve^{1

13}, Victoria Deleray¹, Mohamed S Donia¹⁴, Mutsawashe B Dzveta¹⁵, Yasin El Abiead¹, Ronald J Ellis^{16

17}, Donald Franklin Jr^{18

17}, Neha Garg^{19

20}, Harsha Gouda¹, Claude Y Hamany Djande¹⁵, Anastasia Hiskia²¹, Benjamin N Ho¹, Chambers C Hughes^{22

23

24}, Sunghoon Hwang¹⁴, Sofia Iliakopoulou²⁵, Jennifer E Iudicello^{18

17}, Alan K Jarmusch^{1

26}, Triantafyllos Kaloudis^{25

21}, Irina Koester^{7

27}, Robert Konkel²⁸, Hector H F Koolen¹¹, Kine Eide Kvitne¹, Sabina Leanti La Rosa²⁹, Anny Lam¹, Santosh Lamichhane³⁰, Motseoa Lephatsi¹⁵, Scott Letendre^{17

31}, Sarolt Magyari^{1

32}, Hanna Mazur-Marzec²⁸, Daniel McDonald³³, Ipsita Mohanty¹, Mónica Monge-Loría¹⁹, David J Moore^{18

17}, Thiago André Moura Veiga³⁴, Musiwalo S Mulaudzi¹⁵, Lerato Nephali³⁵, Griffith Nguyen¹, Martin Orságh^{36

37}, Abubaker Patan¹, Tomáš Pluskal³⁶, Phillip B Pope^{29

38}, Lívia Soman de Medeiros³⁴, Paolo Stincone³⁹, Andrej Tekel^{36

37}, Sydney Thomas¹, Ralph R Torres⁷, Shirley M Tsunoda¹, Fidele Tugizimana¹⁵, Martijn van Faassen⁴⁰, Felipe Vasquez-Castro¹, Giovanni A Vitale³⁹, Berenike C Wagner³⁹, Crystal X Wang^{18

17}, Sevasti-Kiriaki Zervou²¹, Haoqi Nina Zhao¹, Simone Zuffa¹, Daniel Petras^{39

41}, Laura-Isobel McCall⁴², Rob Knight^{33

43

44

45

46

47}, Mingxun Wang⁴⁸, Pieter C Dorrestein^{1

49

50

51}

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
² Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo State, Brazil.
³ Amazon Integrated Metabolomics Center (CIMAZON), Institute of Natural and Exact Sciences, Federal University of Pará, Rua Augusto Corrêa, 01 - Guamá 66075-110, Belém, PA, Brazil.
⁴ Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.
⁵ Robert A.
⁶ Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
⁷ Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
⁸ Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
⁹ Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA.
¹⁰ Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA.
¹¹ Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, 69065-001 Manaus-AM, Brazil.
¹² Instituto de Ciências Exatas e Tecnologia, Universidade Federal do Amazonas, 69103-128 Itacoatiara-AM, Brazil.
¹³ Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
¹⁴ Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
¹⁵ Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
¹⁶ Department of Neurosciences, University of California San Diego, San Diego, CA 92093, USA.
¹⁷ HIV Neurobehavioral Research Program, University of California San Diego, San Diego, CA 92093, USA.
¹⁸ Department of Psychiatry, University of California San Diego, San Diego, CA 92093, USA.
¹⁹ School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.
²⁰ Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.
²¹ Institute of Nanoscience & Nanotechnology, NCSR Demokritos, Athens, Greece.
²² Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, 72076 Tübingen, Germany.
²³ Cluster of Excellence EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, 72076 Tübingen, Germany.
²⁴ German Center for Infection Research (DZIF), Partner Site Tübingen, 72706 Tübingen, Germany.
²⁵ AquOmixLab, Department of Water Quality Control, Athens Water Supply & Sewerage Company (EYDAP SA), Athens, Greece.
²⁶ National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
²⁷ Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
²⁸ Department of Marine Biology and Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Gdynia, Poland.
²⁹ Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway.
³⁰ Institute 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.
³¹ Department of Medicine, University of California San Diego, La Jolla, CA, USA.
³² Department of Chemistry, Simon Fraser University, 8888 University Drive,Burnaby, Canada.
³³ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
³⁴ Institute of Environmental, Chemical and Pharmaceutical Sciences, Department of Chemistry, Federal University of São Paulo, Diadema, 09972-270, Brazil.
³⁵ Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
³⁶ Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
³⁷ Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Albertov 6, 120 00 Prague 2, Czech Republic.
³⁸ The Centre for Microbiome Research, Queensland University of Technology, 4102, Woolloongabba, Australia.
³⁹ University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany.
⁴⁰ Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands.
⁴¹ Department of Biochemistry, University of California Riverside, Riverside, CA, USA.
⁴² Department of Chemistry and Biochemistry, San Diego State University, San Diego, California, USA.
⁴³ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
⁴⁴ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
⁴⁵ Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
⁴⁶ Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA.
⁴⁷ Hong Kong University of Science and Technology Jockey Club Institute for Advanced Study, Hong Kong SAR, China.
⁴⁸ Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA.
⁴⁹ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92093, USA.
⁵⁰ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
⁵¹ Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.

PMID: 41659575
PMCID: PMC12874021
DOI: 10.64898/2026.01.24.701521

Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data

Helena Mannochio-Russo et al. bioRxiv. 2026.

[Preprint]. 2026 Jan 26:2026.01.24.701521.

doi: 10.64898/2026.01.24.701521.

Authors

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
² Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo State, Brazil.
³ Amazon Integrated Metabolomics Center (CIMAZON), Institute of Natural and Exact Sciences, Federal University of Pará, Rua Augusto Corrêa, 01 - Guamá 66075-110, Belém, PA, Brazil.
⁴ Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.
⁵ Robert A.
⁶ Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
⁷ Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
⁸ Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
⁹ Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA.
¹⁰ Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA.
¹¹ Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, 69065-001 Manaus-AM, Brazil.
¹² Instituto de Ciências Exatas e Tecnologia, Universidade Federal do Amazonas, 69103-128 Itacoatiara-AM, Brazil.
¹³ Laboratory of Integrative Metabolomics, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
¹⁴ Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
¹⁵ Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
¹⁶ Department of Neurosciences, University of California San Diego, San Diego, CA 92093, USA.
¹⁷ HIV Neurobehavioral Research Program, University of California San Diego, San Diego, CA 92093, USA.
¹⁸ Department of Psychiatry, University of California San Diego, San Diego, CA 92093, USA.
¹⁹ School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.
²⁰ Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.
²¹ Institute of Nanoscience & Nanotechnology, NCSR Demokritos, Athens, Greece.
²² Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, 72076 Tübingen, Germany.
²³ Cluster of Excellence EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, 72076 Tübingen, Germany.
²⁴ German Center for Infection Research (DZIF), Partner Site Tübingen, 72706 Tübingen, Germany.
²⁵ AquOmixLab, Department of Water Quality Control, Athens Water Supply & Sewerage Company (EYDAP SA), Athens, Greece.
²⁶ National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
²⁷ Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
²⁸ Department of Marine Biology and Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Gdynia, Poland.
²⁹ Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway.
³⁰ Institute 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.
³¹ Department of Medicine, University of California San Diego, La Jolla, CA, USA.
³² Department of Chemistry, Simon Fraser University, 8888 University Drive,Burnaby, Canada.
³³ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
³⁴ Institute of Environmental, Chemical and Pharmaceutical Sciences, Department of Chemistry, Federal University of São Paulo, Diadema, 09972-270, Brazil.
³⁵ Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
³⁶ Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
³⁷ Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Albertov 6, 120 00 Prague 2, Czech Republic.
³⁸ The Centre for Microbiome Research, Queensland University of Technology, 4102, Woolloongabba, Australia.
³⁹ University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany.
⁴⁰ Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands.
⁴¹ Department of Biochemistry, University of California Riverside, Riverside, CA, USA.
⁴² Department of Chemistry and Biochemistry, San Diego State University, San Diego, California, USA.
⁴³ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
⁴⁴ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
⁴⁵ Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
⁴⁶ Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA.
⁴⁷ Hong Kong University of Science and Technology Jockey Club Institute for Advanced Study, Hong Kong SAR, China.
⁴⁸ Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA.
⁴⁹ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92093, USA.
⁵⁰ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
⁵¹ Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.

PMID: 41659575
PMCID: PMC12874021
DOI: 10.64898/2026.01.24.701521

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.

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Figures

**Figure 1.. Overview of the CMMC-KB capabilities and depositions.**
**(a)** Inputs accepted for community depositions and current numbers as of December 2025. **(b)** CMMC enrichment workflow in GNPS2, which annotates molecular networks (generated from Classical or Feature-Based Molecular Networking^,) by matching experimental spectra to the CMMC-KB and retrieving associated metadata. **(c)** Download options as MGF and TSV files, enabling reuse in third-party software and in-house workflows. **(d)** The CMMC-Dashboard is a web application that enables users to utilize outputs from the FBMN and CMMC enrichment workflows, along with uploaded metadata, to generate visualizations for exploring matches to the CMMC-KB (e.g., boxplots for statistical evaluation, structure cards, UpSet-style overviews, and microbeMASST integration). Distribution of the deposited compounds (December 2025) by **(e)** molecule source and **(f)** molecule origin. Icons were obtained from Bioicons.com.

**Figure 2.. Application of CMMC-KB enrichment to fecal metabolomics data from the American Gut Project.**
**(a)** Source distribution of metabolites matched to the CMMC-KB from a subset of the American Gut Project (n = 1,993 samples). The UpSet plot was generated using the CMMC-Dashboard. **(b)** Molecular network visualization with nodes colored by metabolite source annotation from the CMMC-KB. Each node represents a unique mass spectral feature, and edges connect features with similar MS/MS spectra (cosine similarity threshold set to 0.5). **(c-e)** Zoomed-in views of selected molecular networks with distinct source annotations. These subnetworks illustrate the tool’s capability to rapidly identify and visualize structurally related compounds sharing common sources within complex metabolomic datasets. The colors of the nodes in **b-e** match the upset plot colors in a.

See this image and copyright information in PMC

References

1. Quinn R. A. et al. Global chemical effects of the microbiome include new bile-acid conjugations. Nature 579, 123–129 (2020). - PMC - PubMed
1. Tremaroli V. & Bäckhed F. Functional interactions between the gut microbiota and host metabolism. Nature 489, 242–249 (2012). - PubMed
1. Oliphant K. & Allen-Vercoe E. Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health. Microbiome 7, 91 (2019). - PMC - PubMed
1. Hadadi N., Berweiler V., Wang H. & Trajkovski M. Intestinal microbiota as a route for micronutrient bioavailability. Curr. Opin. Endocr. Metab. Res. 20, 100285 (2021).
1. Wilson I. D. & Nicholson J. K. Gut microbiome interactions with drug metabolism, efficacy, and toxicity. Transl. Res. 179, 204–222 (2017). - PMC - PubMed

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This is a preprint.

Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data

Affiliations

Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data

Authors

Affiliations

Abstract

Figures

References

Publication types

LinkOut - more resources

Full Text Sources

Miscellaneous