microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

Simone Zuffa^#^{1

2}, Robin Schmid^#^{1

2}, Anelize Bauermeister^#^{1

2

3}, Paulo Wender P Gomes^{1

2}, Andres M Caraballo-Rodriguez^{1

2}, Yasin El Abiead^{1

2}, Allegra T Aron⁴, Emily C Gentry⁵, Jasmine Zemlin^{1

6}, Michael J Meehan¹, Nicole E Avalon⁷, Robert H Cichewicz⁸, Ekaterina Buzun⁹, Marvic Carrillo Terrazas⁹, Chia-Yun Hsu⁹, Renee Oles⁹, Adriana Vasquez Ayala⁹, Jiaqi Zhao⁹, Hiutung Chu^{9

10}, Mirte C M Kuijpers¹¹, Sara L Jackrel¹¹, Fidele Tugizimana^{12

13}, Lerato Pertunia Nephali¹², Ian A Dubery¹², Ntakadzeni Edwin Madala¹⁴, Eduarda Antunes Moreira¹⁵, Leticia Veras Costa-Lotufo³, Norberto Peporine Lopes¹⁵, Paula Rezende-Teixeira³, Paula C Jimenez¹⁶, Bipin Rimal¹⁷, Andrew D Patterson¹⁷, Matthew F Traxler¹⁸, Rita de Cassia Pessotti¹⁸, Daniel Alvarado-Villalobos¹⁹, Giselle Tamayo-Castillo^{19

20}, Priscila Chaverri^{21

22

23}, Efrain Escudero-Leyva²⁴, Luis-Manuel Quiros-Guerrero^{25

26}, Alexandre Jean Bory^{25

26}, Juliette Joubert^{25

26}, Adriano Rutz^{25

26

27}, Jean-Luc Wolfender^{25

26}, Pierre-Marie Allard^{25

26

28}, Andreas Sichert²⁷, Sammy Pontrelli²⁷, Benjamin S Pullman²⁹, Nuno Bandeira^{1

29}, William H Gerwick^{1

7}, Katia Gindro³⁰, Josep Massana-Codina³⁰, Berenike C Wagner³¹, Karl Forchhammer³¹, Daniel Petras³², Nicole Aiosa³³, Neha Garg^{33

34}, Manuel Liebeke^{35

36}, Patric Bourceau³⁵, Kyo Bin Kang³⁷, Henna Gadhavi^{38

39}, Luiz Pedro Sorio de Carvalho^{38

40}, Mariana Silva Dos Santos⁴¹, Alicia Isabel Pérez-Lorente⁴², Carlos Molina-Santiago⁴², Diego Romero⁴², Raimo Franke⁴³, Mark Brönstrup^{43

44}, Arturo Vera Ponce de León⁴⁵, Phillip Byron Pope^{45

46}, Sabina Leanti La Rosa^{45

46}, Giorgia La Barbera⁴⁷, Henrik M Roager⁴⁷, Martin Frederik Laursen⁴⁸, Fabian Hammerle⁴⁹, Bianka Siewert⁴⁹, Ursula Peintner⁵⁰, Cuauhtemoc Licona-Cassani⁵¹, Lorena Rodriguez-Orduña⁵¹, Evelyn Rampler⁵², Felina Hildebrand^{52

53}, Gunda Koellensperger^{52

54}, Harald Schoeny⁵², Katharina Hohenwallner^{52

53}, Lisa Panzenboeck^{52

53}, Rachel Gregor⁵⁵, Ellis Charles O'Neill⁵⁶, Eve Tallulah Roxborough⁵⁶, Jane Odoi⁵⁷, Nicole J Bale⁵⁸, Su Ding⁵⁸, Jaap S Sinninghe Damsté⁵⁸, Xue Li Guan⁵⁹, Jerry J Cui⁶⁰, Kou-San Ju^{60

61

62

63}, Denise Brentan Silva⁶⁴, Fernanda Motta Ribeiro Silva⁶⁴, Gilvan Ferreira da Silva⁶⁵, Hector H F Koolen⁶⁶, Carlismari Grundmann⁶⁷, Jason A Clement⁶⁸, Hosein Mohimani⁶⁹, Kirk Broders⁷⁰, Kerry L McPhail⁷¹, Sidnee E Ober-Singleton⁷², Christopher M Rath⁷³, Daniel McDonald⁷⁴, Rob Knight^{29

74

75}, Mingxun Wang⁷⁶, Pieter C Dorrestein^{77

78}

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
² Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
³ Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
⁴ Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA.
⁵ Department of Chemistry, Virginia Tech, Blacksburg, VA, USA.
⁶ Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA.
⁷ Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
⁸ Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, Norman, OK, USA.
⁹ Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA.
¹⁰ Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, San Diego, CA, USA.
¹¹ Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA.
¹² Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa.
¹³ International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, Johannesburg, South Africa.
¹⁴ Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Thohoyandou, South Africa.
¹⁵ Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
¹⁶ Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Santos, Brazil.
¹⁷ Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA.
¹⁸ Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA.
¹⁹ Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica.
²⁰ Escuela de Química, Universidad de Costa Rica, San José, Costa Rica.
²¹ Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica.
²² Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica.
²³ Department of Natural Sciences, Bowie State University, Bowie, MD, USA.
²⁴ Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica.
²⁵ School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
²⁶ Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland.
²⁷ Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
²⁸ Department of Biology, University of Fribourg, Fribourg, Switzerland.
²⁹ Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
³⁰ Plant Protection, Mycology group, Agroscope, Nyon, Switzerland.
³¹ Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany.
³² Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tuebingen, Tuebingen, Germany.
³³ School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
³⁴ Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
³⁵ Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany.
³⁶ Department for Metabolomics, Kiel University, Kiel, Germany.
³⁷ Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Korea.
³⁸ Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK.
³⁹ King's College London, London, UK.
⁴⁰ Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA.
⁴¹ Metabolomics Science Technology Platform, The Francis Crick Institute, London, UK.
⁴² Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain.
⁴³ Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
⁴⁴ German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany.
⁴⁵ Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
⁴⁶ Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
⁴⁷ Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark.
⁴⁸ National Food Institute, Technical University of Denmark, Lyngby, Denmark.
⁴⁹ Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria.
⁵⁰ Department of Microbiology, University of Innsbruck, Innsbruck, Austria.
⁵¹ Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico.
⁵² Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
⁵³ Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria.
⁵⁴ Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria.
⁵⁵ Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁵⁶ School of Chemistry, University of Nottingham, Nottingham, UK.
⁵⁷ Faculty of Engineering, University of Nottingham, Nottingham, UK.
⁵⁸ Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands.
⁵⁹ Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
⁶⁰ Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA.
⁶¹ Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA.
⁶² Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA.
⁶³ Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.
⁶⁴ Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.
⁶⁵ Embrapa Amazônia Ocidental, Manaus, Brazil.
⁶⁶ Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil.
⁶⁷ Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.
⁶⁸ Baruch S. Blumberg Institute, Doylestown, PA, USA.
⁶⁹ Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
⁷⁰ USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, USA.
⁷¹ Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA.
⁷² Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, Eugene, OR, USA.
⁷³ , Emeryville, CA, USA.
⁷⁴ Department of Pediatrics, University of California San Diego, San Diego, CA, USA.
⁷⁵ Department of Bioengineering, University of California San Diego, San Diego, CA, USA.
⁷⁶ Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA.
⁷⁷ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA. pdorrestein@health.ucsd.edu.
⁷⁸ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA. pdorrestein@health.ucsd.edu.

^# Contributed equally.

PMID: 38316926
PMCID: PMC10847041
DOI: 10.1038/s41564-023-01575-9

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

Simone Zuffa et al. Nat Microbiol. 2024 Feb.

. 2024 Feb;9(2):336-345.

doi: 10.1038/s41564-023-01575-9. Epub 2024 Feb 5.

Authors

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
² Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
³ Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
⁴ Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA.
⁵ Department of Chemistry, Virginia Tech, Blacksburg, VA, USA.
⁶ Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA.
⁷ Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
⁸ Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, Norman, OK, USA.
⁹ Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA.
¹⁰ Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, San Diego, CA, USA.
¹¹ Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA.
¹² Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa.
¹³ International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, Johannesburg, South Africa.
¹⁴ Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Thohoyandou, South Africa.
¹⁵ Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
¹⁶ Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Santos, Brazil.
¹⁷ Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA.
¹⁸ Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA.
¹⁹ Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica.
²⁰ Escuela de Química, Universidad de Costa Rica, San José, Costa Rica.
²¹ Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica.
²² Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica.
²³ Department of Natural Sciences, Bowie State University, Bowie, MD, USA.
²⁴ Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica.
²⁵ School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
²⁶ Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland.
²⁷ Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
²⁸ Department of Biology, University of Fribourg, Fribourg, Switzerland.
²⁹ Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
³⁰ Plant Protection, Mycology group, Agroscope, Nyon, Switzerland.
³¹ Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany.
³² Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tuebingen, Tuebingen, Germany.
³³ School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
³⁴ Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
³⁵ Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany.
³⁶ Department for Metabolomics, Kiel University, Kiel, Germany.
³⁷ Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Korea.
³⁸ Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK.
³⁹ King's College London, London, UK.
⁴⁰ Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA.
⁴¹ Metabolomics Science Technology Platform, The Francis Crick Institute, London, UK.
⁴² Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain.
⁴³ Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
⁴⁴ German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany.
⁴⁵ Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
⁴⁶ Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
⁴⁷ Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark.
⁴⁸ National Food Institute, Technical University of Denmark, Lyngby, Denmark.
⁴⁹ Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria.
⁵⁰ Department of Microbiology, University of Innsbruck, Innsbruck, Austria.
⁵¹ Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico.
⁵² Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
⁵³ Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria.
⁵⁴ Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria.
⁵⁵ Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁵⁶ School of Chemistry, University of Nottingham, Nottingham, UK.
⁵⁷ Faculty of Engineering, University of Nottingham, Nottingham, UK.
⁵⁸ Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands.
⁵⁹ Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
⁶⁰ Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA.
⁶¹ Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA.
⁶² Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA.
⁶³ Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.
⁶⁴ Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.
⁶⁵ Embrapa Amazônia Ocidental, Manaus, Brazil.
⁶⁶ Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil.
⁶⁷ Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.
⁶⁸ Baruch S. Blumberg Institute, Doylestown, PA, USA.
⁶⁹ Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
⁷⁰ USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, USA.
⁷¹ Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA.
⁷² Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, Eugene, OR, USA.
⁷³ , Emeryville, CA, USA.
⁷⁴ Department of Pediatrics, University of California San Diego, San Diego, CA, USA.
⁷⁵ Department of Bioengineering, University of California San Diego, San Diego, CA, USA.
⁷⁶ Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA.
⁷⁷ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA. pdorrestein@health.ucsd.edu.
⁷⁸ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA. pdorrestein@health.ucsd.edu.

^# Contributed equally.

PMID: 38316926
PMCID: PMC10847041
DOI: 10.1038/s41564-023-01575-9

Abstract

microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.

PubMed Disclaimer

Conflict of interest statement

P.C.D. is an advisor to Cybele, consulted for MSD animal health in 2023 and is a co-founder and scientific advisor for Ometa Labs, Arome and Enveda, with previous approval from the University of California, San Diego. M.W. is a co-founder of Ometa labs. There are no known conflicts of interest in this work by the USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. R.K. is a scientific advisory board member and consultant for BiomeSense, Inc., where he has equity and receives income. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict-of-interest policies. The other authors declare no competing interests.

Figures

**Fig. 1. The microbeMASST search tool and reference database.**
a, Community contributions of data and knowledge to GNPS, ReDU and MassIVE from 2014 to 2022 were used to generate the microbeMASST reference database. In addition, a public invitation to deposit data in June 2022 resulted in the further deposition of LC–MS/MS files from 25 different laboratories from 15 different countries across the globe, leading to the curation of a total of 60,781 LC–MS/MS files of microbial monoculture extracts. b, microbeMASST comprises 1,858 unique lineages across three different domains of life mapped to 541 unique strains, 1,336 species, 539 genera, 264 families, 109 orders, 41 classes and 16 phyla. c, Examples of medically relevant small molecules known to be produced by bacteria or fungi. Lovastatin, a cholesterol-lowering drug originally isolated from *Aspergillus* genus; salinosporamide A, a Phase III candidate to treat glioblastoma produced by *Salinispora tropica*; and commendamide, a human G-protein-coupled receptor agonist. d, microbeMASST search outputs of the three different molecules of interest confirm that they were exclusively found in monocultures of the only known producers. Pie charts display the proportion of MS/MS matches found in the deposited reference database. Blue indicates a match with a monoculture, while yellow represents a non-match. Searches were performed using MS/MS spectra deposited in the GNPS reference library: lovastatin (CCMSLIB00005435737), salinosporamide A (CCMSLIB00010013003) and commendamide (CCMSLIB00004679239). GNPS, ReDU and microbeMASST logos reproduced under a Creative Commons license CC BY 4.0.

**Fig. 2. microbeMASST can identify microbial MS/MS spectra within mouse and human datasets.**
a, Workflow to extract microbial MS/MS spectra from biochemical profiles of 29 different tissues and biofluids of SPF mice that are not observed in GF mice. The MS/MS spectra unique to SPF mice (10,047) were searched with microbeMASST. A total of 3,262 MS/MS spectra had a match; those MS/MS also matching human cell lines were removed, leaving a total of 2,425 putative microbial MS/MS spectra (see Methods to download .mgf file). b, The presence of the 2,425 MS/MS spectra was evaluated in an additional animal study looking at antibiotic usage. A total of 512 MS/MS spectra, out of the 621 overlapping, were exclusively found in animals not receiving antibiotics. c, UpSet plot of the distribution of the detected MS/MS spectra (512) across bacterial phyla. Terpenoids were more commonly observed across phyla, while amino acids and peptides appeared to be more phylum specific. d, The 512 MS/MS spectra were searched in human datasets and 455 were found to have a match. These MS/MS spectra were present in both healthy individuals and individuals affected by different diseases. e, Most of the MS/MS spectra (n = 411) matched faecal samples (n = 110,973 matches), followed by blood, oral cavity, breast milk, urine and several other organs. CSF, cerebral spinal fluid; COVID-19, coronavirus disease 2019; HIV, human immunodeficiency virus; PBI, primary bacterial infectious disease; SD, sleep disorder; AD, Alzheimer’s disease; IS, ischaemic stroke; KD, Kawasaki disease; IBD, inflammatory bowel disease; T2D, type II diabetes. GNPS and and microbeMASST logos reproduced under a Creative Commons license CC BY 4.0; SIRIUS logo reproduced under a Creative Commons license CC BY 4.0-ND.

See this image and copyright information in PMC

Update of

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data.
Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SL, Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Si… See abstract for full author list ➔ Zuffa S, et al. Res Sq [Preprint]. 2023 Aug 3:rs.3.rs-3189768. doi: 10.21203/rs.3.rs-3189768/v1. Res Sq. 2023. Update in: Nat Microbiol. 2024 Feb;9(2):336-345. doi: 10.1038/s41564-023-01575-9. PMID: 37577622 Free PMC article. Updated. Preprint.

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microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

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microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

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