A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

Simone Zuffa; Robin Schmid; Anelize Bauermeister; Paulo Wender P Gomes; Andres M Caraballo-Rodriguez; Yasin El Abiead; Allegra T Aron; Emily C Gentry; Jasmine Zemlin; Michael J Meehan; Nicole E Avalon; Robert H Cichewicz; Ekaterina Buzun; Marvic Carrillo Terrazas; Chia-Yun Hsu; Renee Oles; Adriana Vasquez Ayala; Jiaqi Zhao; Hiutung Chu; Mirte C M Kuijpers; Sara L Jackrel; Fidele Tugizimana; Lerato Pertunia Nephali; Ian A Dubery; Ntakadzeni Edwin Madala; Eduarda Antunes Moreira; Leticia Veras Costa-Lotufo; Norberto Peporine Lopes; Paula Rezende-Teixeira; Paula C Jimenez; Bipin Rimal; Andrew D Patterson; Matthew F Traxler; Rita de Cassia Pessotti; Daniel Alvarado-Villalobos; Giselle Tamayo-Castillo; Priscila Chaverri; Efrain Escudero-Leyva; Luis-Manuel Quiros-Guerrero; Alexandre Jean Bory; Juliette Joubert; Adriano Rutz; Jean-Luc Wolfender; Pierre-Marie Allard; Andreas Sichert; Sammy Pontrelli; Benjamin S Pullman; Nuno Bandeira; William H Gerwick; Katia Gindro; Josep Massana-Codina; Berenike C Wagner; Karl Forchhammer; Daniel Petras; Nicole Aiosa; Neha Garg; Manuel Liebeke; Patric Bourceau; Kyo Bin Kang; Henna Gadhavi; Luiz Pedro Sorio de Carvalho; Mariana Silva Dos Santos; Alicia Isabel Pérez-Lorente; Carlos Molina-Santiago; Diego Romero; Raimo Franke; Mark Brönstrup; Arturo Vera Ponce de León; Phillip Byron Pope; Sabina Leanti La Rosa; Giorgia La Barbera; Henrik M Roager; Martin Frederik Laursen; Fabian Hammerle; Bianka Siewert; Ursula Peintner; Cuauhtemoc Licona-Cassani; Lorena Rodriguez-Orduña; Evelyn Rampler; Felina Hildebrand; Gunda Koellensperger; Harald Schoeny; Katharina Hohenwallner; Lisa Panzenboeck; Rachel Gregor; Ellis Charles O'Neill; Eve Tallulah Roxborough; Jane Odoi; Nicole J Bale; Su Ding; Jaap S Sinninghe Damsté; Xueli Li Guan; Jerry J Cui; Kou-San Ju; Denise Brentan Silva; Fernanda Motta Ribeiro Silva; Gilvan Ferreira da Silva; Hector H F Koolen; Carlismari Grundmann; Jason A Clement; Hosein Mohimani; Kirk Broders; Kerry L McPhail; Sidnee E Ober-Singleton; Christopher M Rath; Daniel McDonald; Rob Knight; Mingxun Wang; Pieter C Dorrestein

doi:10.21203/rs.3.rs-3189768/v1

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

Res Sq [Preprint]. 2023 Aug 3:rs.3.rs-3189768. doi: 10.21203/rs.3.rs-3189768/v1.

Authors

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 Patterson¹⁸, Matthew F Traxler¹⁹, Rita de Cassia Pessotti¹⁹, Daniel Alvarado-Villalobos²⁰, Giselle Tamayo-Castillo^{20

21}, Priscila Chaverri^{22

23

24}, Efrain Escudero-Leyva²⁵, Luis-Manuel Quiros-Guerrero^{26

27}, Alexandre Jean Bory^{26

27}, Juliette Joubert^{26

27}, Adriano Rutz^{26

27

28}, Jean-Luc Wolfender^{26

27}, Pierre-Marie Allard^{29

26

27}, Andreas Sichert²⁸, Sammy Pontrelli²⁸, Benjamin S Pullman³⁰, Nuno Bandeira^{30

1}, William H Gerwick^{31

1}, Katia Gindro³², Josep Massana-Codina³², Berenike C Wagner³³, Karl Forchhammer³³, Daniel Petras³⁴, Nicole Aiosa³⁵, Neha Garg^{35

36}, Manuel Liebeke³⁷, Patric Bourceau³⁷, Kyo Bin Kang³⁸, Henna Gadhavi^{39

40}, Luiz Pedro Sorio de Carvalho^{39

41}, Mariana Silva Dos Santos⁴², Alicia Isabel Pérez-Lorente⁴³, Carlos Molina-Santiago⁴³, Diego Romero⁴³, Raimo Franke⁴⁴, Mark Brönstrup^{44

45}, Arturo Vera Ponce de León⁴⁶, Phillip Byron Pope^{47

46}, Sabina Leanti La Rosa⁴⁶, Giorgia La Barbera⁴⁸, Henrik M Roager⁴⁸, Martin Frederik Laursen⁴⁹, Fabian Hammerle⁵⁰, Bianka Siewert⁵⁰, Ursula Peintner⁵¹, Cuauhtemoc Licona-Cassani⁵², Lorena Rodriguez-Orduña⁵², Evelyn Rampler⁵³, Felina Hildebrand^{53

54}, Gunda Koellensperger^{53

55}, Harald Schoeny⁵³, Katharina Hohenwallner^{53

54}, Lisa Panzenboeck^{53

54}, Rachel Gregor⁵⁶, Ellis Charles O'Neill⁵⁷, Eve Tallulah Roxborough⁵⁷, Jane Odoi⁵⁸, Nicole J Bale⁵⁹, Su Ding⁵⁹, Jaap S Sinninghe Damsté⁵⁹, Xueli Li Guan⁶⁰, Jerry J Cui⁶¹, Kou-San Ju^{61

62

63

64}, Denise Brentan Silva⁶⁵, Fernanda Motta Ribeiro Silva⁶⁵, Gilvan Ferreira da Silva⁶⁶, Hector H F Koolen⁶⁷, Carlismari Grundmann⁶⁸, Jason A Clement⁶⁹, Hosein Mohimani⁷⁰, Kirk Broders⁷¹, Kerry L McPhail⁷², Sidnee E Ober-Singleton⁷³, Christopher M Rath⁷⁴, Daniel McDonald⁷⁵, Rob Knight^{75

30

76}, Mingxun Wang⁷⁷, Pieter C Dorrestein^{1

2}

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States.
² Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States.
³ Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil.
⁴ Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, United States.
⁵ Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, United States.
⁶ Center for Microbiome Innovation, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States.
⁷ Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, United States.
⁸ Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States.
⁹ Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States.
¹⁰ Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States.
¹¹ Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States.
¹² Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa.
¹³ International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, 178 Montecasino Boulevard, Fourways, Johannesburg, Gauteng, 2191, South Africa.
¹⁴ Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Private Bag X5050, Thohoyandou, Limpopo, 950, South Africa.
¹⁵ Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil.
¹⁶ Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Rua Carvalho de Mendonça, 144, Santos, SP, 11070-100, Brazil.
¹⁷ Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 319 Life Sciences Building, University Park, PA, 16802, United States.
¹⁸ Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 320 Life Sciences Building, University Park, PA, 16802, United States.
¹⁹ Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, 311 Koshland Hall, Berkeley, CA, 94270, United States.
²⁰ Metabolomics & Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica.
²¹ Escuela de Química, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica.
²² Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) & Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica.
²³ Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica.
²⁴ Department of Natural Sciences, Bowie State University, Bowie, Maryland, 20715, United States.
²⁵ Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica.
²⁶ School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland.
²⁷ Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland.
²⁸ Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland.
²⁹ Department of Biology, University of Fribourg, Chemin du Musée, 10, Fribourg, FR, 1700, Switzerland.
³⁰ Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States.
³¹ Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States.
³² Plant Protection, Mycology group, Agroscope, Rte de Duillier, 50, Nyon, VD, 1260, Switzerland.
³³ Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, Tuebingen, 72076, Germany.
³⁴ Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Auf der Morgenstelle 24, Tuebingen, 72076, Germany.
³⁵ School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States.
³⁶ Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, United States.
³⁷ Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany.
³⁸ Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Cheongpa-ro 47 gil 100, Seoul, 04310, Korea.
³⁹ Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
⁴⁰ King's College London, Strand, London, WC2R 2LS, UK.
⁴¹ Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 110 Scripps Way, Jupiter, FL, 33458, United States.
⁴² Metabolomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
⁴³ 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), Málaga, Málaga, 29071, Spain.
⁴⁴ Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany.
⁴⁵ German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, 38124, Germany.
⁴⁶ Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway.
⁴⁷ Faculty of Biosciences, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway.
⁴⁸ Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, Frederiksberg, 1958, Denmark.
⁴⁹ National Food Institute, Technical University of Denmark, Kemitorvet B202, Lyngby, 2800, Denmark.
⁵⁰ Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria.
⁵¹ Department of Microbiology, University of Innsbruck, Technikerstr. 25, Innsbruck, 6020, Austria.
⁵² Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon, 64849, Mexico.
⁵³ Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria.
⁵⁴ Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria.
⁵⁵ Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14,, Vienna, 1090, Austria.
⁵⁶ Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02142, United States.
⁵⁷ School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK.
⁵⁸ Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG72RD, UK.
⁵⁹ Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands.
⁶⁰ Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, Singapore, 636921, Singapore.
⁶¹ Department of Microbiology, College of Arts and Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States.
⁶² Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States.
⁶³ Center for Applied Plant Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States.
⁶⁴ Infectious Diseases Institute, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States.
⁶⁵ Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Av. Costa e Silva, s/n, Campo Grande, MS, 79070-900, Brazil.
⁶⁶ Embrapa Amazônia Ocidental, AM-010 Roadway, Manaus, AM, 69010-970, Brazil.
⁶⁷ Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, 1777 Carvalho Leal Avenue, Manaus, AM, 69065-001, Brazil.
⁶⁸ Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil.
⁶⁹ Baruch S. Blumberg Institute, 3805 Old Easton Rd., Doylestown, PA, 18902, United States.
⁷⁰ Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, United States.
⁷¹ USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL, 61604, United States.
⁷² Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Weniger Hall, room 341, Corvallis, OR, 97331, United States.
⁷³ Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, 1255 E 13th Ave, Basement, Eugene, OR, 97402, United States.
⁷⁴ 1480 64th St #300, Emeryville, CA, 94608, United States.
⁷⁵ Department of Pediatrics, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States.
⁷⁶ Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States.
⁷⁷ Department of Computer Science and Engineering, University of California Riverside, 900 University Ave., Riverside, CA, 92521, United States.

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 microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms' role in ecology and human health.

Keywords: bacteria; fungi; metabolomics; microbiome; search tool.

Publication types

Preprint

Abstract

Publication types

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