1
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Wood PL, Le A, Palazzolo DL. Comparative Lipidomics of Oral Commensal and Opportunistic Bacteria. Metabolites 2024; 14:240. [PMID: 38668368 PMCID: PMC11052126 DOI: 10.3390/metabo14040240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
The oral cavity contains a vast array of microbes that contribute to the balance between oral health and disease. In addition, oral bacteria can gain access to the circulation and contribute to other diseases and chronic conditions. There are a limited number of publications available regarding the comparative lipidomics of oral bacteria and fungi involved in the construction of oral biofilms, hence our decision to study the lipidomics of representative oral bacteria and a fungus. We performed high-resolution mass spectrometric analyses (<2.0 ppm mass error) of the lipidomes from five Gram-positive commensal bacteria: Streptococcus oralis, Streptococcus intermedius, Streptococcus mitis, Streptococcus sanguinis, and Streptococcus gordonii; five Gram-positive opportunistic bacteria: Streptococcus mutans, Staphylococcus epidermis, Streptococcus acidominimus, Actinomyces viscosus, and Nanosynbacter lyticus; seven Gram-negative opportunistic bacteria: Porphyromonas gingivalis. Prevotella brevis, Proteus vulgaris, Fusobacterium nucleatum, Veillonella parvula, Treponema denticola, and Alkermansia muciniphila; and one fungus: Candida albicans. Our mass spectrometric analytical platform allowed for a detailed evaluation of the many structural modifications made by microbes for the three major lipid scaffolds: glycerol, sphingosine and fatty acyls of hydroxy fatty acids (FAHFAs).
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Affiliation(s)
- Paul L. Wood
- Metabolomics Unit, College of Veterinary Medicine, Lincoln Memorial University, 6965 Cumberland Gap Pkwy., Harrogate, TN 37752, USA
| | - Annie Le
- Clinical Training Program, DeBusk College of Osteopathic Medicine, Lincoln Memorial University, 6965 Cumberland Gap Pkwy., Harrogate, TN 37752, USA
| | - Dominic L. Palazzolo
- Department of Physiology, DeBusk College of Osteopathic Medicine, Lincoln Memorial University, 6965 Cumberland Gap Pkwy., Harrogate, TN 37752, USA;
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2
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Elmassry MM, Sugihara K, Chankhamjon P, Camacho FR, Wang S, Sugimoto Y, Chatterjee S, Chen LA, Kamada N, Donia MS. A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579278. [PMID: 38370680 PMCID: PMC10871352 DOI: 10.1101/2024.02.07.579278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Changes in the gut microbiome have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a multi-cohort analysis of small molecule biosynthetic gene clusters (BGCs) in 5,306 metagenomic samples of the gut microbiome from 2,033 Inflammatory Bowel Disease (IBD) patients and 833 matched healthy subjects and identified a group of Clostridia-derived BGCs that are significantly associated with IBD. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the IBD-enriched BGCs. Using two mouse models of colitis, we show that the discovered small molecules disrupt gut permeability and exacerbate inflammation in chemically and genetically susceptible mice. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of microbiome-host interactions in the context of microbiome-associated diseases.
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Affiliation(s)
- Moamen M Elmassry
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Kohei Sugihara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | | | - Francine R Camacho
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, 08544, USA
| | - Shuo Wang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, 08544, USA
| | - Yuki Sugimoto
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Seema Chatterjee
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Lea Ann Chen
- Department of Medicine, Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, 08901, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, 08544, USA
- Lead Contact
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3
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Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, 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, Pessotti RDC, 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, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La 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 Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat Microbiol 2024; 9:336-345. [PMID: 38316926 PMCID: PMC10847041 DOI: 10.1038/s41564-023-01575-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/29/2023] [Indexed: 02/07/2024]
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.
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Affiliation(s)
- Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paulo Wender P Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Andres M Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Emily C Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA
| | - Michael J Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, Norman, OK, USA
| | - Ekaterina Buzun
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Marvic Carrillo Terrazas
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Chia-Yun Hsu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Renee Oles
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Jiaqi Zhao
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
| | - Hiutung Chu
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA
- Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, San Diego, CA, USA
| | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Sara L Jackrel
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Fidele Tugizimana
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
- International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, Johannesburg, South Africa
| | - Lerato Pertunia Nephali
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ian A Dubery
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Thohoyandou, South Africa
| | - Eduarda Antunes Moreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Norberto Peporine Lopes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula C Jimenez
- Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Santos, Brazil
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - Matthew F Traxler
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Rita de Cassia Pessotti
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA
| | - Daniel Alvarado-Villalobos
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Giselle Tamayo-Castillo
- Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Priscila Chaverri
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, MD, USA
| | - Efrain Escudero-Leyva
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Alexandre Jean Bory
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Juliette Joubert
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Andreas Sichert
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Benjamin S Pullman
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Katia Gindro
- Plant Protection, Mycology group, Agroscope, Nyon, Switzerland
| | | | - Berenike C Wagner
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Karl Forchhammer
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Daniel Petras
- Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Manuel Liebeke
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department for Metabolomics, Kiel University, Kiel, Germany
| | - Patric Bourceau
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Henna Gadhavi
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- King's College London, London, UK
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
- Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
| | | | - Alicia Isabel Pérez-Lorente
- 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
| | - Carlos Molina-Santiago
- 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
| | - Diego Romero
- 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
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany
| | - Arturo Vera Ponce de León
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip Byron Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Giorgia La Barbera
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | | | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Lorena Rodriguez-Orduña
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Katharina Hohenwallner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Jane Odoi
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Su Ding
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands
| | - Xue Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jerry J Cui
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
| | - Kou-San Ju
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA
| | - Denise Brentan Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Fernanda Motta Ribeiro Silva
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Hector H F Koolen
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Carlismari Grundmann
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kirk Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Sidnee E Ober-Singleton
- Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, Eugene, OR, USA
| | | | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
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4
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Roach J, Mital R, Haffner JJ, Colwell N, Coats R, Palacios HM, Liu Z, Godinho JLP, Ness M, Peramuna T, McCall LI. Microbiome metabolite quantification methods enabling insights into human health and disease. Methods 2024; 222:81-99. [PMID: 38185226 DOI: 10.1016/j.ymeth.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/27/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
Many of the health-associated impacts of the microbiome are mediated by its chemical activity, producing and modifying small molecules (metabolites). Thus, microbiome metabolite quantification has a central role in efforts to elucidate and measure microbiome function. In this review, we cover general considerations when designing experiments to quantify microbiome metabolites, including sample preparation, data acquisition and data processing, since these are critical to downstream data quality. We then discuss data analysis and experimental steps to demonstrate that a given metabolite feature is of microbial origin. We further discuss techniques used to quantify common microbial metabolites, including short-chain fatty acids (SCFA), secondary bile acids (BAs), tryptophan derivatives, N-acyl amides and trimethylamine N-oxide (TMAO). Lastly, we conclude with challenges and future directions for the field.
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Affiliation(s)
- Jarrod Roach
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Rohit Mital
- Department of Biology, University of Oklahoma
| | - Jacob J Haffner
- Department of Anthropology, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma
| | - Nathan Colwell
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Randy Coats
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Horvey M Palacios
- Department of Anthropology, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma
| | - Zongyuan Liu
- Department of Chemistry and Biochemistry, University of Oklahoma
| | | | - Monica Ness
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Thilini Peramuna
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, University of Oklahoma; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma; Department of Chemistry and Biochemistry, San Diego State University.
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5
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Lunjani N, Ambikan AT, Hlela C, Levin M, Mankahla A, Heldstab‐Kast JI, Boonpiyathad T, Tan G, Altunbulakli C, Gray C, Nadeau KC, Neogi U, Akdis CA, O'Mahony L. Rural and urban exposures shape early life immune development in South African children with atopic dermatitis and nonallergic children. Allergy 2024; 79:65-79. [PMID: 37534631 PMCID: PMC10952395 DOI: 10.1111/all.15832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/01/2023] [Accepted: 07/04/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND Immunological traits and functions have been consistently associated with environmental exposures and are thought to shape allergic disease susceptibility and protection. In particular, specific exposures in early life may have more significant effects on the developing immune system, with potentially long-term impacts. METHODS We performed RNA-Seq on peripheral blood mononuclear cells (PBMCs) from 150 children with atopic dermatitis and healthy nonallergic children in rural and urban settings from the same ethnolinguistic AmaXhosa background in South Africa. We measured environmental exposures using questionnaires. RESULTS A distinct PBMC gene expression pattern was observed in those children with atopic dermatitis (132 differentially expressed genes [DEGs]). However, the predominant influences on the immune cell transcriptome were related to early life exposures including animals, time outdoors, and types of cooking and heating fuels. Sample clustering revealed two rural groups (Rural_1 and Rural_2) that separated from the urban group (3413 and 2647 DEGs, respectively). The most significantly regulated pathways in Rural_1 children were related to innate activation of the immune system (e.g., TLR and cytokine signaling), changes in lymphocyte polarization (e.g., TH17 cells), and immune cell metabolism (i.e., oxidative phosphorylation). The Rural_2 group displayed evidence for ongoing lymphocyte activation (e.g., T cell receptor signaling), with changes in immune cell survival and proliferation (e.g., mTOR signaling, insulin signaling). CONCLUSIONS This study highlights the importance of the exposome on immune development in early life and identifies potentially protective (e.g., animal) exposures and potentially detrimental (e.g., pollutant) exposures that impact key immunological pathways.
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Affiliation(s)
- Nonhlanhla Lunjani
- Division of DermatologyUniversity of Cape TownCape TownSouth Africa
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Anoop T. Ambikan
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory MedicineKarolinska Institute, ANA FuturaStockholmSweden
| | - Carol Hlela
- Division of DermatologyUniversity of Cape TownCape TownSouth Africa
| | - Michael Levin
- Division of Paediatric Allergy, Department of Paediatrics and Child HealthUniversity of Cape TownCape TownSouth Africa
| | - Avumile Mankahla
- The Division of Dermatology, Department of Medicine and PharmacologyWalter Sisulu UniversityMthathaEastern CapeSouth Africa
| | | | - Tadech Boonpiyathad
- Swiss Institute of Allergy and Asthma Research (SIAF), University of ZurichDavosSwitzerland
| | - Ge Tan
- Swiss Institute of Allergy and Asthma Research (SIAF), University of ZurichDavosSwitzerland
| | - Can Altunbulakli
- Swiss Institute of Allergy and Asthma Research (SIAF), University of ZurichDavosSwitzerland
| | - Clive Gray
- Division of ImmunologyUniversity of Cape TownCape TownSouth Africa
| | - Kari C. Nadeau
- Department of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory MedicineKarolinska Institute, ANA FuturaStockholmSweden
| | - Cezmi A. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of ZurichDavosSwitzerland
- Christine Kühne‐Center for Allergy Research and EducationDavosSwitzerland
| | - Liam O'Mahony
- APC Microbiome IrelandUniversity College CorkCorkIreland
- Department of MedicineUniversity College CorkCorkIreland
- School of MicrobiologyUniversity College CorkCorkIreland
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Roussel C, Sola M, Lessard-Lord J, Nallabelli N, Généreux P, Cavestri C, Azeggouar Wallen O, Villano R, Raymond F, Flamand N, Silvestri C, Di Marzo V. Human gut microbiota and their production of endocannabinoid-like mediators are directly affected by a dietary oil. Gut Microbes 2024; 16:2335879. [PMID: 38695302 PMCID: PMC11067990 DOI: 10.1080/19490976.2024.2335879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/25/2024] [Indexed: 05/05/2024] Open
Abstract
Dietary omega-3 polyunsaturated fatty acids (n-3 PUFAs) and the gut microbiome affect each other. We investigated the impact of supplementation with Buglossoides arvensis oil (BO), rich in stearidonic acid (SDA), on the human gut microbiome. Employing the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), we simulated the ileal and ascending colon microbiomes of four donors. Our results reveal two distinct microbiota clusters influenced by BO, exhibiting shared and contrasting shifts. Notably, Bacteroides and Clostridia abundance underwent similar changes in both clusters, accompanied by increased propionate production in the colon. However, in the ileum, cluster 2 displayed a higher metabolic activity in terms of BO-induced propionate levels. Accordingly, a triad of bacterial members involved in propionate production through the succinate pathway, namely Bacteroides, Parabacteroides, and Phascolarctobacterium, was identified particularly in this cluster, which also showed a surge of second-generation probiotics, such as Akkermansia, in the colon. Finally, we describe for the first time the capability of gut bacteria to produce N-acyl-ethanolamines, and particularly the SDA-derived N-stearidonoyl-ethanolamine, following BO supplementation, which also stimulated the production of another bioactive endocannabinoid-like molecule, commendamide, in both cases with variations across individuals. Spearman correlations enabled the identification of bacterial genera potentially involved in endocannabinoid-like molecule production, such as, in agreement with previous reports, Bacteroides in the case of commendamide. This study suggests that the potential health benefits on the human microbiome of certain dietary oils may be amenable to stratified nutrition strategies and extend beyond n-3 PUFAs to include microbiota-derived endocannabinoid-like mediators.
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Affiliation(s)
- Charlène Roussel
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Quebec, QC, Canada
- Centre Nutrition, Santé et Société (NUTRISS), INAF Laval University, Quebec, QC, Canada
- Canada Excellence Research Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health, Laval University, Quebec, QC, Canada
| | - Mathilde Sola
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Quebec, QC, Canada
- Canada Excellence Research Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health, Laval University, Quebec, QC, Canada
| | - Jacob Lessard-Lord
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Quebec, QC, Canada
- Centre Nutrition, Santé et Société (NUTRISS), INAF Laval University, Quebec, QC, Canada
| | - Nayudu Nallabelli
- Faculty of Medicine, Department of Medicine, Laval University, Quebec, QC, Canada
| | - Pamela Généreux
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Quebec, QC, Canada
| | - Camille Cavestri
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Quebec, QC, Canada
| | - Oumaima Azeggouar Wallen
- Canada Excellence Research Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health, Laval University, Quebec, QC, Canada
- Faculty of Medicine, Department of Medicine, Laval University, Quebec, QC, Canada
| | - Rosaria Villano
- Institute of Biomolecular Chemistry, Consiglio Nazionale delle Ricerche (CNR), Pozzuoli (Napoli), Italy
| | - Frédéric Raymond
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Quebec, QC, Canada
- Centre Nutrition, Santé et Société (NUTRISS), INAF Laval University, Quebec, QC, Canada
- Canada Excellence Research Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health, Laval University, Quebec, QC, Canada
| | - Nicolas Flamand
- Canada Excellence Research Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health, Laval University, Quebec, QC, Canada
- Faculty of Medicine, Department of Medicine, Laval University, Quebec, QC, Canada
| | - Cristoforo Silvestri
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Quebec, QC, Canada
- Centre Nutrition, Santé et Société (NUTRISS), INAF Laval University, Quebec, QC, Canada
- Canada Excellence Research Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health, Laval University, Quebec, QC, Canada
- Faculty of Medicine, Department of Medicine, Laval University, Quebec, QC, Canada
| | - Vincenzo Di Marzo
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Quebec, QC, Canada
- Centre Nutrition, Santé et Société (NUTRISS), INAF Laval University, Quebec, QC, Canada
- Canada Excellence Research Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health, Laval University, Quebec, QC, Canada
- Faculty of Medicine, Department of Medicine, Laval University, Quebec, QC, Canada
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Mathieu E, Léjard V, Ezzine C, Govindin P, Morat A, Giat M, Lapaque N, Doré J, Blottière HM. An Insight into Functional Metagenomics: A High-Throughput Approach to Decipher Food-Microbiota-Host Interactions in the Human Gut. Int J Mol Sci 2023; 24:17630. [PMID: 38139456 PMCID: PMC10744307 DOI: 10.3390/ijms242417630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/08/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Our understanding of the symbiotic relationship between the microbiota and its host has constantly evolved since our understanding that the "self" was not only defined by our genetic patrimony but also by the genomes of bugs living in us. The first culture-based methods highlighted the important functions of the microbiota. However, these methods had strong limitations and did not allow for a full understanding of the complex relationships that occur at the interface between the microbiota and the host. The recent development of metagenomic approaches has been a groundbreaking step towards this understanding. Its use has provided new insights and perspectives. In the present chapter, we will describe the advances of functional metagenomics to decipher food-microbiota and host-microbiota interactions. This powerful high-throughput approach allows for the assessment of the microbiota as a whole (including non-cultured bacteria) and enabled the discovery of new signaling pathways and functions involved in the crosstalk between food, the gut microbiota and its host. We will present the pipeline and highlight the most important studies that helped to develop the field. To conclude, we will emphasize the most recent developments and hot topics in functional metagenomics.
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Affiliation(s)
- Elliot Mathieu
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
| | - Véronique Léjard
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
| | - Chaima Ezzine
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
| | - Pauline Govindin
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
| | - Aurélien Morat
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
| | - Margot Giat
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
| | - Nicolas Lapaque
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France;
| | - Joël Doré
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France;
| | - Hervé M. Blottière
- Université Paris-Saclay, INRAE, MGP Metagenopolis, 78350 Jouy-en-Josas, France; (E.M.); (V.L.); (C.E.); (P.G.); (A.M.); (M.G.); (J.D.)
- Nantes Université, INRAE, UMR 1280, PhAN, 44000 Nantes, France
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8
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Lee YJ. Examining the functional space of gut microbiome-derived peptides. Microbiologyopen 2023; 12:e1393. [PMID: 38129980 PMCID: PMC10714122 DOI: 10.1002/mbo3.1393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
The human gut microbiome contains thousands of small, novel peptides that could play a role in microbe-microbe and host-microbe interactions, contributing to human health and disease. Although these peptides have not yet been systematically characterized, computational tools can be used to elucidate the bioactivities they may have. This article proposes probing the functional space of gut microbiome-derived peptides (MDPs) using in silico approaches for three bioactivities: antimicrobial, anticancer, and nucleomodulins. Machine learning programs that support peptide and protein queries are provided for each bioactivity. Considering the biases of an activity-centric approach, activity-agnostic tools using structural and chemical similarity and target prediction are also described. Gut MDPs represent a vast functional space that can not only contribute to our understanding of microbiome interactions but potentially even serve as a source of life-changing therapeutics.
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Affiliation(s)
- Ying‐Chiang J. Lee
- Department of Molecular BiologyPrinceton UniversityPrincetonNew JerseyUSA
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9
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Hwang HG, Ye DY, Jung GY. Biosensor-guided discovery and engineering of metabolic enzymes. Biotechnol Adv 2023; 69:108251. [PMID: 37690614 DOI: 10.1016/j.biotechadv.2023.108251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
A variety of chemicals have been produced through metabolic engineering approaches, and enhancing biosynthesis performance can be achieved by using enzymes with high catalytic efficiency. Accordingly, a number of efforts have been made to discover enzymes in nature for various applications. In addition, enzyme engineering approaches have been attempted to suit specific industrial purposes. However, a significant challenge in enzyme discovery and engineering is the efficient screening of enzymes with the desired phenotype from extensive enzyme libraries. To overcome this bottleneck, genetically encoded biosensors have been developed to specifically detect target molecules produced by enzyme activity at the intracellular level. Especially, the biosensors facilitate high-throughput screening (HTS) of targeted enzymes, expanding enzyme discovery and engineering strategies with advances in systems and synthetic biology. This review examines biosensor-guided HTS systems and highlights studies that have utilized these tools to discover enzymes in diverse areas and engineer enzymes to enhance their properties, such as catalytic efficiency, specificity, and stability.
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Affiliation(s)
- Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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10
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Wan T, Wang Y, He K, Zhu S. Microbial sensing in the intestine. Protein Cell 2023; 14:824-860. [PMID: 37191444 PMCID: PMC10636641 DOI: 10.1093/procel/pwad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023] Open
Abstract
The gut microbiota plays a key role in host health and disease, particularly through their interactions with the immune system. Intestinal homeostasis is dependent on the symbiotic relationships between the host and the diverse gut microbiota, which is influenced by the highly co-evolved immune-microbiota interactions. The first step of the interaction between the host and the gut microbiota is the sensing of the gut microbes by the host immune system. In this review, we describe the cells of the host immune system and the proteins that sense the components and metabolites of the gut microbes. We further highlight the essential roles of pattern recognition receptors (PRRs), the G protein-coupled receptors (GPCRs), aryl hydrocarbon receptor (AHR) and the nuclear receptors expressed in the intestinal epithelial cells (IECs) and the intestine-resident immune cells. We also discuss the mechanisms by which the disruption of microbial sensing because of genetic or environmental factors causes human diseases such as the inflammatory bowel disease (IBD).
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Affiliation(s)
- Tingting Wan
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yalong Wang
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Kaixin He
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Shu Zhu
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei 230601, China
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11
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Aleti G, Troyer EA, Hong S. G protein-coupled receptors: A target for microbial metabolites and a mechanistic link to microbiome-immune-brain interactions. Brain Behav Immun Health 2023; 32:100671. [PMID: 37560037 PMCID: PMC10407893 DOI: 10.1016/j.bbih.2023.100671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 07/30/2023] [Indexed: 08/11/2023] Open
Abstract
Human-microorganism interactions play a key role in human health. However, the underlying molecular mechanisms remain poorly understood. Small-molecules that offer a functional readout of microbe-microbe-human relationship are of great interest for deeper understanding of the inter-kingdom crosstalk at the molecular level. Recent studies have demonstrated that small-molecules from gut microbiota act as ligands for specific human G protein-coupled receptors (GPCRs) and modulate a range of human physiological functions, offering a mechanistic insight into the microbe-human interaction. To this end, we focused on analysis of bacterial metabolites that are currently recognized to bind to GPCRs and are found to activate the known downstream signaling pathways. We further mapped the distribution of these molecules across the public mass spectrometry-based metabolomics data, to identify the presence of these molecules across body sites and their association with health status. By combining this with RNA-Seq expression and spatial localization of GPCRs from a public human protein atlas database, we inferred the most predominant GPCR-mediated microbial metabolite-human cell interactions regulating gut-immune-brain axis. Furthermore, by evaluating the intestinal absorption properties and blood-brain barrier permeability of the small-molecules we elucidated their molecular interactions with specific human cell receptors, particularly expressed on human intestinal epithelial cells, immune cells and the nervous system that are shown to hold much promise for clinical translational potential. Furthermore, we provide an overview of an open-source resource for simultaneous interrogation of bioactive molecules across the druggable human GPCRome, a useful framework for integration of microbiome and metabolite cataloging with mechanistic studies for an improved understanding of gut microbiota-immune-brain molecular interactions and their potential therapeutic use.
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Affiliation(s)
- Gajender Aleti
- Department of Food and Animal Sciences, Tennessee State University, Nashville, TN, 37209, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Emily A. Troyer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Suzi Hong
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
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12
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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 SLL, Barbera GL, 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 Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data. RESEARCH SQUARE 2023:rs.3.rs-3189768. [PMID: 37577622 PMCID: PMC10418563 DOI: 10.21203/rs.3.rs-3189768/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
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.
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Affiliation(s)
- Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- 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
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- 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
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- 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
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Paulo Wender P. Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- 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
| | - Andres M. Caraballo-Rodriguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- 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
| | - Yasin El Abiead
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- 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
| | - Allegra T. Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, United States
| | - Emily C. Gentry
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, United States
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Center for Microbiome Innovation, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Michael J. Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Nicole E. Avalon
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, United States
| | - Robert H. Cichewicz
- Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Ekaterina Buzun
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Marvic Carrillo Terrazas
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Chia-Yun Hsu
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Renee Oles
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Adriana Vasquez Ayala
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Jiaqi Zhao
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Hiutung Chu
- Department of Pathology, School of Medicine, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Mirte C. M. Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Sara L. Jackrel
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Fidele Tugizimana
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
- International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, 178 Montecasino Boulevard, Fourways, Johannesburg, Gauteng, 2191, South Africa
| | - Lerato Pertunia Nephali
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Private Bag X5050, Thohoyandou, Limpopo, 950, South Africa
| | - Eduarda Antunes Moreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Norberto Peporine Lopes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Paula Rezende-Teixeira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes 1524, São Paulo, SP, 05508-000, Brazil
| | - Paula C. Jimenez
- Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Rua Carvalho de Mendonça, 144, Santos, SP, 11070-100, Brazil
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 319 Life Sciences Building, University Park, PA, 16802, United States
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 320 Life Sciences Building, University Park, PA, 16802, United States
| | - Matthew F. Traxler
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, 311 Koshland Hall, Berkeley, CA, 94270, United States
| | - Rita de Cassia Pessotti
- Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, 311 Koshland Hall, Berkeley, CA, 94270, United States
| | - Daniel Alvarado-Villalobos
- 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
| | - Giselle Tamayo-Castillo
- 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
- Escuela de Química, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Priscila Chaverri
- 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
- Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, 20715, United States
| | - Efrain Escudero-Leyva
- Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 2061, Costa Rica
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Alexandre Jean Bory
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Juliette Joubert
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, Genève, GE, 1206, Switzerland
- Department of Biology, University of Fribourg, Chemin du Musée, 10, Fribourg, FR, 1700, Switzerland
| | - Andreas Sichert
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, Zürich, 8093, Switzerland
| | - Benjamin S Pullman
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - William H. Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Katia Gindro
- Plant Protection, Mycology group, Agroscope, Rte de Duillier, 50, Nyon, VD, 1260, Switzerland
| | - Josep Massana-Codina
- Plant Protection, Mycology group, Agroscope, Rte de Duillier, 50, Nyon, VD, 1260, Switzerland
| | - Berenike C. Wagner
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, Tuebingen, 72076, Germany
| | - Karl Forchhammer
- Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, Tuebingen, 72076, Germany
| | - Daniel Petras
- Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI), University of Tuebingen, Auf der Morgenstelle 24, Tuebingen, 72076, Germany
| | - Nicole Aiosa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, United States
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, United States
| | - Manuel Liebeke
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Patric Bourceau
- Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women’s University, Cheongpa-ro 47 gil 100, Seoul, 04310, Korea
| | - Henna Gadhavi
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- King’s College London, Strand, London, WC2R 2LS, UK
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 110 Scripps Way, Jupiter, FL, 33458, United States
| | - Mariana Silva dos Santos
- Metabolomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alicia Isabel Pérez-Lorente
- 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
| | - Carlos Molina-Santiago
- 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
| | - Diego Romero
- 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
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, 38124, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, 38124, Germany
| | - Arturo Vera Ponce de León
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Phillip Byron Pope
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, BIotechnology and Food Science, Norwegian University of Life Sciences, Postboks 5003, Ås, 1433, Norway
| | - Giorgia La Barbera
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, Frederiksberg, 1958, Denmark
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, Frederiksberg, 1958, Denmark
| | - Martin Frederik Laursen
- National Food Institute, Technical University of Denmark, Kemitorvet B202, Lyngby, 2800, Denmark
| | - Fabian Hammerle
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria
| | - Bianka Siewert
- Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, Innsbruck, 6020, Austria
| | - Ursula Peintner
- Department of Microbiology, University of Innsbruck, Technikerstr. 25, Innsbruck, 6020, Austria
| | - Cuauhtemoc Licona-Cassani
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon, 64849, Mexico
| | - Lorena Rodriguez-Orduña
- Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon, 64849, Mexico
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
| | - Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14,, Vienna, 1090, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
| | - Katharina Hohenwallner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Lisa Panzenboeck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, Vienna, 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Waehringer Str. 42, Vienna, 1090, Austria
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02142, United States
| | - Ellis Charles O’Neill
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | | | - Jane Odoi
- Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Su Ding
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, t Horntje (Texel), 1797 SZ, Netherlands
| | - Xueli Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, Singapore, 636921, Singapore
| | - Jerry J. Cui
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
| | - Kou-San Ju
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Center for Applied Plant Sciences, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
- Infectious Diseases Institute, The Ohio State University, 484 W. 12th Ave, Columbus, OH, 43210, United States
| | - Denise Brentan Silva
- 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
| | - Fernanda Motta Ribeiro Silva
- 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
| | | | - Hector H. F. Koolen
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, 1777 Carvalho Leal Avenue, Manaus, AM, 69065-001, Brazil
| | - Carlismari Grundmann
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café, Ribeirão Preto, SP, 14040-903, Brazil
| | - Jason A. Clement
- Baruch S. Blumberg Institute, 3805 Old Easton Rd., Doylestown, PA, 18902, United States
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, United States
| | - Kirk Broders
- 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
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Weniger Hall, room 341, Corvallis, OR, 97331, United States
| | - Sidnee E. Ober-Singleton
- Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, 1255 E 13th Ave, Basement, Eugene, OR, 97402, United States
| | | | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, 900 University Ave., Riverside, CA, 92521, United States
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr., San Diego, CA, 92093, United States
- 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
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Seyedsayamdost MR, Clardy J. Discovering functional small molecules in the gut microbiome. Curr Opin Chem Biol 2023; 75:102309. [PMID: 37163788 PMCID: PMC10524162 DOI: 10.1016/j.cbpa.2023.102309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/25/2023] [Indexed: 05/12/2023]
Abstract
The human microbiome has emerged as a source of bacterially produced, functional small molecules that help regulate health and disease, and their discovery and annotation has become a popular research topic. Identifying these molecules provides an essential step in unraveling the molecular mechanisms underlying biological outcomes. The relevance of specific bacterial members of the microbiome has been demonstrated in a variety of correlative studies, and there are many possible paths from these correlations to the responsible metabolites. Herein, we summarize two studies that have recently identified gut microbiome metabolites that modulate immune responses or promote physical activity. Aside from the deep insights gained, these studies provide blueprints for successfully uncovering the molecules and mechanisms that control important physiological pathways.
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Affiliation(s)
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA.
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Steffan BN, Calise D, Park SC, Niu M, Yang J, Hammock BD, Jones M, Steele C, Keller NP. Loss of the mammalian G-protein coupled receptor, G2A, modulates severity of invasive pulmonary aspergillosis. Front Immunol 2023; 14:1173544. [PMID: 37435068 PMCID: PMC10331294 DOI: 10.3389/fimmu.2023.1173544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/01/2023] [Indexed: 07/13/2023] Open
Abstract
Background Aspergillus fumigatus is a well-known opportunistic pathogen that causes a range of diseases including the often-fatal disease, invasive pulmonary aspergillosis (IPA), in immunocompromised populations. The severity of IPA is dependent on both host- and pathogen-derived signaling molecules that mediate host immunity and fungal growth. Oxylipins are bioactive oxygenated fatty acids known to influence host immune response and Aspergillus developmental programs. Aspergillus synthesizes 8-HODE and 5,8-diHODE that have structural similarities to 9-HODE and 13-HODE, which are known ligands of the host G-protein-coupled receptor G2A (GPR132). Materials and methods Oxylipins were extracted from infected lung tissue to assess fungal oxylipin production and the Pathhunter β-arrestin assay was used to assess agonist and antagonist activity by fungal oxylipins on G2A. An immunocompetent model of A. fumigatus infection was used to assess changes in survival and immune responses for G2A-/- mice. Results Here we report that Aspergillus oxylipins are produced in lung tissue of infected mice and in vitro ligand assays suggest 8-HODE is a G2A agonist and 5,8-diHODE is a partial antagonist. To address the hypothesis that G2A could be involved in the progression of IPA, we assessed the response of G2A-/- mice to A. fumigatus infection. G2A-/- mice showed a survival advantage over wild-type mice; this was accompanied by increased recruitment of G2A-/- neutrophils and increased levels of inflammatory markers in A. fumigatus-infected lungs. Conclusions We conclude that G2A suppresses host inflammatory responses to Aspergillus fumigatus although it remains unclear if fungal oxylipins are involved in G2A activities.
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Affiliation(s)
- Breanne N. Steffan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States
| | - Dante Calise
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States
| | - Sung Chul Park
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States
| | - Mengyao Niu
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jun Yang
- Department of Entomology, University of California-Davis, Davis, CA, United States
| | - Bruce D. Hammock
- Department of Entomology, University of California-Davis, Davis, CA, United States
| | - MaryJane Jones
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA, United States
| | - Chad Steele
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA, United States
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
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15
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Hussain A, Patwekar U, Mongad DS, Shouche YS. Strategizing the human microbiome for small molecules: Approaches and perspectives. Drug Discov Today 2023; 28:103459. [PMID: 36435302 DOI: 10.1016/j.drudis.2022.103459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 11/03/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022]
Abstract
Studies of the human microbiome are providing a deeper understanding of its significance to human health, and increasing evidence links the microbiota with several diseases. Nevertheless, the exact mechanisms involved in human-microbe interactions are mostly undefined. The genomic potential of the human microbiome to biosynthesize distinct molecules outmatches its known chemical space, and small-molecule discovery in this context remains in its infancy. The profiling of microbiome-derived small molecules and their contextualization through cause-effect mechanistic studies may provide a better understanding of host-microbe interactions, guide new therapeutic interventions, and modulate microbiome-based therapies. This review describes the advances, approaches, and allied challenges in mining new microbial scaffolds from the human microbiome using genomic, microbe cultivation, and chemical analytic platforms. In the future, the complete biological characterization of a single microbe-derived molecule that has a specific therapeutic application could resolve the current limitations of microbiota-modulating therapies.
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Affiliation(s)
- Aehtesham Hussain
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India.
| | - Umera Patwekar
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India
| | - Dattatray S Mongad
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India
| | - Yogesh S Shouche
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra 411007, India
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16
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Chen H, Cao T, Zhang B, Cai H. The regulatory effects of second-generation antipsychotics on lipid metabolism: Potential mechanisms mediated by the gut microbiota and therapeutic implications. Front Pharmacol 2023; 14:1097284. [PMID: 36762113 PMCID: PMC9905135 DOI: 10.3389/fphar.2023.1097284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 01/12/2023] [Indexed: 01/26/2023] Open
Abstract
Second-generation antipsychotics (SGAs) are the mainstay of treatment for schizophrenia and other neuropsychiatric diseases but cause a high risk of disruption to lipid metabolism, which is an intractable therapeutic challenge worldwide. Although the exact mechanisms underlying this lipid disturbance are complex, an increasing body of evidence has suggested the involvement of the gut microbiota in SGA-induced lipid dysregulation since SGA treatment may alter the abundance and composition of the intestinal microflora. The subsequent effects involve the generation of different categories of signaling molecules by gut microbes such as endogenous cannabinoids, cholesterol, short-chain fatty acids (SCFAs), bile acids (BAs), and gut hormones that regulate lipid metabolism. On the one hand, these signaling molecules can directly activate the vagus nerve or be transported into the brain to influence appetite via the gut-brain axis. On the other hand, these molecules can also regulate related lipid metabolism via peripheral signaling pathways. Interestingly, therapeutic strategies directly targeting the gut microbiota and related metabolites seem to have promising efficacy in the treatment of SGA-induced lipid disturbances. Thus, this review provides a comprehensive understanding of how SGAs can induce disturbances in lipid metabolism by altering the gut microbiota.
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Affiliation(s)
- Hui Chen
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China,Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China,Institute of Clinical Pharmacy, Central South University, Changsha, China,International Research Center for Precision Medicine, Transformative Technology and Software Services, Changsha, Hunan, China
| | - Ting Cao
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China,Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China,Institute of Clinical Pharmacy, Central South University, Changsha, China,International Research Center for Precision Medicine, Transformative Technology and Software Services, Changsha, Hunan, China
| | - Bikui Zhang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China,Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China,Institute of Clinical Pharmacy, Central South University, Changsha, China,International Research Center for Precision Medicine, Transformative Technology and Software Services, Changsha, Hunan, China,*Correspondence: Bikui Zhang, ; Hualin Cai,
| | - Hualin Cai
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China,Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China,Institute of Clinical Pharmacy, Central South University, Changsha, China,International Research Center for Precision Medicine, Transformative Technology and Software Services, Changsha, Hunan, China,*Correspondence: Bikui Zhang, ; Hualin Cai,
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17
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Kalia VC, Gong C, Shanmugam R, Lee JK. Prospecting Microbial Genomes for Biomolecules and Their Applications. Indian J Microbiol 2022; 62:516-523. [PMID: 36458216 PMCID: PMC9705627 DOI: 10.1007/s12088-022-01040-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/04/2022] [Indexed: 11/26/2022] Open
Abstract
Bioactive molecules of microbial origin are finding increasing biotechnological applications. Their sources range from the terrestrial, marine, and endophytic to the human microbiome. These biomolecules have unique chemical structures and related groups, which enable them to improve the efficiency of the bioprocesses. This review focuses on the applications of biomolecules in bioremediation, agriculture, food, pharmaceutical industries, and human health.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Chunjie Gong
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, 430068 People’s Republic of China
| | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
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18
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Forde B, Yao L, Shaha R, Murphy S, Lunjani N, O'Mahony L. Immunomodulation by foods and microbes: Unravelling the molecular tango. Allergy 2022; 77:3513-3526. [PMID: 35892227 PMCID: PMC10087875 DOI: 10.1111/all.15455] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/15/2022] [Accepted: 07/23/2022] [Indexed: 01/28/2023]
Abstract
Metabolic health and immune function are intimately connected via diet and the microbiota. Nearly 90% of all immune cells in the body are associated with the gastrointestinal tract and these immune cells are continuously exposed to a wide range of microbes and microbial-derived compounds, with important systemic ramifications. Microbial dysbiosis has consistently been observed in patients with atopic dermatitis, food allergy and asthma and the molecular mechanisms linking changes in microbial populations with disease risk and disease endotypes are being intensively investigated. The discovery of novel bacterial metabolites that impact immune function is at the forefront of host-microbe research. Co-evolution of microbial communities within their hosts has resulted in intertwined metabolic pathways that affect physiological and pathological processes. However, recent dietary and lifestyle changes are thought to negatively influence interactions between microbes and their host. This review provides an overview of some of the critical metabolite-receptor interactions that have been recently described, which may underpin the immunomodulatory effects of the microbiota, and are of relevance for allergy, asthma and infectious diseases.
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Affiliation(s)
- Brian Forde
- APC Microbiome Ireland, UCC, Cork, Ireland.,School of Microbiology, UCC, Cork, Ireland
| | - Lu Yao
- APC Microbiome Ireland, UCC, Cork, Ireland.,School of Microbiology, UCC, Cork, Ireland
| | - Rupin Shaha
- APC Microbiome Ireland, UCC, Cork, Ireland.,School of Microbiology, UCC, Cork, Ireland
| | | | - Nonhlanhla Lunjani
- APC Microbiome Ireland, UCC, Cork, Ireland.,University of Cape Town, Cape Town, South Africa
| | - Liam O'Mahony
- APC Microbiome Ireland, UCC, Cork, Ireland.,School of Microbiology, UCC, Cork, Ireland.,Department of Medicine, UCC, Cork, Ireland
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19
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Li Q, Yin G, Wang J, Li L, Liang Q, Zhao X, Chen Y, Zheng X, Zhao X. An emerging paradigm to develop analytical methods based on immobilized transmembrane proteins and its applications in drug discovery. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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20
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Xavier J, M A, A S F, Ravichandiran V, Kumar N. Intriguing role of Gut-Brain Axis on cognition with emphasis on interaction with Papez circuit. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2022; 22:CNSNDDT-EPUB-124445. [PMID: 35702801 DOI: 10.2174/1871527321666220614124145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/26/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
The gut microbiome is a complicated ecosystem of around a hundred billion symbiotic bacteria cells. Bidirectional communication between the gut and the brain is facilitated by the immune system, the enteric nervous system, the vagus nerve, and microbial compounds such as tryptophan metabolites and short-chain fatty acids (SCFAs). The current study emphasises the relationship of the gut-brain axis with cognitive performance and elucidates the underlying biological components, with a focus on neurotransmitters such as serotonin, indole derivatives, and catecholamine. These biological components play important roles in both the digestive and brain systems. Recent research has linked the gut microbiome to a variety of cognitive disorders, including Alzheimer's (AD). The review describes the intriguing role of the gut-brain axis in recognition memory depending on local network connections within the hippocampal as well as other additional hippocampal portions of the Papez circuit. The available data from various research papers show how the gut microbiota might alter brain function and hence psychotic and cognitive illnesses. The role of supplementary probiotics is emphasized for the reduction of brain-related dysfunction as a viable strategy in handling cognitive disorders. Further, the study elucidates the mode of action of probiotics with reported adverse effects.
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Affiliation(s)
- Joyal Xavier
- Department of Pharmacology and Toxicology,National Institute of Pharmaceutical Education and Research
| | - Anu M
- Biotechnology National Institute of Pharmaceutical Education and Research India
| | - Fathima A S
- Pharamcy practice National Institute of Pharmaceutical Education and Research India
| | - V Ravichandiran
- Natural Product sNational Institute of Pharmaceutical Education and Research India
| | - Nitesh Kumar
- Pharmacology and Toxicology National Institute of Pharmaceutical Education and Research India
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21
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Cohen LJ, Han SM, Lau P, Guisado D, Liang Y, Nakashige TG, Ali T, Chiang D, Rahman A, Brady SF. Unraveling function and diversity of bacterial lectins in the human microbiome. Nat Commun 2022; 13:3101. [PMID: 35661736 PMCID: PMC9166713 DOI: 10.1038/s41467-022-29949-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 04/07/2022] [Indexed: 11/08/2022] Open
Abstract
The mechanisms by which commensal organisms affect human physiology remain poorly understood. Lectins are non-enzymatic carbohydrate binding proteins that all organisms employ as part of establishing a niche, evading host-defenses and protecting against pathogens. Although lectins have been extensively studied in plants, bacterial pathogens and human immune cells for their role in disease pathophysiology and as therapeutics, the role of bacterial lectins in the human microbiome is largely unexplored. Here we report on the characterization of a lectin produced by a common human associated bacterium that interacts with myeloid cells in the blood and intestine. In mouse and cell-based models, we demonstrate that this lectin induces distinct immunologic responses in peripheral and intestinal leukocytes and that these responses are specific to monocytes, macrophages and dendritic cells. Our analysis of human microbiota sequencing data reveal thousands of unique sequences that are predicted to encode lectins, many of which are highly prevalent in the human microbiome yet completely uncharacterized. Based on the varied domain architectures of these lectins we predict they will have diverse effects on the human host. The systematic investigation of lectins in the human microbiome should improve our understanding of human health and provide new therapeutic opportunities.
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Affiliation(s)
- Louis J Cohen
- Department of Medicine, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Sun M Han
- Department of Medicine, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pearson Lau
- Department of Medicine, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniela Guisado
- Department of Medicine, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yupu Liang
- Rockefeller University, New York, NY, USA
| | - Toshiki G Nakashige
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, NY, USA
| | - Thamina Ali
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, NY, USA
| | - David Chiang
- Division of Internal Medicine-Pediatrics, University of Massachusetts Medical School, Worcester, MA, USA
| | - Adeeb Rahman
- Human Immune Monitoring Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, New York, NY, USA.
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22
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Coccurello R, Marrone MC, Maccarrone M. The Endocannabinoids-Microbiota Partnership in Gut-Brain Axis Homeostasis: Implications for Autism Spectrum Disorders. Front Pharmacol 2022; 13:869606. [PMID: 35721203 PMCID: PMC9204215 DOI: 10.3389/fphar.2022.869606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
The latest years have witnessed a growing interest towards the relationship between neuropsychiatric disease in children with autism spectrum disorders (ASD) and severe alterations in gut microbiota composition. In parallel, an increasing literature has focused the attention towards the association between derangement of the endocannabinoids machinery and some mechanisms and symptoms identified in ASD pathophysiology, such as alteration of neural development, immune system dysfunction, defective social interaction and stereotypic behavior. In this narrative review, we put together the vast ground of endocannabinoids and their partnership with gut microbiota, pursuing the hypothesis that the crosstalk between these two complex homeostatic systems (bioactive lipid mediators, receptors, biosynthetic and hydrolytic enzymes and the entire bacterial gut ecosystem, signaling molecules, metabolites and short chain fatty acids) may disclose new ideas and functional connections for the development of synergic treatments combining “gut-therapy,” nutritional intervention and pharmacological approaches. The two separate domains of the literature have been examined looking for all the plausible (and so far known) overlapping points, describing the mutual changes induced by acting either on the endocannabinoid system or on gut bacteria population and their relevance for the understanding of ASD pathophysiology. Both human pathology and symptoms relief in ASD subjects, as well as multiple ASD-like animal models, have been taken into consideration in order to provide evidence of the relevance of the endocannabinoids-microbiota crosstalk in this major neurodevelopmental disorder.
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Affiliation(s)
- Roberto Coccurello
- Institute for Complex Systems (ISC), National Council of Research (CNR), Rome, Italy
- European Center for Brain Research/Santa Lucia Foundation IRCCS, Rome, Italy
- *Correspondence: Roberto Coccurello, ; Mauro Maccarrone,
| | - Maria Cristina Marrone
- Ministry of University and Research, Mission Unity for Recovery and Resilience Plan, Rome, Italy
| | - Mauro Maccarrone
- European Center for Brain Research/Santa Lucia Foundation IRCCS, Rome, Italy
- Department of Biotechnological and Applied Clinical and Sciences, University of L’Aquila, L’Aquila, Italy
- *Correspondence: Roberto Coccurello, ; Mauro Maccarrone,
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23
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Fobofou SA, Savidge T. Microbial metabolites: cause or consequence in gastrointestinal disease? Am J Physiol Gastrointest Liver Physiol 2022; 322:G535-G552. [PMID: 35271353 PMCID: PMC9054261 DOI: 10.1152/ajpgi.00008.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 01/31/2023]
Abstract
Systems biology studies have established that changes in gastrointestinal microbiome composition and function can adversely impact host physiology. Notable diseases synonymously associated with dysbiosis include inflammatory bowel diseases, cancer, metabolic disorders, and opportunistic and recurrent pathogen infections. However, there is a scarcity of mechanistic data that advances our understanding of taxonomic correlations with pathophysiological host-microbiome interactions. Generally, to survive a hostile gut environment, microbes are highly metabolically active and produce trans-kingdom signaling molecules to interact with competing microorganisms and the host. These specialized metabolites likely play important homeostatic roles, and identifying disease-specific taxa and their effector pathways can provide better strategies for diagnosis, treatment, and prevention, as well as the discovery of innovative therapeutics. The signaling role of microbial biotransformation products such as bile acids, short-chain fatty acids, polysaccharides, and dietary tryptophan is increasingly recognized, but little is known about the identity and function of metabolites that are synthesized by microbial biosynthetic gene clusters, including ribosomally synthesized and posttranslationally modified peptides (RiPPs), nonribosomal peptides (NRPs), polyketides (PKs), PK-NRP hybrids, and terpenes. Here we consider how bioactive natural products directly encoded by the human microbiome can contribute to the pathophysiology of gastrointestinal disease, cancer, autoimmune, antimicrobial-resistant bacterial and viral infections (including COVID-19). We also present strategies used to discover these compounds and the biological activities they exhibit, with consideration of therapeutic interventions that could emerge from understanding molecular causation in gut microbiome research.
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Affiliation(s)
- Serge Alain Fobofou
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
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24
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Hou L, Tian HY, Wang L, Ferris ZE, Wang J, Cai M, Older EA, Raja MRK, Xue D, Sun W, Nagarkatti P, Nagarkatti M, Chen H, Fan D, Tang X, Li J. Identification and Biosynthesis of Pro-Inflammatory Sulfonolipids from an Opportunistic Pathogen Chryseobacterium gleum. ACS Chem Biol 2022; 17:1197-1206. [PMID: 35476918 DOI: 10.1021/acschembio.2c00141] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Sulfonolipids (SoLs) are a unique class of sphingolipids featuring a sulfonate group compared to other sphingolipids. However, the biological functions and biosynthesis of SoLs in human microbiota have been poorly understood. Here, we report the discovery and isolation of SoLs from a human opportunistic pathogen Chryseobacterium gleum DSM16776. We show for the first time the pro-inflammatory activity of SoLs with mice primary macrophages. Furthermore, we used both in vivo heterologous expression and in vitro biochemical reconstitution to characterize two enzymes, cysteate synthase and cysteate fatty acyltransferase, that are specifically involved in the biosynthesis of SoLs rather than other sphingolipids. Based on these two SoL-specific enzymes, our bioinformatics analysis showed a wider distribution of SoL biosynthetic genes in microbes that had not been reported as SoL producers. We selected four of these strains and verified their cysteate synthase and cysteate fatty acyltransferase activities in SoL biosynthesis. Considering this wider distribution of SoL-specific biosynthetic enzymes in the context of SoLs' activity in mediating inflammation, a common and fundamental biological process, it may suggest a more comprehensive function of SoLs at play.
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Affiliation(s)
- Lukuan Hou
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Hai-Yan Tian
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Li Wang
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Zachary E Ferris
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Junfeng Wang
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Mingwei Cai
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Ethan A. Older
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Manikanda Raja Keerthi Raja
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Dan Xue
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Wanyang Sun
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Hexin Chen
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Daping Fan
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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25
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Giri R, Hoedt EC, Khushi S, Salim AA, Bergot AS, Schreiber V, Thomas R, McGuckin MA, Florin TH, Morrison M, Capon RJ, Ó Cuív P, Begun J. Secreted NF-κB suppressive microbial metabolites modulate gut inflammation. Cell Rep 2022; 39:110646. [PMID: 35417687 DOI: 10.1016/j.celrep.2022.110646] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 01/24/2022] [Accepted: 03/16/2022] [Indexed: 12/27/2022] Open
Abstract
Emerging evidence suggests that microbiome-host crosstalk regulates intestinal immune activity and predisposition to inflammatory bowel disease (IBD). NF-κB is a master regulator of immune function and a validated target for the treatment of IBD. Here, we identify five Clostridium strains that suppress immune-mediated NF-κB activation in epithelial cell lines, PBMCs, and gut epithelial organoids from healthy human subjects and patients with IBD. Cell-free culture supernatant from Clostridium bolteae AHG0001 strain, but not the reference C. bolteae BAA-613 strain, suppresses inflammatory responses and endoplasmic reticulum stress in gut epithelial organoids derived from Winnie mice. The in vivo responses to Clostridium bolteae AHG0001 and BAA-613 mirror the in vitro activity. Thus, using our in vitro screening of bacteria capable of suppressing NF-κB in the context of IBD and using an ex vivo organoid-based approach, we identify a strain capable of alleviating colitis in a relevant pre-clinical animal model of IBD.
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Affiliation(s)
- Rabina Giri
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia; Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Emily C Hoedt
- Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Shamsunnahar Khushi
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Angela A Salim
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Anne-Sophie Bergot
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Veronika Schreiber
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Michael A McGuckin
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia; Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Timothy H Florin
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Mark Morrison
- Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Robert J Capon
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Páraic Ó Cuív
- Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia; The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Jakob Begun
- Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia; Faculty of Medicine, The University of Queensland, St. Lucia, QLD 4072, Australia.
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26
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Villano R, Tinto F, Di Marzo V. Facile and Sustainable Synthesis of Commendamide and its Analogues. Front Chem 2022; 10:858854. [PMID: 35300384 PMCID: PMC8921460 DOI: 10.3389/fchem.2022.858854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/08/2022] [Indexed: 11/23/2022] Open
Abstract
Commendamide, or N-(3-hydroxypalmitoyl)-glycine 1a, is a gut microbiota-derived bioactive metabolite, structurally similar to long-chain N-acyl-amino acids which belong to the complex lipid signaling system known as endocannabinoidome and play important roles in mammals through activation of, inter alia, G-protein-coupled receptors (GPCRs). In this work, we describe a simple, green and economic method for the preparation of commendamide 1a, a GPCR G2A/132 agonist. The developed protocol is general and could also be applied to the synthesis of deuterated commendamide 1b, as well as to other minor microbiota-derived metabolites, such as the analog 2.
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Affiliation(s)
- Rosaria Villano
- Istituto di Chimica Biomolecolare, Pozzuoli, Italy
- *Correspondence: Rosaria Villano,
| | - Francesco Tinto
- Département de Médecine, Faculté de Médecine, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, QC, Canada
| | - Vincenzo Di Marzo
- Istituto di Chimica Biomolecolare, Pozzuoli, Italy
- Canada Excellence Research Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health, Faculty of Medicine and Faculty of Agricultural and Food Sciences, Centre NUTRISS, Centre de Recherche de l’Institut de Cardiologie et Pneumologie de l’Université et Institut sur la Nutrition et les Aliments Fonctionnels, Université Laval, Quebec City, QC, Canada
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27
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Sartorio MG, Valguarnera E, Hsu FF, Feldman MF. Lipidomics Analysis of Outer Membrane Vesicles and Elucidation of the Inositol Phosphoceramide Biosynthetic Pathway in Bacteroides thetaiotaomicron. Microbiol Spectr 2022; 10:e0063421. [PMID: 35080445 PMCID: PMC8791184 DOI: 10.1128/spectrum.00634-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/19/2021] [Indexed: 12/24/2022] Open
Abstract
Approximately one-third of the human colonic microbiome is formed by bacteria from the genus Bacteroides. These bacteria produce a large amount of uniformly sized outer membrane vesicles (OMVs), which are equipped with hydrolytic enzymes that play a role in the degradation of diet- and host-derived glycans. In this work, we characterize the lipid composition of membranes and OMVs from Bacteroides thetaiotaomicron VPI-5482. Liquid chromatography-mass spectrometry (LC-MS) analysis indicated that OMVs carry sphingolipids, glycerophospholipids, and serine-dipeptide lipids. Sphingolipid species represent more than 50% of the total lipid content of OMVs. The most abundant sphingolipids in OMVs are ethanolamine phosphoceramide (EPC) and inositol phosphoceramide (IPC). Bioinformatics analysis allowed the identification of the BT1522-1526 operon putatively involved in IPC synthesis. Mutagenesis studies revealed that BT1522-1526 is essential for the synthesis of phosphatidylinositol (PI) and IPC, confirming the role of this operon in the biosynthesis of IPC. BT1522-1526 mutant strains lacking IPC produced OMVs that were indistinguishable from the wild-type strain, indicating that IPC sphingolipid species are not involved in OMV biogenesis. Given the known role of sphingolipids in immunomodulation, we suggest that OMVs may act as long-distance vehicles for the delivery of sphingolipids in the human gut. IMPORTANCE Sphingolipids are essential membrane lipid components found in eukaryotes that are also involved in cell signaling processes. Although rare in bacteria, sphingolipids are produced by members of the phylum Bacteroidetes, human gut commensals. Here, we determined that OMVs carry sphingolipids and other lipids of known signaling function. Our results demonstrate that the BT1522-1526 operon is required for IPC biosynthesis in B. thetaiotaomicron.
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Affiliation(s)
- Mariana G. Sartorio
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Ezequiel Valguarnera
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Fong-Fu Hsu
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States
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28
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Schiano Moriello A, Di Marzo V, Petrosino S. Mutual Links between the Endocannabinoidome and the Gut Microbiome, with Special Reference to Companion Animals: A Nutritional Viewpoint. Animals (Basel) 2022; 12:ani12030348. [PMID: 35158670 PMCID: PMC8833664 DOI: 10.3390/ani12030348] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/21/2022] [Accepted: 01/30/2022] [Indexed: 12/07/2022] Open
Abstract
There is growing evidence that perturbation of the gut microbiome, known as “dysbiosis”, is associated with the pathogenesis of human and veterinary diseases that are not restricted to the gastrointestinal tract. In this regard, recent studies have demonstrated that dysbiosis is linked to the pathogenesis of central neuroinflammatory disorders, supporting the existence of the so-called microbiome-gut-brain axis. The endocannabinoid system is a recently recognized lipid signaling system and termed endocannabinoidome monitoring a variety of body responses. Accumulating evidence demonstrates that a profound link exists between the gut microbiome and the endocannabinoidome, with mutual interactions controlling intestinal homeostasis, energy metabolism and neuroinflammatory responses during physiological conditions. In the present review, we summarize the latest data on the microbiome-endocannabinoidome mutual link in health and disease, focalizing the attention on gut dysbiosis and/or altered endocannabinoidome tone that may distort the bidirectional crosstalk between these two complex systems, thus leading to gastrointestinal and metabolic diseases (e.g., idiopathic inflammation, chronic enteropathies and obesity) as well as neuroinflammatory disorders (e.g., neuropathic pain and depression). We also briefly discuss the novel possible dietary interventions based not only on probiotics and/or prebiotics, but also, and most importantly, on endocannabinoid-like modulators (e.g., palmitoylethanolamide) for intestinal health and beyond.
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Affiliation(s)
- Aniello Schiano Moriello
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Napoli, Italy; (A.S.M.); (V.D.M.)
- Epitech Group SpA, Via Einaudi 13, 35030 Padova, Italy
| | - Vincenzo Di Marzo
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Napoli, Italy; (A.S.M.); (V.D.M.)
- Canada Excellence Research Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health, CRIUCPQ and INAF, Centre NUTRISS, Faculties of Medicine and Agriculture and Food Sciences, Université Laval, Quebéc City, QC G1V 4G5, Canada
| | - Stefania Petrosino
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Napoli, Italy; (A.S.M.); (V.D.M.)
- Epitech Group SpA, Via Einaudi 13, 35030 Padova, Italy
- Correspondence:
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29
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Structures and functions of the gut microbial lipidome. Biochim Biophys Acta Mol Cell Biol Lipids 2022; 1867:159110. [PMID: 34995792 DOI: 10.1016/j.bbalip.2021.159110] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/19/2021] [Accepted: 12/24/2021] [Indexed: 12/26/2022]
Abstract
Microbial lipids provide signals that are responsible for maintaining host health and controlling disease. The differences in the structures of microbial lipids have been shown to alter receptor selectivity and agonist/antagonist activity. Advanced lipidomics is an emerging field that helps to elucidate the complex bacterial lipid diversity. The use of cutting-edge technologies is expected to lead to the discovery of new functional metabolites involved in host homeostasis. This review aims to describe recent updates on functional lipid metabolites derived from gut microbiota, their structure-activity relationships, and advanced lipidomics technologies.
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30
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Abstract
The gut microbiome produces chemically diverse small molecules to interact with the host, conveying signals from the gut to the whole system. The microbial metabolites feature several unique modes of interaction with host targets, which fits well into the balanced and networked fashion of biological regulation. Hence, fully unveiling the targetome of signaling microbial metabolites may offer new insights into host health and disease, expand the repertoire of druggable targets, and enlighten a bioinspired path to drug design and discovery. In this review, we present an updated understanding of how microbial metabolite interaction with host targets finely orchestrates and integrates multiple signals to pathophysiological phenotypes, contributing new insights into organ crosstalk and holistic homeostasis maintenance in biological systems. We discuss strategies and open questions for mining and biomimicking the microbial metabolite-targetome interactions for pharmacological manipulation, which may lead to a new paradigm of drug discovery.
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Affiliation(s)
- Xiao Zheng
- State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaoying Cai
- State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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31
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Next-generation microbial drugs developed from microbiome's natural products. ADVANCES IN GENETICS 2021; 108:341-382. [PMID: 34844715 DOI: 10.1016/bs.adgen.2021.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Scientists working in natural products chemistry have been enticed by the current advancements being made in the discovery of novel "magic bullets" from microbes homed to all conceivable environments. Even though researchers continue to face challenges funneling the novel bioactive compounds in the global therapeutic industries, it seems most likely that the discovery of some "hit molecules" with significant biomedical applications is not that far. We applaud novel natural products for their ability to combat the spread of superbugs and aid in the prevention of currently observed antibiotic resistance. This in-depth investigation covers a wide range of microbiomes with a proclivity for synthesizing novel compounds to combat the spread of superbugs. Furthermore, we use this opportunity to explore various groups of secondary metabolites and their biosynthetic pathways in various microbiota found in mammals, insects, and humans. This systematic study, when taken as a whole, offers detail understanding on the biomedical fate of various groups of compounds originated from diverse microbiomes. For gathering all information that has been uncovered and released so far, we have also presented the huge diversity of microbes that are associated with humans and their metabolic products. To conclude, this concrete review suggests novel ideas that will prove immensely helpful in reducing the danger posed by superbugs while also improving the efficacy of antibiotics.
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32
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Bishai JD, Palm NW. Small Molecule Metabolites at the Host-Microbiota Interface. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:1725-1733. [PMID: 34544815 PMCID: PMC8500551 DOI: 10.4049/jimmunol.2100528] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/09/2021] [Indexed: 01/15/2023]
Abstract
The trillions of bacteria that constitutively colonize the human gut collectively generate thousands of unique small molecules. These microbial metabolites can accumulate both locally and systemically and potentially influence nearly all aspects of mammalian biology, including immunity, metabolism, and even mood and behavior. In this review, we briefly summarize recent work identifying bioactive microbiota metabolites, the means through which they are synthesized, and their effects on host physiology. Rather than offering an exhaustive list of all known bioactive microbial small molecules, we select a few examples from each key class of metabolites to illustrate the diverse impacts of microbiota-derived compounds on the host. In addition, we attempt to address the microbial logic behind specific biotransformations. Finally, we outline current and emerging strategies for identifying previously undiscovered bioactive microbiota metabolites that may shape human health and disease.
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Affiliation(s)
- Jason D Bishai
- Department of Microbial Pathogenesis, Yale School of Medicine, Yale University, New Haven, CT; and
| | - Noah W Palm
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
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33
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Piscotta FJ, Whitfield ST, Nakashige TG, Estrela AB, Ali T, Brady SF. Multiplexed functional metagenomic analysis of the infant microbiome identifies effectors of NF-κB, autophagy, and cellular redox state. Cell Rep 2021; 36:109746. [PMID: 34551287 PMCID: PMC8480279 DOI: 10.1016/j.celrep.2021.109746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/19/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023] Open
Abstract
The human microbiota plays a critical role in host health. Proper development of the infant microbiome is particularly important. Its dysbiosis leads to both short-term health issues and long-term disorders lasting into adulthood. A central way in which the microbiome interacts with the host is through the production of effector molecules, such as proteins and small molecules. Here, a metagenomic library constructed from 14 infant stool microbiomes is analyzed for the production of effectors that modulate three distinct host pathways: immune response (nuclear factor κB [NF-κB] activation), autophagy (LC3-B puncta formation), and redox potential (NADH:NAD ratio). We identify microbiome-encoded bioactive metabolites, including commendamide and hydrogen sulfide and their associated biosynthetic genes, as well as a previously uncharacterized autophagy-inducing operon from Klebsiella spp. This work extends our understanding of microbial effector molecules that are known to influence host pathways. Parallel functional screening of metagenomic libraries can be easily expanded to investigate additional host processes. Construction of a metagenomic library from stool of infants A multiplexed screen for bacterial effectors of host cellular processes Identification of microbiome-encoded effectors hydrogen sulfide and commendamide The products of a Klebsiella pneumoniae operon induce autophagy
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Affiliation(s)
- Frank J Piscotta
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Shawn T Whitfield
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Toshiki G Nakashige
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Andreia B Estrela
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Thahmina Ali
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA.
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34
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Dalal N, Jalandra R, Bayal N, Yadav AK, Sharma M, Makharia GK, Kumar P, Singh R, Solanki PR, Kumar A. Gut microbiota-derived metabolites in CRC progression and causation. J Cancer Res Clin Oncol 2021; 147:3141-3155. [PMID: 34273006 DOI: 10.1007/s00432-021-03729-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/04/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Based on recent research reports, dysbiosis and improper concentrations of microbial metabolites in the gut may result into the carcinogenesis of colorectal cancer. Recent advancement also highlights the involvement of bacteria and their secreted metabolites in the cancer causation. Gut microbial metabolites are functional output of the host-microbiota interactions and produced by anaerobic fermentation of food components in the diet. They contribute to influence variety of biological mechanisms including inflammation, cell signaling, cell-cycle disruption which are majorly disrupted in carcinogenic activities. PURPOSE In this review, we intend to discuss recent updates and possible molecular mechanisms to provide the role of bacterial metabolites, gut bacteria and diet in the colorectal carcinogenesis. Recent evidences have proposed the role of bacteria, such as Fusobacterium nucleaturm, Streptococcus bovis, Helicobacter pylori, Bacteroides fragilis and Clostridium septicum, in the carcinogenesis of CRC. Metagenomic study confirmed that these bacteria are in increased abundance in CRC patient as compared to healthy individuals and can cause inflammation and DNA damage which can lead to development of cancer. These bacteria produce metabolites, such as secondary bile salts from primary bile salts, hydrogen sulfide, trimethylamine-N-oxide (TMAO), which are likely to promote inflammation and subsequently cancer development. CONCLUSION Recent studies suggest that gut microbiota-derived metabolites have a role in CRC progression and causation and hence, could be implicated in CRC diagnosis, prognosis and therapy.
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Affiliation(s)
- Nishu Dalal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
- Department of Environmental Science, Satyawati College, Delhi University, Delhi, 110052, India
| | - Rekha Jalandra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
- Department of Zoology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Nitin Bayal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
| | - Amit K Yadav
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Minakshi Sharma
- Department of Zoology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Govind K Makharia
- Department of Gastroenterology and Human Nutrition, AIIMS, New Delhi, 110029, India
| | - Pramod Kumar
- Sri Aurobindo College, Delhi University, New Delhi, 110067, India
| | - Rajeev Singh
- Department of Environmental Science, Satyawati College, Delhi University, Delhi, 110052, India
| | - Pratima R Solanki
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India.
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35
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Crofts TS, McFarland AG, Hartmann EM. Mosaic Ends Tagmentation (METa) Assembly for Highly Efficient Construction of Functional Metagenomic Libraries. mSystems 2021; 6:e0052421. [PMID: 34184912 PMCID: PMC8269240 DOI: 10.1128/msystems.00524-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/07/2021] [Indexed: 11/20/2022] Open
Abstract
Functional metagenomic libraries, physical bacterial libraries which allow the high-throughput capture and expression of microbiome genes, have been instrumental in the sequence-naive and cultivation-independent exploration of metagenomes. However, preparation of these libraries is often limited by their high DNA input requirement and their low cloning efficiency. Here, we describe a new method, mosaic ends tagmentation (METa) assembly, for highly efficient functional metagenomic library preparation. We applied tagmentation to metagenomic DNA from soil and gut microbiomes to prepare DNA inserts for high-throughput cloning into functional metagenomic libraries. The presence of mosaic end sequences in the resulting DNA fragments synergized with homology-based assembly cloning to result in a 300-fold increase in cloning efficiency compared to traditional blunt-cloning-based protocols. We show that compared to published libraries prepared by state-of-the-art protocols, METa assembly is on average ca. 20- to 200-fold more efficient and can prepare gigabase-sized libraries with as little as 200 ng of input DNA. We show the usefulness of METa assembly first by using a normative 5-μg mass of soil metagenomic DNA to prepare a 700-Gb library that allowed us to discover novel nourseothricin resistance genes and a potentially new mode of resistance to this antibiotic and second by using only 300 ng of goose fecal metagenomic DNA to prepare a 27-Gb library that captured numerous tetracycline and colistin resistance genes. METa assembly provides a streamlined, flexible, and efficient method for preparing functional metagenomic libraries, enabling new avenues of genetic and biochemical research into low-biomass or scarce microbiomes. IMPORTANCE Medically and industrially important genes can be recovered from microbial communities by high-throughput sequencing, but precise annotation is often limited to characterized genes and their relatives. Cloning a metagenome en masse into an expression host to produce a functional metagenomic library, directly connecting genes to functions, is a sequence-naive and cultivation-independent method to discover novel genes. The process of preparing these libraries is DNA greedy and inefficient, however. Here, we describe a library preparation method that is an order of magnitude more efficient and less DNA greedy. This method is consistently efficient across libraries prepared from cultures, a soil microbiome, and a goose fecal microbiome and allowed us to discover new antibiotic resistance genes and mechanisms. This library preparation method will potentially allow the functional metagenomic exploration of microbiomes that were previously off limits due to their rarity or low microbial biomass, such as biomedical swabs or exotic samples.
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Affiliation(s)
- Terence S. Crofts
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Alexander G. McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
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36
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Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids. Nat Microbiol 2021; 6:792-805. [PMID: 33846627 DOI: 10.1038/s41564-021-00887-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/01/2021] [Indexed: 02/01/2023]
Abstract
Human physiology is regulated by endogenous signalling compounds, including fatty acid amides (FAAs), chemical mimics of which are made by bacteria. The molecules produced by human-associated microbes are difficult to identify because they may only be made in a local niche or they require a substrate sourced from the host, diet or other microbes. We identified a set of uncharacterized gene clusters in metagenomics data from the human gut microbiome. These clusters were discovered to make FAAs by fusing exogenous fatty acids with amines. Using an in vitro assay, we tested their ability to incorporate 25 fatty acids and 53 amines known to be present in the human gut, from which the production of six FAAs was deduced (oleoyl dopamine, oleoyl tyramine, lauroyl tryptamine, oleoyl aminovaleric acid, α-linolenoyl phenylethylamine and caproyl tryptamine). These molecules were screened against panels of human G-protein-coupled receptors to deduce their putative human targets. Lauroyl tryptamine is found to be an antagonist to the immunomodulatory receptor EBI2 against its native oxysterol ligand (0.98 μM half-maximal inhibitory concentration), is produced in culture by Eubacterium rectale and is present in human faecal samples. FAAs produced by Clostridia may serve as a mechanism to modulate their host by mimicking human signalling molecules.
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37
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Sharma N, Akhade AS, Ismaeel S, Qadri A. Serum-borne lipids amplify TLR-activated inflammatory responses. J Leukoc Biol 2021; 109:821-831. [PMID: 32717772 DOI: 10.1002/jlb.3ab0720-241rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/10/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
TLRs recognize conserved pathogen associated molecular patterns and generate innate immune responses. Several circulating and cell membrane associated proteins have been shown to collaborate with TLRs in sensing microbial ligands and promoting inflammatory responses. Here, we show that serum and serum-borne lipids including lysophosphatidylcholine (LPC) amplify inflammatory responses from intestinal epithelial cells and mononuclear phagocytes primed with microbial TLR ligands. Treatment with the inhibitors of G protein-coupled receptor (GPCR) signaling, suramin, or pertussis toxin (PT), the inhibitor of JNK-MAPK, or knockdown of LPC response-regulating GPCR, G2A, decreases the augmentation brought about by serum or LPC in TLR-induced inflammatory response. In vivo administration of PT or anti-G2A antibody reduces TLR2-activated cytokine secretion. The ability of host lipids to costimulate TLR-generated cellular responses represents a novel pathway for the amplification of innate immunity and inflammation.
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Affiliation(s)
- Naveen Sharma
- Hybridoma Laboratory, National Institute of Immunology, New Delhi, India
- Department of Immunology, The University of Texas MD Anderson Cancer Centre, Houston, Texas, USA
| | - Ajay Suresh Akhade
- Hybridoma Laboratory, National Institute of Immunology, New Delhi, India
- Institute for Systems Biology, Seattle, Washington, USA
| | - Sana Ismaeel
- Hybridoma Laboratory, National Institute of Immunology, New Delhi, India
| | - Ayub Qadri
- Hybridoma Laboratory, National Institute of Immunology, New Delhi, India
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38
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Abstract
The human microbiome encodes a second genome that dwarfs the genetic capacity of the host. Microbiota-derived small molecules can directly target human cells and their receptors or indirectly modulate host responses through functional interactions with other microbes in their ecological niche. Their biochemical complexity has profound implications for nutrition, immune system development, disease progression, and drug metabolism, as well as the variation in these processes that exists between individuals. While the species composition of the human microbiome has been deeply explored, detailed mechanistic studies linking specific microbial molecules to host phenotypes are still nascent. In this review, we discuss challenges in decoding these interaction networks, which require interdisciplinary approaches that combine chemical biology, microbiology, immunology, genetics, analytical chemistry, bioinformatics, and synthetic biology. We highlight important classes of microbiota-derived small molecules and notable examples. An understanding of these molecular mechanisms is central to realizing the potential of precision microbiome editing in health, disease, and therapeutic responses.
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Affiliation(s)
- Emilee E Shine
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA; .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA.,Current affiliation: Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Jason M Crawford
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06536, USA; .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA.,Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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39
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Lamousé-Smith E, Kelly D, De Cremoux I. Designing bugs as drugs: exploiting the gut microbiome. Am J Physiol Gastrointest Liver Physiol 2021; 320:G295-G303. [PMID: 33264062 PMCID: PMC8609565 DOI: 10.1152/ajpgi.00381.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The extensive investigation of the human microbiome and the accumulating evidence regarding its critical relationship to human health and disease has advanced recognition of its potential as the next frontier of drug development. The rapid development of technologies, directed at understanding the compositional and functional dynamics of the human microbiome, and the ability to mine for novel therapeutic targets and biomarkers are leading innovative efforts to develop microbe-derived drugs that can prevent and treat autoimmune, metabolic, and infectious diseases. Increasingly, academics, biotechs, investors, and large pharmaceutical companies are partnering to collectively advance various therapeutic modalities ranging from live bacteria to small molecules. We review the leading platforms in current development focusing on live microbial consortia, engineered microbes, and microbial-derived metabolites. We will also touch on how the field is addressing and challenging the traditional definitions of pharmacokinetics and pharmacodynamics, dosing, toxicity, and safety to advance the development of these novel and cutting-edge therapeutics into the clinic.
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40
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Icke C, Hodges FJ, Pullela K, McKeand SA, Bryant JA, Cunningham AF, Cole JA, Henderson IR. Glycine acylation and trafficking of a new class of bacterial lipoprotein by a composite secretion system. eLife 2021; 10:63762. [PMID: 33625358 PMCID: PMC7943197 DOI: 10.7554/elife.63762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/23/2021] [Indexed: 01/21/2023] Open
Abstract
Protein acylation is critical for many cellular functions across all domains of life. In bacteria, lipoproteins have important roles in virulence and are targets for the development of antimicrobials and vaccines. Bacterial lipoproteins are secreted from the cytosol via the Sec pathway and acylated on an N-terminal cysteine residue through the action of three enzymes. In Gram-negative bacteria, the Lol pathway transports lipoproteins to the outer membrane. Here, we demonstrate that the Aat secretion system is a composite system sharing similarity with elements of a type I secretion systems and the Lol pathway. During secretion, the AatD subunit acylates the substrate CexE on a highly conserved N-terminal glycine residue. Mutations disrupting glycine acylation interfere with membrane incorporation and trafficking. Our data reveal CexE as the first member of a new class of glycine-acylated lipoprotein, while Aat represents a new secretion system that displays the substrate lipoprotein on the cell surface.
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Affiliation(s)
- Christopher Icke
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Freya J Hodges
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Karthik Pullela
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | | | | | - Adam F Cunningham
- Institute of Microbiology and Infection, Birmingham, United Kingdom.,Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Jeff A Cole
- Institute of Microbiology and Infection, Birmingham, United Kingdom
| | - Ian R Henderson
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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41
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The endocannabinoid system. Essays Biochem 2021; 64:485-499. [PMID: 32648908 DOI: 10.1042/ebc20190086] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 12/21/2022]
Abstract
Thirty years ago, the discovery of a cannabinoid (CB) receptor that interacts with the psychoactive compound in Cannabis led to the identification of anandamide, an endogenous receptor ligand or endocannabinoid. Research on endocannabinoids has since exploded, and additional receptors along with their lipid mediators and signaling pathways continue to be revealed. Specifically, in humans, the release of endocannabinoids from membrane lipids occurs on demand and the signaling process is rapidly attenuated by the breakdown of the ligand suggesting a tight regulation of the endocannabinoid system (ECS). Additionally, the varying distribution of CB receptors between the central nervous system and other tissues allows for the ECS to participate in a wide range of cognitive and physiological processes. Select plant-derived 'phyto'cannabinoids such as Δ-9-tetrahydrocannabinol (Δ9-THC) bind to the CB receptors and trigger the ECS, and in the case of Δ9-THC, while it has therapeutic value, can also produce detrimental effects. Current research is aimed at the identification of additional phytocannabinoids with minimal psychotropic effects with potential for therapeutic development. Although decades of research on the ECS and its components have expanded our understanding of the mechanisms and implications of endocannabinoid signaling in mammals, it continues to evolve. Here, we provide a brief overview of the ECS and its overlap with other related lipid-mediated signaling pathways.
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42
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Abstract
Historically, the focus of type II diabetes mellitus (T2DM) research has been on host metabolism and hormone action. However, emerging evidence suggests that the gut microbiome, commensal microbes that colonize the gastrointestinal tract, also play a significant role in T2DM pathogenesis. Specifically, gut microbes metabolize what is available to them through the host diet to produce small molecule metabolites that can have endocrine-like effects on human cells. In fact, the meta-organismal crosstalk between gut microbe-generated metabolites and host receptor systems may represent an untapped therapeutic target for those at risk for or suffering from T2DM. Recent evidence suggests that gut microbe-derived metabolites can impact host adiposity, insulin resistance, and hormone secretion to collectively impact T2DM progression. Here we review the current evidence that structurally diverse gut microbe-derived metabolites, including short chain fatty acids, secondary bile acids, aromatic metabolites, trimethylamine-N-oxide, polyamines, and N-acyl amides, that can engage with host receptors in an endocrine-like manner to promote host metabolic disturbance associated with T2DM. Although these microbe-host signaling circuits are not as well understood as host hormonal signaling, they hold untapped potential as new druggable targets to improve T2DM complications. Whether drugs that selectively target meta-organismal endocrinology will be safe and efficacious in treating T2DM is a key new question in the field of endocrinology. Here we discuss the opportunities and challenges in targeting the gut microbial endocrine organ for the treatment of diabetes and potentially many other diseases where diet-microbe-host interactions play a contributory role.
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Affiliation(s)
- William Massey
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, OH, USA
- Center for Microbiome and Human Health, Lerner Research Institute of the Cleveland Clinic, Cleveland, OH, USA
| | - J Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute of the Cleveland Clinic, Cleveland, OH, USA
- Center for Microbiome and Human Health, Lerner Research Institute of the Cleveland Clinic, Cleveland, OH, USA
- Correspondence: J. Mark Brown, Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA.
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43
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Lamichhane S, Sen P, Alves MA, Ribeiro HC, Raunioniemi P, Hyötyläinen T, Orešič M. Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations. Metabolites 2021; 11:55. [PMID: 33467644 PMCID: PMC7830997 DOI: 10.3390/metabo11010055] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/09/2021] [Accepted: 01/12/2021] [Indexed: 02/08/2023] Open
Abstract
Various studies aiming to elucidate the role of the gut microbiome-metabolome co-axis in health and disease have primarily focused on water-soluble polar metabolites, whilst non-polar microbial lipids have received less attention. The concept of microbiota-dependent lipid biotransformation is over a century old. However, only recently, several studies have shown how microbial lipids alter intestinal and circulating lipid concentrations in the host, thus impacting human lipid homeostasis. There is emerging evidence that gut microbial communities play a particularly significant role in the regulation of host cholesterol and sphingolipid homeostasis. Here, we review and discuss recent research focusing on microbe-host-lipid co-metabolism. We also discuss the interplay of human gut microbiota and molecular lipids entering host systemic circulation, and its role in health and disease.
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Affiliation(s)
- Santosh Lamichhane
- Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; (P.S.); (M.A.A.); (H.C.R.); (P.R.); (M.O.)
| | - Partho Sen
- Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; (P.S.); (M.A.A.); (H.C.R.); (P.R.); (M.O.)
- School of Medical Sciences, Orebro University, 702 81 Orebro, Sweden
| | - Marina Amaral Alves
- Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; (P.S.); (M.A.A.); (H.C.R.); (P.R.); (M.O.)
| | - Henrique C. Ribeiro
- Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; (P.S.); (M.A.A.); (H.C.R.); (P.R.); (M.O.)
| | - Peppi Raunioniemi
- Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; (P.S.); (M.A.A.); (H.C.R.); (P.R.); (M.O.)
| | | | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; (P.S.); (M.A.A.); (H.C.R.); (P.R.); (M.O.)
- School of Medical Sciences, Orebro University, 702 81 Orebro, Sweden
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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A microbial metabolite synergizes with endogenous serotonin to trigger C. elegans reproductive behavior. Proc Natl Acad Sci U S A 2020; 117:30589-30598. [PMID: 33199611 DOI: 10.1073/pnas.2017918117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Natural products are a major source of small-molecule therapeutics, including those that target the nervous system. We have used a simple serotonin-dependent behavior of the roundworm Caenorhabditis elegans, egg laying, to perform a behavior-based screen for natural products that affect serotonin signaling. Our screen yielded agonists of G protein-coupled serotonin receptors, protein kinase C agonists, and a microbial metabolite not previously known to interact with serotonin signaling pathways: the disulfide-bridged 2,5-diketopiperazine gliotoxin. Effects of gliotoxin on egg-laying behavior required the G protein-coupled serotonin receptors SER-1 and SER-7, and the Gq ortholog EGL-30. Furthermore, mutants lacking serotonergic neurons and mutants that cannot synthesize serotonin were profoundly resistant to gliotoxin. Exogenous serotonin restored their sensitivity to gliotoxin, indicating that this compound synergizes with endogenous serotonin to elicit behavior. These data show that a microbial metabolite with no structural similarity to known serotonergic agonists potentiates an endogenous serotonin signal to affect behavior. Based on this study, we suggest that microbial metabolites are a rich source of functionally novel neuroactive molecules.
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Herrema H, Niess JH. Intestinal microbial metabolites in human metabolism and type 2 diabetes. Diabetologia 2020; 63:2533-2547. [PMID: 32880688 PMCID: PMC7641949 DOI: 10.1007/s00125-020-05268-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022]
Abstract
Humans with the metabolic syndrome and type 2 diabetes have an altered gut microbiome. Emerging evidence indicates that it is not only the microorganisms and their structural components, but also their metabolites that influences the host and contributes to the development of the metabolic syndrome and type 2 diabetes. Here, we discuss some of the mechanisms underlying how microbial metabolites are recognised by the host or are further processed endogenously in the context of type 2 diabetes. We discuss the possibility that gut-derived microbial metabolites fuel the development of the metabolic syndrome and type 2 diabetes. Graphical abstract.
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Affiliation(s)
- Hilde Herrema
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands.
| | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, Hebelstrasse 20, CH-4031, Basel, Switzerland.
- University Center for Gastrointestinal and Liver Diseases, St Clara Hospital and University Hospital of Basel, Basel, Switzerland.
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Rodriguez J, Olivares M, Delzenne NM. Implication of the Gut Microbiota in Metabolic Inflammation Associated with Nutritional Disorders and Obesity. Mol Nutr Food Res 2020; 65:e1900481. [PMID: 33111450 DOI: 10.1002/mnfr.201900481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/22/2020] [Indexed: 12/12/2022]
Abstract
SCOPE More than a decade ago, the concept of "metabolic endotoxemia" is elaborated on the fact that some bacterial components, classified as microbial associated membrane pathogens (MAMPs) can pass through the gut barrier and create a systemic low tone inflammation. METHODS AND RESULTS The translocation of lipopolysaccharides and its contribution to systemic inflammation are largely studied in murine models of obesity, allowing to unravel the molecular pathways involved in the process. Many different pathological contexts evoke the loss of gut barrier as an event contributing to inflammation and thereby driving metabolic and behavioral alterations. CONCLUSION This review describes the role of nutrition as a modulator of metabolic regulation and focuses on the contribution of the gut microbiota in the process of the production of a large diversity of bioactive metabolites. The two first sections of the review will be dedicated to the impact of nutritional disorders on both the gut microbiota composition and on metabolic inflammation. The last and more prominent section will describe the role of different nutrient-derived gut metabolites on the gut barrier integrity, metabolic inflammation, and peripheral tissue alterations during obesity or associated complications.
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Affiliation(s)
- Julie Rodriguez
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, 1200, Belgium
| | - Marta Olivares
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, 1200, Belgium
| | - Nathalie M Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, 1200, Belgium
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Naz F, Arish M. GPCRs as an emerging host-directed therapeutic target against mycobacterial infection: From notion to reality. Br J Pharmacol 2020; 179:4899-4909. [PMID: 33150959 DOI: 10.1111/bph.15315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/12/2020] [Accepted: 10/22/2020] [Indexed: 11/26/2022] Open
Abstract
Mycobacterium tuberculosis (M. tb) is one of the successful pathogens and claim millions of deaths across the globe. The emergence of drug resistance in M. tb has created new hurdles in the tuberculosis elimination programme worldwide. Hence, there is an unmet medical need for alternative therapy, which could be achieved by targeting the host's critical signalling pathways that are compromised during M. tb infection. In this review, we have summarized some of the findings involving the modulation of host GPCRs in the regulation of the mycobacterial infection. Understanding the role of these GPCRs not only unravels signalling pathways during infection but also provides clues for targeting critical signalling intermediates for the development of GPCR-based host-directive therapy.
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Affiliation(s)
- Farha Naz
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohd Arish
- JH-Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India.,Department of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, 55905, USA
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Jackson MI, Waldy C, Jewell DE. Dietary resistant starch preserved through mild extrusion of grain alters fecal microbiome metabolism of dietary macronutrients while increasing immunoglobulin A in the cat. PLoS One 2020; 15:e0241037. [PMID: 33141838 PMCID: PMC7608938 DOI: 10.1371/journal.pone.0241037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
Dietary digestion-resistant starch (RS) provides health benefits to the host via gut microbiome-mediated metabolism. The degree to which cats manifest beneficial changes in response to RS intake was examined. Healthy cats (N = 36) were fed identically formulated foods processed under high (n = 17) or low (n = 19) shear extrusion conditions (low and high RS levels [LRS and HRS], respectively). Fecal samples collected after 3 and 6 weeks' feeding were assayed for stool firmness score, short-chain fatty acids, ammonia, and changes to the global metabolome and microbiome; fecal immunoglobulin A (IgA) was analyzed at week 6. Few differences were seen in proximate analyses of the foods; stool firmness scores did not differ. In cats consuming HRS food, concentrations of fecal butyrate and the straight chain:branched chain fatty acid ratio were significantly greater in feces at both weeks 3 and 6, while fecal ammonia was reduced at week 6 relative to feces from LRS-fed cats. Fecal IgA concentrations were significantly higher at week 6 with HRS food. RS consumption altered 47% of the fecal metabolome; RS-derived sugars and metabolites associated with greater gut health, including indoles and polyamines, increased in the cats consuming HRS food relative to those fed the LS food, while endocannabinoid N-acylethanolamines decreased. Consumption of HRS food increased concentrations of the ketone body 3-hydroxybutyrate in feces and elevated concentrations of reduced members of NADH-coupled redox congeners and NADH precursors. At the microbiome genus-level, 21% of operational taxonomic units were significantly different between food types; many involved taxa with known saccharolytic or proteolytic proclivities. Microbiome taxa richness and Shannon and Simpson alpha diversity were significantly higher in the HRS group at both weeks. These data show that feline consumption of grain-derived RS produces potentially beneficial shifts in microbiota-mediated metabolism and increases IgA production.
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Affiliation(s)
- Matthew I. Jackson
- Pet Nutrition Center, Hill's Pet Nutrition, Inc., Topeka, KS, United States of America
| | - Christopher Waldy
- Pet Nutrition Center, Hill's Pet Nutrition, Inc., Topeka, KS, United States of America
| | - Dennis E. Jewell
- Pet Nutrition Center, Hill's Pet Nutrition, Inc., Topeka, KS, United States of America
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Abstract
Observational findings achieved during the past two decades suggest that the intestinal microbiota may contribute to the metabolic health of the human host and, when aberrant, to the pathogenesis of various common metabolic disorders including obesity, type 2 diabetes, non-alcoholic liver disease, cardio-metabolic diseases and malnutrition. However, to gain a mechanistic understanding of how the gut microbiota affects host metabolism, research is moving from descriptive microbiota census analyses to cause-and-effect studies. Joint analyses of high-throughput human multi-omics data, including metagenomics and metabolomics data, together with measures of host physiology and mechanistic experiments in humans, animals and cells hold potential as initial steps in the identification of potential molecular mechanisms behind reported associations. In this Review, we discuss the current knowledge on how gut microbiota and derived microbial compounds may link to metabolism of the healthy host or to the pathogenesis of common metabolic diseases. We highlight examples of microbiota-targeted interventions aiming to optimize metabolic health, and we provide perspectives for future basic and translational investigations within the nascent and promising research field.
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Feature-based molecular networking in the GNPS analysis environment. Nat Methods 2020; 17:905-908. [PMID: 32839597 PMCID: PMC7885687 DOI: 10.1038/s41592-020-0933-6] [Citation(s) in RCA: 527] [Impact Index Per Article: 131.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 07/22/2020] [Indexed: 12/13/2022]
Abstract
Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present Feature-Based Molecular Networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. The FBMN method brings quantitative analyses, isomeric resolution, including from ion-mobility spectrometry, into molecular networks.
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