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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Beauchamp-Walters J, Aleti G, Herrera L, Debelius J, Lima N, Dalal P, Hong S, Knight R, Rhee KE. Impact of exclusive enteral nutrition on the gut microbiome of children with medical complexity. JPEN J Parenter Enteral Nutr 2023; 47:77-86. [PMID: 35526141 DOI: 10.1002/jpen.2392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/19/2022] [Accepted: 05/01/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Children with medical complexity (CMC) often require enteral tube feedings to meet their nutrition needs. Many, however, experience symptoms of feeding intolerance, such as vomiting and pain. The goal of this analysis was to examine the relationship between diet and the gut microbiome, controlling for medications, among CMC receiving enteral tube feedings, CMC consuming oral nutrition, and healthy controls. Given the variety of available commercial formula preparations, we were also interested in examining the impact of different formula types on the CMC microbiome. METHODS Fecal samples from 91 children (57 CMC and 34 healthy controls) were collected and analyzed. Parents completed clinical and dietary questionnaires. 16S ribosomal RNA amplicon sequencing was completed using the QIIME2 pipeline. RESULTS A significant decrease in alpha diversity among CMC receiving exclusive enteral nutrition (CMC EEN) compared with healthy controls (Shannon P = 0.006 and Faith's phylogenetic distance P = 0.006) was found that was not observed between CMC receiving oral nutrition and healthy controls. Significant differences in beta diversity were also observed between CMC EEN and healthy controls, with CMC EEN having a greater relative abundance of Enterobacteriaceae and obligate anaerobes. Differences were also noted between CMC EEN and CMC receiving oral nutrition (Aitchison distance P = 0.001); however, no differences were observed between CMC receiving oral nutrition and healthy controls. CONCLUSION Despite similarities in medication profiles, CMC EEN have decreased alpha diversity and differences in beta diversity compared with healthy controls not observed in CMC receiving oral nutrition, highlighting the impact of diet over medications.
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Affiliation(s)
- Julia Beauchamp-Walters
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Rady's Children's Hospital, San Diego, California, USA
| | - Gajender Aleti
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA
| | - Lourdes Herrera
- Department of Pediatrics, Billings Clinic, Billings, Montana, USA
| | - Justine Debelius
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie Lima
- Crean College of Health and Behavioral Sciences, Chapman University, Orange, California, USA
| | - Pritha Dalal
- Rady's Children's Hospital, San Diego, California, USA.,Department of Orthopedics, University of California San Diego, La Jolla, California, USA
| | - Suzi Hong
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA.,Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA.,Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Kyung E Rhee
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Rady's Children's Hospital, San Diego, California, USA
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3
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Terlouw BR, Blin K, Navarro-Muñoz JC, Avalon NE, Chevrette MG, Egbert S, Lee S, Meijer D, Recchia MJ, Reitz Z, van Santen J, Selem-Mojica N, Tørring T, Zaroubi L, Alanjary M, Aleti G, Aguilar C, Al-Salihi SA, Augustijn H, Avelar-Rivas J, Avitia-Domínguez L, Barona-Gómez F, Bernaldo-Agüero J, Bielinski VA, Biermann F, Booth T, Carrion Bravo V, Castelo-Branco R, Chagas F, Cruz-Morales P, Du C, Duncan K, Gavriilidou A, Gayrard D, Gutiérrez-García K, Haslinger K, Helfrich EN, van der Hooft JJ, Jati A, Kalkreuter E, Kalyvas N, Kang K, Kautsar S, Kim W, Kunjapur A, Li YX, Lin GM, Loureiro C, Louwen JR, Louwen NL, Lund G, Parra J, Philmus B, Pourmohsenin B, Pronk LU, Rego A, Rex D, Robinson S, Rosas-Becerra L, Roxborough E, Schorn M, Scobie D, Singh K, Sokolova N, Tang X, Udwary D, Vigneshwari A, Vind K, Vromans SJM, Waschulin V, Williams S, Winter J, Witte T, Xie H, Yang D, Yu J, Zdouc M, Zhong Z, Collemare J, Linington R, Weber T, Medema M. MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Res 2022; 51:D603-D610. [PMID: 36399496 PMCID: PMC9825592 DOI: 10.1093/nar/gkac1049] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/07/2022] [Accepted: 10/21/2022] [Indexed: 11/19/2022] Open
Abstract
With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.
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Affiliation(s)
| | | | - Jorge C Navarro-Muñoz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0212, USA
| | - Marc G Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Susan Egbert
- Department of Chemistry, University of Manitoba, 66 Chancellors Cir, Winnipeg, MB R3T 2N2, Canada
| | - Sanghoon Lee
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - David Meijer
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Michael J J Recchia
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Zachary L Reitz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Jeffrey A van Santen
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada,Unnatural Products, 2161 Delaware Ave. Suite A, Santa Cruz, CA 95060, USA
| | | | - Thomas Tørring
- Department of Biological and Chemical Engineering, Aarhus University, Denmark
| | - Liana Zaroubi
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Gajender Aleti
- Food and Animal Sciences, Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - César Aguilar
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | | | - Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands
| | - J Abraham Avelar-Rivas
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México
| | - Luis A Avitia-Domínguez
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands,Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México
| | - Francisco Barona-Gómez
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands,Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México
| | - Jordan Bernaldo-Agüero
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Friederike Biermann
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Institute of Molecular Bio Science, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Thomas J Booth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark,School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Victor J Carrion Bravo
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands,Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Raquel Castelo-Branco
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal,Faculty of Sciences, University of Porto, 4150-179 Porto, Portugal
| | - Fernanda O Chagas
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Pablo Cruz-Morales
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Chao Du
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow, G4 ORE UK
| | - Athina Gavriilidou
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany,Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Damien Gayrard
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Karina Gutiérrez-García
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA
| | - Kristina Haslinger
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Eric J N Helfrich
- Institute of Molecular Bio Science, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Afif P Jati
- Indonesian Society of Bioinformatics And Biodiversity, Indonesia
| | - Edward Kalkreuter
- Department of Chemistry, University of Florida Scripps Biomedical Research, 110 Scripps Way, Jupiter, FL 33458, USA
| | - Nikolaos Kalyvas
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women's University, Seoul, South Korea
| | - Satria Kautsar
- Department of Chemistry, University of Florida Scripps Biomedical Research, 110 Scripps Way, Jupiter, FL 33458, USA
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National Universtiy, Suncheon, South Korea
| | - Aditya M Kunjapur
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P.R. China
| | - Geng-Min Lin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catarina Loureiro
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Joris J R Louwen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Nico L L Louwen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - George Lund
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Jonathan Parra
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, 11501-2060, Costa Rica,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica,Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, USA
| | - Bita Pourmohsenin
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany,Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Lotte J U Pronk
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Adriana Rego
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Portugal
| | | | - Serina Robinson
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - L Rodrigo Rosas-Becerra
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands,Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México
| | - Eve T Roxborough
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Darren J Scobie
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow, G4 ORE UK
| | - Kumar Saurabh Singh
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Nika Sokolova
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | | | - Kristiina Vind
- Host-Microbe Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands,NAICONS Srl, 20139 Milan, Italy
| | - Sophie P J M Vromans
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Valentin Waschulin
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK
| | - Sam E Williams
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Jaclyn M Winter
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Thomas E Witte
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Huali Xie
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Key laboratory of Detection for Biotoxins, Ministry of Agriculture and Rural Affairs and Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, China
| | - Dong Yang
- Department of Chemistry and Natural Products Discovery Center, UF Scripps Biomedical Research, University of Florida, Jupiter, FL 33458, USA
| | - Jingwei Yu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Mitja Zdouc
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Zheng Zhong
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Tilmann Weber
- Correspondence may also be addressed to Tilmann Weber. Tel: +45 24896132;
| | - Marnix H Medema
- To whom correspondence should be addressed. Tel: +31 317484706;
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4
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Aleti G, Kohn JN, Troyer EA, Weldon K, Huang S, Tripathi A, Dorrestein PC, Swafford AD, Knight R, Hong S. Salivary bacterial signatures in depression-obesity comorbidity are associated with neurotransmitters and neuroactive dipeptides. BMC Microbiol 2022; 22:75. [PMID: 35287577 PMCID: PMC8919597 DOI: 10.1186/s12866-022-02483-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/25/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Depression and obesity are highly prevalent, often co-occurring conditions marked by inflammation. Microbiome perturbations are implicated in obesity-inflammation-depression interrelationships, but how the microbiome mechanistically contributes to pathology remains unclear. Metabolomic investigations into microbial neuroactive metabolites may offer mechanistic insights into host-microbe interactions. Using 16S sequencing and untargeted mass spectrometry of saliva, and blood monocyte inflammation regulation assays, we identified key microbes, metabolites and host inflammation in association with depressive symptomatology, obesity, and depressive symptomatology-obesity comorbidity. RESULTS Gram-negative bacteria with inflammation potential were enriched relative to Gram-positive bacteria in comorbid obesity-depression, supporting the inflammation-oral microbiome link in obesity-depression interrelationships. Oral microbiome was more highly predictive of depressive symptomatology-obesity co-occurrences than of obesity or depressive symptomatology independently, suggesting specific microbial signatures associated with obesity-depression co-occurrences. Mass spectrometry analysis revealed significant changes in levels of signaling molecules of microbiota, microbial or dietary derived signaling peptides and aromatic amino acids among depressive symptomatology, obesity and comorbid obesity-depression. Furthermore, integration of the microbiome and metabolomics data revealed that key oral microbes, many previously shown to have neuroactive potential, co-occurred with potential neuropeptides and biosynthetic precursors of the neurotransmitters dopamine, epinephrine and serotonin. CONCLUSIONS Together, our findings offer novel insights into oral microbial-brain connection and potential neuroactive metabolites involved.
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Affiliation(s)
- Gajender Aleti
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jordan N Kohn
- 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
| | - Kelly Weldon
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Shi Huang
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Anupriya Tripathi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Pieter C Dorrestein
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, 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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5
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Torralba MG, Aleti G, Li W, Moncera KJ, Lin YH, Yu Y, Masternak MM, Golusinski W, Golusinski P, Lamperska K, Edlund A, Freire M, Nelson KE. Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma. Microb Ecol 2021; 82:1030-1046. [PMID: 33155101 PMCID: PMC8551143 DOI: 10.1007/s00248-020-01596-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/01/2020] [Indexed: 05/14/2023]
Abstract
The human microbiome has been the focus of numerous research efforts to elucidate the pathogenesis of human diseases including cancer. Oral cancer mortality is high when compared with other cancers, as diagnosis often occurs during late stages. Its prevalence has increased in the USA over the past decade and accounts for over 40,000 new cancer patients each year. Additionally, oral cancer pathogenesis is not fully understood and is likely multifactorial. To unravel the relationships that are associated with the oral microbiome and their virulence factors, we used 16S rDNA and metagenomic sequencing to characterize the microbial composition and functional content in oral squamous cell carcinoma (OSCC) tumor tissue, non-tumor tissue, and saliva from 18 OSCC patients. Results indicate a higher number of bacteria belonging to the Fusobacteria, Bacteroidetes, and Firmicutes phyla associated with tumor tissue when compared with all other sample types. Additionally, saliva metaproteomics revealed a significant increase of Prevotella in five OSCC subjects, while Corynebacterium was mostly associated with ten healthy subjects. Lastly, we determined that there are adhesion and virulence factors associated with Streptococcus gordonii as well as from known oral pathogens belonging to the Fusobacterium genera found mostly in OSCC tissues. From these results, we propose that not only will the methods utilized in this study drastically improve OSCC diagnostics, but the organisms and specific virulence factors from the phyla detected in tumor tissue may be excellent biomarkers for characterizing disease progression.
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Affiliation(s)
- Manolito G Torralba
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.
| | - Gajender Aleti
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Weizhong Li
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Kelvin Jens Moncera
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Yi-Han Lin
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Yanbao Yu
- Department of Genomic Medicine, J. Craig Venter Institute, 9605 Medical Center Drive Suite 150, Rockville, MD, 20850, USA
| | - Michal M Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Central Florida Blvd, Orlando, FL, 32827, USA
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Garbary 15, 61-866, Poznan, Poland
| | - Pawel Golusinski
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Garbary 15, 61-866, Poznan, Poland
- Department of Otolaryngology and Maxillofacial Surgery, University of Zielona Gora, Podgórna 50, 65-246, Zielona Góra, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15th Garbary Street, room 5025, 61-866, Poznan, Poland
| | - Anna Edlund
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Marcelo Freire
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Karen E Nelson
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
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6
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Torralba MG, Aleti G, Li W, Moncera KJ, Lin YH, Yu Y, Masternak MM, Golusinski W, Golusinski P, Lamperska K, Edlund A, Freire M, Nelson KE. Correction to: Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma. Microb Ecol 2021; 82:1047. [PMID: 33219400 PMCID: PMC9172741 DOI: 10.1007/s00248-020-01641-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Manolito G Torralba
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.
| | - Gajender Aleti
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Weizhong Li
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Kelvin Jens Moncera
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Yi-Han Lin
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Yanbao Yu
- Department of Genomic Medicine, J. Craig Venter Institute, 9605 Medical Center Drive Suite 150, Rockville, MD, 20850, USA
| | - Michal M Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Central Florida Blvd, Orlando, FL, 32827, USA
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan University of Medical Sciences, Garbary 15, 61-866, Poznań, Poland
| | - Pawel Golusinski
- Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan University of Medical Sciences, Garbary 15, 61-866, Poznań, Poland
- Department of Otolaryngology and Maxillofacial Surgery, University of Zielona Gora, Podgórna 50, 65-246, Zielona Góra, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866, Poznan, Poland
| | - Anna Edlund
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Marcelo Freire
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Karen E Nelson
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
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7
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Schmid R, Petras D, Nothias LF, Wang M, Aron AT, Jagels A, Tsugawa H, Rainer J, Garcia-Aloy M, Dührkop K, Korf A, Pluskal T, Kameník Z, Jarmusch AK, Caraballo-Rodríguez AM, Weldon KC, Nothias-Esposito M, Aksenov AA, Bauermeister A, Albarracin Orio A, Grundmann CO, Vargas F, Koester I, Gauglitz JM, Gentry EC, Hövelmann Y, Kalinina SA, Pendergraft MA, Panitchpakdi M, Tehan R, Le Gouellec A, Aleti G, Mannochio Russo H, Arndt B, Hübner F, Hayen H, Zhi H, Raffatellu M, Prather KA, Aluwihare LI, Böcker S, McPhail KL, Humpf HU, Karst U, Dorrestein PC. Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment. Nat Commun 2021; 12:3832. [PMID: 34158495 PMCID: PMC8219731 DOI: 10.1038/s41467-021-23953-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 04/26/2021] [Indexed: 12/21/2022] Open
Abstract
Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.
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Affiliation(s)
- Robin Schmid
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, Germany
| | - Louis-Félix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Annika Jagels
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Johannes Rainer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Mar Garcia-Aloy
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Kai Dührkop
- Chair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany
| | - Ansgar Korf
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Zdeněk Kameník
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | | | - Kelly C Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Melissa Nothias-Esposito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
- Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Andrea Albarracin Orio
- IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina
| | - Carlismari O Grundmann
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
- School of Pharmaceutical Sciences of Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Irina Koester
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Julia M Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Yannick Hövelmann
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | | | - Matthew A Pendergraft
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Richard Tehan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Audrey Le Gouellec
- Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France
| | - Gajender Aleti
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Helena Mannochio Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
- NuBBE, Institute of Chemistry, , São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Birgit Arndt
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Florian Hübner
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Hui Zhi
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA
| | - Kimberly A Prather
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lihini I Aluwihare
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, San Diego, CA, USA.
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8
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Schorn MA, Verhoeven S, Ridder L, Huber F, Acharya DD, Aksenov AA, Aleti G, Moghaddam JA, Aron AT, Aziz S, Bauermeister A, Bauman KD, Baunach M, Beemelmanns C, Beman JM, Berlanga-Clavero MV, Blacutt AA, Bode HB, Boullie A, Brejnrod A, Bugni TS, Calteau A, Cao L, Carrión VJ, Castelo-Branco R, Chanana S, Chase AB, Chevrette MG, Costa-Lotufo LV, Crawford JM, Currie CR, Cuypers B, Dang T, de Rond T, Demko AM, Dittmann E, Du C, Drozd C, Dujardin JC, Dutton RJ, Edlund A, Fewer DP, Garg N, Gauglitz JM, Gentry EC, Gerwick L, Glukhov E, Gross H, Gugger M, Guillén Matus DG, Helfrich EJN, Hempel BF, Hur JS, Iorio M, Jensen PR, Kang KB, Kaysser L, Kelleher NL, Kim CS, Kim KH, Koester I, König GM, Leao T, Lee SR, Lee YY, Li X, Little JC, Maloney KN, Männle D, Martin H C, McAvoy AC, Metcalf WW, Mohimani H, Molina-Santiago C, Moore BS, Mullowney MW, Muskat M, Nothias LF, O'Neill EC, Parkinson EI, Petras D, Piel J, Pierce EC, Pires K, Reher R, Romero D, Roper MC, Rust M, Saad H, Saenz C, Sanchez LM, Sørensen SJ, Sosio M, Süssmuth RD, Sweeney D, Tahlan K, Thomson RJ, Tobias NJ, Trindade-Silva AE, van Wezel GP, Wang M, Weldon KC, Zhang F, Ziemert N, Duncan KR, Crüsemann M, Rogers S, Dorrestein PC, Medema MH, van der Hooft JJJ. A community resource for paired genomic and metabolomic data mining. Nat Chem Biol 2021; 17:363-368. [PMID: 33589842 PMCID: PMC7987574 DOI: 10.1038/s41589-020-00724-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.
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Affiliation(s)
- Michelle A Schorn
- Laboratory of Microbiology, Department of Agricultural and Food Sciences, Wageningen University, Wageningen, the Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | | | - Lars Ridder
- Netherlands eScience Center, Amsterdam, the Netherlands
| | - Florian Huber
- Netherlands eScience Center, Amsterdam, the Netherlands
| | - Deepa D Acharya
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Gajender Aleti
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jamshid Amiri Moghaddam
- Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI), Jena, Germany
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Saefuddin Aziz
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- Microbiology Department, Biology Faculty, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Katherine D Bauman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Martin Baunach
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI), Jena, Germany
| | - J Michael Beman
- Department of Life and Environmental Sciences, University of California Merced, Merced, CA, USA
- Sierra Nevada Research Institute, University of California Merced, Merced, CA, USA
| | - María Victoria Berlanga-Clavero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Alex A Blacutt
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Anne Boullie
- Institut Pasteur, Collection of Cyanobacteria, Paris, France
| | - Asker Brejnrod
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexandra Calteau
- Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Liu Cao
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Víctor J Carrión
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands
| | - Raquel Castelo-Branco
- Interdisciplinary Centre of Marine and Environmental Research), University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Shaurya Chanana
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexander B Chase
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Marc G Chevrette
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Bart Cuypers
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tam Dang
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany
| | - Chao Du
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Christopher Drozd
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Anna Edlund
- J. Craig Venter Institute, Genomic Medicine Group, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - David P Fewer
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Harald Gross
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Muriel Gugger
- Institut Pasteur, Collection of Cyanobacteria, Paris, France
| | - Dulce G Guillén Matus
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Eric J N Helfrich
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Benjamin-Florian Hempel
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
- Charité, University Medicine Berlin, Berlin-Brandenburg Center for Regenerative Therapy (BCRT), Campus Virchow Klinikum, Berlin, Germany
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Sunchon, Republic of Korea
| | | | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Leonard Kaysser
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Chung Sub Kim
- Department of Chemistry, Yale University, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Irina Koester
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Tiago Leao
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seoung Rak Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Yi-Yuan Lee
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xuanji Li
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jessica C Little
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Daniel Männle
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Christian Martin H
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Panama, Republic of Panama
| | - Andrew C McAvoy
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Willam W Metcalf
- Carl R. Woese Institute for Genomic Biology and Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Mitchell Muskat
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ellis C O'Neill
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Elizabeth I Parkinson
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Emily C Pierce
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Karine Pires
- Instituto Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Raphael Reher
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - M Caroline Roper
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Michael Rust
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Hamada Saad
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- Phytochemistry and Plant Systematics Department, Division of Pharmaceutical Industries, National Research Centre, Cairo, Egypt
| | - Carmen Saenz
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | | | | | | | - Douglas Sweeney
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, Canada
| | - Regan J Thomson
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Nicholas J Tobias
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Amaro E Trindade-Silva
- Departamento de Fisiologia e Farmacologia, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Gilles P van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Fan Zhang
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI, USA
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, UK
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Simon Rogers
- School of Computing Science, University of Glasgow, Glasgow, UK
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology and Pediatrics, University of California San Diego, La Jolla, CA, USA.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
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9
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Troyer EA, Kohn JN, Ecklu-Mensah G, Aleti G, Rosenberg DR, Hong S. Searching for host immune-microbiome mechanisms in obsessive-compulsive disorder: A narrative literature review and future directions. Neurosci Biobehav Rev 2021; 125:517-534. [PMID: 33639178 DOI: 10.1016/j.neubiorev.2021.02.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 02/09/2021] [Accepted: 02/22/2021] [Indexed: 12/20/2022]
Abstract
Obsessive-compulsive disorder (OCD) is disabling and often treatment-refractory. Host immunity and gut microbiota have bidirectional communication with each other and with the brain. Perturbations to this axis have been implicated in neuropsychiatric disorders, but immune-microbiome signaling in OCD is relatively underexplored. We review support for further pursuing such investigations in OCD, including: 1) gut microbiota has been associated with OCD, but causal pathogenic mechanisms remain unclear; 2) early environmental risk factors for OCD overlap with critical periods of immune-microbiome development; 3) OCD is associated with increased risk of immune-mediated disorders and changes in immune parameters, which are separately associated with the microbiome; and 4) gut microbiome manipulations in animal models are associated with changes in immunity and some obsessive-compulsive symptoms. Theoretical pathogenic mechanisms could include microbiota programming of cytokine production, promotion of expansion and trafficking of peripheral immune cells to the CNS, and regulation of microglial function. Immune-microbiome signaling in OCD requires further exploration, and may offer novel insights into pathogenic mechanisms and potential treatment targets for this disabling disorder.
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Affiliation(s)
- Emily A Troyer
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States.
| | - Jordan N Kohn
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States
| | - Gertrude Ecklu-Mensah
- Department of Medicine and Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States
| | - Gajender Aleti
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States
| | - David R Rosenberg
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University, Detroit, Michigan, United States
| | - Suzi Hong
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States; Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, California, United States
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10
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Jarmusch AK, Wang M, Aceves CM, Advani RS, Aguirre S, Aksenov AA, Aleti G, Aron AT, Bauermeister A, Bolleddu S, Bouslimani A, Caraballo Rodriguez AM, Chaar R, Coras R, Elijah EO, Ernst M, Gauglitz JM, Gentry EC, Husband M, Jarmusch SA, Jones KL, Kamenik Z, Le Gouellec A, Lu A, McCall LI, McPhail KL, Meehan MJ, Melnik AV, Menezes RC, Montoya Giraldo YA, Nguyen NH, Nothias LF, Nothias-Esposito M, Panitchpakdi M, Petras D, Quinn RA, Sikora N, van der Hooft JJJ, Vargas F, Vrbanac A, Weldon KC, Knight R, Bandeira N, Dorrestein PC. ReDU: a framework to find and reanalyze public mass spectrometry data. Nat Methods 2020; 17:901-904. [PMID: 32807955 DOI: 10.1038/s41592-020-0916-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 07/10/2020] [Indexed: 11/09/2022]
Abstract
We present ReDU ( https://redu.ucsd.edu/ ), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one's own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking.
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Affiliation(s)
- Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rohit S Advani
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shaden Aguirre
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gajender Aleti
- Department of Psychiatry, Stein Clinical Research, University of California, San Diego, La Jolla, CA, USA
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Sanjana Bolleddu
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Andres Mauricio Caraballo Rodriguez
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rama Chaar
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Roxana Coras
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Center for Newborn Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Makhai Husband
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Scott A Jarmusch
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, UK
| | - Kenneth L Jones
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Zdenek Kamenik
- Institute of Microbiology, Czech Academy of Sciences, Videnska, Czech Republic
| | - Audrey Le Gouellec
- TIMC-IMAG, Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, Grenoble, France
| | - Aileen Lu
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Riya C Menezes
- Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yessica Alejandra Montoya Giraldo
- Grupo de Investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Universidad EAFIT, Medellín, Colombia
| | - Ngoc Hung Nguyen
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI, USA
| | - Nicole Sikora
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Justin J J van der Hooft
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Alison Vrbanac
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA. .,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA. .,Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
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11
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Kohn JN, Kosciolek T, Marotz C, Aleti G, Guay-Ross RN, Hong SH, Hansen S, Swafford A, Knight R, Hong S. Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults. Brain Behav Immun 2020; 87:591-602. [PMID: 32061904 DOI: 10.1016/j.bbi.2020.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/04/2020] [Accepted: 02/09/2020] [Indexed: 12/14/2022] Open
Affiliation(s)
| | - Tomasz Kosciolek
- Department of Pediatrics, United States; Current affiliation: Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | | | | | | | | | | | - Rob Knight
- Department of Pediatrics, United States; Center for Microbiome Innovation, United States; Department of Computer Science and Engineering, United States; Department of Bioengineering, United States
| | - Suzi Hong
- Department of Psychiatry, United States; Center for Microbiome Innovation, United States; Department of Family Medicine and Public Health, University of California, San Diego, United States.
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12
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Pessoa L, Aleti G, Choudhury S, Nguyen D, Yaskell T, Zhang Y, Li W, Nelson KE, Neto LLS, Sant'Ana ACP, Freire M. Host-Microbial Interactions in Systemic Lupus Erythematosus and Periodontitis. Front Immunol 2019; 10:2602. [PMID: 31781106 PMCID: PMC6861327 DOI: 10.3389/fimmu.2019.02602] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/21/2019] [Indexed: 12/31/2022] Open
Abstract
Background: Systemic lupus erythematosus (SLE) is a potentially fatal complex autoimmune disease, that is characterized by widespread inflammation manifesting tissue damage and comorbidities across the human body including heart, blood vessels, joints, skin, liver, kidneys, and periodontal tissues. The etiology of SLE is partially attributed to a deregulated inflammatory response to microbial dysbiosis and environmental changes. In the mouth, periodontal environment provides an optimal niche for local and systemic inflammation. Our aim was to evaluate the reciprocal impact of periodontal subgingival microbiome on SLE systemic inflammation. Methods: Ninety-one female subjects were recruited, including healthy (n = 31), SLE-inactive (n = 29), and SLE-active (n = 31). Patients were screened for probing depth, bleeding on probing, clinical attachment level, and classified according to CDC/AAP criteria with or without periodontal dysbiosis. Serum inflammatory cytokines were measured by human cytokine panel and a targeted pathogenic subgingival biofilm panel was examined by DNA-DNA checkerboard from subgingival plaque samples. Results: The results showed significant upregulation of serum proinflammatory cytokines in individuals with SLE when compared to controls. Stratification of subject's into SLE-inactive (I) and SLE-active (A) phenotypes or periodontitis and non-periodontitis groups provided new insights into SLE pathophysiology. Ten proinflammatory cytokines were upregulated in serum of SLE-I only and one in SLE-A only. Four molecules overlapped in SLE-A and SLE-I. Anti-inflammatory cytokines included IL-4 IL-10, which were upregulated in SLE-I sera (but not SLE-A), controlling clinical phenotypes. Out of 24 significant differential oral microbial abundances found in SLE, 14 unique subgingival bacteria profiles were found to be elevated in SLE. The most severe oral pathogens (Treponema denticola and Tannerella forsythia) showed increase abundances on SLE-A periodontal sites when compared to SLE-I and healthy controls. Inflammation as measured by cytokine-microbial correlations showed that periodontal pathogens dominating the environment increased proinflammatory cytokines systemically. Conclusions: Altogether, low-grade systemic inflammation that influenced SLE disease activity and severity was correlated to dysbiotic changes of the oral microbiota present in periodontal diseases.
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Affiliation(s)
- Larissa Pessoa
- Department of Prosthodontics and Periodontics, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - Gajender Aleti
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, United States
| | - Saibyasachi Choudhury
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, United States
| | - Daniel Nguyen
- Applied Oral Sciences, The Forsyth Institute, Cambridge, MA, United States
| | - Tina Yaskell
- Applied Oral Sciences, The Forsyth Institute, Cambridge, MA, United States
| | - Yun Zhang
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, United States
| | - Weizhong Li
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, United States
| | - Karen E Nelson
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, United States.,Department of Genomic Medicine, J. Craig Venter Institute, Rockville, MD, United States
| | | | - Adriana C P Sant'Ana
- Department of Prosthodontics and Periodontics, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - Marcelo Freire
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, United States
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13
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Gauglitz JM, Aceves CM, Aksenov AA, Aleti G, Almaliti J, Bouslimani A, Brown EA, Campeau A, Caraballo-Rodríguez AM, Chaar R, da Silva RR, Demko AM, Di Ottavio F, Elijah E, Ernst M, Ferguson LP, Holmes X, Jarmusch AK, Jiang L, Kang KB, Koester I, Kwan B, Li J, Li Y, Melnik AV, Molina-Santiago C, Ni B, Oom AL, Panitchpakdi MW, Petras D, Quinn R, Sikora N, Spengler K, Teke B, Tripathi A, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vrbanac A, Vu AQ, Wang SC, Weldon K, Wilson K, Wozniak JM, Yoon M, Bandeira N, Dorrestein PC. Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages. Food Chem 2019; 302:125290. [PMID: 31404873 DOI: 10.1016/j.foodchem.2019.125290] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/19/2019] [Accepted: 07/28/2019] [Indexed: 10/26/2022]
Abstract
In our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrometry analysis of food samples has the potential to increase our chemical understanding of these processes by detecting a broad spectrum of chemicals. We performed a time-based analysis of the chemical changes in foods during common preparations, such as fermentation, brewing, and ripening, using untargeted mass spectrometry and molecular networking. The data analysis workflow presented implements an approach to study changes in food chemistry that can reveal global alterations in chemical profiles, identify changes in abundance, as well as identify specific chemicals and their transformation products. The data generated in this study are publicly available, enabling the replication and re-analysis of these data in isolation, and serve as a baseline dataset for future investigations.
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Affiliation(s)
- Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Center for Microbiome Innovation, University of California, San Diego, United States.
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Gajender Aleti
- Mammalian Genomics, J. Craig Venter Institute, San Diego, United States
| | - Jehad Almaliti
- Scripps Institution of Oceanography, University of California, San Diego, United States; Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Elizabeth A Brown
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Anaamika Campeau
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Department of Pharmacology, University of California, San Diego, United States
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Rama Chaar
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Ricardo R da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Alyssa M Demko
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Francesca Di Ottavio
- Faculty of Bioscience and Technology for Food, Agriculture, and Environment, University of Teramo, TE, Italy
| | - Emmanuel Elijah
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - L Paige Ferguson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Xavier Holmes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Lingjing Jiang
- Department of Family Medicine and Public Health, University of California, San Diego, United States
| | - Kyo Bin Kang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Irina Koester
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Brian Kwan
- Department of Family Medicine and Public Health, University of California, San Diego, United States
| | - Jie Li
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Yueying Li
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Center for Microbiome Innovation, University of California, San Diego, United States
| | - Carlos Molina-Santiago
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - Bohan Ni
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Aaron L Oom
- Department of Medicine, University of California, San Diego, United States
| | - Morgan W Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Center for Microbiome Innovation, University of California, San Diego, United States; Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Robert Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Nicole Sikora
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Katharina Spengler
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Bahar Teke
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Anupriya Tripathi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Sabah Ul-Hasan
- School of Natural Sciences, University of California Merced, Merced, CA 95343, United States
| | - Justin J J van der Hooft
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States
| | - Alison Vrbanac
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States
| | - Anthony Q Vu
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States
| | - Steven C Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States
| | - Kelly Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Center for Microbiome Innovation, University of California, San Diego, United States
| | - Kayla Wilson
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Jacob M Wozniak
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Department of Pharmacology, University of California, San Diego, United States
| | - Michael Yoon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Department of Computer Science and Engineering, University of California, San Diego, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Departments of Pharmacology and Pediatrics, University of California, San Diego, United States.
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14
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Aleti G, Baker JL, Tang X, Alvarez R, Dinis M, Tran NC, Melnik AV, Zhong C, Ernst M, Dorrestein PC, Edlund A. Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease. mBio 2019; 10:e00321-19. [PMID: 30992349 PMCID: PMC6469967 DOI: 10.1128/mbio.00321-19] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/12/2019] [Indexed: 01/03/2023] Open
Abstract
Small molecules are the primary communication media of the microbial world. Recent bioinformatic studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria and their connection to health versus disease in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for more than 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals either with good oral health or with dental caries or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Coabundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in healthy individuals but greatly reduced in individuals with dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the world's most common chronic diseases.IMPORTANCE The healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the world's most common and costly chronic infectious diseases and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome and how it devolves in the case of two prominent diseases.
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Affiliation(s)
- Gajender Aleti
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California, USA
| | - Jonathon L Baker
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California, USA
| | - Xiaoyu Tang
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California, USA
| | - Ruth Alvarez
- School of Dentistry, The University of California, Los Angeles, California, USA
| | - Márcia Dinis
- School of Dentistry, The University of California, Los Angeles, California, USA
| | - Nini C Tran
- School of Dentistry, The University of California, Los Angeles, California, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, California, USA
| | - Cuncong Zhong
- Department of Electric Engineering and Computer Science, The University of Kansas, Lawrence, Kansas, USA
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, California, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, California, USA
| | - Anna Edlund
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California, USA
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15
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Sarwar A, Brader G, Corretto E, Aleti G, Ullah MA, Sessitsch A, Hafeez FY. Correction: Qualitative analysis of biosurfactants from Bacillus species exhibiting antifungal activity. PLoS One 2018; 13:e0201624. [PMID: 30048549 PMCID: PMC6062110 DOI: 10.1371/journal.pone.0201624] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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16
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Hussain I, Aleti G, Naidu R, Puschenreiter M, Mahmood Q, Rahman MM, Wang F, Shaheen S, Syed JH, Reichenauer TG. Microbe and plant assisted-remediation of organic xenobiotics and its enhancement by genetically modified organisms and recombinant technology: A review. Sci Total Environ 2018; 628-629:1582-1599. [PMID: 30045575 DOI: 10.1016/j.scitotenv.2018.02.037] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/31/2018] [Accepted: 02/03/2018] [Indexed: 05/18/2023]
Abstract
Environmental problems such as the deterioration of groundwater quality, soil degradation and various threats to human, animal and ecosystem health are closely related to the presence of high concentrations of organic xenobiotics in the environment. Employing appropriate technologies to remediate contaminated soils is crucial due to the site-specificity of most remediation methods. The limitations of conventional remediation technologies include poor environmental compatibility, high cost of implementation and poor public acceptability. This raises the call to employ biological methods for remediation. Bioremediation and microbe-assisted bioremediation (phytoremediation) offer many ecological and cost-associated benefits. The overall efficiency and performance of bio- and phytoremediation approaches can be enhanced by genetically modified microbes and plants. Moreover, phytoremediation can also be stimulated by suitable plant-microbe partnerships, i.e. plant-endophytic or plant-rhizospheric associations. Synergistic interactions between recombinant bacteria and genetically modified plants can further enhance the restoration of environments impacted by organic pollutants. Nevertheless, releasing genetically modified microbes and plants into the environment does pose potential risks. These can be minimized by adopting environmental biotechnological techniques and guidelines provided by environmental protection agencies and other regulatory frameworks. The current contribution provides a comprehensive overview on enhanced bioremediation and phytoremediation approaches using transgenic plants and microbes. It also sheds light on the mitigation of associated environmental risks.
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Affiliation(s)
- Imran Hussain
- AIT Austrian Institute of Technology, Centre for Energy, Environmental Resources and Technologies, Tulln, Austria; Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Austria
| | - Gajender Aleti
- AIT Austrian Institute of Technology, Centre for Energy, Environmental Resources and Technologies, Tulln, Austria
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, New South Wales, Australia
| | - Markus Puschenreiter
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Qaisar Mahmood
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Mohammad Mahmudur Rahman
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, New South Wales, Australia
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shahida Shaheen
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Jabir Hussain Syed
- Department of Meteorology, COMSATS Institute of Information Technology, Park Road Tarlai Kalan 45550, Islamabad, Pakistan; Department of Civil and Environmental Engineering, Hong Kong Polytechnic University, Hong Kong.
| | - Thomas G Reichenauer
- AIT Austrian Institute of Technology, Centre for Energy, Environmental Resources and Technologies, Tulln, Austria.
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17
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Aleti G, Lehner S, Bacher M, Compant S, Nikolic B, Plesko M, Schuhmacher R, Sessitsch A, Brader G. Surfactin variants mediate species-specific biofilm formation and root colonization in Bacillus. Environ Microbiol 2016; 18:2634-45. [PMID: 27306252 DOI: 10.1111/1462-2920.13405] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclic lipopeptides (cLP) and especially surfactins produced by Bacillus spp. trigger biofilm formation and root colonization and are crucial for biocontrol activity and systemic resistance in plants. Bacillus atrophaeus 176s isolated from the moss Tortella tortuosa produces the cLP fengycins, iturins and surfactins, possesses antifungal activities and can protect tomato, lettuce and sugar beet against Rhizoctonia solani infection. In B. atrophaeus we identified for the first time the variant surfactin C, which differs from surfactin A produced by B. subtilis and B. amyloliquefaciens by an isoleucine instead of a leucine at position 7 of the lipopeptide backbone. The analysis of the complete surfactin gene clusters revealed that the dissimilarity is encoded in the adenylation domain of srfC and show that surfactin variations are distributed in a species-specific manner in bacilli. We demonstrate that the surfactin A and C with subtle structural differences have varying signal strengths on biofilm formation and root colonization and act specifically on the respective producing strain. This became evident as biofilm formation and root colonization but not swarming motility in surfactin biosynthesis mutants was restored differentially in the presence of exogenously supplemented cognate and non-cognate surfactin variants.
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Affiliation(s)
- Gajender Aleti
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Sylvia Lehner
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Markus Bacher
- Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), UFT Research Center Tulln, Konrad-Lorenz-Str. 24, Tulln, A-3430, Austria
| | - Stéphane Compant
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Branislav Nikolic
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Maja Plesko
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Angela Sessitsch
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
| | - Günter Brader
- Health & Environment Department, Bioresources Unit, AIT Austrian Institute of Technology GmbH, AIT, Konrad Lorenz Strasse 24, Tulln, A-3430, Austria
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