1
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Noecker C, Turnbaugh PJ. Emerging tools and best practices for studying gut microbial community metabolism. Nat Metab 2024; 6:1225-1236. [PMID: 38961185 DOI: 10.1038/s42255-024-01074-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
The human gut microbiome vastly extends the set of metabolic reactions catalysed by our own cells, with far-reaching consequences for host health and disease. However, our knowledge of gut microbial metabolism relies on a handful of model organisms, limiting our ability to interpret and predict the metabolism of complex microbial communities. In this Perspective, we discuss emerging tools for analysing and modelling the metabolism of gut microorganisms and for linking microorganisms, pathways and metabolites at the ecosystem level, highlighting promising best practices for researchers. Continued progress in this area will also require infrastructure development to facilitate cross-disciplinary synthesis of scientific findings. Collectively, these efforts can enable a broader and deeper understanding of the workings of the gut ecosystem and open new possibilities for microbiome manipulation and therapy.
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Affiliation(s)
- Cecilia Noecker
- Department of Biological Sciences, Minnesota State University, Mankato, Mankato, MN, USA
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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2
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Cickovski T, Mathee K, Aguirre G, Tatke G, Hermida A, Narasimhan G, Stollstorff M. Attention Deficit Hyperactivity Disorder (ADHD) and the gut microbiome: An ecological perspective. PLoS One 2023; 18:e0273890. [PMID: 37594987 PMCID: PMC10437823 DOI: 10.1371/journal.pone.0273890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
Attention Deficit Hyperactivity Disorder (ADHD) is an increasingly prevalent neuropsychiatric disorder characterized by hyperactivity, inattention, and impulsivity. Symptoms emerge from underlying deficiencies in neurocircuitry, and recent research has suggested a role played by the gut microbiome. The gut microbiome is an ecosystem of interdependent taxa involved in an exponentially complex web of interactions, plus host gene and reaction pathways, some of which involve neurotransmitters with roles in ADHD neurocircuitry. Studies have analyzed the ADHD gut microbiome using macroscale metrics such as diversity and differential abundance, and have proposed several taxa as elevated or reduced in ADHD compared to Control. Few studies have delved into the complex underlying dynamics ultimately responsible for the emergence of such metrics, leaving a largely incomplete, sometimes contradictory, and ultimately inconclusive picture. We aim to help complete this picture by venturing beyond taxa abundances and into taxa relationships (i.e. cooperation and competition), using a publicly available gut microbiome dataset (targeted 16S, v3-4 region, qPCR) from an observational, case-control study of 30 Control (15 female, 15 male) and 28 ADHD (15 female, 13 male) undergraduate students. We first perform the same macroscale analyses prevalent in ADHD gut microbiome literature (diversity, differential abundance, and composition) to observe the degree of correspondence, or any new trends. We then estimate two-way ecological relationships by producing Control and ADHD Microbial Co-occurrence Networks (MCNs), using SparCC correlations (p ≤ 0.01). We perform community detection to find clusters of taxa estimated to mutually cooperate along with their centroids, and centrality calculations to estimate taxa most vital to overall gut ecology. We finally summarize our results, providing conjectures on how they can guide future experiments, some methods for improving our experiments, and general implications for the field.
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Affiliation(s)
- Trevor Cickovski
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, United States of America
| | - Kalai Mathee
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL United States of America
- Biomolecular Sciences Institute, Florida International University, Miami, FL, United States of America
| | - Gloria Aguirre
- Department of Biological Sciences, College of Arts, Sciences and Education, Florida International University, Miami, FL, United States of America
| | - Gorakh Tatke
- Department of Biological Sciences, College of Arts, Sciences and Education, Florida International University, Miami, FL, United States of America
| | - Alejandro Hermida
- Cognitive Neuroscience Laboratory, Department of Psychology, Florida International University, Miami, FL, United States of America
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, United States of America
| | - Melanie Stollstorff
- Cognitive Neuroscience Laboratory, Department of Psychology, Florida International University, Miami, FL, United States of America
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3
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Zhong J, Wu D, Zeng Y, Wu G, Zheng N, Huang W, Li Y, Tao X, Zhu W, Sheng L, Shen X, Zhang W, Zhu R, Li H. The Microbial and Metabolic Signatures of Patients with Stable Coronary Artery Disease. Microbiol Spectr 2022; 10:e0246722. [PMID: 36354350 PMCID: PMC9769616 DOI: 10.1128/spectrum.02467-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/17/2022] [Indexed: 11/12/2022] Open
Abstract
Growing evidence indicates an association between gut dysbiosis and coronary artery disease (CAD). However, the underlying mechanisms relevant to stable CAD (SCAD) pathogenesis, based on microbe-host metabolism interactions, are poorly explored. Here, we constructed a quasi-paired cohort based on the metabolic background of metagenomic samples by the propensity score matching (PSM) principle. Compared to healthy controls (HCs), gut microbiome disturbances were observed in SCAD patients, accompanied by differences in serum metabolome, mainly including elevated acylcarnitine and decreased unsaturated fatty acids in SCAD patients, which implicated the reduced cardiac fatty acid oxidation. Moreover, we identified Ralstonia pickettii as the core strain responsible for impaired microbial homeostasis in SCAD patientsm and may be partly responsible for the decrease of host unsaturated fatty acid levels. These findings highlight the importance of unsaturated fatty acids, R. pickettii, and their interaction in the pathogenesis of SCAD. IMPORTANCE Stable coronary artery disease (SCAD) is an early stage of CAD development. It is important to understand the pathogenesis of SCAD and find out the possible prevention and control targets for delaying the progression of CAD. We observed reduced levels of unsaturated fatty acids (USFAs) in SCAD patients. However, the reduced USFAs may be related to Ralstonia Pickettii, which was the core strain responsible for the impaired gut microbial function in SCAD patients, and further affected the host's cardiovascular health by altering amino acids, vitamin B metabolism, and LPS biosynthesis. These findings not only emphasized the importance of USFAs for cardiovascular health, but also R. Pickettii for maintaining microbial function homeostasis. More importantly, our study revealed, for the first time, that enriched R. Pickettii might be responsible for the reduced USFAs in SCAD patients, which adds new evidence on the role of altered gut microbiota for SCAD formation.
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Affiliation(s)
- Jing Zhong
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Dingfeng Wu
- National Clinical Research Center for Child Health, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Yuanyuan Zeng
- Cardiology Department of Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- The First Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Gaosong Wu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ningning Zheng
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wenjin Huang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yan Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xin Tao
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Weize Zhu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lili Sheng
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoxu Shen
- Cardiology Department of Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- The First Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Weidong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Ruixin Zhu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, People’s Republic of China
| | - Houkai Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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4
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Singh R, Dutta A, Bose T, Mande SS. A compendium of predicted growths and derived symbiotic relationships between 803 gut microbes in 13 different diets. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100127. [PMID: 35909605 PMCID: PMC9325735 DOI: 10.1016/j.crmicr.2022.100127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/11/2022] [Accepted: 03/20/2022] [Indexed: 11/30/2022] Open
Abstract
Simulated growth of 803 gut microbes in mono- and co-cultures in 13 distinct diets. Inferred symbiotic relationships and metabolic co-operation among gut microbes. Diet-based variations in metabolic co-operation among gut microbes. Validation of in silico findings against existing literature evidence.
Gut health is intimately linked to dietary habits and the microbial community (microbiota) that flourishes within. The delicate dependency of the latter on nutritional availability is also strongly influenced by interactions (such as, parasitic or mutualistic) between the resident microbes, often affecting their growth rate and ability to produce key metabolites. Since, cultivating the entire repertoire of gut microbes is a challenging task, metabolic models (genome-based metabolic reconstructions) could be employed to predict their growth patterns and interactions. Here, we have used 803 gut microbial metabolic models from the Virtual Metabolic Human repository, and subsequently optimized and simulated them to grow on 13 dietary compositions. The presented pairwise interaction data (https://osf.io/ay8bq/) and the associated bacterial growth rates are expected to be useful for (a) deducing microbial association patterns, (b) diet-based inference of personalised gut profiles, and (c) as a steppingstone for studying multi-species metabolic interactions.
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5
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Pettersen VK, Antunes LCM, Dufour A, Arrieta MC. Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics. Comput Struct Biotechnol J 2021; 20:274-286. [PMID: 35024099 PMCID: PMC8718658 DOI: 10.1016/j.csbj.2021.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 12/17/2022] Open
Abstract
Humans have a long-standing coexistence with microorganisms. In particular, the microbial community that populates the human gastrointestinal tract has emerged as a critical player in governing human health and disease. DNA and RNA sequencing techniques that map taxonomical composition and genomic potential of the gut community have become invaluable for microbiome research. However, deriving a biochemical understanding of how activities of the gut microbiome shape host development and physiology requires an expanded experimental design that goes beyond these approaches. In this review, we explore advances in high-throughput techniques based on liquid chromatography-mass spectrometry. These omics methods for the identification of proteins and metabolites have enabled direct characterisation of gut microbiome functions and the crosstalk with the host. We discuss current metaproteomics and metabolomics workflows for producing functional profiles, the existing methodological challenges and limitations, and recent studies utilising these techniques with a special focus on early life gut microbiome.
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Affiliation(s)
- Veronika Kuchařová Pettersen
- Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Pediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Centre for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway
| | - Luis Caetano Martha Antunes
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
- National Institute of Science and Technology of Innovation on Diseases of Neglected Populations, Center for Technological Development in Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - Marie-Claire Arrieta
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
- International Microbiome Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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6
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Dusad V, Thiel D, Barahona M, Keun HC, Oyarzún DA. Opportunities at the Interface of Network Science and Metabolic Modeling. Front Bioeng Biotechnol 2021; 8:591049. [PMID: 33569373 PMCID: PMC7868444 DOI: 10.3389/fbioe.2020.591049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/22/2020] [Indexed: 12/17/2022] Open
Abstract
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key to understand how cells respond to genetic, environmental, or therapeutic perturbations. Here we discuss the roles of two complementary strategies for the analysis of genome-scale metabolic models: Flux Balance Analysis (FBA) and network science. While FBA estimates metabolic flux on the basis of an optimization principle, network approaches reveal emergent properties of the global metabolic connectivity. We highlight how the integration of both approaches promises to deliver insights on the structure and function of metabolic systems with wide-ranging implications in discovery science, precision medicine and industrial biotechnology.
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Affiliation(s)
- Varshit Dusad
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Denise Thiel
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Hector C Keun
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom.,Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Diego A Oyarzún
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.,School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
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7
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Dalal N, Jalandra R, Sharma M, Prakash H, Makharia GK, Solanki PR, Singh R, Kumar A. Omics technologies for improved diagnosis and treatment of colorectal cancer: Technical advancement and major perspectives. Biomed Pharmacother 2020; 131:110648. [PMID: 33152902 DOI: 10.1016/j.biopha.2020.110648] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/09/2020] [Accepted: 08/16/2020] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) ranks third among the most commonly occurring cancers worldwide, and it causes half a million deaths annually. Alongside mechanistic study for CRC detection and treatment by conventional techniques, new technologies have been developed to study CRC. These technologies include genomics, transcriptomics, proteomics, and metabolomics which elucidate DNA markers, RNA transcripts, protein and, metabolites produced inside the colon and rectum part of the gut. All these approaches form the omics arena, which presents a remarkable opportunity for the discovery of novel prognostic, diagnostic and therapeutic biomarkers and also delineate the underlying mechanism of CRC causation, which may further help in devising treatment strategies. This review also mentions the latest developments in metagenomics and culturomics as emerging evidence suggests that metagenomics of gut microbiota has profound implications in the causation, prognosis, and treatment of CRC. A majority of bacteria cannot be studied as they remain unculturable, so culturomics has also been strengthened to develop culture conditions suitable for the growth of unculturable bacteria and identify unknown bacteria. The overall purpose of this review is to succinctly evaluate the application of omics technologies in colorectal cancer research for improving the diagnosis and treatment strategies.
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Affiliation(s)
- Nishu Dalal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India; Department of Environmental Science, Satyawati College, Delhi University, Delhi 110052, India
| | - Rekha Jalandra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India; Department of Zoology, Maharshi Dayanand University, Rohtak 124001, India
| | - Minakshi Sharma
- Department of Zoology, Maharshi Dayanand University, Rohtak 124001, India
| | - Hridayesh Prakash
- Amity Institute of Virology and Immunology, Amity University, Sector 125, Noida 201313, Uttar Pradesh, India
| | - Govind K Makharia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pratima R Solanki
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajeev Singh
- Department of Environmental Science, Satyawati College, Delhi University, Delhi 110052, India.
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India.
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8
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Zhang M, Chu Y, Meng Q, Ding R, Shi X, Wang Z, He Y, Zhang J, Liu J, Zhang J, Yu J, Kang Y, Wang J. A quasi-paired cohort strategy reveals the impaired detoxifying function of microbes in the gut of autistic children. SCIENCE ADVANCES 2020; 6:eaba3760. [PMID: 33087359 PMCID: PMC7577716 DOI: 10.1126/sciadv.aba3760] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Growing evidence suggests that autism spectrum disorder (ASD) is strongly associated with dysbiosis in the gut microbiome, with the exact mechanisms still unclear. We have proposed a novel analytic strategy-quasi-paired cohort-and applied it to a metagenomic study of the ASD microbiome. By comparing paired samples of ASD and neurotypical subjects, we have identified significant deficiencies in ASD children in detoxifying enzymes and pathways, which show a strong correlation with biomarkers of mitochondrial dysfunction. Diagnostic models based on these detoxifying enzymes accurately distinguished ASD individuals from controls, and the dysfunction score inferred from the model increased with the clinical rating scores of ASD. In summary, our results suggest a previously undiscovered potential role of impaired intestinal microbial detoxification in toxin accumulation and mitochondrial dysfunction, a core component of ASD pathogenesis. These findings pave the way for designing future therapeutic strategies to restore microbial detoxification capabilities for patients with ASD.
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Affiliation(s)
- Mengxiang Zhang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Yanan Chu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
| | - Qingren Meng
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Rui Ding
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
- Autism Research Center of Peking University Health Science Center, Beijing 100191, China
| | - Xing Shi
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Zuqun Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
- Autism Research Center of Peking University Health Science Center, Beijing 100191, China
| | - Yi He
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
- Autism Research Center of Peking University Health Science Center, Beijing 100191, China
| | - Juan Zhang
- Department of Pediatrics, Peking University Third Hospital, Beijing 100191, China
| | - Jing Liu
- Key Laboratory of Mental Health, Ministry of Health, Peking University Institute of Mental Health, Peking University Sixth Hospital, Beijing 100191, China
| | - Jie Zhang
- Children Health Care Center, Xi'an Children's Hospital, Xi'an 710003, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
| | - Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China.
| | - Juan Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China.
- Autism Research Center of Peking University Health Science Center, Beijing 100191, China
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9
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Rosario D, Boren J, Uhlen M, Proctor G, Aarsland D, Mardinoglu A, Shoaie S. Systems Biology Approaches to Understand the Host-Microbiome Interactions in Neurodegenerative Diseases. Front Neurosci 2020; 14:716. [PMID: 32733199 PMCID: PMC7360858 DOI: 10.3389/fnins.2020.00716] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative diseases (NDDs) comprise a broad range of progressive neurological disorders with multifactorial etiology contributing to disease pathophysiology. Evidence of the microbiome involvement in the gut-brain axis urges the interest in understanding metabolic interactions between the microbiota and host physiology in NDDs. Systems Biology offers a holistic integrative approach to study the interplay between the different biologic systems as part of a whole, and may elucidate the host–microbiome interactions in NDDs. We reviewed direct and indirect pathways through which the microbiota can modulate the bidirectional communication of the gut-brain axis, and explored the evidence of microbial dysbiosis in Alzheimer’s and Parkinson’s diseases. As the gut microbiota being strongly affected by diet, the potential approaches to targeting the human microbiota through diet for the stimulation of neuroprotective microbial-metabolites secretion were described. We explored the potential of Genome-scale metabolic models (GEMs) to infer microbe-microbe and host-microbe interactions and to identify the microbiome contribution to disease development or prevention. Finally, a systemic approach based on GEMs and ‘omics integration, that would allow the design of sustainable personalized anti-inflammatory diets in NDDs prevention, through the modulation of gut microbiota was described.
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Affiliation(s)
- Dorines Rosario
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Jan Boren
- Department of Molecular and Clinical Medicine, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Gordon Proctor
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom
| | - Dag Aarsland
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom.,Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, United Kingdom.,Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
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10
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Blanco-Míguez A, Fdez-Riverola F, Sánchez B, Lourenço A. Resources and tools for the high-throughput, multi-omic study of intestinal microbiota. Brief Bioinform 2020; 20:1032-1056. [PMID: 29186315 DOI: 10.1093/bib/bbx156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/23/2017] [Indexed: 12/18/2022] Open
Abstract
The human gut microbiome impacts several aspects of human health and disease, including digestion, drug metabolism and the propensity to develop various inflammatory, autoimmune and metabolic diseases. Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts. These efforts demonstrate the power of standardized and reproducible computational workflows for integrating and analysing varied omics data and gaining deeper insights into microbe community structure and function as well as host-microbe interactions.
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Affiliation(s)
| | | | | | - Anália Lourenço
- Dpto. de Informática - Universidade de Vigo, ESEI - Escuela Superior de Ingeniería Informática, Edificio politécnico, Campus Universitario As Lagoas s/n, 32004 Ourense, Spain
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11
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Zeisel SH. Precision (Personalized) Nutrition: Understanding Metabolic Heterogeneity. Annu Rev Food Sci Technol 2020; 11:71-92. [DOI: 10.1146/annurev-food-032519-051736] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
People differ in their requirements for and responses to nutrients and bioactive molecules in the diet. Many inputs contribute to metabolic heterogeneity (including variations in genetics, epigenetics, microbiome, lifestyle, diet intake, and environmental exposure). Precision nutrition is not about developing unique prescriptions for individual people but rather about stratifying people into different subgroups of the population on the basis of biomarkers of the above-listed sources of metabolic variation and then using this stratification to better estimate the different subgroups’ dietary requirements, thereby enabling better dietary recommendations and interventions. The hope is that we will be able to subcategorize people into ever-smaller groups that can be targeted in terms of recommendations, but we will never achieve this at the individual level, thus, the choice of precision nutrition rather than personalized nutrition to designate this new field. This review focuses mainly on genetically related sources of metabolic heterogeneity and identifies challenges that need to be overcome to achieve a full understanding of the complex interactions between the many sources of metabolic heterogeneity that make people differ from one another in their requirements for and responses to foods. It also discusses the commercial applications of precision nutrition.
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Affiliation(s)
- Steven H. Zeisel
- Nutrition Research Institute, Department of Nutrition, University of North Carolina, Kannapolis, North Carolina 28081, USA
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12
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Chowdhury S, Fong SS. Computational Modeling of the Human Microbiome. Microorganisms 2020; 8:microorganisms8020197. [PMID: 32023941 PMCID: PMC7074762 DOI: 10.3390/microorganisms8020197] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/20/2022] Open
Abstract
The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.
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Affiliation(s)
- Shomeek Chowdhury
- Integrative Life Sciences, Virginia Commonwealth University, 1000 West Cary Street, Richmond, VA 23284 USA;
| | - Stephen S. Fong
- Chemical and Life Science Engineering, Virginia Commonwealth University, 601 West Main Street, Richmond, VA 23284, USA
- Correspondence:
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13
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Noecker C, Chiu HC, McNally CP, Borenstein E. Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies. mSystems 2019; 4:e00579-19. [PMID: 31848305 PMCID: PMC6918031 DOI: 10.1128/msystems.00579-19] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 11/20/2019] [Indexed: 01/24/2023] Open
Abstract
Correlation-based analysis of paired microbiome-metabolome data sets is becoming a widespread research approach, aiming to comprehensively identify microbial drivers of metabolic variation. To date, however, the limitations of this approach and other microbiome-metabolome analysis methods have not been comprehensively evaluated. To address this challenge, we have introduced a mathematical framework to quantify the contribution of each taxon to metabolite variation based on uptake and secretion fluxes. We additionally used a multispecies metabolic model to simulate simplified gut communities, generating idealized microbiome-metabolome data sets. We then compared observed taxon-metabolite correlations in these data sets to calculated ground truth taxonomic contribution values. We found that in simulations of both a representative simple 10-species community and complex human gut microbiota, correlation-based analysis poorly identified key contributors, with an extremely low predictive value despite the idealized setting. We further demonstrate that the predictive value of correlation analysis is strongly influenced by both metabolite and taxon properties, as well as by exogenous environmental variation. We finally discuss the practical implications of our findings for interpreting microbiome-metabolome studies.IMPORTANCE Identifying the key microbial taxa responsible for metabolic differences between microbiomes is an important step toward understanding and manipulating microbiome metabolism. To achieve this goal, researchers commonly conduct microbiome-metabolome association studies, comprehensively measuring both the composition of species and the concentration of metabolites across a set of microbial community samples and then testing for correlations between microbes and metabolites. Here, we evaluated the utility of this general approach by first developing a rigorous mathematical definition of the contribution of each microbial taxon to metabolite variation and then examining these contributions in simulated data sets of microbial community metabolism. We found that standard correlation-based analysis of our simulated microbiome-metabolome data sets can identify true contributions with very low predictive value and that its performance depends strongly on specific properties of both metabolites and microbes, as well as on those of the surrounding environment. Combined, our findings can guide future interpretation and validation of microbiome-metabolome studies.
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Affiliation(s)
- Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Hsuan-Chao Chiu
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Colin P McNally
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Santa Fe Institute, Santa Fe, New Mexico, USA
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14
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Hooks KB, O'Malley MA. Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research. J Eukaryot Microbiol 2019; 67:279-295. [PMID: 31583780 PMCID: PMC7154641 DOI: 10.1111/jeu.12766] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/11/2019] [Accepted: 09/25/2019] [Indexed: 12/25/2022]
Abstract
Most discussions of human microbiome research have focused on bacterial investigations and findings. Our target is to understand how human eukaryotic microbiome research is developing, its potential distinctiveness, and how problems can be addressed. We start with an overview of the entire eukaryotic microbiome literature (578 papers), show tendencies in the human‐based microbiome literature, and then compare the eukaryotic field to more developed human bacterial microbiome research. We are particularly concerned with problems of interpretation that are already apparent in human bacterial microbiome research (e.g. disease causality, probiotic interventions, evolutionary claims). We show where each field converges and diverges, and what this might mean for progress in human eukaryotic microbiome research. Our analysis then makes constructive suggestions for the future of the field.
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Affiliation(s)
- Katarzyna B Hooks
- CBiB, University of Bordeaux, Bordeaux, 33076, France.,CNRS/LaBRI, University of Bordeaux, Talence, 33405, France
| | - Maureen A O'Malley
- School of History and Philosophy of Science, University of Sydney, Sydney, NSW, 2006, Australia
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15
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Rettberg P, Antunes A, Brucato J, Cabezas P, Collins G, Haddaji A, Kminek G, Leuko S, McKenna-Lawlor S, Moissl-Eichinger C, Fellous JL, Olsson-Francis K, Pearce D, Rabbow E, Royle S, Saunders M, Sephton M, Spry A, Walter N, Wimmer Schweingruber R, Treuet JC. Biological Contamination Prevention for Outer Solar System Moons of Astrobiological Interest: What Do We Need to Know? ASTROBIOLOGY 2019; 19:951-974. [PMID: 30762429 PMCID: PMC6767865 DOI: 10.1089/ast.2018.1996] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
To ensure that scientific investments in space exploration are not compromised by terrestrial contamination of celestial bodies, special care needs to be taken to preserve planetary conditions for future astrobiological exploration. Significant effort has been made and is being taken to address planetary protection in the context of inner Solar System exploration. In particular for missions to Mars, detailed internationally accepted guidelines have been established. For missions to the icy moons in the outer Solar System, Europa and Enceladus, the planetary protection requirements are so far based on a probabilistic approach and a conservative estimate of poorly known parameters. One objective of the European Commission-funded project, Planetary Protection of Outer Solar System, was to assess the existing planetary protection approach, to identify inherent knowledge gaps, and to recommend scientific investigations necessary to update the requirements for missions to the icy moons.
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Affiliation(s)
- Petra Rettberg
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
- Address correspondence to: Petra Rettberg, German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Research Group Astrobiology, Linder Höhe, 51147 Köln, Germany
| | - André Antunes
- GEMM—Group for Extreme and Marine Microbiology, Department of Biology, Edge Hill University, Ormskirk, United Kingdom
| | - John Brucato
- Department of Physics and Astronomy, Astrophysical Observatory of Arcetri, National Institute for Astrophysics (INAF), Florence, Italy
| | - Patricia Cabezas
- Science Connect–European Science Foundation (ESF), Strasbourg, France
| | - Geoffrey Collins
- Department of Physics and Astronomy, Wheaton College, Massachusetts, Norton, Massachusetts
| | - Alissa Haddaji
- Committee on Space Research (COSPAR), Montpellier, France
| | - Gerhard Kminek
- Committee on Space Research (COSPAR), Montpellier, France
| | - Stefan Leuko
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | | | | | - Jean-Louis Fellous
- Department of Physics and Astronomy, Wheaton College, Massachusetts, Norton, Massachusetts
| | - Karen Olsson-Francis
- Faculty of Science, Technology, Engineering & Mathematics, School of Environment, Earth & Ecosystem Sciences, The Open University, Milton Keynes, United Kingdom
| | - David Pearce
- Department of Applied Sciences, Northumbria University, Newcastle, United Kingdom
| | - Elke Rabbow
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | - Samuel Royle
- Faculty of Engineering, Department of Earth Science & Engineering, Imperial College, London, United Kingdom
| | - Mark Saunders
- Independent Consultant for the US National Academies of Sciences (NAS), Washington, District of Columbia
| | - Mark Sephton
- Faculty of Engineering, Department of Earth Science & Engineering, Imperial College, London, United Kingdom
| | - Andy Spry
- Carl Sagan Center, SETI, Mountain View, California
| | - Nicolas Walter
- Science Connect–European Science Foundation (ESF), Strasbourg, France
| | - Robert Wimmer Schweingruber
- Institut für Experimentelle und Angewandte Physik, Abteilung Extraterrestrische Physik, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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16
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Bang S, Yoo D, Kim SJ, Jhang S, Cho S, Kim H. Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data. Sci Rep 2019; 9:10189. [PMID: 31308384 PMCID: PMC6629854 DOI: 10.1038/s41598-019-46249-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/12/2019] [Indexed: 12/17/2022] Open
Abstract
Diseases prediction has been performed by machine learning approaches with various biological data. One of the representative data is the gut microbial community, which interacts with the host's immune system. The abundance of a few microorganisms has been used as markers to predict diverse diseases. In this study, we hypothesized that multi-classification using machine learning approach could distinguish the gut microbiome from following six diseases: multiple sclerosis, juvenile idiopathic arthritis, myalgic encephalomyelitis/chronic fatigue syndrome, acquired immune deficiency syndrome, stroke and colorectal cancer. We used the abundance of microorganisms at five taxonomy levels as features in 696 samples collected from different studies to establish the best prediction model. We built classification models based on four multi-class classifiers and two feature selection methods including a forward selection and a backward elimination. As a result, we found that the performance of classification is improved as we use the lower taxonomy levels of features; the highest performance was observed at the genus level. Among four classifiers, LogitBoost-based prediction model outperformed other classifiers. Also, we suggested the optimal feature subsets at the genus-level obtained by backward elimination. We believe the selected feature subsets could be used as markers to distinguish various diseases simultaneously. The finding in this study suggests the potential use of selected features for the diagnosis of several diseases.
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Affiliation(s)
- Sohyun Bang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Republic of Korea
- C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea
| | - DongAhn Yoo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Republic of Korea
| | - Soo-Jin Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Soyun Jhang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Republic of Korea
- C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea
| | - Seoae Cho
- C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Republic of Korea.
- C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
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17
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Müller J, Spriewald S, Stecher B, Stadler E, Fuchs TM. Evolutionary Stability of Salmonella Competition with the Gut Microbiota: How the Environment Fosters Heterogeneity in Exploitative and Interference Competition. J Mol Biol 2019; 431:4732-4748. [PMID: 31260689 DOI: 10.1016/j.jmb.2019.06.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/19/2019] [Accepted: 06/19/2019] [Indexed: 11/27/2022]
Abstract
Following ingestion, gastrointestinal pathogens compete against the gastrointestinal microbiota and overcome host immune defenses in order to cause infections. Besides employing direct killing mechanisms, the commensal microbiota occupies metabolic niches to outcompete invading pathogens. Salmonella enterica serovar Typhimurium (S. Typhimurium) uses several strategies to successfully colonize the gut and establish infection, of which an increasing number is based on phenotypic heterogeneity within the S. Typhimurium population. The utilization of myo-inositol (MI) and the production of colicin confer a selective advantage over the microbiota in terms of exploitative and interference competition, respectively. In this review, we summarize the genetic basis underlying bistability of MI catabolism and colicin production. As demonstrated by single-cell analyses, a stochastic switch in the expression of the genes responsible for colicin production and MI degradation constitutes the heterogeneity of the two phenotypes. Both genetic systems are tightly regulated to avoid their expression under non-appropriate conditions and possible detrimental effects on bacterial fitness. Moreover, evolutionary mechanisms underlying formation and stability of these phenotypes in S. Typhimurium are discussed. We propose that both MI catabolism and colicin production create a bet-hedging strategy, which provides an adaptive benefit for S. Typhimurium in the fluctuating environment of the mammalian gut.
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Affiliation(s)
- Johannes Müller
- Technische Universität München, Centre for Mathematical Sciences, Boltzmannstr. 3, 85747 Garching, Germany; Institute for Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Stefanie Spriewald
- Max von Pettenkofer-Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany
| | - Bärbel Stecher
- Max von Pettenkofer-Institute, LMU Munich, Pettenkoferstr. 9a, 80336 Munich, Germany
| | - Eva Stadler
- Technische Universität München, Centre for Mathematical Sciences, Boltzmannstr. 3, 85747 Garching, Germany
| | - Thilo M Fuchs
- Friedrich-Loeffler-Institut, Institut für Molekulare Pathogenese, Naumburger Str. 96a, 07743 Jena, Germany.
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18
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Zeisel SH. A Conceptual Framework for Studying and Investing in Precision Nutrition. Front Genet 2019; 10:200. [PMID: 30936893 PMCID: PMC6431609 DOI: 10.3389/fgene.2019.00200] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 02/25/2019] [Indexed: 12/15/2022] Open
Abstract
Nutrients and food-derived bioactive molecules must transit complex metabolic pathways, and these pathways vary between people. Metabolic heterogeneity is caused by genetic variation, epigenetic variation, differences in microbiome composition and function, lifestyle differences and by variation in environmental exposures. This review discusses a number of these sources of metabolic heterogeneity and presents some of the research investments that will be needed to make applications of precision nutrition practical.
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Affiliation(s)
- Steven H Zeisel
- Nutrition Research Institute, The University of North Carolina at Chapel Hill, Kannapolis, NC, United States
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19
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Mendez R, Banerjee S, Bhattacharya SK, Banerjee S. Lung inflammation and disease: A perspective on microbial homeostasis and metabolism. IUBMB Life 2019; 71:152-165. [PMID: 30466159 PMCID: PMC6352907 DOI: 10.1002/iub.1969] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/05/2018] [Accepted: 10/17/2018] [Indexed: 12/20/2022]
Abstract
It is now well appreciated that the human microbiome plays a significant role in a number of processes in the body, significantly affecting its metabolic, inflammatory, and immune homeostasis. Recent research has revealed that almost every mucosal surface in the human body is associated with a resident commensal microbiome of its own. While the gut microbiome and its role in regulation of host metabolism along with its alteration in a disease state has been well studied, there is a lacuna in understanding the resident microbiota of other mucosal surfaces. Among these, the scientific information on the role of lung microbiota in pulmonary diseases is currently severely limited. Historically, lungs have been considered to be sterile and lung diseases have only been studied in the context of bacterial pathogenesis. Recently however, studies have revealed a resilient microbiome in the upper and lower respiratory tracts and there is increased evidence on its central role in respiratory diseases. Knowledge of lung microbiome and its metabolic fallout (local and systemic) is still in its nascent stages and attracting immense interest in recent times. In this review, we will provide a perspective on lung-associated metabolic disorders defined for lung diseases (e.g., chronic obstructive pulmonary disease, asthma, and respiratory depression due to infection) and correlate it with lung microbial perturbation. Such perturbations may be due to altered biochemical or metabolic stress as well. Finally, we will draw evidence from microbiome and classical microbiology literature to demonstrate how specific lung morbidities associate with specific metabolic characteristics of the disease, and with the role of microbiome in this context. © 2018 IUBMB Life, 71(1):152-165, 2019.
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Affiliation(s)
- Roberto Mendez
- Surgery, Miller School of Medicine, University of Miami, Florida, USA
| | - Sulagna Banerjee
- Surgery, Miller School of Medicine, University of Miami, Florida, USA
- Miami Integrative Metabolomics Research Center, University of Miami, Florida, USA
| | - Sanjoy K. Bhattacharya
- Bascom Palmer Eye Institute, University of Miami, Florida, USA
- Miami Integrative Metabolomics Research Center, University of Miami, Florida, USA
| | - Santanu Banerjee
- Surgery, Miller School of Medicine, University of Miami, Florida, USA
- Miami Integrative Metabolomics Research Center, University of Miami, Florida, USA
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20
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du Teil Espina M, Gabarrini G, Harmsen HJM, Westra J, van Winkelhoff AJ, van Dijl JM. Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis. FEMS Microbiol Rev 2019; 43:1-18. [PMID: 30219863 DOI: 10.1093/femsre/fuy035] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/13/2018] [Indexed: 02/07/2023] Open
Abstract
Microbial communities inhabiting the human body, collectively called the microbiome, are critical modulators of immunity. This notion is underpinned by associations between changes in the microbiome and particular autoimmune disorders. Specifically, in rheumatoid arthritis, one of the most frequently occurring autoimmune disorders worldwide, changes in the oral and gut microbiomes have been implicated in the loss of tolerance against self-antigens and in increased inflammatory events promoting the damage of joints. In the present review, we highlight recently gained insights in the roles of microbes in the etiology of rheumatoid arthritis. In addition, we address important immunomodulatory processes, including biofilm formation and neutrophil function, which have been implicated in host-microbe interactions relevant for rheumatoid arthritis. Lastly, we present recent advances in the development and evaluation of emerging microbiome-based therapeutic approaches. Altogether, we conclude that the key to uncovering the etiopathogenesis of rheumatoid arthritis will lie in the immunomodulatory functions of the oral and gut microbiomes.
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Affiliation(s)
- Marines du Teil Espina
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Giorgio Gabarrini
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, 9700 RB Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Center for Dentistry and Oral Hygiene, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands
| | - Hermie J M Harmsen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Johanna Westra
- University of Groningen, University Medical Center Groningen, Department of Rheumatology and Clinical Immunology, Hanzeplein 1, 9700 RB Groningen, the Netherlands
| | - Arie Jan van Winkelhoff
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, 9700 RB Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Center for Dentistry and Oral Hygiene, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands
| | - Jan Maarten van Dijl
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, 9700 RB Groningen, the Netherlands
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21
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Wang PH, Correia K, Ho HC, Venayak N, Nemr K, Flick R, Mahadevan R, Edwards EA. An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community. ISME JOURNAL 2019; 13:1042-1055. [PMID: 30607026 DOI: 10.1038/s41396-018-0333-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 11/09/2022]
Abstract
Microbes in ecosystems often develop coordinated metabolic interactions. Therefore, understanding metabolic interdependencies between microbes is critical to deciphering ecosystem function. In this study, we sought to deconstruct metabolic interdependencies in organohalide-respiring consortium ACT-3 containing Dehalobacter restrictus using a combination of metabolic modeling and experimental validation. D. restrictus possesses a complete set of genes for amino acid biosynthesis yet when grown in isolation requires amino acid supplementation. We reconciled this discrepancy using flux balance analysis considering cofactor availability, enzyme promiscuity, and shared protein expression patterns for several D. restrictus strains. Experimentally, 13C incorporation assays, growth assays, and metabolite analysis of D. restrictus strain PER-K23 cultures were performed to validate the model predictions. The model resolved that the amino acid dependency of D. restrictus resulted from restricted NADPH regeneration and predicted that malate supplementation would replenish intracellular NADPH. Interestingly, we observed unexpected export of pyruvate and glutamate in parallel to malate consumption in strain PER-K23 cultures. Further experimental analysis using the ACT-3 transfer cultures suggested the occurrence of an interspecies malate-pyruvate shuttle reconciling a redox imbalance, reminiscent of the mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study suggests that redox imbalance and metabolic complementarity are important driving forces for metabolite exchange in anaerobic microbial communities.
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Affiliation(s)
- Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kevin Correia
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Han-Chen Ho
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kayla Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.
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22
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Huitzil S, Sandoval-Motta S, Frank A, Aldana M. Modeling the Role of the Microbiome in Evolution. Front Physiol 2018; 9:1836. [PMID: 30618841 PMCID: PMC6307544 DOI: 10.3389/fphys.2018.01836] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/06/2018] [Indexed: 12/17/2022] Open
Abstract
There is undeniable evidence showing that bacteria have strongly influenced the evolution and biological functions of multicellular organisms. It has been hypothesized that many host-microbial interactions have emerged so as to increase the adaptive fitness of the holobiont (the host plus its microbiota). Although this association has been corroborated for many specific cases, general mechanisms explaining the role of the microbiota in the evolution of the host are yet to be understood. Here we present an evolutionary model in which a network representing the host adapts in order to perform a predefined function. During its adaptation, the host network (HN) can interact with other networks representing its microbiota. We show that this interaction greatly accelerates and improves the adaptability of the HN without decreasing the adaptation of the microbial networks. Furthermore, the adaptation of the HN to perform several functions is possible only when it interacts with many different bacterial networks in a specialized way (each bacterial network participating in the adaptation of one function). Disrupting these interactions often leads to non-adaptive states, reminiscent of dysbiosis, where none of the networks the holobiont consists of can perform their respective functions. By considering the holobiont as a unit of selection and focusing on the adaptation of the host to predefined but arbitrary functions, our model predicts the need for specialized diversity in the microbiota. This structural and dynamical complexity in the holobiont facilitates its adaptation, whereas a homogeneous (non-specialized) microbiota is inconsequential or even detrimental to the holobiont's evolution. To our knowledge, this is the first model in which symbiotic interactions, diversity, specialization and dysbiosis in an ecosystem emerge as a result of coevolution. It also helps us understand the emergence of complex organisms, as they adapt more easily to perform multiple tasks than non-complex ones.
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Affiliation(s)
- Saúl Huitzil
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Santiago Sandoval-Motta
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Consejo Nacional de Ciencia y Tecnología, Cátedras CONACyT, Mexico City, Mexico
| | - Alejandro Frank
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Member of El Colegio Nacional, Mexico City, Mexico
| | - Maximino Aldana
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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23
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Adamowicz EM, Flynn J, Hunter RC, Harcombe WR. Cross-feeding modulates antibiotic tolerance in bacterial communities. ISME JOURNAL 2018; 12:2723-2735. [PMID: 29991761 PMCID: PMC6194032 DOI: 10.1038/s41396-018-0212-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 05/18/2018] [Accepted: 06/11/2018] [Indexed: 12/29/2022]
Abstract
Microbes frequently rely on metabolites excreted by other bacterial species, but little is known about how this cross-feeding influences the effect of antibiotics. We hypothesized that when species rely on each other for essential metabolites, the minimum inhibitory concentration (MIC) for all species will drop to that of the “weakest link”—the species least resistant in monoculture. We tested this hypothesis in an obligate cross-feeding system that was engineered between Escherichia coli, Salmonella enterica, and Methylobacterium extorquens. The effect of tetracycline and ampicillin were tested on both liquid and solid media. In all cases, resistant species were inhibited at significantly lower antibiotic concentrations in the cross-feeding community than in monoculture or a competitive community. However, deviation from the “weakest link” hypothesis was also observed in cross-feeding communities apparently as result of changes in the timing of growth and cross-protection. Comparable results were also observed in a clinically relevant system involving facultative cross-feeding between Pseudomonas aeruginosa and an anaerobic consortium found in the lungs of cystic fibrosis patients. P. aeruginosa was inhibited by lower concentrations of ampicillin when cross-feeding than when grown in isolation. These results suggest that cross-feeding significantly alters tolerance to antibiotics in a variety of systems.
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Affiliation(s)
- Elizabeth M Adamowicz
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA.,Department of Ecology and Evolutionary Biology, University of Minnesota, St. Paul, MN, USA
| | - Jeffrey Flynn
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Ryan C Hunter
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - William R Harcombe
- Department of Ecology and Evolutionary Biology, University of Minnesota, St. Paul, MN, USA. .,BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.
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24
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O’Malley MA, Skillings DJ. Methodological Strategies in Microbiome Research and their Explanatory Implications. ACTA ACUST UNITED AC 2018. [DOI: 10.1162/posc_a_00274] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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25
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Koo H, Hakim JA, Morrow CD, Andersen DT, Bej AK. Microbial Community Composition and Predicted Functional Attributes of Antarctic Lithobionts Using Targeted Next-Generation Sequencing and Bioinformatics Tools. J Microbiol Methods 2018. [DOI: 10.1016/bs.mim.2018.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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26
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Gerardo N, Hurst G. Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes. BMC Biol 2017; 15:126. [PMID: 29282064 PMCID: PMC5744397 DOI: 10.1186/s12915-017-0455-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Over the past decade, there has been a pronounced shift in the study of host-microbe associations, with recognition that many of these associations are beneficial, and often critical, for a diverse array of hosts. There may also be pronounced benefits for the microbes, though this is less well empirically understood. Significant progress has been made in understanding how ecology and evolution shape simple associations between hosts and one or a few microbial species, and this work can serve as a foundation to study the ecology and evolution of host associations with their often complex microbial communities (microbiomes).
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Affiliation(s)
- Nicole Gerardo
- Department of Biology, Emory University, 1510 Clifton RD, Atlanta, Georgia, 30322, USA.
| | - Gregory Hurst
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
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Ghoul M, Andersen SB, West SA. Sociomics: Using Omic Approaches to Understand Social Evolution. Trends Genet 2017; 33:408-419. [PMID: 28506494 DOI: 10.1016/j.tig.2017.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/29/2017] [Indexed: 12/31/2022]
Abstract
All of life is social, from genes cooperating to form organisms, to animals cooperating to form societies. Omic approaches offer exceptional opportunities to solve major outstanding problems in the study of how sociality evolves. First, omics can be used to clarify the extent and form of sociality in natural populations. This is especially useful in species where it is difficult to study social traits in natural populations, such as bacteria and other microbes. Second, omics can be used to examine the consequences of sociality for genome evolution and gene expression. This is especially useful in cases where there is clear variation in the level of sociality, such as the social insects. Major tasks for the future are to apply these approaches to a wider range of non-model organisms, and to move from exploratory analyses to the testing of evolutionary theory.
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Affiliation(s)
- Melanie Ghoul
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
| | - Sandra B Andersen
- Langone Medical Center, New York University, 423 East 23rd Street, New York, NY 10010, USA.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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28
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Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr 2017; 57:1-24. [PMID: 28393285 PMCID: PMC5847071 DOI: 10.1007/s00394-017-1445-8] [Citation(s) in RCA: 1319] [Impact Index Per Article: 188.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 03/23/2017] [Indexed: 02/07/2023]
Abstract
The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays.
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29
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Kim WJ, Kim HU, Lee SY. Current state and applications of microbial genome-scale metabolic models. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.03.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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30
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Fischer CN, Trautman EP, Crawford JM, Stabb EV, Handelsman J, Broderick NA. Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior. eLife 2017; 6. [PMID: 28068220 PMCID: PMC5222558 DOI: 10.7554/elife.18855] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/12/2016] [Indexed: 12/12/2022] Open
Abstract
Animals host multi-species microbial communities (microbiomes) whose properties may result from inter-species interactions; however, current understanding of host-microbiome interactions derives mostly from studies in which elucidation of microbe-microbe interactions is difficult. In exploring how Drosophila melanogaster acquires its microbiome, we found that a microbial community influences Drosophila olfactory and egg-laying behaviors differently than individual members. Drosophila prefers a Saccharomyces-Acetobacter co-culture to the same microorganisms grown individually and then mixed, a response mainly due to the conserved olfactory receptor, Or42b. Acetobacter metabolism of Saccharomyces-derived ethanol was necessary, and acetate and its metabolic derivatives were sufficient, for co-culture preference. Preference correlated with three emergent co-culture properties: ethanol catabolism, a distinct volatile profile, and yeast population decline. Egg-laying preference provided a context-dependent fitness benefit to larvae. We describe a molecular mechanism by which a microbial community affects animal behavior. Our results support a model whereby emergent metabolites signal a beneficial multispecies microbiome. DOI:http://dx.doi.org/10.7554/eLife.18855.001 Animals associate with communities of microorganisms, also known as their microbiome, that live in or on their bodies. Within these communities, microbes – such as yeast and bacteria – interact by producing chemical compounds called metabolites that can influence the activity of other members of the community. These metabolites can also affect the host, helping with nutrition or causing disease. The behavior of an animal may help it to acquire its microbiome, although this has not been properly explored experimentally. For example, the fruit fly Drosophila melanogaster acquires members of its microbiome from the microbes found on the fermented fruit that it eats. It is possible that the flies – and other animals – respond to microbial metabolites, which act as signals or cues that cause the animal to avoid or seek the microbial community. The fruit fly microbiome is commonly studied in the laboratory because it has a much simpler composition than mammalian microbiomes. Previous studies have explored how the flies respond to odors produced by individual types of microbes, but none have explored how the behavior of the flies changes in response to the odors produced by a mixed microbial community. Fischer et al. now show that fruit flies are preferentially attracted to microbiome members that are interacting with each other. The flies detected members of the microbiome by responding to chemicals that are only produced when community members grew together. For example, one member of the microbial community produces ethanol that is then converted to acetate by another community member. Neither ethanol nor acetate alone attracted flies as strongly. Fischer et al. also discovered that both adult fruit flies and their larvae benefit from acquiring a mixture of different microbes at the same time. Adult flies benefit by avoiding harmful concentrations of either ethanol or acetic acid, and larvae benefit from developing in an environment that reduces how quickly disease-causing microbes can grow. Overall, the results presented by Fischer et al. detail how flies select a beneficial, interactive microbiome from an external reservoir of microorganisms. Flies also have internal mechanisms, like their immune system, that help them to select their microbiome. Therefore a future challenge will be to integrate the behavioral and internal selection mechanisms into a single model of microbiome acquisition. DOI:http://dx.doi.org/10.7554/eLife.18855.002
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Affiliation(s)
- Caleb N Fischer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Eric P Trautman
- Department of Chemistry, Yale University, New Haven, United States
| | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, United States
| | - Eric V Stabb
- Department of Microbiology, University of Georgia, Athens, United States
| | - Jo Handelsman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Nichole A Broderick
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States.,Institute for Systems Genomics, University of Connecticut, Storrs, United States
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31
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Noecker C, McNally CP, Eng A, Borenstein E. High-resolution characterization of the human microbiome. Transl Res 2017; 179:7-23. [PMID: 27513210 PMCID: PMC5164958 DOI: 10.1016/j.trsl.2016.07.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 12/29/2022]
Abstract
The human microbiome plays an important and increasingly recognized role in human health. Studies of the microbiome typically use targeted sequencing of the 16S rRNA gene, whole metagenome shotgun sequencing, or other meta-omic technologies to characterize the microbiome's composition, activity, and dynamics. Processing, analyzing, and interpreting these data involve numerous computational tools that aim to filter, cluster, annotate, and quantify the obtained data and ultimately provide an accurate and interpretable profile of the microbiome's taxonomy, functional capacity, and behavior. These tools, however, are often limited in resolution and accuracy and may fail to capture many biologically and clinically relevant microbiome features, such as strain-level variation or nuanced functional response to perturbation. Over the past few years, extensive efforts have been invested toward addressing these challenges and developing novel computational methods for accurate and high-resolution characterization of microbiome data. These methods aim to quantify strain-level composition and variation, detect and characterize rare microbiome species, link specific genes to individual taxa, and more accurately characterize the functional capacity and dynamics of the microbiome. These methods and the ability to produce detailed and precise microbiome information are clearly essential for informing microbiome-based personalized therapies. In this review, we survey these methods, highlighting the challenges each method sets out to address and briefly describing methodological approaches.
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Affiliation(s)
- Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Colin P McNally
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Computer Science and Engineering, University of Washington, Seattle, WA
- Santa Fe Institute, Santa Fe, NM
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32
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Deines P, Bosch TCG. Transitioning from Microbiome Composition to Microbial Community Interactions: The Potential of the Metaorganism Hydra as an Experimental Model. Front Microbiol 2016; 7:1610. [PMID: 27790207 PMCID: PMC5061769 DOI: 10.3389/fmicb.2016.01610] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/26/2016] [Indexed: 01/08/2023] Open
Abstract
Animals are home to complex microbial communities, which are shaped through interactions within the community, interactions with the host, and through environmental factors. The advent of high-throughput sequencing methods has led to novel insights in changing patterns of community composition and structure. However, deciphering the different types of interactions among community members, with their hosts and their interplay with their environment is still a challenge of major proportion. The emerging fields of synthetic microbial ecology and community systems biology have the potential to decrypt these complex relationships. Studying host-associated microbiota across multiple spatial and temporal scales will bridge the gap between individual microorganism studies and large-scale whole community surveys. Here, we discuss the unique potential of Hydra as an emerging experimental model in microbiome research. Through in vivo, in vitro, and in silico approaches the interaction structure of host-associated microbial communities and the effects of the host on the microbiota and its interactions can be disentangled. Research in the model system Hydra can unify disciplines from molecular genetics to ecology, opening up the opportunity to discover fundamental rules that govern microbiome community stability.
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Affiliation(s)
- Peter Deines
- Zoological Institute and Interdisciplinary Research Center, Kiel Life Science, Christian-Albrechts-Universität zu Kiel Kiel, Germany
| | - Thomas C G Bosch
- Zoological Institute and Interdisciplinary Research Center, Kiel Life Science, Christian-Albrechts-Universität zu Kiel Kiel, Germany
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33
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Ruiz L, Hidalgo C, Blanco-Míguez A, Lourenço A, Sánchez B, Margolles A. Tackling probiotic and gut microbiota functionality through proteomics. J Proteomics 2016; 147:28-39. [DOI: 10.1016/j.jprot.2016.03.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/19/2016] [Accepted: 03/10/2016] [Indexed: 12/24/2022]
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34
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Aguiar-Pulido V, Huang W, Suarez-Ulloa V, Cickovski T, Mathee K, Narasimhan G. Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis. Evol Bioinform Online 2016; 12:5-16. [PMID: 27199545 PMCID: PMC4869604 DOI: 10.4137/ebo.s36436] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/26/2016] [Accepted: 01/31/2016] [Indexed: 01/21/2023] Open
Abstract
Microbiomes are ubiquitous and are found in the ocean, the soil, and in/on other living organisms. Changes in the microbiome can impact the health of the environmental niche in which they reside. In order to learn more about these communities, different approaches based on data from multiple omics have been pursued. Metagenomics produces a taxonomical profile of the sample, metatranscriptomics helps us to obtain a functional profile, and metabolomics completes the picture by determining which byproducts are being released into the environment. Although each approach provides valuable information separately, we show that, when combined, they paint a more comprehensive picture. We conclude with a review of network-based approaches as applied to integrative studies, which we believe holds the key to in-depth understanding of microbiomes.
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Affiliation(s)
- Vanessa Aguiar-Pulido
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Wenrui Huang
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Victoria Suarez-Ulloa
- Chromatin Structure and Evolution Group (Chromevol), Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Trevor Cickovski
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA.; Department of Computer Science, Eckerd College, St. Petersburg, FL, USA
| | - Kalai Mathee
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.; Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.; Global Health Consortium, Florida International University, Miami, FL, USA
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA.; Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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35
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From Hype to Hope: The Gut Microbiota in Enteric Infectious Disease. Cell 2016; 163:1326-32. [PMID: 26638069 DOI: 10.1016/j.cell.2015.11.032] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 12/12/2022]
Abstract
One of the clearest functions of the gut microbiota in humans is resistance to colonization by enteric bacterial pathogens. Reconstitution of the microbiota offers an exciting therapeutic approach, but great challenges must be overcome.
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36
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Predicting microbial interactions through computational approaches. Methods 2016; 102:12-9. [PMID: 27025964 DOI: 10.1016/j.ymeth.2016.02.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/15/2016] [Accepted: 02/23/2016] [Indexed: 11/22/2022] Open
Abstract
Microorganisms play a vital role in various ecosystems and characterizing interactions between them is an essential step towards understanding the organization and function of microbial communities. Computational prediction has recently become a widely used approach to investigate microbial interactions. We provide a thorough review of emerging computational methods organized by the type of data they employ. We highlight three major challenges in inferring interactions using metagenomic survey data and discuss the underlying assumptions and mathematics of interaction inference algorithms. In addition, we review interaction prediction methods relying on metabolic pathways, which are increasingly used to reveal mechanisms of interactions. Furthermore, we also emphasize the importance of mining the scientific literature for microbial interactions - a largely overlooked data source for experimentally validated interactions.
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37
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Rebollar EA, Antwis RE, Becker MH, Belden LK, Bletz MC, Brucker RM, Harrison XA, Hughey MC, Kueneman JG, Loudon AH, McKenzie V, Medina D, Minbiole KPC, Rollins-Smith LA, Walke JB, Weiss S, Woodhams DC, Harris RN. Using "Omics" and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases. Front Microbiol 2016; 7:68. [PMID: 26870025 PMCID: PMC4735675 DOI: 10.3389/fmicb.2016.00068] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 01/14/2016] [Indexed: 12/20/2022] Open
Abstract
Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called "omics," are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the Kolmogorov-Smirnov Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics, or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.
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Affiliation(s)
- Eria A. Rebollar
- Department of Biology, James Madison UniversityHarrisonburg, VA, USA
| | - Rachael E. Antwis
- Unit for Environmental Sciences and Management, North-West UniversityPotchefstroom, South Africa
- Institute of Zoology, Zoological Society of LondonLondon, UK
- School of Environment and Life Sciences, University of SalfordSalford, UK
| | - Matthew H. Becker
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological ParkWashington, DC, USA
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Molly C. Bletz
- Zoological Institute, Technische Universität BraunschweigBraunschweig, Germany
| | | | | | - Myra C. Hughey
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Jordan G. Kueneman
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Andrew H. Loudon
- Department of Zoology, Biodiversity Research Centre, University of British ColumbiaVancouver, BC, Canada
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | | | - Louise A. Rollins-Smith
- Department of Pathology, Microbiology and Immunology and Department of Pediatrics, Vanderbilt University School of Medicine, Department of Biological Sciences, Vanderbilt UniversityNashville, TN, USA
| | - Jenifer B. Walke
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado at BoulderBoulder, CO, USA
| | | | - Reid N. Harris
- Department of Biology, James Madison UniversityHarrisonburg, VA, USA
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38
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Marbouty M, Koszul R. Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data. Trends Genet 2015; 31:673-682. [PMID: 26608779 DOI: 10.1016/j.tig.2015.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/15/2015] [Accepted: 10/15/2015] [Indexed: 01/26/2023]
Abstract
Microbial communities are complex and constitute important parts of our environment. Genomic analysis of these populations is a dynamic research area but remains limited by the difficulty in assembling full genomes of individual species. Recently, a new method for metagenome assembly/analysis based on chromosome conformation capture has emerged (meta3C). This approach quantifies the collisions experienced by DNA molecules to identify those sharing the same cellular compartments, allowing the characterization of genomes present within complex mixes of species. The exploitation of these chromosome 3D signatures holds promising perspectives for genome sequencing of discrete species in complex populations. It also has the potential to assign correctly extra-chromosomal elements, such as plasmids, mobile elements and phages, to their host cells.
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Affiliation(s)
- Martial Marbouty
- Institut Pasteur, Department of Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015 Paris, France; CNRS, UMR 3525, 75015 Paris, France
| | - Romain Koszul
- Institut Pasteur, Department of Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015 Paris, France; CNRS, UMR 3525, 75015 Paris, France.
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39
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Host Genetic Control of the Microbiota Mediates the Drosophila Nutritional Phenotype. Appl Environ Microbiol 2015; 82:671-9. [PMID: 26567306 DOI: 10.1128/aem.03301-15] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/08/2015] [Indexed: 02/07/2023] Open
Abstract
A wealth of studies has demonstrated that resident microorganisms (microbiota) influence the pattern of nutrient allocation to animal protein and energy stores, but it is unclear how the effects of the microbiota interact with other determinants of animal nutrition, including animal genetic factors and diet. Here, we demonstrate that members of the gut microbiota in Drosophila melanogaster mediate the effect of certain animal genetic determinants on an important nutritional trait, triglyceride (lipid) content. Parallel analysis of the taxonomic composition of the associated bacterial community and host nutritional indices (glucose, glycogen, triglyceride, and protein contents) in multiple Drosophila genotypes revealed significant associations between the abundance of certain microbial taxa, especially Acetobacteraceae and Xanthamonadaceae, and host nutritional phenotype. By a genome-wide association study of Drosophila lines colonized with a defined microbiota, multiple host genes were statistically associated with the abundance of one bacterium, Acetobacter tropicalis. Experiments using mutant Drosophila validated the genetic association evidence and reveal that host genetic control of microbiota abundance affects the nutritional status of the flies. These data indicate that the abundance of the resident microbiota is influenced by host genotype, with consequent effects on nutrient allocation patterns, demonstrating that host genetic control of the microbiome contributes to the genotype-phenotype relationship of the animal host.
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40
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Belden LK, Hughey MC, Rebollar EA, Umile TP, Loftus SC, Burzynski EA, Minbiole KPC, House LL, Jensen RV, Becker MH, Walke JB, Medina D, Ibáñez R, Harris RN. Panamanian frog species host unique skin bacterial communities. Front Microbiol 2015; 6:1171. [PMID: 26579083 PMCID: PMC4621460 DOI: 10.3389/fmicb.2015.01171] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/09/2015] [Indexed: 01/26/2023] Open
Abstract
Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd), that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species) community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26%) were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in these skin symbiont microbial systems as it is in many macro-systems.
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Affiliation(s)
- Lisa K Belden
- Department of Biological Sciences, Virginia Tech Blacksburg, VA, USA ; Smithsonian Tropical Research Institute Balboa, Ancón, Republic of Panamá
| | - Myra C Hughey
- Department of Biological Sciences, Virginia Tech Blacksburg, VA, USA
| | - Eria A Rebollar
- Smithsonian Tropical Research Institute Balboa, Ancón, Republic of Panamá
| | - Thomas P Umile
- Department of Chemistry, Villanova University Villanova, PA, USA
| | | | | | | | - Leanna L House
- Department of Statistics, Virginia Tech Blacksburg, VA, USA
| | - Roderick V Jensen
- Department of Biological Sciences, Virginia Tech Blacksburg, VA, USA
| | - Matthew H Becker
- Department of Biological Sciences, Virginia Tech Blacksburg, VA, USA
| | - Jenifer B Walke
- Department of Biological Sciences, Virginia Tech Blacksburg, VA, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia Tech Blacksburg, VA, USA
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute Balboa, Ancón, Republic of Panamá
| | - Reid N Harris
- Department of Biology, James Madison University Harrisonburg, VA, USA
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41
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Campbell K, Vowinckel J, Mülleder M, Malmsheimer S, Lawrence N, Calvani E, Miller-Fleming L, Alam MT, Christen S, Keller MA, Ralser M. Self-establishing communities enable cooperative metabolite exchange in a eukaryote. eLife 2015; 4:e09943. [PMID: 26499891 PMCID: PMC4695387 DOI: 10.7554/elife.09943] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/20/2015] [Indexed: 11/13/2022] Open
Abstract
Metabolite exchange among co-growing cells is frequent by nature, however, is not necessarily occurring at growth-relevant quantities indicative of non-cell-autonomous metabolic function. Complementary auxotrophs of Saccharomyces cerevisiae amino acid and nucleotide metabolism regularly fail to compensate for each other's deficiencies upon co-culturing, a situation which implied the absence of growth-relevant metabolite exchange interactions. Contrastingly, we find that yeast colonies maintain a rich exometabolome and that cells prefer the uptake of extracellular metabolites over self-synthesis, indicators of ongoing metabolite exchange. We conceived a system that circumvents co-culturing and begins with a self-supporting cell that grows autonomously into a heterogeneous community, only able to survive by exchanging histidine, leucine, uracil, and methionine. Compensating for the progressive loss of prototrophy, self-establishing communities successfully obtained an auxotrophic composition in a nutrition-dependent manner, maintaining a wild-type like exometabolome, growth parameters, and cell viability. Yeast, as a eukaryotic model, thus possesses extensive capacity for growth-relevant metabolite exchange and readily cooperates in metabolism within progressively establishing communities.
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Affiliation(s)
- Kate Campbell
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Jakob Vowinckel
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Michael Mülleder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Silke Malmsheimer
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Nicola Lawrence
- The Wellcome Trust Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Enrica Calvani
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Leonor Miller-Fleming
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Mohammad T Alam
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Stefan Christen
- Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Markus A Keller
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
- Mill Hill Laboratory, The Francis Crick Institute, London, United Kingdom
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42
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Affiliation(s)
- Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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43
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Mueller U, Sachs J. Engineering Microbiomes to Improve Plant and Animal Health. Trends Microbiol 2015; 23:606-617. [DOI: 10.1016/j.tim.2015.07.009] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/08/2015] [Accepted: 07/22/2015] [Indexed: 12/22/2022]
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From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems. Cell Mol Life Sci 2015; 72:4287-308. [PMID: 26254872 PMCID: PMC4611022 DOI: 10.1007/s00018-015-2004-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 12/30/2022]
Abstract
Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.
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45
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Shoaie S, Ghaffari P, Kovatcheva-Datchary P, Mardinoglu A, Sen P, Pujos-Guillot E, de Wouters T, Juste C, Rizkalla S, Chilloux J, Hoyles L, Nicholson JK, Dore J, Dumas ME, Clement K, Bäckhed F, Nielsen J. Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome. Cell Metab 2015; 22:320-31. [PMID: 26244934 DOI: 10.1016/j.cmet.2015.07.001] [Citation(s) in RCA: 275] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 03/02/2015] [Accepted: 06/11/2015] [Indexed: 12/25/2022]
Abstract
The human gut microbiome is known to be associated with various human disorders, but a major challenge is to go beyond association studies and elucidate causalities. Mathematical modeling of the human gut microbiome at a genome scale is a useful tool to decipher microbe-microbe, diet-microbe and microbe-host interactions. Here, we describe the CASINO (Community And Systems-level INteractive Optimization) toolbox, a comprehensive computational platform for analysis of microbial communities through metabolic modeling. We first validated the toolbox by simulating and testing the performance of single bacteria and whole communities in vitro. Focusing on metabolic interactions between the diet, gut microbiota, and host metabolism, we demonstrated the predictive power of the toolbox in a diet-intervention study of 45 obese and overweight individuals and validated our predictions by fecal and blood metabolomics data. Thus, modeling could quantitatively describe altered fecal and serum amino acid levels in response to diet intervention.
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Affiliation(s)
- Saeed Shoaie
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Pouyan Ghaffari
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Petia Kovatcheva-Datchary
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, 41345 Gothenburg, Sweden
| | - Adil Mardinoglu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Partho Sen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Estelle Pujos-Guillot
- Institut National de la Recherche 'Agronomique (INRA), Nutrition Humaine, Plateforme Exploration du Métabolisme, 63000 Clermont-Ferrand, France
| | - Tomas de Wouters
- Institut National de la Recherche 'Agronomique (INRA), UMR1319 Micalis and USR1367 MetaGenoPolis, 78352 Jouy-en-Josas, France
| | - Catherine Juste
- Institut National de la Recherche 'Agronomique (INRA), UMR1319 Micalis and USR1367 MetaGenoPolis, 78352 Jouy-en-Josas, France
| | - Salwa Rizkalla
- Institute of Cardiometabolism and Nutrition (ICAN), Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, 75013 Paris, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1166, NutriOmics Team 6, 75013 Paris, France
| | - Julien Chilloux
- Section of Biomolecular Medicine, Department of Surgery and Cancer, Division of Computational and Systems Medicine, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Lesley Hoyles
- Section of Biomolecular Medicine, Department of Surgery and Cancer, Division of Computational and Systems Medicine, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Jeremy K Nicholson
- Section of Biomolecular Medicine, Department of Surgery and Cancer, Division of Computational and Systems Medicine, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | | | - Joel Dore
- Institut National de la Recherche 'Agronomique (INRA), UMR1319 Micalis and USR1367 MetaGenoPolis, 78352 Jouy-en-Josas, France
| | - Marc E Dumas
- Section of Biomolecular Medicine, Department of Surgery and Cancer, Division of Computational and Systems Medicine, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Karine Clement
- Institute of Cardiometabolism and Nutrition (ICAN), Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, 75013 Paris, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1166, NutriOmics Team 6, 75013 Paris, France; Sorbonne Universités, UPMC University Paris 06, UMR S-1166, Team 6, 75013 Paris, France
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, 41345 Gothenburg, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden.
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Abstract
Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable. To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology. Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., "holobionts." As such, their collective genomes forge a "hologenome," and models of animal and plant biology that do not account for these intergenomic associations are incomplete. Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation. Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany. We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines. At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology.
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Affiliation(s)
- Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kevin R. Theis
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
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47
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Biggs MB, Medlock GL, Kolling GL, Papin JA. Metabolic network modeling of microbial communities. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:317-34. [PMID: 26109480 DOI: 10.1002/wsbm.1308] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 12/15/2022]
Abstract
Genome-scale metabolic network reconstructions and constraint-based analyses are powerful methods that have the potential to make functional predictions about microbial communities. Genome-scale metabolic networks are used to characterize the metabolic functions of microbial communities via several techniques including species compartmentalization, separating species-level and community-level objectives, dynamic analysis, the 'enzyme-soup' approach, multiscale modeling, and others. There are many challenges in the field, including a need for tools that accurately assign high-level omics signals to individual community members, the need for improved automated network reconstruction methods, and novel algorithms for integrating omics data and engineering communities. As technologies and modeling frameworks improve, we expect that there will be corresponding advances in the fields of ecology, health science, and microbial community engineering.
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Affiliation(s)
- Matthew B Biggs
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Gregory L Medlock
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Glynis L Kolling
- Department of Medicine, Infectious Diseases, University of Virginia, Charlottesville, VA, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
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48
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Ji B, Nielsen J. From next-generation sequencing to systematic modeling of the gut microbiome. Front Genet 2015; 6:219. [PMID: 26157455 PMCID: PMC4477173 DOI: 10.3389/fgene.2015.00219] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 06/03/2015] [Indexed: 12/31/2022] Open
Abstract
Changes in the human gut microbiome are associated with altered human metabolism and health, yet the mechanisms of interactions between microbial species and human metabolism have not been clearly elucidated. Next-generation sequencing has revolutionized the human gut microbiome research, but most current applications concentrate on studying the microbial diversity of communities and have at best provided associations between specific gut bacteria and human health. However, little is known about the inner metabolic mechanisms in the gut ecosystem. Here we review recent progress in modeling the metabolic interactions of gut microbiome, with special focus on the utilization of metabolic modeling to infer host–microbe interactions and microbial species interactions. The systematic modeling of metabolic interactions could provide a predictive understanding of gut microbiome, and pave the way to synthetic microbiota design and personalized-microbiome medicine and healthcare. Finally, we discuss the integration of metabolic modeling and gut microbiome engineering, which offer a new way to explore metabolic interactions across members of the gut microbiota.
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Affiliation(s)
- Boyang Ji
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology , Göteborg, Sweden
| | - Jens Nielsen
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology , Göteborg, Sweden
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49
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Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico. Appl Environ Microbiol 2015; 81:4049-61. [PMID: 25841013 DOI: 10.1128/aem.00101-15] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/31/2015] [Indexed: 12/31/2022] Open
Abstract
The human gut is inhabited by thousands of microbial species, most of which are still uncharacterized. Gut microbes have adapted to each other's presence as well as to the host and engage in complex cross feeding. Constraint-based modeling has been successfully applied to predicting microbe-microbe interactions, such as commensalism, mutualism, and competition. Here, we apply a constraint-based approach to model pairwise interactions between 11 representative gut microbes. Microbe-microbe interactions were computationally modeled in conjunction with human small intestinal enterocytes, and the microbe pairs were subjected to three diets with various levels of carbohydrate, fat, and protein in normoxic or anoxic environments. Each microbe engaged in species-specific commensal, parasitic, mutualistic, or competitive interactions. For instance, Streptococcus thermophilus efficiently outcompeted microbes with which it was paired, in agreement with the domination of streptococci in the small intestinal microbiota. Under anoxic conditions, the probiotic organism Lactobacillus plantarum displayed mutualistic behavior toward six other species, which, surprisingly, were almost entirely abolished under normoxic conditions. This finding suggests that the anoxic conditions in the large intestine drive mutualistic cross feeding, leading to the evolvement of an ecosystem more complex than that of the small intestinal microbiota. Moreover, we predict that the presence of the small intestinal enterocyte induces competition over host-derived nutrients. The presented framework can readily be expanded to a larger gut microbial community. This modeling approach will be of great value for subsequent studies aiming to predict conditions favoring desirable microbes or suppressing pathogens.
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50
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Abstract
The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics of the microbial communities that populate diverse habitats. Over the past decade, these advances have yielded an avalanche of metagenomic data. The current stage of "van Leeuwenhoek"-like cataloguing, as well as functional analyses, will likely accelerate as DNA and RNA sequencing, plus protein and metabolic profiling capacities and computational tools, continue to improve. However, it is time to consider: what's next for microbiome research? The short pieces included here briefly consider the challenges and opportunities awaiting microbiome research.
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