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Kong Y, Chen H, Huang X, Chang L, Yang B, Chen W. Precise metabolic modeling in post-omics era: accomplishments and perspectives. Crit Rev Biotechnol 2024:1-19. [PMID: 39198033 DOI: 10.1080/07388551.2024.2390089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 09/01/2024]
Abstract
Microbes have been extensively utilized for their sustainable and scalable properties in synthesizing desired bio-products. However, insufficient knowledge about intracellular metabolism has impeded further microbial applications. The genome-scale metabolic models (GEMs) play a pivotal role in facilitating a global understanding of cellular metabolic mechanisms. These models enable rational modification by exploring metabolic pathways and predicting potential targets in microorganisms, enabling precise cell regulation without experimental costs. Nonetheless, simplified GEM only considers genome information and network stoichiometry while neglecting other important bio-information, such as enzyme functions, thermodynamic properties, and kinetic parameters. Consequently, uncertainties persist particularly when predicting microbial behaviors in complex and fluctuant systems. The advent of the omics era with its massive quantification of genes, proteins, and metabolites under various conditions has led to the flourishing of multi-constrained models and updated algorithms with improved predicting power and broadened dimension. Meanwhile, machine learning (ML) has demonstrated exceptional analytical and predictive capacities when applied to training sets of biological big data. Incorporating the discriminant strength of ML with GEM facilitates mechanistic modeling efficiency and improves predictive accuracy. This paper provides an overview of research innovations in the GEM, including multi-constrained modeling, analytical approaches, and the latest applications of ML, which may contribute comprehensive knowledge toward genetic refinement, strain development, and yield enhancement for a broad range of biomolecules.
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Affiliation(s)
- Yawen Kong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Xinlei Huang
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
| | - Lulu Chang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Bo Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, P. R. China
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2
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Cui X, Wu Z, Zhou Y, Deng L, Chen Y, Huang H, Sun X, Li Y, Wang H, Zhang L, He J. A bibliometric study of global trends in T1DM and intestinal flora research. Front Microbiol 2024; 15:1403514. [PMID: 39027096 PMCID: PMC11254799 DOI: 10.3389/fmicb.2024.1403514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
Background Type 1 diabetes mellitus (T1DM) is a chronic metabolic disease that seriously jeopardizes human physical and mental health and reduces quality of life. Intestinal flora is one of the critical areas of exploration in T1DM research. Objective This study aims to explore the research hotspot and development trend of T1DM and intestinal flora to provide research direction and ideas for researchers. Methods We used the Web of Science (WOS) Core Collection and searched up to 18 November 2023, for articles on studies of the correlation between T1DM and intestinal flora. CiteSpace, VOSviewers and R package "bibliometrix" were used to conduct this bibliometric analysis. Results Eventually, 534 documents met the requirements to be included, and as of 18 November 2023, there was an upward trend in the number of publications in the field, with a significant increase in the number of articles published after 2020. In summary, F Susan Wong (UK) was the author with the most publications (21), the USA was the country with the most publications (198), and the State University System of Florida (the United States) was the institution with the most publications (32). The keywords that appeared more frequently were T cells, fecal transplants, and short-chain fatty acids. The results of keywords with the most robust citation bursts suggest that Faecalibacterium prausnitzii and butyrate may become a focus of future research. Conclusion In the future, intestinal flora will remain a research focus in T1DM. Future research can start from Faecalibacterium prausnitzii and combine T cells, fecal bacteria transplantation, and short-chain fatty acids to explore the mechanism by which intestinal flora affects blood glucose in patients with T1DM, which may provide new ideas for the prevention and treatment of T1DM.
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Affiliation(s)
- Xinxin Cui
- Department of Public Health, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Zhen Wu
- Department of Public Health, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Yangbo Zhou
- Department of Public Health, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Longji Deng
- Department of Public Health, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Yu Chen
- Department of Public Health, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Hanqiao Huang
- Department of Public Health, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Xiangbin Sun
- Department of Public Health, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Yu Li
- Department of Public Health, Shihezi University School of Medicine, Shihezi, Xinjiang, China
- Key Laboratory for Prevention and Control of Emerging Infectious Diseases and Public Health Security, The Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
- Department of Public Health and Key Laboratory of Xinjiang Endemic and Ethnic Diseases of the Ministry of Education, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Haixia Wang
- Department of Public Health, Shihezi University School of Medicine, Shihezi, Xinjiang, China
- Key Laboratory for Prevention and Control of Emerging Infectious Diseases and Public Health Security, The Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
- Department of Public Health and Key Laboratory of Xinjiang Endemic and Ethnic Diseases of the Ministry of Education, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Li Zhang
- Department of Public Health, Shihezi University School of Medicine, Shihezi, Xinjiang, China
- Key Laboratory for Prevention and Control of Emerging Infectious Diseases and Public Health Security, The Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
- Department of Public Health and Key Laboratory of Xinjiang Endemic and Ethnic Diseases of the Ministry of Education, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Jia He
- Department of Public Health, Shihezi University School of Medicine, Shihezi, Xinjiang, China
- Key Laboratory for Prevention and Control of Emerging Infectious Diseases and Public Health Security, The Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
- Department of Public Health and Key Laboratory of Xinjiang Endemic and Ethnic Diseases of the Ministry of Education, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
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3
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Liu N, Liu S, Xu X, Nong X, Chen H. Organoids as an in vitro model to study human tumors and bacteria. J Surg Oncol 2024; 129:1390-1400. [PMID: 38534036 DOI: 10.1002/jso.27626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024]
Abstract
Organoids faithfully replicate the morphological structure, physiological functions, stable phenotype of the source tissue. Recent research indicates that bacteria can significantly influence the initiation, advancement, and treatment of tumors. This article provides a comprehensive review of the applications of organoid technology in tumor research, the relationship between bacteria and the genesis and development of tumors, and the exploration of the impact of bacteria on tumors and their applications in research.
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Affiliation(s)
- Naiyu Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shuxi Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaoyue Xu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - XianXian Nong
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hong Chen
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
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4
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Madison AA, Bailey MT. Stressed to the Core: Inflammation and Intestinal Permeability Link Stress-Related Gut Microbiota Shifts to Mental Health Outcomes. Biol Psychiatry 2024; 95:339-347. [PMID: 38353184 PMCID: PMC10867428 DOI: 10.1016/j.biopsych.2023.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/02/2023] [Accepted: 10/22/2023] [Indexed: 02/16/2024]
Abstract
Stress levels are surging, alongside the incidence of stress-related psychiatric disorders. Perhaps a related phenomenon, especially in urban areas, the human gut contains fewer bacterial species than ever before. Although the functional implications of this absence are unclear, one consequence may be reduced stress resilience. Preclinical and clinical evidence has shown how stress exposure can alter the gut microbiota and their metabolites, affecting host physiology. Also, stress-related shifts in the gut microbiota jeopardize tight junctions of the gut barrier. In this context, bacteria and bacterial products can translocate from the gut to the bloodstream, lymph nodes, and other organs, thereby modifying systemic inflammatory responses. Heightened circulating inflammation can be an etiological factor in stress-related psychiatric disorders, including some cases of depression. In this review, we detail preclinical and clinical evidence that traces these brain-to-gut-to-brain pathways that underlie stress-related psychiatric disorders and potentially affect their responsivity to conventional psychiatric medications. We also review evidence for interventions that modulate the gut microbiota (e.g., antibiotics, probiotics, prebiotics) to reduce stress responses and psychiatric symptoms. Lastly, we discuss challenges to translation and opportunities for innovations that could impact future psychiatric clinical practice.
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Affiliation(s)
- Annelise A Madison
- Institute for Behavioral Medicine Research, Ohio State University College of Medicine, Columbus, Ohio; Department of Psychology, Ohio State University, Columbus, Ohio.
| | - Michael T Bailey
- Institute for Behavioral Medicine Research, Ohio State University College of Medicine, Columbus, Ohio; Department of Pediatrics, Ohio State University College of Medicine, Columbus, Ohio; Center for Microbial Pathogenesis and the Oral and Gastrointestinal Microbiology Research Affinity Group, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio.
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5
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Paraskevaidis I, Xanthopoulos A, Tsougos E, Triposkiadis F. Human Gut Microbiota in Heart Failure: Trying to Unmask an Emerging Organ. Biomedicines 2023; 11:2574. [PMID: 37761015 PMCID: PMC10526035 DOI: 10.3390/biomedicines11092574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
There is a bidirectional relationship between the heart and the gut. The gut microbiota, the community of gut micro-organisms themselves, is an excellent gut-homeostasis keeper since it controls the growth of potentially harmful bacteria and protects the microbiota environment. There is evidence suggesting that a diet rich in fatty acids can be metabolized and converted by gut microbiota and hepatic enzymes to trimethyl-amine N-oxide (TMAO), a product that is associated with atherogenesis, platelet dysfunction, thrombotic events, coronary artery disease, stroke, heart failure (HF), and, ultimately, death. HF, by inducing gut ischemia, congestion, and, consequently, gut barrier dysfunction, promotes the intestinal leaking of micro-organisms and their products, facilitating their entrance into circulation and thus stimulating a low-grade inflammation associated with an immune response. Drugs used for HF may alter the gut microbiota, and, conversely, gut microbiota may modify the pharmacokinetic properties of the drugs. The modification of lifestyle based mainly on exercise and a Mediterranean diet, along with the use of pre- or probiotics, may be beneficial for the gut microbiota environment. The potential role of gut microbiota in HF development and progression is the subject of this review.
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Affiliation(s)
| | - Andrew Xanthopoulos
- Department of Cardiology, University Hospital of Larissa, 41110 Larissa, Greece; (A.X.); (F.T.)
| | - Elias Tsougos
- 6th Department of Cardiology, Hygeia Hospital, 15123 Athens, Greece
| | - Filippos Triposkiadis
- Department of Cardiology, University Hospital of Larissa, 41110 Larissa, Greece; (A.X.); (F.T.)
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6
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Wang J, Lou Y, Ma D, Feng K, Chen C, Zhao L, Xing D. Co-treatment with free nitrous acid and calcium peroxide regulates microbiome and metabolic functions of acidogenesis and methanogenesis in sludge anaerobic digestion. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 870:161924. [PMID: 36736410 DOI: 10.1016/j.scitotenv.2023.161924] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Wasted activated sludge (WAS) is a promising feedstock for carbon management because of its abundance and carbon-neutral features. Currently, the goal is to maximize the energy in WAS and avoid secondary toxic effects or accumulation of harmful substances in the environment. Chemical pretreatment is an effective strategy for enhancing WAS disintegration and production of short chain fatty acids (SCFAs). However, the role of pretreatment in shaping the core microbiome and functional metabolism of anaerobic microorganisms remains obscure. Here, the mechanisms of SCFA synthesis and microbiome response to free nitrous acid (FNA) and calcium peroxide (CaO2) co-treatment during sludge anaerobic digestion (AD) were investigated. The combination of FNA and CaO2 enriched acidogenic Macellibacteroides, Petrimonas, and Sedimentibacter to a relative abundance of 15.0%, 10.3%, and 7.3%, respectively, resulting in an apparent increase in SCFA production. Metagenome analysis indicated that FNA + CaO2 co-treatment facilitated glycolysis, phosphate acetyltransferase-acetate kinase pathway, amino acid metabolism, and acetate transport, but inhibited CO2 reduction and common pathway of methanogenesis compared with the untreated control. This work provides theoretical insights into the functional activity and interaction of microorganisms with ecological factors.
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Affiliation(s)
- Jing Wang
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yu Lou
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Dongmei Ma
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kun Feng
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Chuan Chen
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lei Zhao
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Defeng Xing
- State Key Lab of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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7
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Woo AYM, Aguilar Ramos MA, Narayan R, Richards-Corke KC, Wang ML, Sandoval-Espinola WJ, Balskus EP. Targeting the human gut microbiome with small-molecule inhibitors. NATURE REVIEWS. CHEMISTRY 2023; 7:319-339. [PMID: 37117817 DOI: 10.1038/s41570-023-00471-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 04/30/2023]
Abstract
The human gut microbiome is a complex microbial community that is strongly linked to both host health and disease. However, the detailed molecular mechanisms underlying the effects of these microorganisms on host biology remain largely uncharacterized. The development of non-lethal, small-molecule inhibitors that target specific gut microbial activities enables a powerful but underutilized approach to studying the gut microbiome and a promising therapeutic strategy. In this Review, we will discuss the challenges of studying this microbial community, the historic use of small-molecule inhibitors in microbial ecology, and recent applications of this strategy. We also discuss the evidence suggesting that host-targeted drugs can affect the growth and metabolism of gut microbes. Finally, we address the issues of developing and implementing microbiome-targeted small-molecule inhibitors and define important future directions for this research.
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Affiliation(s)
- Amelia Y M Woo
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | | | - Rohan Narayan
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | | | - Michelle L Wang
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
| | - Walter J Sandoval-Espinola
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA
- Universidad Nacional de Asunción, Facultad de Ciencias Exactas y Naturales, Departamento de Biotecnología, Laboratorio de Biotecnología Microbiana, San Lorenzo, Paraguay
| | - Emily P Balskus
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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8
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Lupu VV, Adam Raileanu A, Mihai CM, Morariu ID, Lupu A, Starcea IM, Frasinariu OE, Mocanu A, Dragan F, Fotea S. The Implication of the Gut Microbiome in Heart Failure. Cells 2023; 12:1158. [PMID: 37190067 PMCID: PMC10136760 DOI: 10.3390/cells12081158] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Heart failure is a worldwide health problem with important consequences for the overall wellbeing of affected individuals as well as for the healthcare system. Over recent decades, numerous pieces of evidence have demonstrated that the associated gut microbiota represent an important component of human physiology and metabolic homeostasis, and can affect one's state of health or disease directly, or through their derived metabolites. The recent advances in human microbiome studies shed light on the relationship between the gut microbiota and the cardiovascular system, revealing its contribution to the development of heart failure-associated dysbiosis. HF has been linked to gut dysbiosis, low bacterial diversity, intestinal overgrowth of potentially pathogenic bacteria and a decrease in short chain fatty acids-producing bacteria. An increased intestinal permeability allowing microbial translocation and the passage of bacterial-derived metabolites into the bloodstream is associated with HF progression. A more insightful understanding of the interactions between the human gut microbiome, HF and the associated risk factors is mandatory for optimizing therapeutic strategies based on microbiota modulation and offering individualized treatment. The purpose of this review is to summarize the available data regarding the influence of gut bacterial communities and their derived metabolites on HF, in order to obtain a better understanding of this multi-layered complex relationship.
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Affiliation(s)
- Vasile Valeriu Lupu
- Faculty of General Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania (I.M.S.)
| | - Anca Adam Raileanu
- Faculty of General Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania (I.M.S.)
| | | | - Ionela Daniela Morariu
- Faculty of Pharmacy, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Ancuta Lupu
- Faculty of General Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania (I.M.S.)
| | - Iuliana Magdalena Starcea
- Faculty of General Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania (I.M.S.)
| | - Otilia Elena Frasinariu
- Faculty of General Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania (I.M.S.)
| | - Adriana Mocanu
- Faculty of General Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania (I.M.S.)
| | - Felicia Dragan
- Faculty of Medicine and Pharmacy, University of Oradea, 410087 Oradea, Romania
| | - Silvia Fotea
- Medical Department, Faculty of Medicine and Pharmacy, “Dunarea de Jos” University of Galati, 800008 Galati, Romania
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9
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Kalia VC, Gong C, Shanmugam R, Lee JK. Prospecting Microbial Genomes for Biomolecules and Their Applications. Indian J Microbiol 2022; 62:516-523. [PMID: 36458216 PMCID: PMC9705627 DOI: 10.1007/s12088-022-01040-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/04/2022] [Indexed: 11/26/2022] Open
Abstract
Bioactive molecules of microbial origin are finding increasing biotechnological applications. Their sources range from the terrestrial, marine, and endophytic to the human microbiome. These biomolecules have unique chemical structures and related groups, which enable them to improve the efficiency of the bioprocesses. This review focuses on the applications of biomolecules in bioremediation, agriculture, food, pharmaceutical industries, and human health.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Chunjie Gong
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, 430068 People’s Republic of China
| | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
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10
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Bhosle A, Wang Y, Franzosa EA, Huttenhower C. Progress and opportunities in microbial community metabolomics. Curr Opin Microbiol 2022; 70:102195. [PMID: 36063685 DOI: 10.1016/j.mib.2022.102195] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 01/25/2023]
Abstract
The metabolome lies at the interface of host-microbiome crosstalk. Previous work has established links between chemically diverse microbial metabolites and a myriad of host physiological processes and diseases. Coupled with scalable and cost-effective technologies, metabolomics is thus gaining popularity as a tool for characterization of microbial communities, particularly when combined with metagenomics as a window into microbiome function. A systematic interrogation of microbial community metabolomes can uncover key microbial compounds, metabolic capabilities of the microbiome, and also provide critical mechanistic insights into microbiome-linked host phenotypes. In this review, we discuss methods and accompanying resources that have been developed for these purposes. The accomplishments of these methods demonstrate that metabolomes can be used to functionally characterize microbial communities, and that microbial properties can be used to identify and investigate chemical compounds.
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Affiliation(s)
- Amrisha Bhosle
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ya Wang
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eric A Franzosa
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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11
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Zhang Y, Bhosle A, Bae S, McIver LJ, Pishchany G, Accorsi EK, Thompson KN, Arze C, Wang Y, Subramanian A, Kearney SM, Pawluk A, Plichta DR, Rahnavard A, Shafquat A, Xavier RJ, Vlamakis H, Garrett WS, Krueger A, Huttenhower C, Franzosa EA. Discovery of bioactive microbial gene products in inflammatory bowel disease. Nature 2022; 606:754-760. [PMID: 35614211 PMCID: PMC9913614 DOI: 10.1038/s41586-022-04648-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/15/2022] [Indexed: 01/26/2023]
Abstract
Microbial communities and their associated bioactive compounds1-3 are often disrupted in conditions such as the inflammatory bowel diseases (IBD)4. However, even in well-characterized environments (for example, the human gastrointestinal tract), more than one-third of microbial proteins are uncharacterized and often expected to be bioactive5-7. Here we systematically identified more than 340,000 protein families as potentially bioactive with respect to gut inflammation during IBD, about half of which have not to our knowledge been functionally characterized previously on the basis of homology or experiment. To validate prioritized microbial proteins, we used a combination of metagenomics, metatranscriptomics and metaproteomics to provide evidence of bioactivity for a subset of proteins that are involved in host and microbial cell-cell communication in the microbiome; for example, proteins associated with adherence or invasion processes, and extracellular von Willebrand-like factors. Predictions from high-throughput data were validated using targeted experiments that revealed the differential immunogenicity of prioritized Enterobacteriaceae pilins and the contribution of homologues of von Willebrand factors to the formation of Bacteroides biofilms in a manner dependent on mucin levels. This methodology, which we term MetaWIBELE (workflow to identify novel bioactive elements in the microbiome), is generalizable to other environmental communities and human phenotypes. The prioritized results provide thousands of candidate microbial proteins that are likely to interact with the host immune system in IBD, thus expanding our understanding of potentially bioactive gene products in chronic disease states and offering a rational compendium of possible therapeutic compounds and targets.
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Affiliation(s)
- Yancong Zhang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Amrisha Bhosle
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sena Bae
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Lauren J. McIver
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Gleb Pishchany
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Emma K. Accorsi
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Kelsey N. Thompson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Cesar Arze
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ya Wang
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ayshwarya Subramanian
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sean M. Kearney
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - April Pawluk
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Damian R. Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ali Rahnavard
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Afrah Shafquat
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ramnik J. Xavier
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wendy S. Garrett
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andy Krueger
- Takeda Pharmaceutical Company Limited, Cambridge, MA, USA
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Eric A. Franzosa
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA,These authors jointly supervised this work: Curtis Huttenhower & Eric A. Franzosa
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12
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Malla MA, Dubey A, Raj A, Kumar A, Upadhyay N, Yadav S. Emerging frontiers in microbe-mediated pesticide remediation: Unveiling role of omics and In silico approaches in engineered environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 299:118851. [PMID: 35085655 DOI: 10.1016/j.envpol.2022.118851] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
The overuse of pesticides for augmenting agriculture productivity always comes at the cost of environment, biodiversity, and human health and has put the land, water, and environmental footprints under severe threat throughout the globe. Underpinning and maximizing the microbiome functions in pesticide-contaminated environments has become a prerequisite for a sustainable environment and resilient agriculture. It is imperative to elucidate the metabolic network of the microbial communities and environmental variables at the contaminated site to predict the best strategy for remediation and soil microbe-pesticide interactions. High throughput next-generation sequencing and in silico analysis allow us to identify and discern the members and characteristics of core microbiomes at the contaminated site. Integration of modern high throughput multi-omics investigations and informatics pipelines provide novel approaches and pathways to capitalize on the core microbiomes for enhancing environmental functioning and mitigation. The role of eco-genomics tools in visualising the microbial network, taxonomy, functional potential, and environmental variables in contaminated habitats is discussed in this review. The integrated role of the potential microbe identification as individual or consortia, mechanistic approach for pesticide degradation, identification of responsible enzymes/genes, and in silico approach is emphasized for the prospects of the area.
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Affiliation(s)
- Muneer Ahmad Malla
- Department of Zoology, Dr. Harisingh Gour University (Central University), Sagar, 470003, MP, India; Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar, 470003, MP, India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar, 470003, MP, India
| | - Aman Raj
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar, 470003, MP, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar, 470003, MP, India.
| | - Niraj Upadhyay
- Department of Chemistry, Dr. Harisingh Gour University (Central University), Sagar, 470003, MP, India
| | - Shweta Yadav
- Department of Zoology, Dr. Harisingh Gour University (Central University), Sagar, 470003, MP, India
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13
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Zhou H, Beltrán JF, Brito IL. Host-microbiome protein-protein interactions capture disease-relevant pathways. Genome Biol 2022; 23:72. [PMID: 35246229 PMCID: PMC8895870 DOI: 10.1186/s13059-022-02643-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/22/2022] [Indexed: 01/02/2023] Open
Abstract
Background Host-microbe interactions are crucial for normal physiological and immune system development and are implicated in a variety of diseases, including inflammatory bowel disease (IBD), colorectal cancer (CRC), obesity, and type 2 diabetes (T2D). Despite large-scale case-control studies aimed at identifying microbial taxa or genes involved in pathogeneses, the mechanisms linking them to disease have thus far remained elusive. Results To identify potential pathways through which human-associated bacteria impact host health, we leverage publicly-available interspecies protein-protein interaction (PPI) data to find clusters of microbiome-derived proteins with high sequence identity to known human-protein interactors. We observe differential targeting of putative human-interacting bacterial genes in nine independent metagenomic studies, finding evidence that the microbiome broadly targets human proteins involved in immune, oncogenic, apoptotic, and endocrine signaling pathways in relation to IBD, CRC, obesity, and T2D diagnoses. Conclusions This host-centric analysis provides a mechanistic hypothesis-generating platform and extensively adds human functional annotation to commensal bacterial proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02643-9.
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Affiliation(s)
- Hao Zhou
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Juan Felipe Beltrán
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Ilana Lauren Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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14
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Yan D, Cao L, Zhou M, Mohimani H. TransDiscovery: Discovering Biotransformation from Human Microbiota by Integrating Metagenomic and Metabolomic Data. Metabolites 2022; 12:metabo12020119. [PMID: 35208194 PMCID: PMC8877437 DOI: 10.3390/metabo12020119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 12/27/2022] Open
Abstract
The human microbiome is a complex community of microorganisms, their enzymes, and the molecules they produce or modify. Recent studies show that imbalances in human microbial ecosystems can cause disease. Our microbiome affects our health through the products of biochemical reactions catalyzed by microbial enzymes (microbial biotransformations). Despite their significance, currently, there are no systematic strategies for identifying these chemical reactions, their substrates and molecular products, and their effects on health and disease. We present TransDiscovery, a computational algorithm that integrates molecular networks (connecting related molecules with similar mass spectra), association networks (connecting co-occurring molecules and microbes) and knowledge bases of microbial enzymes to discover microbial biotransformations, their substrates, and their products. After searching the metabolomics and metagenomics data from the American Gut Project and the Global Foodomic Project, TranDiscovery identified 17 potentially novel biotransformations from the human gut microbiome, along with the corresponding microbial species, substrates, and products.
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15
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Urinary Metabolic Markers of Bladder Cancer: A Reflection of the Tumor or the Response of the Body? Metabolites 2021; 11:metabo11110756. [PMID: 34822414 PMCID: PMC8621503 DOI: 10.3390/metabo11110756] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
This work will review the metabolic information that various studies have obtained in recent years on bladder cancer, with particular attention to discovering biomarkers in urine for the diagnosis and prognosis of this disease. In principle, they would be capable of complementing cystoscopy, an invasive but nowadays irreplaceable technique or, in the best case, of replacing it. We will evaluate the degree of reproducibility that the different experiments have shown in the indication of biomarkers, and a synthesis will be attempted to obtain a consensus list that is more likely to become a guideline for clinical practice. In further analysis, we will inquire into the origin of these dysregulated metabolites in patients with bladder cancer. For this purpose, it will be helpful to compare the imbalances measured in urine with those known inside tumor cells or tissues. Although the urine analysis is sometimes considered a liquid biopsy because of its direct contact with the tumor in the bladder wall, it contains metabolites from all organs and tissues of the body, and the tumor is separated from urine by the most impermeable barrier found in mammals. The distinction between the specific and systemic responses can help understand the disease and its consequences in more depth.
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16
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Zhang Y, Thompson KN, Branck T, Yan Yan, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annu Rev Biomed Data Sci 2021; 4:279-311. [PMID: 34465175 DOI: 10.1146/annurev-biodatasci-031121-103035] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.
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Affiliation(s)
- Yancong Zhang
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Tobyn Branck
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Yan
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Eric A Franzosa
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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17
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McCoubrey LE, Gaisford S, Orlu M, Basit AW. Predicting drug-microbiome interactions with machine learning. Biotechnol Adv 2021; 54:107797. [PMID: 34260950 DOI: 10.1016/j.biotechadv.2021.107797] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023]
Abstract
Pivotal work in recent years has cast light on the importance of the human microbiome in maintenance of health and physiological response to drugs. It is now clear that gastrointestinal microbiota have the metabolic power to promote, inactivate, or even toxify the efficacy of a drug to a level of clinically relevant significance. At the same time, it appears that drug intake has the propensity to alter gut microbiome composition, potentially affecting health and response to other drugs. Since the precise composition of an individual's microbiome is unique, one's drug-microbiome relationship is similarly unique. Thus, in the age of evermore personalised medicine, the ability to predict individuals' drug-microbiome interactions is highly sought. Machine learning (ML) offers a powerful toolkit capable of characterising and predicting drug-microbiota interactions at the individual patient level. ML techniques have the potential to learn the mechanisms operating drug-microbiome activities and measure patients' risk of such occurrences. This review will outline current knowledge at the drug-microbiota interface, and present ML as a technique for examining and forecasting personalised drug-microbiome interactions. When harnessed effectively, ML could alter how the pharmaceutical industry and healthcare professionals consider the drug-microbiome axis in patient care.
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Affiliation(s)
| | | | - Mine Orlu
- University College London, London, United Kingdom
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18
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Yang Z, Kulik HJ. Protein Dynamics and Substrate Protonation States Mediate the Catalytic Action of trans-4-Hydroxy-l-Proline Dehydratase. J Phys Chem B 2021; 125:7774-7784. [PMID: 34236200 DOI: 10.1021/acs.jpcb.1c05320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzyme trans-4-hydroxy-l-proline (Hyp) dehydratase (HypD) is among the most abundant glycyl radical enzymes (GREs) in the healthy human gut microbiome and is considered a promising antibiotic target for the prominent antibiotic-resistant pathogen Clostridium difficile. Although an enzymatic mechanism has been proposed, the role of the greater HypD protein environment in mediating radical reactivity is not well understood. To fill this gap in understanding, we investigate HypD across multiple time- and length-scales using electronic structure modeling and classical molecular dynamics. We observe that the Hyp substrate protonation state significantly alters both its enzyme-free reactivity and its dynamics within the enzyme active site. Accurate coupled-cluster modeling suggests the deprotonated form of Hyp to be the most reactive protonation state for C5-Hpro-S activation. In the protein environment, hydrophobic interactions modulate the positioning of the Cys434 radical to enhance the reactivity of C5-Hpro-S abstraction. Long-time dynamics reveal that changing Hyp protonation states triggers the switching of a Leu643-gated water tunnel, a functional feature that has not yet been observed for members of the GRE superfamily.
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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19
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Yang KL, Lejeune A, Chang G, Scher JU, Koralov SB. Microbial-derived antigens and metabolites in spondyloarthritis. Semin Immunopathol 2021; 43:163-172. [PMID: 33569635 DOI: 10.1007/s00281-021-00844-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/20/2021] [Indexed: 12/30/2022]
Abstract
Spondyloarthritis (SpA) is a group of chronic, immune-mediated, inflammatory diseases affecting the bone, synovium, and enthesis. Microbiome, the community of microorganisms that has co-evolved with human hosts, plays a pivotal role in human health and disease. This invisible "essential organ" supplies the host with a myriad of chemicals and molecules. In turn, microbial metabolites can serve as messengers for microbes to communicate with each other and in the cross-talk with host cells. Gut dysbiosis in SpA is associated with altered microbial metabolites, and an accumulated body of research has contributed to the understanding that changes in intestinal microbiota can modulate disease pathogenesis. We review the novel findings from human and animal studies to provide an overview of the contribution of individual microbial metabolites and antigens to SpA.
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Affiliation(s)
- Katharine Lu Yang
- Department of Pathology, NYU School of Medicine, 522 First Ave. Smilow Research Bldg 511, New York, NY, 10016, USA
| | - Alannah Lejeune
- Department of Pathology, NYU School of Medicine, 522 First Ave. Smilow Research Bldg 511, New York, NY, 10016, USA
| | - Gregory Chang
- Department of Radiology, NYU School of Medicine, New York, NY, 10016, USA
| | - Jose U Scher
- Division of Rheumatology, Department of Medicine, NYU School of Medicine, New York, NY, 10016, USA. .,Division of Rheumatology and Psoriatic Arthritis Center, 301 East 17th St, Room 1608, New York, NY, 10003, USA.
| | - Sergei B Koralov
- Department of Pathology, NYU School of Medicine, 522 First Ave. Smilow Research Bldg 511, New York, NY, 10016, USA.
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20
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Dash NR, Al Bataineh MT. Metagenomic Analysis of the Gut Microbiome Reveals Enrichment of Menaquinones (Vitamin K2) Pathway in Diabetes Mellitus. Diabetes Metab J 2021; 45:77-85. [PMID: 32431114 PMCID: PMC7850878 DOI: 10.4093/dmj.2019.0202] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease with a high prevalence worldwide, especially among overweight and obese populations. T2DM is multifactorial with several genetic and acquired risk factors that lead to insulin resistance. Mounting evidence indicates that alteration of gut microbiome composition contribute to insulin resistance and inflammation. However, the precise link between T2DM and gut microbiome role and composition remains unknown. METHODS We evaluated the metabolic capabilities of the gut microbiome of twelve T2DM and six healthy individuals through shotgun metagenomics using MiSeq platform. RESULTS We identified no significant differences in the overall taxonomic composition between healthy and T2DM subjects when controlling for differences in diet. However, results showed that T2DM enriched in metabolic pathways involved in menaquinone (vitamin K2) superpathway biosynthesis (PWY-5838) as compared to healthy individuals. Covariance analysis between the bacterial genera and metabolic pathways displaying difference in abundance (analysis of variance P<0.05) in T2DM as compared to healthy subjects revealed that genera belonging Firmicutes, Actinobacteria, and Bacteroidetes phyla contribute significantly to vitamin K2 biosynthesis. Further, the microbiome corresponding to T2DM with high glycosylated hemoglobin (HbA1c) (>6.5%) exhibit high abundance of genes involved in lysine biosynthesis and low abundance of genes involved in creatinine degradation as compared to T2DM with lower HbA1c (<6.5%). CONCLUSION The identified differences in metabolic capabilities provide important information that may eventually lead to the development of novel biomarkers and more effective management strategies to treat T2DM.
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Affiliation(s)
- Nihar Ranjan Dash
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohammad Tahseen Al Bataineh
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Research Institute for Medical & Health Sciences at University of Sharjah, Sharjah, United Arab Emirates
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21
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Jarman R, Ribeiro-Milograna S, Kalle W. Potential of the Microbiome as a Biomarker for Early Diagnosis and Prognosis of Breast Cancer. J Breast Cancer 2020; 23:579-587. [PMID: 33408884 PMCID: PMC7779729 DOI: 10.4048/jbc.2020.23.e60] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
Breast cancer affects 1 in 8 women globally, and is the leading cause of cancer-related deaths in female patients. The majority of breast cancer cases are of unknown cause; few are linked to genetic predisposition, and some arise sporadically. Finding the cause of these sporadic cases is an important area in cancer research. Investigations into the microbiome show links between microbiome dysbiosis and breast cancer, with possible mechanisms in the association of the microbiome and breast cancer, including estrogen metabolism and the 'oestrobolome,' immune regulation, propensity for obesity, and the regulation of the tumor microenvironment. This paper reviews the literature and discusses the potential implications of links between the microbiome and breast cancer, and concludes that the microbiome may have significant applications as a biomarker for breast cancer diagnosis, prognosis, and management. Further investigation is crucial, since modification of the microbiome can, at the most basic level, be achieved via dietary modification.
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Affiliation(s)
- Robyn Jarman
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia
| | | | - Wouter Kalle
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia
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22
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Holmes A, Finger C, Morales-Scheihing D, Lee J, McCullough LD. Gut dysbiosis and age-related neurological diseases; an innovative approach for therapeutic interventions. Transl Res 2020; 226:39-56. [PMID: 32755639 PMCID: PMC7590960 DOI: 10.1016/j.trsl.2020.07.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/14/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023]
Abstract
The gut microbiota is a complex ecosystem of bacteria, fungi, and viruses that acts as a critical regulator in microbial, metabolic, and immune responses in the host organism. Imbalances in the gut microbiota, termed "dysbiosis," often induce aberrant immune responses, which in turn disrupt the local and systemic homeostasis of the host. Emerging evidence has highlighted the importance of gut microbiota in intestinal diseases, and more recently, in age-related central nervous systems diseases, for example, stroke and Alzheimer's disease. It is now generally recognized that gut microbiota significantly influences host behaviors and modulates the interaction between microbiota, gut, and brain, via the "microbiota-gut-brain axis." Several approaches have been utilized to reduce age-related dysbiosis in experimental models and in clinical studies. These include strategies to manipulate the microbiome via fecal microbiota transplantation, administration of prebiotics and probiotics, and dietary interventions. In this review, we explore both clinical and preclinical therapies for treating age-related dysbiosis.
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Affiliation(s)
- Aleah Holmes
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Carson Finger
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Diego Morales-Scheihing
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Juneyoung Lee
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Louise D McCullough
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.
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23
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Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med 2020; 12:71. [PMID: 32791981 PMCID: PMC7427293 DOI: 10.1186/s13073-020-00765-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome. While it is now more obvious how pathogenic strain variants are detrimental to human health, the consequences of subtle genetic variation in the microbiome have only recently been exposed. Here, we review the operational definitions of strains (e.g., genetic and structural variants) as they can now be identified from microbial communities using different high-throughput, often culture-independent techniques. We summarize the distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs. We list methods for identifying, quantifying, and tracking strains, utilizing high-throughput sequencing along with other molecular and “culturomics” technologies. Finally, we discuss implications of population studies in bridging experimental gaps and leading to a better understanding of the health effects of strains in the human microbiome.
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Affiliation(s)
- Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Long H Nguyen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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24
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Brown EM, Kenny DJ, Xavier RJ. Gut Microbiota Regulation of T Cells During Inflammation and Autoimmunity. Annu Rev Immunol 2020; 37:599-624. [PMID: 31026411 DOI: 10.1146/annurev-immunol-042718-041841] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The intestinal microbiota plays a crucial role in influencing the development of host immunity, and in turn the immune system also acts to regulate the microbiota through intestinal barrier maintenance and immune exclusion. Normally, these interactions are homeostatic, tightly controlled, and organized by both innate and adaptive immune responses. However, a combination of environmental exposures and genetic defects can result in a break in tolerance and intestinal homeostasis. The outcomes of these interactions at the mucosal interface have broad, systemic effects on host immunity and the development of chronic inflammatory or autoimmune disease. The underlying mechanisms and pathways the microbiota can utilize to regulate these diseases are just starting to emerge. Here, we discuss the recent evidence in this area describing the impact of microbiota-immune interactions during inflammation and autoimmunity, with a focus on barrier function and CD4+ T cell regulation.
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Affiliation(s)
- Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; , .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Douglas J Kenny
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; , .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; , .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA;
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25
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Abstract
Shotgun metagenomic sequencing has revolutionized our ability to detect and characterize the diversity and function of complex microbial communities. In this review, we highlight the benefits of using metagenomics as well as the breadth of conclusions that can be made using currently available analytical tools, such as greater resolution of species and strains across phyla and functional content, while highlighting challenges of metagenomic data analysis. Major challenges remain in annotating function, given the dearth of functional databases for environmental bacteria compared to model organisms, and the technical difficulties of metagenome assembly and phasing in heterogeneous environmental samples. In the future, improvements and innovation in technology and methodology will lead to lowered costs. Data integration using multiple technological platforms will lead to a better understanding of how to harness metagenomes. Subsequently, we will be able not only to characterize complex microbiomes but also to manipulate communities to achieve prosperous outcomes for health, agriculture, and environmental sustainability.
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Affiliation(s)
- Felicia N New
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, USA;
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, USA;
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26
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Microbial Alterations and Risk Factors of Breast Cancer: Connections and Mechanistic Insights. Cells 2020; 9:cells9051091. [PMID: 32354130 PMCID: PMC7290701 DOI: 10.3390/cells9051091] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer-related mortality remains high worldwide, despite tremendous advances in diagnostics and therapeutics; hence, the quest for better strategies for disease management, as well as the identification of modifiable risk factors, continues. With recent leaps in genomic technologies, microbiota have emerged as major players in most cancers, including breast cancer. Interestingly, microbial alterations have been observed with some of the established risk factors of breast cancer, such as obesity, aging and periodontal disease. Higher levels of estrogen, a risk factor for breast cancer that cross-talks with other risk factors such as alcohol intake, obesity, parity, breastfeeding, early menarche and late menopause, are also modulated by microbial dysbiosis. In this review, we discuss the association between known breast cancer risk factors and altered microbiota. An important question related to microbial dysbiosis and cancer is the underlying mechanisms by which alterations in microbiota can support cancer progression. To this end, we review the involvement of microbial metabolites as effector molecules, the modulation of the metabolism of xenobiotics, the induction of systemic immune modulation, and altered responses to therapy owing to microbial dysbiosis. Given the association of breast cancer risk factors with microbial dysbiosis and the multitude of mechanisms altered by dysbiotic microbiota, an impaired microbiome is, in itself, an important risk factor.
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27
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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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28
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Ditz B, Christenson S, Rossen J, Brightling C, Kerstjens HAM, van den Berge M, Faiz A. Sputum microbiome profiling in COPD: beyond singular pathogen detection. Thorax 2020; 75:338-344. [PMID: 31996401 PMCID: PMC7231454 DOI: 10.1136/thoraxjnl-2019-214168] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/19/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023]
Abstract
Culture-independent microbial sequencing techniques have revealed that the respiratory tract harbours a complex microbiome not detectable by conventional culturing methods. The contribution of the microbiome to chronic obstructive pulmonary disease (COPD) pathobiology and the potential for microbiome-based clinical biomarkers in COPD are still in the early phases of investigation. Sputum is an easily obtainable sample and has provided a wealth of information on COPD pathobiology, and thus has been a preferred sample type for microbiome studies. Although the sputum microbiome likely reflects the respiratory microbiome only in part, there is increasing evidence that microbial community structure and diversity are associated with disease severity and clinical outcomes, both in stable COPD and during the exacerbations. Current evidence has been limited to mainly cross-sectional studies using 16S rRNA gene sequencing, attempting to answer the question 'who is there?' Longitudinal studies using standardised protocols are needed to answer outstanding questions including differences between sputum sampling techniques. Further, with advancing technologies, microbiome studies are shifting beyond the examination of the 16S rRNA gene, to include whole metagenome and metatranscriptome sequencing, as well as metabolome characterisation. Despite being technically more challenging, whole-genome profiling and metabolomics can address the questions 'what can they do?' and 'what are they doing?' This review provides an overview of the basic principles of high-throughput microbiome sequencing techniques, current literature on sputum microbiome profiling in COPD, and a discussion of the associated limitations and future perspectives.
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Affiliation(s)
- Benedikt Ditz
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Stephanie Christenson
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, the United States
| | - John Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center, University of Groningen, Groningen, the Netherlands
| | - Chris Brightling
- Institute of Lung Health, University of Leicester, Leicester, UK
| | - Huib A M Kerstjens
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Maarten van den Berge
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alen Faiz
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, New South Wales, Australia
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29
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From Association to Causality: the Role of the Gut Microbiota and Its Functional Products on Host Metabolism. Mol Cell 2020; 78:584-596. [PMID: 32234490 DOI: 10.1016/j.molcel.2020.03.005] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/30/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022]
Abstract
Many genomic studies have revealed associations between the gut microbiota composition and host metabolism. These observations led to the idea that a causal relationship could exist between the microbiota and metabolic diseases, a concept supported by studies showing compositional changes in the microbial community in metabolic diseases and transmissibility of host phenotype via microbiota transfer. Accumulating data suggest that the microbiota may affect host metabolic phenotypes through the production of metabolites. These bioactive microbial metabolites, sensitive fingerprints of microbial function, can act as inter-kingdom signaling messengers via penetration into host blood circulation and tissues. These fingerprints may be used for diagnostic purposes, and increased understanding of strain specificity in producing microbial metabolites can identify bacterial strains or specific metabolites that can be used for therapeutic purposes. Here, we will review data supporting the causal role of the gut microbiota in metabolism and discuss mechanisms and potential clinical implications.
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30
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Backman LRF, Huang YY, Andorfer MC, Gold B, Raines RT, Balskus EP, Drennan CL. Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme. eLife 2020; 9:e51420. [PMID: 32180548 PMCID: PMC7077986 DOI: 10.7554/elife.51420] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/19/2020] [Indexed: 02/04/2023] Open
Abstract
The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, trans-4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to (S)-Δ1-pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen Clostridioides difficile with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration.
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Affiliation(s)
- Lindsey RF Backman
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Yolanda Y Huang
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Mary C Andorfer
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Brian Gold
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
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31
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Chilakapati SR, Ricciuti J, Zsiros E. Microbiome and cancer immunotherapy. Curr Opin Biotechnol 2020; 65:114-117. [PMID: 32192986 DOI: 10.1016/j.copbio.2020.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 12/13/2022]
Abstract
Immunomodulation has become a promising and growing field of cancer research. Compelling results from a variety of studies provide strong evidence for the importance of commensal bacteria on oncologic outcomes and response to antitumor immunotherapies. The gut microbiome has emerged as a new prognostic biomarker and a potential therapeutic target to enhance the efficacy of immunotherapy.
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Affiliation(s)
| | - Jason Ricciuti
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Emese Zsiros
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA; Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
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32
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Fu B, Balskus EP. Discovery of CC bond-forming and bond-breaking radical enzymes: enabling transformations for metabolic engineering. Curr Opin Biotechnol 2020; 65:94-101. [PMID: 32171888 PMCID: PMC7670169 DOI: 10.1016/j.copbio.2020.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 11/23/2022]
Abstract
Radical enzymes catalyze difficult C—C bond-forming and bond-breaking transformations. Radical enzymes catalyzing unprecedented reactions continue to be discovered. The products of radical enzymes are often of high value. Understanding mechanisms of radical enzymes will aid metabolic engineering efforts.
Radical enzymes catalyze some of the most chemically challenging C—C bond-forming and bond-breaking reactions. Advances in DNA sequencing have accelerated the discovery of radical enzymes from microbes, including radical S-adenosylmethionine (rSAM) enzymes, glycyl radical enzymes (GREs), and diiron enzymes. These enzymes catalyze various reactions that yield products of industrial relevance (e.g. aromatics, hydrocarbons, and natural product derivatives), making their incorporation into engineered metabolic pathways enticing. Elucidating the mechanisms of radical enzymes that cleave and construct C—C bonds will enable further enzyme discovery and engineering efforts.
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Affiliation(s)
- Beverly Fu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, MA 02138, United States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, MA 02138, United States.
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33
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Nazeen S, Yu YW, Berger B. Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads. Genome Biol 2020; 21:47. [PMID: 32093762 PMCID: PMC7038607 DOI: 10.1186/s13059-020-1933-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 01/10/2020] [Indexed: 01/09/2023] Open
Abstract
Microbial populations exhibit functional changes in response to different ambient environments. Although whole metagenome sequencing promises enough raw data to study those changes, existing tools are limited in their ability to directly compare microbial metabolic function across samples and studies. We introduce Carnelian, an end-to-end pipeline for metabolic functional profiling uniquely suited to finding functional trends across diverse datasets. Carnelian is able to find shared metabolic pathways, concordant functional dysbioses, and distinguish Enzyme Commission (EC) terms missed by existing methodologies. We demonstrate Carnelian's effectiveness on type 2 diabetes, Crohn's disease, Parkinson's disease, and industrialized and non-industrialized gut microbiome cohorts.
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Affiliation(s)
- Sumaiya Nazeen
- Computer Science and Artificial Intelligence Laboratory, MIT, 77 Massachusetts Ave, Cambridge, MA 02139 USA
| | - Yun William Yu
- Department of Mathematics, University of Toronto, Toronto, M5S 2E4 ON Canada
- Department of Computer and Mathematical Sciences, University of Toronto at Scarborough, Toronto, M1C 1A4 ON Canada
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, MIT, 77 Massachusetts Ave, Cambridge, MA 02139 USA
- Department of Mathematics, MIT, 77 Massachusetts Ave, Cambridge, MA 02139 USA
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34
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Baffy G. Gut Microbiota and Cancer of the Host: Colliding Interests. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1219:93-107. [PMID: 32130695 DOI: 10.1007/978-3-030-34025-4_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cancer develops in multicellular organisms from cells that ignore the rules of cooperation and escape the mechanisms of anti-cancer surveillance. Tumorigenesis is jointly encountered by the host and microbiota, a vast collection of microorganisms that live on the external and internal epithelial surfaces of the body. The largest community of human microbiota resides in the gastrointestinal tract where commensal, symbiotic and pathogenic microorganisms interact with the intestinal barrier and gut mucosal lymphoid tissue, creating a tumor microenvironment in which cancer cells thrive or perish. Aberrant composition and function of the gut microbiota (dysbiosis) has been associated with tumorigenesis by inducing inflammation, promoting cell growth and proliferation, weakening immunosurveillance, and altering food and drug metabolism or other biochemical functions of the host. However, recent research has also identified several mechanisms through which gut microbiota support the host in the fight against cancer. These mechanisms include the use of antigenic mimicry, biotransformation of chemotherapeutic agents, and other mechanisms to boost anti-cancer immune responses and improve the efficacy of cancer immunotherapy. Further research in this rapidly advancing field is expected to identify additional microbial metabolites with tumor suppressing properties, map the complex interactions of host-microbe 'transkingdom network' with cancer cells, and elucidate cellular and molecular pathways underlying the impact of specific intestinal microbial configurations on immune checkpoint inhibitor therapy.
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Affiliation(s)
- Gyorgy Baffy
- Department of Medicine, VA Boston Healthcare System and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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35
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Prabha R, Singh DP, Gupta S, Gupta VK, El-Enshasy HA, Verma MK. Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities. Microorganisms 2019; 7:microorganisms7120608. [PMID: 31771141 PMCID: PMC6956225 DOI: 10.3390/microorganisms7120608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
Multifunctionalities linked with the microbial communities associated with the millet crop rhizosphere has remained unexplored. In this study, we are analyzing microbial communities inhabiting rhizosphere of kodo millet and their associated functions and its impact over plant growth and survival. Metagenomics of Paspalum scrobiculatum L.(kodo millet) rhizopshere revealed taxonomic communities with functional capabilities linked to support growth and development of the plants under nutrient-deprived, semi-arid and dry biotic conditions. Among 65 taxonomically diverse phyla identified in the rhizobiome, Actinobacteria were the most abundant followed by the Proteobacteria. Functions identified for different genes/proteins led to revelations that multifunctional rhizobiome performs several metabolic functions including carbon fixation, nitrogen, phosphorus, sulfur, iron and aromatic compound metabolism, stress response, secondary metabolite synthesis and virulence, disease, and defense. Abundance of genes linked with N, P, S, Fe and aromatic compound metabolism and phytohormone synthesis—along with other prominent functions—clearly justifies growth, development, and survival of the plants under nutrient deprived dry environment conditions. The dominance of actinobacteria, the known antibiotic producing communities shows that the kodo rhizobiome possesses metabolic capabilities to defend themselves against biotic stresses. The study opens avenues to revisit multi-functionalities of the crop rhizosphere for establishing link between taxonomic abundance and targeted functions that help plant growth and development in stressed and nutrient deprived soil conditions. It further helps in understanding the role of rhizosphere microbiome in adaptation and survival of plants in harsh abiotic conditions.
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Affiliation(s)
- Ratna Prabha
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
| | - Dhananjaya P. Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275101, UP, India
- Correspondence:
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock 18057, Germany;
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia;
| | - Hesham A. El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia, Skudai 81310, Johor Bahru, Johor, Malaysia;
| | - Mukesh K. Verma
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
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36
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Schmidt R, Ulanova D, Wick LY, Bode HB, Garbeva P. Microbe-driven chemical ecology: past, present and future. ISME JOURNAL 2019; 13:2656-2663. [PMID: 31289346 DOI: 10.1038/s41396-019-0469-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 11/09/2022]
Abstract
In recent years, research in the field of Microbial Ecology has revealed the tremendous diversity and complexity of microbial communities across different ecosystems. Microbes play a major role in ecosystem functioning and contribute to the health and fitness of higher organisms. Scientists are now facing many technological and methodological challenges in analyzing these complex natural microbial communities. The advances in analytical and omics techniques have shown that microbial communities are largely shaped by chemical interaction networks mediated by specialized (water-soluble and volatile) metabolites. However, studies concerning microbial chemical interactions need to consider biotic and abiotic factors on multidimensional levels, which require the development of new tools and approaches mimicking natural microbial habitats. In this review, we describe environmental factors affecting the production and transport of specialized metabolites. We evaluate their ecological functions and discuss approaches to address future challenges in microbial chemical ecology (MCE). We aim to emphasize that future developments in the field of MCE will need to include holistic studies involving organisms at all levels and to consider mechanisms underlying the interactions between viruses, micro-, and macro-organisms in their natural environments.
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Affiliation(s)
- Ruth Schmidt
- INRS-Institut Armand-Frappier, Laval, H7V 1B7, Canada.,Quebec Center for Biodiversity Sciences (QCBS), H3A 1B1, Montréal, Canada
| | - Dana Ulanova
- Faculty of Agriculture and Marine Science, Kochi University, Kochi, 783-8502, Japan.,Center for Advanced Marine Core Research, Kochi University, Kochi, 783-8502, Japan
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, D-04318, Leipzig, Germany
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Frankfurt am Main, 60438, Germany
| | - Paolina Garbeva
- Netherlands Institute of Ecology, Wageningen, 6708 PB, The Netherlands.
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37
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Sieow BFL, Nurminen TJ, Ling H, Chang MW. Meta-Omics- and Metabolic Modeling-Assisted Deciphering of Human Microbiota Metabolism. Biotechnol J 2019; 14:e1800445. [PMID: 31144773 DOI: 10.1002/biot.201800445] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/24/2019] [Indexed: 12/15/2022]
Abstract
The human microbiota is a complex community of commensal, symbiotic, and pathogenic microbes that play a crucial role in maintaining the homeostasis of human health. Such a homeostasis is maintained through the collective functioning of enzymatic genes responsible for the production of metabolites, enabling the interaction and signaling within microbiota as well as between microbes and the human host. Understanding microbial genes, their associated chemistries and functions would be valuable for engineering systemic metabolic pathways within the microbiota to manage human health and diseases. Given that there are many unknown gene metabolic functions and interactions, increasing efforts have been made to gain insights into the underlying functions of microbiota metabolism. This can be achieved through culture-independent metagenomic approaches and metabolic modeling to simulate the microenvironment of human microbiota. In this article, the recent advances in metagenome mining and functional profiling for the discovery of the genetic and biochemical links in human microbiota metabolism as well as metabolic modeling for simulation and prediction of metabolic fluxes in the human microbiota are reviewed. This review provides useful insights into the understanding, reconstruction, and modulation of the human microbiota guided by the knowledge acquired from the basic understanding of the human microbiota metabolism.
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Affiliation(s)
- Brendan Fu-Long Sieow
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore.,NUS Graduate School of Integrative Sciences and Engineering (NGS), University Hall, Tan Chin Tuan Wing, National University of Singapore, Singapore, 119077, Singapore
| | - Toni Juhani Nurminen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore.,NUS Graduate School of Integrative Sciences and Engineering (NGS), University Hall, Tan Chin Tuan Wing, National University of Singapore, Singapore, 119077, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore.,NUS Graduate School of Integrative Sciences and Engineering (NGS), University Hall, Tan Chin Tuan Wing, National University of Singapore, Singapore, 119077, Singapore
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38
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Kumar H, Park W, Srikanth K, Choi BH, Cho ES, Lee KT, Kim JM, Kim K, Park J, Lim D, Park JE. Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and their Functional Annotations. Genes (Basel) 2019; 10:E382. [PMID: 31137556 PMCID: PMC6562920 DOI: 10.3390/genes10050382] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/16/2019] [Accepted: 05/16/2019] [Indexed: 12/18/2022] Open
Abstract
The microbial composition in the cecum of pig influences host health, immunity, nutrient digestion, and feeding requirements significantly. Advancements in metagenome sequencing technologies such as 16S rRNAs have made it possible to explore cecum microbial population. In this study, we performed a comparative analysis of cecum microbiota of crossbred Korean native pigs at two different growth stages (stage L = 10 weeks, and stage LD = 26 weeks) using 16S rRNA sequencing technology. Our results revealed remarkable differences in microbial composition, α and β diversity, and differential abundance between the two stages. Phylum composition analysis with respect to SILVA132 database showed Firmicutes to be present at 51.87% and 48.76% in stages L and LD, respectively. Similarly, Bacteroidetes were present at 37.28% and 45.98% in L and LD, respectively. The genera Prevotella, Anaerovibrio, Succinivibrio, Megasphaera were differentially enriched in stage L, whereas Clostridium, Terrisporobacter, Rikenellaceae were enriched in stage LD. Functional annotation of microbiome by level-three KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that glycine, serine, threonine, valine, leucine, isoleucine arginine, proline, and tryptophan metabolism were differentially enriched in stage L, whereas alanine, aspartate, glutamate, cysteine, methionine, phenylalanine, tyrosine, and tryptophan biosynthesis metabolism were differentially enriched in stage LD. Through machine-learning approaches such as LEfSe (linear discriminant analysis effect size), random forest, and Pearson's correlation, we found pathways such as amino acid metabolism, transport systems, and genetic regulation of metabolism are commonly enriched in both stages. Our findings suggest that the bacterial compositions in cecum content of pigs are heavily involved in their nutrient digestion process. This study may help to meet the demand of human food and can play significant roles in medicinal application.
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Affiliation(s)
- Himansu Kumar
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Wanju 55365, Korea.
| | - Woncheol Park
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Wanju 55365, Korea.
| | - Krishnamoorthy Srikanth
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Wanju 55365, Korea.
| | - Bong-Hwan Choi
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Wanju 55365, Korea.
| | - Eun-Seok Cho
- Swine Science Division, National Institute of Animal Science, RDA, Cheonan 31000, Korea.
| | - Kyung-Tai Lee
- Animal Genetics and Breeding Division, National Institute of Animal Science, RDA, Cheonan 31000, Korea.
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea.
| | | | | | - Dajeong Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Wanju 55365, Korea.
| | - Jong-Eun Park
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Wanju 55365, Korea.
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Metatranscriptomic Analysis of Sub-Acute Ruminal Acidosis in Beef Cattle. Animals (Basel) 2019; 9:ani9050232. [PMID: 31083622 PMCID: PMC6562385 DOI: 10.3390/ani9050232] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 05/03/2019] [Accepted: 05/10/2019] [Indexed: 01/08/2023] Open
Abstract
Simple Summary This study evaluated the functional activity of rumen microbiota during sub-acute ruminal acidosis, a metabolic disease of ruminants characterized by low pH caused by feeding highly fermentable carbohydrate feeds. The abundance of rumen bacteria that degrade cellulose (Fibrobacter succinogenes, Ruminococcus albus, and R. bicirculans) were reduced by induced acidotic challenge. Genes mapped to carbohydrate, amino acid, energy, vitamin and co-factor metabolism pathways, and bacterial biofilm formation pathways were enriched in beef cattle challenged with sub-acute acidosis. This study enhances our understanding of the response of rumen microbiota to sub-acute ruminal acidosis by revealing transcriptionally active taxa and metabolic pathways of rumen microbiota. Abstract Subacute ruminal acidosis (SARA) is a metabolic disease of ruminants characterized by low pH, with significant impacts on rumen microbial activity, and animal productivity and health. Microbial changes during subacute ruminal acidosis have previously been analyzed using quantitative PCR and 16S rRNA sequencing, which do not reveal the actual activity of the rumen microbial population. Here, we report the functional activity of the rumen microbiota during subacute ruminal acidosis. Eight rumen-cannulated Holstein steers were assigned randomly to acidosis-inducing or control diet. Rumen fluid samples were taken at 0, 3, 6, and 9 h relative to feeding from both treatments on the challenge day. A metatranscriptome library was prepared from RNA extracted from the samples and the sequencing of the metatranscriptome library was performed on Illumina HiSeq4000 following a 2 × 150 bp index run. Cellulolytic ruminal bacteria including Fibrobacter succinogenes, Ruminococcus albus, and R. bicirculans were reduced by an induced acidotic challenge. Up to 68 functional genes were differentially expressed between the two treatments. Genes mapped to carbohydrate, amino acid, energy, vitamin and co-factor metabolism pathways, and bacterial biofilm formation pathways were enriched in beef cattle challenged with sub-acute acidosis. This study reveals transcriptionally active taxa and metabolic pathways of rumen microbiota during induced acidotic challenge.
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Abstract
Covering: up to the end of 2017 The human body is composed of an equal number of human and microbial cells. While the microbial community inhabiting the human gastrointestinal tract plays an essential role in host health, these organisms have also been connected to various diseases. Yet, the gut microbial functions that modulate host biology are not well established. In this review, we describe metabolic functions of the human gut microbiota that involve metalloenzymes. These activities enable gut microbial colonization, mediate interactions with the host, and impact human health and disease. We highlight cases in which enzyme characterization has advanced our understanding of the gut microbiota and examples that illustrate the diverse ways in which metalloenzymes facilitate both essential and unique functions of this community. Finally, we analyze Human Microbiome Project sequencing datasets to assess the distribution of a prominent family of metalloenzymes in human-associated microbial communities, guiding future enzyme characterization efforts.
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Klebsiella oxytoca enterotoxins tilimycin and tilivalline have distinct host DNA-damaging and microtubule-stabilizing activities. Proc Natl Acad Sci U S A 2019; 116:3774-3783. [PMID: 30808763 PMCID: PMC6397511 DOI: 10.1073/pnas.1819154116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Human gut microbes form a complex community with vast biosynthetic potential. Microbial products and metabolites released in the gut impact human health and disease. However, defining causative relationships between specific bacterial products and disease initiation and progression remains an immense challenge. This study advances understanding of the functional capacity of the gut microbiota by determining the presence, concentration, and spatial and temporal variability of two enterotoxic metabolites produced by the gut-resident Klebsiella oxytoca. We present a detailed mode of action for the cytotoxins and recapitulate their functionalities in disease models in vivo. The findings provide distinct molecular mechanisms for the enterotoxicity of the metabolites allowing them to act in tandem to damage the intestinal epithelium and cause colitis. Establishing causal links between bacterial metabolites and human intestinal disease is a significant challenge. This study reveals the molecular basis of antibiotic-associated hemorrhagic colitis (AAHC) caused by intestinal resident Klebsiella oxytoca. Colitogenic strains produce the nonribosomal peptides tilivalline and tilimycin. Here, we verify that these enterotoxins are present in the human intestine during active colitis and determine their concentrations in a murine disease model. Although both toxins share a pyrrolobenzodiazepine structure, they have distinct molecular targets. Tilimycin acts as a genotoxin. Its interaction with DNA activates damage repair mechanisms in cultured cells and causes DNA strand breakage and an increased lesion burden in cecal enterocytes of colonized mice. In contrast, tilivalline binds tubulin and stabilizes microtubules leading to mitotic arrest. To our knowledge, this activity is unique for microbiota-derived metabolites of the human intestine. The capacity of both toxins to induce apoptosis in intestinal epithelial cells—a hallmark feature of AAHC—by independent modes of action, strengthens our proposal that these metabolites act collectively in the pathogenicity of colitis.
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Gong L, Chi J, Zhang Y, Wang J, Sun B. In vitro evaluation of the bioaccessibility of phenolic acids in different whole wheats as potential prebiotics. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2018.10.071] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Whidbey C, Sadler NC, Nair RN, Volk RF, DeLeon AJ, Bramer LM, Fansler SJ, Hansen JR, Shukla AK, Jansson JK, Thrall BD, Wright AT. A Probe-Enabled Approach for the Selective Isolation and Characterization of Functionally Active Subpopulations in the Gut Microbiome. J Am Chem Soc 2018; 141:42-47. [PMID: 30541282 DOI: 10.1021/jacs.8b09668] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Commensal microorganisms in the mammalian gut play important roles in host health and physiology, but a central challenge remains in achieving a detailed mechanistic understanding of specific microbial contributions to host biochemistry. New function-based approaches are needed that analyze gut microbial function at the molecular level by coupling detection and measurements of in situ biochemical activity with identification of the responsible microbes and enzymes. We developed a platform employing β-glucuronidase selective activity-based probes to detect, isolate, and identify microbial subpopulations in the gut responsible for this xenobiotic metabolism. We find that metabolic activity of gut microbiota can be plastic and that between individuals and during perturbation, phylogenetically disparate populations can provide β-glucuronidase activity. Our work links biochemical activity with molecular-scale resolution without relying on genomic inference.
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Affiliation(s)
- Christopher Whidbey
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Natalie C Sadler
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Reji N Nair
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Regan F Volk
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Adrian J DeLeon
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Lisa M Bramer
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Sarah J Fansler
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Joshua R Hansen
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Anil K Shukla
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Janet K Jansson
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Brian D Thrall
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Aaron T Wright
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering , Washington State University , Pullman , Washington 99163 , United States
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44
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Discovering radical-dependent enzymes in the human gut microbiota. Curr Opin Chem Biol 2018; 47:86-93. [DOI: 10.1016/j.cbpa.2018.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/28/2018] [Accepted: 09/11/2018] [Indexed: 12/21/2022]
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Esteban-Torres M, Santamaría L, Cabrera-Rubio R, Plaza-Vinuesa L, Crispie F, de Las Rivas B, Cotter P, Muñoz R. A Diverse Range of Human Gut Bacteria Have the Potential To Metabolize the Dietary Component Gallic Acid. Appl Environ Microbiol 2018; 84:e01558-18. [PMID: 30054365 PMCID: PMC6146992 DOI: 10.1128/aem.01558-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/24/2018] [Indexed: 12/27/2022] Open
Abstract
The human gut microbiota contains a broad variety of bacteria that possess functional genes, with resultant metabolites that affect human physiology and therefore health. Dietary gallates are phenolic components that are present in many foods and beverages and are regarded as having health-promoting attributes. However, the potential for metabolism of these phenolic compounds by the human microbiota remains largely unknown. The emergence of high-throughput sequencing (HTS) technologies allows this issue to be addressed. In this study, HTS was used to assess the incidence of gallate-decarboxylating bacteria within the gut microbiota of healthy individuals for whom bacterial diversity was previously determined to be high. This process was facilitated by the design and application of degenerate PCR primers to amplify a region encoding the catalytic C subunit of gallate decarboxylase (LpdC) from total metagenomic DNA extracted from human fecal samples. HTS resulted in the generation of a total of 3,261,967 sequence reads and revealed that the primary gallate-decarboxylating microbial phyla in the intestinal microbiota were Firmicutes (74.6%), Proteobacteria (17.6%), and Actinobacteria (7.8%). These reads corresponded to 53 genera, i.e., 47% of the bacterial genera detected previously in these samples. Among these genera, Anaerostipes and Klebsiella accounted for the majority of reads (40%). The usefulness of the HTS-lpdC method was demonstrated by the production of pyrogallol from gallic acid, as expected for functional gallate decarboxylases, among representative strains belonging to species identified in the human gut microbiota by this method.IMPORTANCE Despite the increasing wealth of sequencing data, the health contributions of many bacteria found in the human gut microbiota have yet to be elucidated. This study applies a novel experimental approach to predict the ability of gut microbes to carry out a specific metabolic activity, i.e., gallate metabolism. The study showed that, while gallate-decarboxylating bacteria represented 47% of the bacterial genera detected previously in the same human fecal samples, no gallate decarboxylase homologs were identified from representatives of Bacteroidetes The presence of functional gallate decarboxylases was demonstrated in representative Proteobacteria and Firmicutes strains from the human microbiota, an observation that could be of considerable relevance to the in vivo production of pyrogallol, a physiologically important bioactive compound.
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Affiliation(s)
- María Esteban-Torres
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Laura Santamaría
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Laura Plaza-Vinuesa
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Blanca de Las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
| | | | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC), Madrid, Spain
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Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ. The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature 2018; 562:589-594. [PMID: 30356183 PMCID: PMC6296767 DOI: 10.1038/s41586-018-0620-2] [Citation(s) in RCA: 491] [Impact Index Per Article: 81.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 09/06/2018] [Indexed: 12/12/2022]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that targets pancreatic islet beta cells and incorporates genetic and environmental factors1, including complex genetic elements2, patient exposures3 and the gut microbiome4. Viral infections5 and broader gut dysbioses6 have been identified as potential causes or contributing factors; however, human studies have not yet identified microbial compositional or functional triggers that are predictive of islet autoimmunity or T1D. Here we analyse 10,913 metagenomes in stool samples from 783 mostly white, non-Hispanic children. The samples were collected monthly from three months of age until the clinical end point (islet autoimmunity or T1D) in the The Environmental Determinants of Diabetes in the Young (TEDDY) study, to characterize the natural history of the early gut microbiome in connection to islet autoimmunity, T1D diagnosis, and other common early life events such as antibiotic treatments and probiotics. The microbiomes of control children contained more genes that were related to fermentation and the biosynthesis of short-chain fatty acids, but these were not consistently associated with particular taxa across geographically diverse clinical centres, suggesting that microbial factors associated with T1D are taxonomically diffuse but functionally more coherent. When we investigated the broader establishment and development of the infant microbiome, both taxonomic and functional profiles were dynamic and highly individualized, and dominated in the first year of life by one of three largely exclusive Bifidobacterium species (B. bifidum, B. breve or B. longum) or by the phylum Proteobacteria. In particular, the strain-specific carriage of genes for the utilization of human milk oligosaccharide within a subset of B. longum was present specifically in breast-fed infants. These analyses of TEDDY gut metagenomes provide, to our knowledge, the largest and most detailed longitudinal functional profile of the developing gut microbiome in relation to islet autoimmunity, T1D and other early childhood events. Together with existing evidence from human cohorts7,8 and a T1D mouse model9, these data support the protective effects of short-chain fatty acids in early-onset human T1D.
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Affiliation(s)
- Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Randall Schwager
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Kendra Vehik
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital SUS, Malmo, Sweden
| | | | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Munich, Germany
- Forschergruppe Diabetes, Technische Universität München, Klinikum Rechts der Isar, Munich, Germany
- Forschergruppe Diabetes e.V. at Helmholtz Zentrum München, Munich, Germany
| | - Beena Akolkar
- National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD, USA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Dirk Gevers
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Janssen Human Microbiome Institute, Janssen Research and Development, Cambridge, MA, USA
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, and Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.
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Huang YY, Martínez-del Campo A, Balskus EP. Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity. Gut Microbes 2018; 9:437-451. [PMID: 29405826 PMCID: PMC6219649 DOI: 10.1080/19490976.2018.1435244] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ1-pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.
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Affiliation(s)
- Yolanda Y. Huang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA,CONTACT Emily P. Balskus Commense Inc., 100 Edwin H. Land Blvd, Cambridge, MA 02142
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Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome. mSystems 2018; 3:mSystems00195-17. [PMID: 29600285 PMCID: PMC5872301 DOI: 10.1128/msystems.00195-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 02/23/2018] [Indexed: 11/25/2022] Open
Abstract
Human gut microbiome research has been supported by advances in DNA sequencing that make it possible to obtain gigabases of sequence data from metagenomes but is limited by a lack of knowledge of gene function that leads to incomplete annotation of these data sets. There is a need for the development of methods that can provide experimental data regarding microbial gene function. Functional metagenomics is one such method, but functional screens are often carried out using hosts that may not be able to express the bulk of the environmental DNA being screened. We expand the range of current screening hosts and demonstrate that human gut-derived metagenomic libraries can be introduced into the gut microbe Bacteroides thetaiotaomicron to identify genes based on activity screening. Our results support the continuing development of genetically tractable systems to obtain information about gene function. Functional metagenomics is a powerful method that allows the isolation of genes whose role may not have been predicted from DNA sequence. In this approach, first, environmental DNA is cloned to generate metagenomic libraries that are maintained in Escherichia coli, and second, the cloned DNA is screened for activities of interest. Typically, functional screens are carried out using E. coli as a surrogate host, although there likely exist barriers to gene expression, such as lack of recognition of native promoters. Here, we describe efforts to develop Bacteroides thetaiotaomicron as a surrogate host for screening metagenomic DNA from the human gut. We construct a B. thetaiotaomicron-compatible fosmid cloning vector, generate a fosmid clone library using DNA from the human gut, and show successful functional complementation of a B. thetaiotaomicron glycan utilization mutant. Though we were unable to retrieve the physical fosmid after complementation, we used genome sequencing to identify the complementing genes derived from the human gut microbiome. Our results demonstrate that the use of B. thetaiotaomicron to express metagenomic DNA is promising, but they also exemplify the challenges that can be encountered in the development of new surrogate hosts for functional screening. IMPORTANCE Human gut microbiome research has been supported by advances in DNA sequencing that make it possible to obtain gigabases of sequence data from metagenomes but is limited by a lack of knowledge of gene function that leads to incomplete annotation of these data sets. There is a need for the development of methods that can provide experimental data regarding microbial gene function. Functional metagenomics is one such method, but functional screens are often carried out using hosts that may not be able to express the bulk of the environmental DNA being screened. We expand the range of current screening hosts and demonstrate that human gut-derived metagenomic libraries can be introduced into the gut microbe Bacteroides thetaiotaomicron to identify genes based on activity screening. Our results support the continuing development of genetically tractable systems to obtain information about gene function.
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Targeted Synthesis and Characterization of a Gene Cluster Encoding NAD(P)H-Dependent 3α-, 3β-, and 12α-Hydroxysteroid Dehydrogenases from Eggerthella CAG:298, a Gut Metagenomic Sequence. Appl Environ Microbiol 2018; 84:AEM.02475-17. [PMID: 29330189 DOI: 10.1128/aem.02475-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/07/2018] [Indexed: 01/11/2023] Open
Abstract
Gut metagenomic sequences provide a rich source of microbial genes, the majority of which are annotated by homology or unknown. Genes and gene pathways that encode enzymes catalyzing biotransformation of host bile acids are important to identify in gut metagenomic sequences due to the importance of bile acids in gut microbiome structure and host physiology. Hydroxysteroid dehydrogenases (HSDHs) are pyridine nucleotide-dependent enzymes with stereospecificity and regiospecificity for bile acid and steroid hydroxyl groups. HSDHs have been identified in several protein families, including medium-chain and short-chain dehydrogenase/reductase families as well as the aldo-keto reductase family. These protein families are large and contain diverse functionalities, making prediction of HSDH-encoding genes difficult and necessitating biochemical characterization. We located a gene cluster in Eggerthella sp. CAG:298 predicted to encode three HSDHs (CDD59473, CDD59474, and CDD59475) and synthesized the genes for heterologous expression in Escherichia coli We then screened bile acid substrates against the purified recombinant enzymes. CDD59475 is a novel 12α-HSDH, and we determined that CDD59474 (3α-HSDH) and CDD59473 (3β-HSDH) constitute novel enzymes in an iso-bile acid pathway. Phylogenetic analysis of these HSDHs with other gut bacterial HSDHs and closest homologues in the database revealed predictable clustering of HSDHs by function and identified several likely HSDH sequences from bacteria isolated or sequenced from diverse mammalian and avian gut samples.IMPORTANCE Bacterial HSDHs have the potential to significantly alter the physicochemical properties of bile acids, with implications for increased/decreased toxicity for gut bacteria and the host. The generation of oxo-bile acids is known to inhibit host enzymes involved in glucocorticoid metabolism and may alter signaling through nuclear receptors such as farnesoid X receptor and G-protein-coupled receptor TGR5. Biochemical or similar approaches are required to fill in many gaps in our ability to link a particular enzymatic function with a nucleic acid or amino acid sequence. In this regard, we have identified a novel 12α-HSDH and a novel set of genes encoding an iso-bile acid pathway (3α-HSDH and 3β-HSDH) involved in epimerization and detoxification of harmful secondary bile acids.
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Hydrogen-water ameliorates radiation-induced gastrointestinal toxicity via MyD88's effects on the gut microbiota. Exp Mol Med 2018; 50:e433. [PMID: 29371696 PMCID: PMC5799803 DOI: 10.1038/emm.2017.246] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 07/04/2017] [Accepted: 07/30/2017] [Indexed: 12/22/2022] Open
Abstract
Although radiation therapy is a cornerstone of modern management of malignancies, various side effects are inevitably linked to abdominal and pelvic cancer after radiotherapy. Radiation-mediated gastrointestinal (GI) toxicity impairs the life quality of cancer survivors and even shortens their lifespan. Hydrogen has been shown to protect against tissue injuries caused by oxidative stress and excessive inflammation, but its effect on radiation-induced intestinal injury was previously unknown. In the present study, we found that oral gavage with hydrogen-water increased the survival rate and body weight of mice exposed to total abdominal irradiation (TAI); oral gavage with hydrogen-water was also associated with an improvement in GI tract function and the epithelial integrity of the small intestine. Mechanistically, microarray analysis revealed that hydrogen-water administration upregulated miR-1968-5p levels, thus resulting in parallel downregulation of MyD88 expression in the small intestine after TAI exposure. Additionally, high-throughput sequencing showed that hydrogen-water oral gavage resulted in retention of the TAI-shifted intestinal bacterial composition in mice. Collectively, our findings suggested that hydrogen-water might be used as a potential therapeutic to alleviate intestinal injury induced by radiotherapy for abdominal and pelvic cancer in preclinical settings.
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