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Lee J, Menon N, Lim CT. Dissecting Gut-Microbial Community Interactions using a Gut Microbiome-on-a-Chip. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2302113. [PMID: 38414327 PMCID: PMC11132043 DOI: 10.1002/advs.202302113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/21/2023] [Indexed: 02/29/2024]
Abstract
While the human gut microbiota has a significant impact on gut health and disease, understanding of the roles of gut microbes, interactions, and collective impact of gut microbes on various aspects of human gut health is limited by the lack of suitable in vitro model system that can accurately replicate gut-like environment and enable the close visualization on causal and mechanistic relationships between microbial constitutents and the gut. , In this study, we present a scalable Gut Microbiome-on-a-Chip (GMoC) with great imaging capability and scalability, providing a physiologically relevant dynamic gut-microbes interfaces. This chip features a reproducible 3D stratified gut epithelium derived from Caco-2 cells (µGut), mimicking key intestinal architecture, functions, and cellular complexity, providing a physiolocially relevant gut environment for microbes residing in the gut. Incorporating tumorigenic bacteria, enterotoxigenic Bacteroides fragilis (ETBF), into the GMoC enable the observation of pathogenic behaviors of ETBF, leading to µGut disruption and pro-tumorigenic signaling activations. Pre-treating the µGut with a beneficial gut microbe Lactobacillus spp., effectively prevent ETBF-mediated gut pathogenesis, preserving the healthy state of the µGut through competition-mediated colonization resistance. The GMoC holds potential as a valuable tool for exploring unknown roles of gut microbes in microbe-induced pathogenesis and microbe-based therapeutic development.
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Affiliation(s)
- Jeeyeon Lee
- Institute for Health Innovation and Technology (iHealthtech)National University of SingaporeSingapore117599Singapore
| | - Nishanth Menon
- Department of Biomedical EngineeringNational University of SingaporeSingapore117583Singapore
| | - Chwee Teck Lim
- Institute for Health Innovation and Technology (iHealthtech)National University of SingaporeSingapore117599Singapore
- Department of Biomedical EngineeringNational University of SingaporeSingapore117583Singapore
- Mechanobiology InstituteNational University of SingaporeSingapore117411Singapore
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2
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Khan MT, Dwibedi C, Sundh D, Pradhan M, Kraft JD, Caesar R, Tremaroli V, Lorentzon M, Bäckhed F. Synergy and oxygen adaptation for development of next-generation probiotics. Nature 2023; 620:381-385. [PMID: 37532933 PMCID: PMC10412450 DOI: 10.1038/s41586-023-06378-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/27/2023] [Indexed: 08/04/2023]
Abstract
The human gut microbiota has gained interest as an environmental factor that may contribute to health or disease1. The development of next-generation probiotics is a promising strategy to modulate the gut microbiota and improve human health; however, several key candidate next-generation probiotics are strictly anaerobic2 and may require synergy with other bacteria for optimal growth. Faecalibacterium prausnitzii is a highly prevalent and abundant human gut bacterium associated with human health, but it has not yet been developed into probiotic formulations2. Here we describe the co-isolation of F. prausnitzii and Desulfovibrio piger, a sulfate-reducing bacterium, and their cross-feeding for growth and butyrate production. To produce a next-generation probiotic formulation, we adapted F. prausnitzii to tolerate oxygen exposure, and, in proof-of-concept studies, we demonstrate that the symbiotic product is tolerated by mice and humans (ClinicalTrials.gov identifier: NCT03728868 ) and is detected in the human gut in a subset of study participants. Our study describes a technology for the production of next-generation probiotics based on the adaptation of strictly anaerobic bacteria to tolerate oxygen exposures without a reduction in potential beneficial properties. Our technology may be used for the development of other strictly anaerobic strains as next-generation probiotics.
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Affiliation(s)
- Muhammad Tanweer Khan
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Metabogen, Mölndal, Sweden
| | - Chinmay Dwibedi
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Sundh
- Sahlgrenska Osteoporosis Centre, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Meenakshi Pradhan
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jamie D Kraft
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Robert Caesar
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Mattias Lorentzon
- Sahlgrenska Osteoporosis Centre, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Geriatric Medicine Clinic, Sahlgrenska University Hospital Mölndal, Mölndal, Sweden
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia
| | - Fredrik Bäckhed
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
- Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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Paunkov A, Hummel K, Strasser D, Sóki J, Leitsch D. Proteomic analysis of metronidazole resistance in the human facultative pathogen Bacteroides fragilis. Front Microbiol 2023; 14:1158086. [PMID: 37065137 PMCID: PMC10102347 DOI: 10.3389/fmicb.2023.1158086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
The anaerobic gut bacteria and opportunistic pathogen Bacteroides fragilis can cause life-threatening infections when leaving its niche and reaching body sites outside of the gut. The antimicrobial metronidazole is a mainstay in the treatment of anaerobic infections and also highly effective against Bacteroides spp. Although resistance rates have remained low in general, metronidazole resistance does occur in B. fragilis and can favor fatal disease outcomes. Most metronidazole-resistant Bacteroides isolates harbor nim genes, commonly believed to encode for nitroreductases which deactivate metronidazole. Recent research, however, suggests that the mode of resistance mediated by Nim proteins might be more complex than anticipated because they affect the cellular metabolism, e.g., by increasing the activity of pyruvate:ferredoxin oxidoreductase (PFOR). Moreover, although nim genes confer only low-level metronidazole resistance to Bacteroides, high-level resistance can be much easier induced in the laboratory in the presence of a nim gene than without. Due to these observations, we hypothesized that nim genes might induce changes in the B. fragilis proteome and performed comparative mass-spectrometric analyses with B. fragilis 638R, either with or without the nimA gene. Further, we compared protein expression profiles in both strains after induction of high-level metronidazole resistance. Interestingly, only few proteins were repeatedly found to be differentially expressed in strain 638R with the nimA gene, one of them being the flavodiiron protein FprA, an enzyme involved in oxygen scavenging. After induction of metronidazole resistance, a far higher number of proteins were found to be differentially expressed in 638R without nimA than in 638R with nimA. In the former, factors for the import of hemin were strongly downregulated, indicating impaired iron import, whereas in the latter, the observed changes were not only less numerous but also less specific. Both resistant strains, however, displayed a reduced capability of scavenging oxygen. Susceptibility to metronidazole could be widely restored in resistant 638R without nimA by supplementing growth media with ferrous iron sulfate, but not so in resistant 638R with the nimA gene. Finally, based on the results of this study, we present a novel hypothetic model of metronidazole resistance and NimA function.
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Affiliation(s)
- Ana Paunkov
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - Karin Hummel
- VetCore Facility for Research, University of Veterinary Medicine, Vienna, Austria
| | - Doris Strasser
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - József Sóki
- Faculty of Medicine, Institute of Medical Microbiology, University of Szeged, Szeged, Hungary
| | - David Leitsch
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
- *Correspondence: David Leitsch,
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When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence. Nat Rev Microbiol 2021; 19:774-785. [PMID: 34183820 PMCID: PMC9191689 DOI: 10.1038/s41579-021-00583-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2021] [Indexed: 02/06/2023]
Abstract
The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these microorganisms failed to evolve defences to protect themselves from reactive oxygen species (ROS) such as superoxide and hydrogen peroxide, and that this failure is what prevents their expansion to oxic habitats. However, studies reveal that anaerobes actually wield most of the same defences that aerobes possess, and many of them have the capacity to tolerate substantial levels of oxygen. Therefore, to understand the structures and real-world dynamics of microbial communities, investigators have examined how anaerobes such as Bacteroides, Desulfovibrio, Pyrococcus and Clostridium spp. struggle and cope with oxygen. The hypoxic environments in which these organisms dwell - including the mammalian gut, sulfur vents and deep sediments - experience episodic oxygenation. In this Review, we explore the molecular mechanisms by which oxygen impairs anaerobes and the degree to which bacteria protect their metabolic pathways from it. The emergent view of anaerobiosis is that optimal strategies of anaerobic metabolism depend upon radical chemistry and low-potential metal centres. Such catalytic sites are intrinsically vulnerable to direct poisoning by molecular oxygen and ROS. Observations suggest that anaerobes have evolved tactics that either minimize the extent to which oxygen disrupts their metabolism or restore function shortly after the stress has dissipated.
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Liu P, Ye C, Zhang C, He G, Xue C, Liu J, Liu C, Zhang Y, Song Y, Li X, Wang X, Chen J, He H, Herrmann H, Mu Y. Photochemical Aging of Atmospheric Fine Particles as a Potential Source for Gas-Phase Hydrogen Peroxide. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:15063-15071. [PMID: 34705458 DOI: 10.1021/acs.est.1c04453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Atmospheric hydrogen peroxide (H2O2), as an important oxidant, plays a key role in atmospheric sulfate formation, affecting the global radiation budget and causing acid rain deposition. The disproportionation reactions of hydroperoxyl radicals (HO2) in both gas and aqueous phases have long been considered as dominant sources for atmospheric H2O2. However, these known sources cannot explain the significant formation of H2O2 in polluted areas under the conditions of high NO levels and low ambient relative humidity (RH). Here, we show that under relatively dry conditions during daytime, atmospheric fine particles directly produce abundant gas-phase H2O2. The formation of H2O2 is verified to be by a reaction between the particle surface -OH group and HO2 radicals formed by photooxidation of chromophoric dissolved organic matters (CDOMs), which is slightly influenced by the presence of high NO levels but remarkably accelerated by water vapor and O2. In contrast to aqueous-phase chemistry, transition metal ions (TMIs) are found to significantly suppress H2O2 formation from the atmospheric fine particles. The H2O2 formed from relatively dry particles can be directly involved in in situ SO2 oxidation, leading to sulfate formation. As CDOMs are ubiquitous in atmospheric fine particles, their daytime photochemistry is expected to play important roles in formation of H2O2 and sulfate worldwide.
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Affiliation(s)
- Pengfei Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Can Ye
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chenglong Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangzhi He
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaoyang Xue
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Junfeng Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengtang Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuanyuan Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifei Song
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuran Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinming Wang
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianmin Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention, Department of Environmental Science and Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Hong He
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hartmut Herrmann
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention, Department of Environmental Science and Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
- Atmospheric Chemistry Department (ACD), Leibniz Institute for Tropospheric Research (TROPOS), 04318 Leipzig, Germany
- Environmental Research Institute, Shandong University, Jinan 250100, China
| | - Yujing Mu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Do Primocolonizing Bacteria Enable Bacteroides thetaiotaomicron Intestinal Colonization Independently of the Capacity To Consume Oxygen? mSphere 2021; 6:6/3/e00232-19. [PMID: 33952662 PMCID: PMC8103986 DOI: 10.1128/msphere.00232-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Aerobic bacteria are frequent primocolonizers of the human naive intestine. Their generally accepted role is to eliminate oxygen, which would allow colonization by anaerobes that subsequently dominate bacterial gut populations. Aerobic bacteria are frequent primocolonizers of the human naive intestine. Their generally accepted role is to eliminate oxygen, which would allow colonization by anaerobes that subsequently dominate bacterial gut populations. In this hypothesis-based study, we revisited this dogma experimentally in a germfree mouse model as a mimic of the germfree newborn. We varied conditions leading to the establishment of the dominant intestinal anaerobe Bacteroides thetaiotaomicron. Two variables were introduced: Bacteroides inoculum size and preestablishment by bacteria capable or not of consuming oxygen. High Bacteroides inoculum size enabled its primocolonization. At low inocula, we show that bacterial preestablishment was decisive for subsequent Bacteroides colonization. However, even non-oxygen-respiring bacteria, a hemAEscherichia coli mutant and the intestinal obligate anaerobe Clostridium scindens, facilitated Bacteroides establishment. These findings, which are supported by recent reports, revise the long-held assumption that oxygen scavenging is the main role for aerobic primocolonizing bacteria. Instead, we suggest that better survival of aerobic bacteria ex vivo during vectorization between hosts could be a reason for their frequent primocolonization.
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7
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Yekani M, Baghi HB, Vahed SZ, Ghanbari H, Hosseinpur R, Azargun R, Azimi S, Memar MY. Tightly controlled response to oxidative stress; an important factor in the tolerance of Bacteroides fragilis. Res Microbiol 2021; 172:103798. [PMID: 33485914 DOI: 10.1016/j.resmic.2021.103798] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/01/2022]
Abstract
The exposure of Bacteroides fragilis to highly oxygenated tissues induces an oxidative stress due to a shift from the reduced condition of the gastrointestinal tract to an aerobic environment of host tissues. The potent and effective responses to reactive oxygen species (ROS) make the B. fragilis tolerant to atmospheric oxygen for several days. The response to oxidative stress in B. fragilis is a complicated event that is induced and regulated by different agents. In this review, we will focus on the B. fragilis response to oxidative stress and present an overview of the regulators of responses to oxidative stress in this bacterium.
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Affiliation(s)
- Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Hadi Ghanbari
- Department of Pharmacognosy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Rasul Hosseinpur
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Robab Azargun
- Department of Microbiology, Faculty of Medicine, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Somayeh Azimi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Microbiology Department, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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8
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Yadav M, Chauhan NS. Overview of the rules of the microbial engagement in the gut microbiome: a step towards microbiome therapeutics. J Appl Microbiol 2020; 130:1425-1441. [PMID: 33022786 DOI: 10.1111/jam.14883] [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: 08/24/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/14/2022]
Abstract
Human gut microbiome is a diversified, resilient, immuno-stabilized, metabolically active and physiologically essential component of the human body. Scientific explorations have been made to seek in-depth information about human gut microbiome establishment, microbiome functioning, microbiome succession, factors influencing microbial community dynamics and the role of gut microbiome in health and diseases. Extensive investigations have proposed the microbiome therapeutics as a futuristic medicine for various physiological and metabolic disorders. A comprehensive outlook of microbial colonization, host-microbe interactions, microbial adaptation, commensal selection and immuno-survivability is still required to catalogue the essential genetic and physiological features for the commensal engagement. Evolution of a structured human gut microbiome relies on the microbial flexibility towards genetic, immunological and physiological adaptation in the human gut. Key features for commensalism could be utilized in developing tailor-made microbiome-based therapy to overcome various physiological and metabolic disorders. This review describes the key genetics and physiological traits required for host-microbe interaction and successful commensalism to institute a human gut microbiome.
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Affiliation(s)
- M Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
| | - N S Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
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9
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Wang C, Zhao J, Zhang H, Lee YK, Zhai Q, Chen W. Roles of intestinal bacteroides in human health and diseases. Crit Rev Food Sci Nutr 2020; 61:3518-3536. [PMID: 32757948 DOI: 10.1080/10408398.2020.1802695] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacteroides, an abundant genus in the intestines of mammals, has been recently considered as the next generation probiotics (NGP) candidate due to its potential role in promoting host health. However, the role of Bacteroides in the development of intestinal dysfunctions such as diarrhea, inflammatory bowel disease, and colorectal cancer should not be overlooked. In the present study, we focused on nine most widely occurred and abundant Bacteroides species and discussed their roles in host immunity, glucose and lipid metabolism and the prevention or induction of diseases. Besides, we also discussed the current methods used in the safety evaluation of Bacteroides species and key opinions about the concerns of these strains for the future use.
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Affiliation(s)
- Chen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Research Institute, Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine, Wuxi, China.,(Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Yuan-Kun Lee
- Department of Microbiology & Immunology, National University of Singapore, Singapore, Singapore
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, P.R. China
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10
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Shahir NM, Wang JR, Wolber EA, Schaner MS, Frank DN, Ir D, Robertson CE, Chaumont N, Sadiq TS, Koruda MJ, Rahbar R, Nix BD, Newberry RD, Sartor RB, Sheikh SZ, Furey TS. Crohn's Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria. Inflamm Bowel Dis 2020; 26:1843-1855. [PMID: 32469069 PMCID: PMC7676424 DOI: 10.1093/ibd/izaa103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND The intestinal microbiota play a key role in the onset, progression, and recurrence of Crohn disease (CD). Most microbiome studies assay fecal material, which does not provide region-specific information on mucosally adherent bacteria that directly interact with host systems. Changes in luminal oxygen have been proposed as a contributor to CD dybiosis. METHODS The authors generated 16S rRNA data using colonic and ileal mucosal bacteria from patients with CD and without inflammatory bowel disease. We developed profiles reflecting bacterial abundance within defined aerotolerance categories. Bacterial diversity, composition, and aerotolerance profiles were compared across intestinal regions and disease phenotypes. RESULTS Bacterial diversity decreased in CD in both the ileum and the colon. Aerotolerance profiles significantly differed between intestinal segments in patients without inflammatory bowel disease, although both were dominated by obligate anaerobes, as expected. In CD, high relative levels of obligate anaerobes were maintained in the colon and increased in the ileum. Relative abundances of similar and distinct taxa were altered in colon and ileum. Notably, several obligate anaerobes, such as Bacteroides fragilis, dramatically increased in CD in one or both intestinal segments, although specific increasing taxa varied across patients. Increased abundance of taxa from the Proteobacteria phylum was found only in the ileum. Bacterial diversity was significantly reduced in resected tissues of patients who developed postoperative disease recurrence across 2 independent cohorts, with common lower abundance of bacteria from the Bacteroides, Streptococcus, and Blautia genera. CONCLUSIONS Mucosally adherent bacteria in the colon and ileum show distinct alterations in CD that provide additional insights not revealed in fecal material.
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Affiliation(s)
- Nur M Shahir
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina (UNC) at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeremy R Wang
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - E Ashley Wolber
- Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew S Schaner
- Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel N Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Diana Ir
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Charles E Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Nicole Chaumont
- Department of Surgery, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Timothy S Sadiq
- Department of Surgery, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark J Koruda
- Department of Surgery, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Reza Rahbar
- Department of Surgery, REX Healthcare of Wakefield, Wakefield, North Carolina, USA
| | - B Darren Nix
- Division of Gastroenterology, John T. Milliken Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Rodney D Newberry
- Division of Gastroenterology, John T. Milliken Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shehzad Z Sheikh
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Terrence S Furey
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Lineberger Comprehensive Cancer Center, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Biology, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Address correspondence to: Terrence S. Furey, PhD, Departments of Genetics and Biology, University of North Carolina at Chapel Hill, 5022 Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC 27599 ()
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11
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Valguarnera E, Wardenburg JB. Good Gone Bad: One Toxin Away From Disease for Bacteroides fragilis. J Mol Biol 2019; 432:765-785. [PMID: 31857085 DOI: 10.1016/j.jmb.2019.12.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 11/27/2019] [Accepted: 12/05/2019] [Indexed: 02/06/2023]
Abstract
The human gut is colonized by hundreds of trillions of microorganisms whose acquisition begins during early infancy. Species from the Bacteroides genus are ubiquitous commensals, comprising about thirty percent of the human gut microbiota. Bacteroides fragilis is one of the least abundant Bacteroides species, yet is the most common anaerobe isolated from extraintestinal infections in humans. A subset of B. fragilis strains carry a genetic element that encodes a metalloprotease enterotoxin named Bacteroides fragilis toxin, or BFT. Toxin-bearing strains, or Enterotoxigenic B. fragilis (ETBF) cause acute and chronic intestinal disease in children and adults. Despite this association with disease, around twenty percent of the human population appear to be asymptomatic carriers of ETBF. BFT damages the colonic epithelial barrier by inducing cleavage of the zonula adherens protein E-cadherin and initiating a cell signaling response characterized by inflammation and c-Myc-dependent pro-oncogenic hyperproliferation. As a consequence, mice harboring genetic mutations that predispose to colonic inflammation or tumor formation are uniquely susceptible to toxin-mediated injury. The recent observation of ETBF-bearing biofilms in colon biopsies from humans with colon cancer susceptibility loci strongly suggests that ETBF is a driver of colorectal cancer. This article will address ETBF biology from a host-pathobiont perspective, including clinical data, analysis of molecular mechanisms of disease, and the complex ecological context of the human gut.
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Affiliation(s)
- Ezequiel Valguarnera
- Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Ave. Box 8208, St. Louis, MO 63110
| | - Juliane Bubeck Wardenburg
- Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Ave. Box 8208, St. Louis, MO 63110.
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O 2-inducible H 2O 2-forming NADPH oxidase is responsible for the hyper O 2 sensitivity of Bifidobacterium longum subsp. infantis. Sci Rep 2018; 8:10750. [PMID: 30013208 PMCID: PMC6048055 DOI: 10.1038/s41598-018-29030-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/04/2018] [Indexed: 01/04/2023] Open
Abstract
Bifidobacteria are beneficial anaerobes, and their O2 sensitivity levels differ among species as a function of unknown molecular mechanisms. Bifidobacterium longum subspecies infantis (B. infantis), a predominant colonizer of the gastrointestinal tract of infants, showed a hyper O2-sensitive growth profile with accompanying a production of H2O2. In this study, we characterized an NADPH oxidase as a key enzyme responsible for this microbe’s hyper O2 sensitivity. A dominant active elution peak of H2O2-forming NADPH oxidase activity was detected in the first step of column chromatography, and the purified NADPH oxidase (NPOX) was identified as a homolog of nitroreductase family proteins. The introduction of the gene encoding B. infantis NPOX (npoxA) into O2-tolerant Bifidobacterium minimum made the strain O2 sensitive and allowed it to produce H2O2. Knockout of the npoxA gene in B. infantis decreased the production of H2O2 and mitigated its B. infantis hyper O2 sensitivity. A transcript of B. infantis npoxA is induced by O2, suggesting that the aerobic production of toxic H2O2 is functionally conserved in B. infantis.
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An insider's perspective: Bacteroides as a window into the microbiome. Nat Microbiol 2017; 2:17026. [PMID: 28440278 DOI: 10.1038/nmicrobiol.2017.26] [Citation(s) in RCA: 341] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/31/2017] [Indexed: 12/22/2022]
Abstract
Over the last decade, our appreciation for the contribution of resident gut microorganisms-the gut microbiota-to human health has surged. However, progress is limited by the sheer diversity and complexity of these microbial communities. Compounding the challenge, the majority of our commensal microorganisms are not close relatives of Escherichia coli or other model organisms and have eluded culturing and manipulation in the laboratory. In this Review, we discuss how over a century of study of the readily cultured, genetically tractable human gut Bacteroides has revealed important insights into the biochemistry, genomics and ecology that make a gut bacterium a gut bacterium. While genome and metagenome sequences are being produced at breakneck speed, the Bacteroides provide a significant 'jump-start' on uncovering the guiding principles that govern microbiota-host and inter-bacterial associations in the gut that will probably extend to many other members of this ecosystem.
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Halpern D, Gruss A. A sensitive bacterial-growth-based test reveals how intestinal Bacteroides meet their porphyrin requirement. BMC Microbiol 2015; 15:282. [PMID: 26715069 PMCID: PMC4696147 DOI: 10.1186/s12866-015-0616-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/16/2015] [Indexed: 12/19/2022] Open
Abstract
Background Bacteroides sp. are dominant constituents of the human and animal intestinal microbiota require porphyrins (i.e., protoporphyrin IX or iron-charged heme) for normal growth. The highly stimulatory effect of porphyrins on Bacteroides growth lead us to propose their use as a potential determinant of bacterial colonization. However, showing a role for porphryins would require sensitive detection methods that work in complex samples such as feces. Results We devised a highly sensitive semi-quantitative porphyrin detection method (detection limit 1-4 ng heme or PPIX) that can be used to assay pure or complex biological samples, based on Bacteroides growth stimulation. The test revealed that healthy colonized or non-colonized murine and human hosts provide porphyrins in feces, which stimulate Bacteroides growth. In addition, a common microbiota constituent, Escherichia coli, is shown to be a porphyrin donor, suggesting a novel basis for intestinal bacterial interactions. Conclusions A highly sensitive method to detect porphyrins based on bacterial growth is devised and is functional in complex biological samples. Host feces, independently of their microbiota, and E. coli, which are present in the intestine, are shown to be porphryin donors. The role of porphyrins as key bioactive molecules can now be assessed for their impact on Bacteroides and other bacterial populations in the gut. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0616-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Halpern
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France, Jouy en Josas, 78352, France.
| | - Alexandra Gruss
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France, Jouy en Josas, 78352, France.
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Leclerc J, Rosenfeld E, Trainini M, Martin B, Meuric V, Bonnaure-Mallet M, Baysse C. The Cytochrome bd Oxidase of Porphyromonas gingivalis Contributes to Oxidative Stress Resistance and Dioxygen Tolerance. PLoS One 2015; 10:e0143808. [PMID: 26629705 PMCID: PMC4668044 DOI: 10.1371/journal.pone.0143808] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/10/2015] [Indexed: 11/18/2022] Open
Abstract
Porphyromonas gingivalis is an etiologic agent of periodontal disease in humans. The disease is associated with the formation of a mixed oral biofilm which is exposed to oxygen and environmental stress, such as oxidative stress. To investigate possible roles for cytochrome bd oxidase in the growth and persistence of this anaerobic bacterium inside the oral biofilm, mutant strains deficient in cytochrome bd oxidase activity were characterized. This study demonstrated that the cytochrome bd oxidase of Porphyromonas gingivalis, encoded by cydAB, was able to catalyse O2 consumption and was involved in peroxide and superoxide resistance, and dioxygen tolerance.
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Affiliation(s)
- Julia Leclerc
- EA1254 Microbiologie—Risques Infectieux, University of Rennes1, Rennes, France
| | - Eric Rosenfeld
- UMR CNRS 7266 LIENSs, University of La Rochelle, La Rochelle, France
| | - Mathieu Trainini
- EA1254 Microbiologie—Risques Infectieux, University of Rennes1, Rennes, France
| | - Bénédicte Martin
- EA1254 Microbiologie—Risques Infectieux, University of Rennes1, Rennes, France
| | - Vincent Meuric
- EA1254 Microbiologie—Risques Infectieux, University of Rennes1, Rennes, France
- UMR CNRS 7266 LIENSs, University of La Rochelle, La Rochelle, France
- CHU Rennes, Rennes, France
| | - Martine Bonnaure-Mallet
- EA1254 Microbiologie—Risques Infectieux, University of Rennes1, Rennes, France
- UMR CNRS 7266 LIENSs, University of La Rochelle, La Rochelle, France
- CHU Rennes, Rennes, France
| | - Christine Baysse
- EA1254 Microbiologie—Risques Infectieux, University of Rennes1, Rennes, France
- * E-mail:
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Evidence for extraintestinal growth of bacteroidales originating from poultry litter. Appl Environ Microbiol 2014; 81:196-202. [PMID: 25326306 DOI: 10.1128/aem.02354-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Water quality monitoring techniques that target microorganisms in the order Bacteroidales are potential alternatives to conventional methods for detection of fecal indicator bacteria. Bacteroidales and members of the genus Bacteroides have been the focus of microbial source tracking (MST) investigations for discriminating sources of fecal pollution (e.g., human or cattle feces) in environmental waters. For accurate source apportionment to occur, one needs to understand both the abundance of Bacteroides in host feces and the survival of these host-associated microbial markers after deposition in the environment. Studies were undertaken to evaluate the abundance, persistence, and potential for growth of Bacteroidales originating from poultry litter under oxic and anoxic environmental conditions. Bacteroidales abundance, as determined by quantitative PCR (qPCR) with GenBac primers and probe, increased 2 to 5 log gene copies ml(-1) and 2 log gene copies g litter(-1) under most conditions during incubation of poultry litter in a variety of laboratory microcosm and field mesocosm studies. DNA sequencing of the Bacteroidales organisms in the litter identified taxa with sequences corresponding exactly to the GenBac primer and probe sequences and that were closely related to Bacteroides uniformis, B. ovatus, and B. vulgatus. These results suggest that MST studies using qPCR methods targeting Bacteroidales in watersheds that are affected by poultry litter should be interpreted cautiously. Growth of Bacteroidales originating from poultry litter in environmental waters may occur while Bacteroidales growth from other fecal sources declines, thus confounding the interpretation of MST results.
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Mishra S, Imlay JA. An anaerobic bacterium, Bacteroides thetaiotaomicron, uses a consortium of enzymes to scavenge hydrogen peroxide. Mol Microbiol 2013; 90:1356-71. [PMID: 24164536 DOI: 10.1111/mmi.12438] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2013] [Indexed: 12/17/2022]
Abstract
Obligate anaerobes are periodically exposed to oxygen, and it has been conjectured that on such occasions their low-potential biochemistry will predispose them to rapid ROS formation. We sought to identify scavenging enzymes that might protect the anaerobe Bacteroides thetaiotaomicron from the H2 O2 that would be formed. Genetic analysis of eight candidate enzymes revealed that four of these scavenge H2 O2 in vivo: rubrerythrins 1 and 2, AhpCF, and catalase E. The rubrerythrins served as key peroxidases under anoxic conditions. However, they quickly lost activity upon aeration, and AhpCF and catalase were induced to compensate. The AhpCF is an NADH peroxidase that effectively degraded low micromolar levels of H2 O2 , while the catalytic cycle of catalase enabled it to quickly degrade higher concentrations that might arise from exogenous sources. Using a non-scavenging mutant we verified that endogenous H2 O2 formation was much higher in aerated B. thetaiotaomicron than in Escherichia coli. Indeed, the OxyR stress response to H2 O2 was induced when B. thetaiotaomicron was aerated, and in that circumstance this response was necessary to forestall cell death. Thus aeration is a serious threat for this obligate anaerobe, and to cope it employs a set of defences that includes a repertoire of complementary scavenging enzymes.
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Affiliation(s)
- Surabhi Mishra
- Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA
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