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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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Tunsakul N, Wongsaroj L, Janchot K, Pongpirul K, Somboonna N. Non-significant influence between aerobic and anaerobic sample transport materials on gut (fecal) microbiota in healthy and fat-metabolic disorder Thai adults. PeerJ 2024; 12:e17270. [PMID: 38650647 PMCID: PMC11034497 DOI: 10.7717/peerj.17270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
Background The appropriate sample handling for human fecal microbiota studies is essential to prevent changes in bacterial composition and quantities that could lead to misinterpretation of the data. Methods This study firstly identified the potential effect of aerobic and anaerobic fecal sample collection and transport materials on microbiota and quantitative microbiota in healthy and fat-metabolic disorder Thai adults aged 23-43 years. We employed metagenomics followed by 16S rRNA gene sequencing and 16S rRNA gene qPCR, to analyze taxonomic composition, alpha diversity, beta diversity, bacterial quantification, Pearson's correlation with clinical factors for fat-metabolic disorder, and the microbial community and species potential metabolic functions. Results Our study successfully obtained microbiota results in percent and quantitative compositions. Each sample exhibited quality sequences with a >99% Good's coverage index, and a relatively plateau rarefaction curve. Alpha diversity indices showed no statistical difference in percent and quantitative microbiota OTU richness and evenness, between aerobic and anaerobic sample transport materials. Obligate and facultative anaerobic species were analyzed and no statistical difference was observed. Supportively, the beta diversity analysis by non-metric multidimensional scale (NMDS) constructed using various beta diversity coefficients showed resembling microbiota community structures between aerobic and anaerobic sample transport groups (P = 0.86). On the other hand, the beta diversity could distinguish microbiota community structures between healthy and fat-metabolic disorder groups (P = 0.02), along with Pearson's correlated clinical parameters (i.e., age, liver stiffness, GGT, BMI, and TC), the significantly associated bacterial species and their microbial metabolic functions. For example, genera such as Ruminococcus and Bifidobacterium in healthy human gut provide functions in metabolisms of cofactors and vitamins, biosynthesis of secondary metabolites against gut pathogens, energy metabolisms, digestive system, and carbohydrate metabolism. These microbial functional characteristics were also predicted as healthy individual biomarkers by LEfSe scores. In conclusion, this study demonstrated that aerobic sample collection and transport (<48 h) did not statistically affect the microbiota and quantitative microbiota analyses in alpha and beta diversity measurements. The study also showed that the short-term aerobic sample collection and transport still allowed fecal microbiota differentiation between healthy and fat-metabolic disorder subjects, similar to anaerobic sample collection and transport. The core microbiota were analyzed, and the findings were consistent. Moreover, the microbiota-related metabolic potentials and bacterial species biomarkers in healthy and fat-metabolic disorder were suggested with statistical bioinformatics (i.e., Bacteroides plebeius).
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Affiliation(s)
- Naruemon Tunsakul
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Lampet Wongsaroj
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Kantima Janchot
- Center of Excellence in Preventive and Integrative Medicine (CE-PIM) and Department of Preventive and Social Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Krit Pongpirul
- Center of Excellence in Preventive and Integrative Medicine (CE-PIM) and Department of Preventive and Social Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Microbiome Research Unit for Probiotics in Food and Cosmetics, Chulalongkorn University, Bangkok, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Multi-Omics for Functional Products in Food, Cosmetics and Animals Research Unit, Chulalongkorn University, Bangkok, Thailand
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Hart JJ, Jamison MN, Porter AM, McNair JN, Szlag DC, Rediske RR. Fecal Impairment Framework, A New Conceptual Framework for Assessing Fecal Contamination in Recreational Waters. ENVIRONMENTAL MANAGEMENT 2024; 73:443-456. [PMID: 37658902 DOI: 10.1007/s00267-023-01878-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
Fecal pollution of surface water is a pervasive problem that negatively affects waterbodies concerning both public health and ecological functions. Current assessment methods monitor fecal indicator bacteria (FIB) to identify pollution sources using culture-based quantification and microbial source tracking (MST). These types of information assist stakeholders in identifying likely sources of fecal pollution, prioritizing them for remediation, and choosing appropriate best management practices. While both culture-based quantification and MST are useful, they yield different kinds of information, potentially increasing uncertainty in prioritizing sources for management. This study presents a conceptual framework that takes separate human health risk estimates based on measured MST and E. coli concentrations as inputs and produces an estimate of the overall fecal impairment risk as its output. The proposed framework is intended to serve as a supplemental screening tool for existing monitoring programs to aid in identifying and prioritizing sites for remediation. In this study, we evaluated the framework by applying it to two primarily agricultural watersheds and several freshwater recreational beaches using existing routine monitoring data. Based on a combination of E. coli and MST results, the proposed fecal impairment framework identified four sites in the watersheds as candidates for remediation and identified temporal trends in the beach application. As these case studies demonstrate, the proposed fecal impairment framework is an easy-to-use and cost-effective supplemental screening tool that provides actionable information to managers using existing routine monitoring data, without requiring specialized expertize.
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Affiliation(s)
- John J Hart
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr, Muskegon, MI, 49441, USA.
| | - Megan N Jamison
- Department of Chemistry, Oakland University, 146 Library Dr., Rochester, MI, 48309, USA
- The Ohio State University, 281 W Lane Ave, Columbus, OH, 43210, USA
| | - Alexis M Porter
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr, Muskegon, MI, 49441, USA
| | - James N McNair
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr, Muskegon, MI, 49441, USA
| | - David C Szlag
- Department of Chemistry, Oakland University, 146 Library Dr., Rochester, MI, 48309, USA
| | - Richard R Rediske
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr, Muskegon, MI, 49441, USA
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4
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Shin JH, Tillotson G, MacKenzie TN, Warren CA, Wexler HM, Goldstein EJC. Bacteroides and related species: The keystone taxa of the human gut microbiota. Anaerobe 2024; 85:102819. [PMID: 38215933 DOI: 10.1016/j.anaerobe.2024.102819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
Microbial communities play a significant role in maintaining ecosystems in a healthy homeostasis. Presently, in the human gastrointestinal tract, there are certain taxonomic groups of importance, though there is no single species that plays a keystone role. Bacteroides spp. are known to be major players in the maintenance of eubiosis in the human gastrointestinal tract. Here we review the critical role that Bacteroides play in the human gut, their potential pathogenic role outside of the gut, and their various methods of adapting to the environment, with a focus on data for B. fragilis and B. thetaiotaomicron. Bacteroides are anaerobic non-sporing Gram negative organisms that are also resistant to bile acids, generally thriving in the gut and having a beneficial relationship with the host. While they are generally commensal organisms, some Bacteroides spp. can be opportunistic pathogens in scenarios of GI disease, trauma, cancer, or GI surgery, and cause infection, most commonly intra-abdominal infection. B. fragilis can develop antimicrobial resistance through multiple mechanisms in large part due to its plasticity and fluid genome. Bacteroidota (formerly, Bacteroidetes) have a very broad metabolic potential in the GI microbiota and can rapidly adapt their carbohydrate metabolism to the available nutrients. Gastrointestinal Bacteroidota species produce short-chain fatty acids such as succinate, acetate, butyrate, and occasionally propionate, as the major end-products, which have wide-ranging and many beneficial influences on the host. Bacteroidota, via bile acid metabolism, also play a role in in colonization-resistance of other organisms, including Clostridioides difficile, and maintenance of gut integrity.
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Affiliation(s)
- Jae Hyun Shin
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | | | | | - Cirle A Warren
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | - Hannah M Wexler
- GLAVAHCS, Los Angeles, CA, USA; David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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Fachi JL, Pral LP, Assis HC, Oliveira S, Rodovalho VR, dos Santos JAC, Fernandes MF, Matheus VA, Sesti-Costa R, Basso PJ, Flóro e Silva M, Câmara NOS, Giorgio S, Colonna M, Vinolo MAR. Hyperbaric oxygen augments susceptibility to C. difficile infection by impairing gut microbiota ability to stimulate the HIF-1α-IL-22 axis in ILC3. Gut Microbes 2024; 16:2297872. [PMID: 38165200 PMCID: PMC10763646 DOI: 10.1080/19490976.2023.2297872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
Hyperbaric oxygen (HBO) therapy is a well-established method for improving tissue oxygenation and is typically used for the treatment of various inflammatory conditions, including infectious diseases. However, its effect on the intestinal mucosa, a microenvironment known to be physiologically hypoxic, remains unclear. Here, we demonstrated that daily treatment with hyperbaric oxygen affects gut microbiome composition, worsening antibiotic-induced dysbiosis. Accordingly, HBO-treated mice were more susceptible to Clostridioides difficile infection (CDI), an enteric pathogen highly associated with antibiotic-induced colitis. These observations were closely linked with a decline in the level of microbiota-derived short-chain fatty acids (SCFAs). Butyrate, a SCFA produced primarily by anaerobic microbial species, mitigated HBO-induced susceptibility to CDI and increased epithelial barrier integrity by improving group 3 innate lymphoid cell (ILC3) responses. Mice displaying tissue-specific deletion of HIF-1 in RORγt-positive cells exhibited no protective effect of butyrate during CDI. In contrast, the reinforcement of HIF-1 signaling in RORγt-positive cells through the conditional deletion of VHL mitigated disease outcome, even after HBO therapy. Taken together, we conclude that HBO induces intestinal dysbiosis and impairs the production of SCFAs affecting the HIF-1α-IL-22 axis in ILC3 and worsening the response of mice to subsequent C. difficile infection.
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Affiliation(s)
- José L. Fachi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Laís. P. Pral
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Helder C. Assis
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Sarah Oliveira
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Vinícius R. Rodovalho
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Jefferson A. C. dos Santos
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Mariane F. Fernandes
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Valquíria A. Matheus
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Renata Sesti-Costa
- Hematology and Hemotherapy Center, University of Campinas, Campinas, Brazil
| | - Paulo J. Basso
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marina Flóro e Silva
- Department of Animal Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Niels O. S. Câmara
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Selma Giorgio
- Department of Animal Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marco A. R. Vinolo
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster, Institute of Biology, University of Campinas, Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, Brazil
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Van Den Ham KM, Little MR, Bednarski OJ, Fusco EM, Mandal RK, Mitra R, Li S, Doumbo S, Doumtabe D, Kayentao K, Ongoiba A, Traore B, Crompton PD, Schmidt NW. Creation of a non-Western humanized gnotobiotic mouse model through the transplantation of rural African fecal microbiota. Microbiol Spectr 2023; 11:e0155423. [PMID: 37819130 PMCID: PMC10714993 DOI: 10.1128/spectrum.01554-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE There is increasing evidence that microbes residing within the intestines (gut microbiota) play important roles in the well-being of humans. Yet, there are considerable challenges in determining the specific role of gut microbiota in human diseases owing to the complexity of diverse internal and environmental factors that can contribute to diseases. Mice devoid of all microorganisms (germ-free mice) can be colonized with human stool samples to examine the specific contribution of the gut microbiota to a disease. These approaches have been primarily focused on stool samples obtained from individuals in Western countries. Thus, there is limited understanding as to whether the same methods used to colonize germ-free mice with stool from Western individuals would apply to the colonization of germ-free mice with stool from non-Western individuals. Here, we report the results from colonizing germ-free mice with stool samples of Malian children.
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Affiliation(s)
- Kristin M. Van Den Ham
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Morgan R. Little
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Olivia J. Bednarski
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Elizabeth M. Fusco
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Rabindra K. Mandal
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Riten Mitra
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky, USA
| | - Shanping Li
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Safiatou Doumbo
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Didier Doumtabe
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Kassoum Kayentao
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Aissata Ongoiba
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Boubacar Traore
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Peter D. Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Nathan W. Schmidt
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Keitel L, Braun K, Finger M, Kosfeld U, Yordanov S, Büchs J. Carbon dioxide and trace oxygen concentrations impact growth and product formation of the gut bacterium Phocaeicola vulgatus. BMC Microbiol 2023; 23:391. [PMID: 38062358 PMCID: PMC10701953 DOI: 10.1186/s12866-023-03127-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The promising yet barely investigated anaerobic species Phocaeicola vulgatus (formerly Bacteroides vulgatus) plays a vital role for human gut health and effectively produces organic acids. Among them is succinate, a building block for high-value-added chemicals. Cultivating anaerobic bacteria is challenging, and a detailed understanding of P. vulgatus growth and metabolism is required to improve succinate production. One significant aspect is the influence of different gas concentrations. CO2 is required for the growth of P. vulgatus. However, it is a greenhouse gas that should not be wasted. Another highly interesting aspect is the sensitivity of P. vulgatus towards O2. In this work, the effects of varying concentrations of both gases were studied in the in-house developed Respiratory Activity MOnitoring System (RAMOS), which provides online monitoring of CO2, O2, and pressure under gassed conditions. The RAMOS was combined with a gas mixing system to test CO2 and O2 concentrations in a range of 0.25-15.0 vol% and 0.0-2.5 vol%, respectively. RESULTS Changing the CO2 concentration in the gas supply revealed a CO2 optimum of 3.0 vol% for total organic acid production and 15.0 vol% for succinate production. It was demonstrated that the organic acid composition changed depending on the CO2 concentration. Furthermore, unrestricted growth of P. vulgatus up to an O2 concentration of 0.7 vol% in the gas supply was proven. The viability decreased rapidly at concentrations larger than or equal to 1.3 vol% O2. CONCLUSIONS The study showed that P. vulgatus requires little CO2, has a distinct O2 tolerance and is therefore well suited for industrial applications.
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Affiliation(s)
- Laura Keitel
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Kristina Braun
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Maurice Finger
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Udo Kosfeld
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Stanislav Yordanov
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jochen Büchs
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
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Abbondio M, Tanca A, De Diego L, Sau R, Bibbò S, Pes GM, Dore MP, Uzzau S. Metaproteomic assessment of gut microbial and host functional perturbations in Helicobacter pylori-infected patients subjected to an antimicrobial protocol. Gut Microbes 2023; 15:2291170. [PMID: 38063474 PMCID: PMC10730194 DOI: 10.1080/19490976.2023.2291170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
The impact of therapeutic interventions on the human gut microbiota (GM) is a clinical issue of paramount interest given the strong interconnection between microbial dynamics and human health. Orally administered antibiotics are known to reduce GM biomass and modify GM taxonomic profile. However, the impact of antimicrobial therapies on GM functions and biochemical pathways has scarcely been studied. Here, we characterized the fecal metaproteome of 10 Helicobacter pylori-infected patients before (T0) and after 10 days (T1) of a successful quadruple therapy (bismuth, tetracycline, metronidazole, and rabeprazole) and 30 days after therapy cessation (T2), to investigate how GM and host functions change during the eradication and healing processes. At T1, the abundance ratio between microbial and host proteins was reversed compared with that at T0 and T2. Several pathobionts (including Klebsiella, Proteus, Enterococcus, Muribaculum, and Enterocloster) were increased at T1. Therapy reshaped the relative contributions of the functions required to produce acetate, propionate, and butyrate. Proteins related to the uptake and processing of complex glycans were increased. Microbial cross-feeding with sialic acid, fucose, and rhamnose was enhanced, whereas hydrogen sulfide production was reduced. Finally, microbial proteins involved in antibiotic resistance and inflammation were more abundant after therapy. Moreover, a reduction in host proteins with known roles in inflammation and H. pylori-mediated carcinogenesis was observed. In conclusion, our results support the use of metaproteomics to monitor drug-induced remodeling of GM and host functions, opening the way for investigating new antimicrobial therapies aimed at preserving gut environmental homeostasis.
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Affiliation(s)
- Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Laura De Diego
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Rosangela Sau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Stefano Bibbò
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Giovanni Mario Pes
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Maria Pina Dore
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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Dyksma S, Pester M. Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium. Nat Commun 2023; 14:6337. [PMID: 37816749 PMCID: PMC10564751 DOI: 10.1038/s41467-023-42074-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Sulfate-reducing microorganisms represent a globally important link between the sulfur and carbon cycles. Recent metagenomic surveys expanded the diversity of microorganisms putatively involved in sulfate reduction underscoring our incomplete understanding of this functional guild. Here, we use genome-centric metatranscriptomics to study the energy metabolism of Acidobacteriota that carry genes for dissimilation of sulfur compounds in a long-term continuous culture running under alternating anoxic and oxic conditions. Differential gene expression analysis reveals the unique metabolic flexibility of a pectin-degrading acidobacterium to switch from sulfate to oxygen reduction when shifting from anoxic to oxic conditions. The combination of facultative anaerobiosis and polysaccharide degradation expands the metabolic versatility among sulfate-reducing microorganisms. Our results highlight that sulfate reduction and aerobic respiration are not mutually exclusive in the same organism, sulfate reducers can mineralize organic polymers, and anaerobic mineralization of complex organic matter is not necessarily a multi-step process involving different microbial guilds but can be bypassed by a single microbial species.
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Affiliation(s)
- Stefan Dyksma
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Microorganisms, Braunschweig, Germany.
| | - Michael Pester
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Microorganisms, Braunschweig, Germany.
- Technical University of Braunschweig, Institute of Microbiology, Braunschweig, Germany.
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10
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Neal M, Thiruppathy D, Zengler K. Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R. PLoS Comput Biol 2023; 19:e1011594. [PMID: 37903176 PMCID: PMC10635569 DOI: 10.1371/journal.pcbi.1011594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 11/09/2023] [Accepted: 10/11/2023] [Indexed: 11/01/2023] Open
Abstract
Bacteroides fragilis is a universal member of the dominant commensal gut phylum Bacteroidetes. Its fermentation products and abundance have been linked to obesity, inflammatory bowel disease, and other disorders through its effects on host metabolic regulation and the immune system. As of yet, there has been no curated systems-level characterization of B. fragilis' metabolism that provides a comprehensive analysis of the link between human diet and B. fragilis' metabolic products. To address this, we developed a genome-scale metabolic model of B. fragilis strain 638R. The model iMN674 contains 1,634 reactions, 1,362 metabolites, three compartments, and reflects the strain's ability to utilize 142 metabolites. Predictions made with this model include its growth rate and efficiency on these substrates, the amounts of each fermentation product it produces under different conditions, and gene essentiality for each biomass component. The model highlights and resolves gaps in knowledge of B. fragilis' carbohydrate metabolism and its corresponding transport proteins. This high quality model provides the basis for rational prediction of B. fragilis' metabolic interactions with its environment and its host.
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Affiliation(s)
- Maxwell Neal
- Department of Bioengineering, University of California, San Diego, California, United States of America
| | - Deepan Thiruppathy
- Department of Bioengineering, University of California, San Diego, California, United States of America
| | - Karsten Zengler
- Department of Bioengineering, University of California, San Diego, California, United States of America
- Department of Pediatrics, University of California, San Diego, California, United States of America
- Center for Microbiome Innovation, University of California, San Diego, California, United States of America
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11
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Wu Z, Nguyen D, Shrestha S, Raskin L, Khanal SK, Lee PH. Evaluation of Nanaerobic Digestion as a Mechanism to Explain Surplus Methane Production in Animal Rumina and Engineered Digesters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12302-12314. [PMID: 37565790 PMCID: PMC10448717 DOI: 10.1021/acs.est.2c07813] [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: 10/28/2022] [Revised: 07/02/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023]
Abstract
Nanaerobes are a newly described class of microorganisms that use a unique cytochrome bd oxidase to achieve nanaerobic respiration at <2 μM dissolved oxygen (∼1% of atmospheric oxygen) but are not viable above this value due to the lack of other terminal oxidases. Although sharing an overlapping ecological niche with methanogenic archaea, the role of nanaerobes in methanogenic systems has not been studied so far. To explore their occurrence and significance, we re-analyzed published meta-omic datasets from animal rumina and waste-to-energy digesters, including conventional anaerobic digesters and anaerobic digesters with ultra-low oxygenation. Results show that animal rumina share broad similarities in the microbial community and system performance with oxygenated digesters, rather than with conventional anaerobic digesters, implying that trace levels of oxygen drive the efficient digestion in ruminants. The rumen system serves as an ideal model for the newly named nanaerobic digestion, as it relies on the synergistic co-occurrence of nanaerobes and methanogens for methane yield enhancement. The most abundant ruminal bacterial family Prevotellaceae contains many nanaerobes, which perform not only anaerobic fermentation but also nanaerobic respiration using cytochrome bd oxidase. These nanaerobes generally accompany hydrogenotrophic methanogens to constitute a thermodynamically and physiologically consistent framework for efficient methane generation. Our findings provide new insights into ruminal methane emissions and strategies to enhance methane generation from biomass.
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Affiliation(s)
- Zhuoying Wu
- Department
of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United
Kingdom
- Shanghai
Shaanxi Coal Hi-tech Research Institute Co., Ltd., Shanghai 201613, China
| | - Duc Nguyen
- Department
of Molecular Biosciences and Bioengineering, University of Hawai’i at Ma̅noa, Honolulu 96822, Hawaii, United States
- The
Lyell Centre, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Shilva Shrestha
- Department
of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor 48109, Michigan, United States
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lutgarde Raskin
- Department
of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor 48109, Michigan, United States
| | - Samir Kumar Khanal
- Department
of Molecular Biosciences and Bioengineering, University of Hawai’i at Ma̅noa, Honolulu 96822, Hawaii, United States
| | - Po-Heng Lee
- Department
of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, United
Kingdom
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12
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Okabe S, Ye S, Lan X, Nukada K, Zhang H, Kobayashi K, Oshiki M. Oxygen tolerance and detoxification mechanisms of highly enriched planktonic anaerobic ammonium-oxidizing (anammox) bacteria. ISME COMMUNICATIONS 2023; 3:45. [PMID: 37137967 PMCID: PMC10156729 DOI: 10.1038/s43705-023-00251-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/05/2023]
Abstract
Oxygen is a key regulatory factor of anaerobic ammonium oxidation (anammox). Although the inhibitory effect of oxygen is evident, a wide range of oxygen sensitivities of anammox bacteria have been reported so far, which makes it difficult to model the marine nitrogen loss and design anammox-based technologies. Here, oxygen tolerance and detoxification mechanisms of four genera of anammox bacteria; one marine species ("Ca. Scalindua sp.") and four freshwater anammox species ("Ca. Brocadia sinica", "Ca. Brocadia sapporoensis", "Ca. Jettenia caeni", and "Ca. Kuenenia stuttgartiensis") were determined and then related to the activities of anti-oxidative enzymes. Highly enriched planktonic anammox cells were exposed to various levels of oxygen, and oxygen inhibition kinetics (50% inhibitory concentration (IC50) and upper O2 limits (DOmax) of anammox activity) were quantitatively determined. A marine anammox species, "Ca. Scalindua sp.", exhibited much higher oxygen tolerance capability (IC50 = 18.0 µM and DOmax = 51.6 µM) than freshwater species (IC50 = 2.7-4.2 µM and DOmax = 10.9-26.6 µM). The upper DO limit of "Ca. Scalindua sp." was much higher than the values reported so far (~20 µM). Furthermore, the oxygen inhibition was reversible even after exposed to ambient air for 12-24 h. The comparative genome analysis confirmed that all anammox species commonly possess the genes considered to function for reduction of O2, superoxide anion (O2•-), and H2O2. However, the superoxide reductase (Sor)-peroxidase dependent detoxification system alone may not be sufficient for cell survival under microaerobic conditions. Despite the fact that anaerobes normally possess no or little superoxide dismutase (Sod) or catalase (Cat), only Scalindua exhibited high Sod activity of 22.6 ± 1.9 U/mg-protein with moderate Cat activity of 1.6 ± 0.7 U/mg-protein, which was consistent with the genome sequence analysis. This Sod-Cat dependent detoxification system could be responsible for the higher O2 tolerance of Scalindua than other freshwater anammox species lacking the Sod activity.
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Affiliation(s)
- Satoshi Okabe
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan.
| | - Shaoyu Ye
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Xi Lan
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Keishi Nukada
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Haozhe Zhang
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Kanae Kobayashi
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Mamoru Oshiki
- Department of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
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13
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Makarchuk I, Kägi J, Gerasimova T, Wohlwend D, Friedrich T, Melin F, Hellwig P. pH-dependent kinetics of NO release from E. coli bd-I and bd-II oxidase reveals involvement of Asp/Glu58 B. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148952. [PMID: 36535430 DOI: 10.1016/j.bbabio.2022.148952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Escherichia coli contains two cytochrome bd oxidases, bd-I and bd-II. The structure of both enzymes is highly similar, but they exhibit subtle differences such as the accessibility of the active site through a putative proton channel. Here, we demonstrate that the duroquinol:dioxygen oxidoreductase activity of bd-I increased with alkaline pH, whereas bd-II showed a broad activity maximum around pH 7. Likewise, the pH dependence of NO release from the reduced active site, an essential property of bd oxidases, differed between the two oxidases as detected by UV/vis spectroscopy. Both findings may be attributed to differences in the proton channel leading to the active site heme d. The channel comprises a titratable residue (Asp58B in bd-I and Glu58B in bd-II). Conservative mutations at this position drastically altered NO release demonstrating its contribution to the process.
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Affiliation(s)
- Iryna Makarchuk
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France
| | - Jan Kägi
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Tatjana Gerasimova
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Frédéric Melin
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France.
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14
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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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15
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Small Intestinal Bacterial Overgrowth and Non-Alcoholic Fatty Liver Disease: What Do We Know in 2023? Nutrients 2023; 15:nu15061323. [PMID: 36986052 PMCID: PMC10052062 DOI: 10.3390/nu15061323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a chronic liver disease associated with the pathological accumulation of lipids inside hepatocytes. Untreated NAFL can progress to non-alcoholic hepatitis (NASH), followed by fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). The common denominator of the above-mentioned metabolic disorders seems to be insulin resistance, which occurs in NAFLD patients. Obesity is the greatest risk factor for lipid accumulation inside hepatocytes, but a part of the NAFLD patient population has a normal body weight according to the BMI index. Obese people with or without NAFLD have a higher incidence of small intestinal bacterial overgrowth (SIBO), and those suffering from NAFLD show increased intestinal permeability, including a more frequent presence of bacterial overgrowth in the small intestine (SIBO). The health consequences of SIBO are primarily malabsorption disorders (vitamin B12, iron, choline, fats, carbohydrates and proteins) and bile salt deconjugation. Undetected and untreated SIBO may lead to nutrient and/or energy malnutrition, thus directly impairing liver function (e.g., folic acid and choline deficiency). However, whether SIBO contributes to liver dysfunction, decreased intestinal barrier integrity, increased inflammation, endotoxemia and bacterial translocation is not yet clear. In this review, we focus on gut–liver axis and discuss critical points, novel insights and the role of nutrition, lifestyle, pre- and probiotics, medication and supplements in the therapy and prevention of both SIBO and NAFLD.
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16
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Wang X, Liu L, Lu B, Duan X, Zhou X, Huang D, Wu H. The thoracoabdominal wall abscess and sepsis caused by Porphyromonas pogonae: Case report and literature review. Heliyon 2023; 9:e14860. [PMID: 37123965 PMCID: PMC10133661 DOI: 10.1016/j.heliyon.2023.e14860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
Background Porphyromonas pogonae was first reported in 2011 from polymicrobial infections in central bearded dragons. Human infections caused by P. pogonae remain rare, with only four cases published in the PubMed database. Herein, we present an unusual Chinese case of the thoracoabdominal wall abscess with sepsis caused by P. pogonae and review the clinical manifestations, diagnostic evaluation, and clinical outcome of the case. Case presentation A 62-year-old female with sinusitis but no diabetes mellitus presented with fever, tenderness under an abdominal mass, and paroxysmal stabbing pain in the chest after receiving augmentation mammoplasty. Cultures of blood and pus yielded P. pogonae, and a diagnosis of sepsis with an abscess in the chest and abdominal wall was made. After repeated debridement and appropriate meropenem antibiotic treatment, the patient was successfully treated and discharged home. Conclusions We report the first human case of P. pogonae causing sepsis in a patient with an abscess in China. The identification of P. pogonae should be considered if the strain grows well under either anaerobic or microaerobic conditions and exhibits strong β-hemolysis with fluorescence. This study retrospectively reviewed patients' infection diagnosis, clinical treatment, and prognosis to enhance awareness of the risk of P. pogonae infection.
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17
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Butler NL, Ito T, Foreman S, Morgan JE, Zagorevsky D, Malamy MH, Comstock LE, Barquera B. Bacteroides fragilis Maintains Concurrent Capability for Anaerobic and Nanaerobic Respiration. J Bacteriol 2023; 205:e0038922. [PMID: 36475831 PMCID: PMC9879120 DOI: 10.1128/jb.00389-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/02/2022] [Indexed: 12/13/2022] Open
Abstract
Bacteroides species can use fumarate and oxygen as terminal electron acceptors during cellular respiration. In the human gut, oxygen diffuses from intestinal epithelial cells supplying "nanaerobic" oxygen levels. Many components of the anaerobic respiratory pathway have been determined, but such analyses have not been performed for nanaerobic respiration. Here, we present genetic, biochemical, enzymatic, and mass spectrometry analyses to elucidate the nanaerobic respiratory pathway in Bacteroides fragilis. Under anaerobic conditions, the transfer of electrons from NADH to the quinone pool has been shown to be contributed by two enzymes, NQR and NDH2. We find that the activity contributed by each under nanaerobic conditions is 77 and 23%, respectively, similar to the activity levels under anaerobic conditions. Using mass spectrometry, we show that the quinone pool also does not differ under these two conditions and consists of a mixture of menaquinone-8 to menaquinone-11, with menaquinone-10 predominant under both conditions. Analysis of fumarate reductase showed that it is synthesized and active under anaerobic and nanaerobic conditions. Previous RNA sequencing data and new transcription reporter assays show that expression of the cytochrome bd oxidase gene does not change under these conditions. Under nanaerobic conditions, we find both increased CydA protein and increased cytochrome bd activity. Reduced-minus-oxidized spectra of membranes showed the presence of heme d when the bacteria were grown in the presence of protoporphyrin IX and iron under both anaerobic and nanaerobic conditions, suggesting that the active oxidase can be assembled with or without oxygen. IMPORTANCE By performing a comprehensive analysis of nanaerobic respiration in Bacteroides fragilis, we show that this organism maintains capabilities for anaerobic respiration on fumarate and nanaerobic respiration on oxygen simultaneously. The contribution of the two NADH:quinone oxidoreductases and the composition of the quinone pool are the same under both conditions. Fumarate reductase and cytochrome bd are both present, and which of these terminal enzymes is active in electron transfer depends on the availability of the final electron acceptor: fumarate or oxygen. The synthesis of cytochrome bd and fumarate reductase under both conditions serves as an adaptation to an environment with low oxygen concentrations so that the bacteria can maximize energy conservation during fluctuating environmental conditions or occupation of different spatial niches.
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Affiliation(s)
- Nicole L. Butler
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Takeshi Ito
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Sara Foreman
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Joel E. Morgan
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Dmitry Zagorevsky
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Michael H. Malamy
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Laurie E. Comstock
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Blanca Barquera
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
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18
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The vermiform cecal appendix, expendable or essential? A narrative review. Curr Opin Gastroenterol 2022; 38:570-576. [PMID: 36165025 DOI: 10.1097/mog.0000000000000881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
PURPOSE OF REVIEW The vermiform cecal appendix is a small thin pouch-like tube of intestinal tissue situated in the lower right abdomen. It is attached at the junction of the large intestine between the ascending colon and small intestine. Historically, the appendix has been labeled redundant with no significant function, a remnant of evolution. This idea was thought to represent a function that may have been critical for survival that became nonsignificant over time. Evolutionary biologists deemed it to be a vestigial organ that early in human evolution was a dedicated organ that was useful and exploited by herbivorous ancestors. RECENT FINDINGS Currently, the vermiform cecal appendix has generated significant renewed research interest. As such it has been reported to present a site with a high concentration of lymphoid tissue and a biofilm microbiome that approximately mirrors that which is found in the large bowel. SUMMARY Research suggests that the vermiform cecal appendix may be the site of a safe-house biofilm that could re-inoculate the large bowel. Given that the appendix has no known role in digestion, the network of lymphoid tissue and microbiome could constitute an initial site of bacterial translocations that can influence early life ontology and immunological tolerance. A dysbiotic microbiome in the appendix is posited to trigger inflammatory sequelae.
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Characterization of the oxidative stress response regulatory network in Bacteroides fragilis: An interaction between BmoR and OxyR regulons promotes abscess formation in a model of intra-abdominal infection. Anaerobe 2022; 78:102668. [DOI: 10.1016/j.anaerobe.2022.102668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/10/2022]
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20
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Xu G, He J. Resilience of organohalide-detoxifying microbial community to oxygen stress in sewage sludge. WATER RESEARCH 2022; 224:119055. [PMID: 36126627 DOI: 10.1016/j.watres.2022.119055] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/20/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Organohalide pollutants are prevalent in the environment, causing harms to wildlife and human. Organohalide-respiring bacteria (OHRB) could detoxify these pollutants in anaerobic environments, but the most competent OHRB (i.e., Dehalococcoides) is susceptible to oxygen. This study reports exceptional resistance and resilience of sewage sludge microbial communities to oxygen stress for attenuation of structurally distinct organohalide pollutants, including tetrachloroethene, tetrabromobisphenol A, and polybrominated diphenyl ethers. The dehalogenation rate constant of these organohalide pollutants in oxygen-exposed sludge microcosms was maintained as 74-120% as that in the control without oxygen exposure. Subsequent top-down experiments clarified that sludge flocs and non-OHRB contributed to alleviating oxygen stress on OHRB. In the dehalogenating microcosms, multiple OHRB (Dehahlococcoides, Dehalogenimonas, and Sulfurospirillum) harboring distinct reductive dehalogenase genes (pceA, pteA, tceA, vcrA, and bdeA) collaborated to detoxify organohalide pollutants but responded differentially to oxygen stress. Comprehensive microbial community analyses (taxonomy, diversity, and structure) demonstrated certain resilience of the sludge-derived dehalogenating microbial communities to oxygen stress. Additionally, microbial co-occurrence networks were intensified by oxygen stress in most microcosms, as a possible stress mitigation strategy. Altogether the mechanistic and ecological findings in this study contribute to remediation of organohalide-contaminated sites encountering oxygen disturbance.
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Affiliation(s)
- Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore; NUS Graduate School - Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, 119077, Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore; NUS Graduate School - Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, 119077, Singapore.
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21
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Pinacho-Guendulain B, Montiel-Castro AJ, Ramos-Fernández G, Pacheco-López G. Social complexity as a driving force of gut microbiota exchange among conspecific hosts in non-human primates. Front Integr Neurosci 2022; 16:876849. [PMID: 36110388 PMCID: PMC9468716 DOI: 10.3389/fnint.2022.876849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The emergent concept of the social microbiome implies a view of a highly connected biological world, in which microbial interchange across organisms may be influenced by social and ecological connections occurring at different levels of biological organization. We explore this idea reviewing evidence of whether increasing social complexity in primate societies is associated with both higher diversity and greater similarity in the composition of the gut microbiota. By proposing a series of predictions regarding such relationship, we evaluate the existence of a link between gut microbiota and primate social behavior. Overall, we find that enough empirical evidence already supports these predictions. Nonetheless, we conclude that studies with the necessary, sufficient, explicit, and available evidence are still scarce. Therefore, we reflect on the benefit of founding future analyses on the utility of social complexity as a theoretical framework.
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Affiliation(s)
- Braulio Pinacho-Guendulain
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana (UAM), Ciudad de México, Mexico
| | - Augusto Jacobo Montiel-Castro
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- *Correspondence: Augusto Jacobo Montiel-Castro,
| | - Gabriel Ramos-Fernández
- Institute for Research on Applied Mathematics and Systems (IIMAS), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Center for Complexity Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Gustavo Pacheco-López
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- Gustavo Pacheco-López,
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22
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Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat Commun 2022; 13:4110. [PMID: 35840579 PMCID: PMC9287336 DOI: 10.1038/s41467-022-31847-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
The Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) "Lutacidiplasmatales" due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota. Phylum-level analysis reveals that Thermoplasmatota evolution had been punctuated by several periods of high levels of novel gene family acquisition. Several essential metabolisms, such as aerobic respiration and acid tolerance, were likely acquired independently by divergent lineages through convergent evolution rather than inherited from a common ancestor. Ultimately, this study describes the terrestrially prevalent Lutacidiciplasmatales and highlights convergent evolution as an important driving force in the evolution of archaeal lineages.
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Potentiation of the Activity of Antibiotics against ATCC and MDR Bacterial Strains with (+)-α-Pinene and (-)-Borneol. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8217380. [PMID: 35663042 PMCID: PMC9159878 DOI: 10.1155/2022/8217380] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/15/2022] [Accepted: 05/07/2022] [Indexed: 12/11/2022]
Abstract
The increasing rates of antimicrobial resistance have demanded the development of new drugs as conventional antibiotics have become significantly less effective. Evidence has identified a variety of phytocompounds with the potential to be used in the combat of infections caused by multidrug-resistant (MDR) bacteria. Considering the verification that terpenes are promising antibacterial compounds, the present research aimed to evaluate the antibacterial and antibiotic-modulating activity of (+)-α-pinene and (-)-borneol against MDR bacterial strains. The broth microdilution method was used to determine the minimum inhibitory concentration (MIC) of the compounds and antibiotics and further evaluate the intrinsic and associated antibiotic activity. These analyses revealed that (+)-α-pinene showed significant antibacterial activity only against E. coli (MIC = 512 μg.mL−1), while no significant inhibition of S. aureus and P. aeruginosa growth was observed (MIC ≥ 1024 μg mL−1). However, when combined with antibiotics, this compound induced a significant improvement in the activity of conventional antibiotics, as observed for ciprofloxacin, amikacin, and gentamicin against Staphylococcus aureus, as well as for amikacin and gentamicin against Escherichia coli, and amikacin against Pseudomonas aeruginosa. On the other hand, (-)-borneol was found to inhibit the growth of E. coli and enhance the antibiotic activity of ciprofloxacin and gentamicin against S. aureus. The present findings indicate that (+)-α-pinene and (-)-borneol are phytocompounds with the potential to be used in the combat of antibacterial resistance.
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Panigrahi MK, Kaliaperumal V, Akella A, Venugopal G, Ramadass B. Mapping microbiome-redox spectrum and evaluating Microbial-Redox Index in chronic gastritis. Sci Rep 2022; 12:8450. [PMID: 35589904 PMCID: PMC9120160 DOI: 10.1038/s41598-022-12431-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/11/2022] [Indexed: 12/27/2022] Open
Abstract
Peptic ulcer disease (PUD) and chronic gastritis are prevalent in developing countries. The role of oxidative stress in the pathogenesis of gastrointestinal mucosal disorders is well recognized. In PUD, the gastric mucosa and its associated microbiome are subject to diet and stress-induced oxidative perturbations. Tissue redox potential (ORP) measurement can quantify oxidative stress, reflecting the balance between prooxidants and antioxidants. This study hypothesizes that the oxidative stress quantified by tissue ORP will be associated with characteristic changes in the mucosa-associated microbiome in PUD and gastritis. In addition, we propose using relative microbial abundance as a quantitative marker of mucosal health. Endoscopy was performed to obtain gastric mucosal biopsies from ten PUD and ten non-ulcer dyspepsia (NUD) patients. The tissue ORP was measured directly with a microelectrode using a biopsy specimen. A second specimen from an adjacent site was subjected to 16s rRNA gene sequencing. From the OTUs, the relative abundance of the microbial taxon in each of the samples was derived. We analyzed the genome of the predominant species for genes encoding the utilization of oxygen as an electron acceptor in respiration and for the presence of antioxidant defense mechanisms. The organisms were then grouped based on their established and inferred redox traits. Shannon diversity index and Species richness were calculated on rarefied data. The relative abundance of organisms that prefer high ORP over those that favor low ORP is conceived as the “Microbial Redox Index (MRI),” an indicator of mucosal health. In the gastric mucosa, aerobic species predominate and are more diverse than the anaerobes. The predominant aerobes are Helicobacter pylori and Sphingobacterium mizutaii. The abundance of these two species had an inverse correlation with the abundance of low ORP preferring anaerobes. Their relative abundance ratio (Microbial Redox Index) correlated with the tissue oxidation–reduction potential (ORP), a direct measure of oxidative stress. Correlation analysis also revealed that the abundance of all anaerobes inversely correlated with the dominant aerobic taxa. In addition, Shannon and Species richness diversity indices, the probable indicators of mucosal health, were negatively correlated with Microbial Redox Index. Using PUD as a prototype mucosal disease, this article describes a generalized approach to infer and quantify mucosal oxidative stress by analyzing the relative abundance of microorganisms that preferentially grow at the extremes of the tissue redox potential. This ratiometric Microbial Redox Index can also be assessed using simple qPCR without the need for sequencing. The approach described herein may be helpful as a widely applicable quantitative measure of mucosal health with prognostic and therapeutic implications.
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Affiliation(s)
- Manas Kumar Panigrahi
- Department of Gastroenterology, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Venkatesh Kaliaperumal
- MYAS-NIN Department of Sports Science, ICMR-National Institute of Nutrition, Hyderabad, India
| | - Abhishek Akella
- Center of Excellence for Clinical Microbiome Research, All India Institute of Medical Sciences, Bhubaneswar, 751019, India
| | - Giriprasad Venugopal
- Center of Excellence for Clinical Microbiome Research, All India Institute of Medical Sciences, Bhubaneswar, 751019, India
| | - Balamurugan Ramadass
- Center of Excellence for Clinical Microbiome Research, All India Institute of Medical Sciences, Bhubaneswar, 751019, India. .,Department of Biochemistry, All India Institute of Medical Sciences, Bhubaneswar, India.
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Li C, Humayun M, Walker GM, Park KY, Connors B, Feng J, Pellitteri Hahn MC, Scarlett CO, Li J, Feng Y, Clark RL, Hefti H, Schrope J, Venturelli OS, Beebe DJ. Under-Oil Autonomously Regulated Oxygen Microenvironments: A Goldilocks Principle-Based Approach for Microscale Cell Culture. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104510. [PMID: 35118834 PMCID: PMC8981459 DOI: 10.1002/advs.202104510] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/20/2021] [Indexed: 05/14/2023]
Abstract
Oxygen levels in vivo are autonomously regulated by a supply-demand balance, which can be altered in disease states. However, the oxygen levels of in vitro cell culture systems, particularly microscale cell culture, are typically dominated by either supply or demand. Further, the oxygen microenvironment in these systems is rarely monitored or reported. Here, a method to establish and dynamically monitor autonomously regulated oxygen microenvironments (AROM) using an oil overlay in an open microscale cell culture system is presented. Using this method, the oxygen microenvironment is dynamically regulated via the supply-demand balance of the system. Numerical simulation and experimental validation of oxygen transport within multi-liquid-phase, microscale culture systems involving a variety of cell types, including mammalian, fungal, and bacterial cells are presented. Finally, AROM is applied to establish a coculture between cells with disparate oxygen demands-primary intestinal epithelial cells (oxygen consuming) and Bacteroides uniformis (an anaerobic species prevalent in the human gut).
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Affiliation(s)
- Chao Li
- Carbone Cancer CenterUniversity of Wisconsin‐MadisonMadisonWI53705USA
| | - Mouhita Humayun
- Department of Biomedical EngineeringUniversity of Wisconsin‐MadisonMadisonWI53705USA
| | - Glenn M. Walker
- Department of Biomedical EngineeringUniversity of Mississippi UniversityMadisonMS38677USA
| | - Keon Young Park
- Department of SurgeryUniversity of California San FranciscoSan FranciscoCA94143USA
| | - Bryce Connors
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWI53706USA
- Department of Chemical and Biological EngineeringUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Jun Feng
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Molly C. Pellitteri Hahn
- Analytical Instrumentation Center‐Mass Spec FacilitySchool of PharmacyUniversity of Wisconsin‐MadisonMadisonWI53705USA
| | - Cameron O. Scarlett
- Analytical Instrumentation Center‐Mass Spec FacilitySchool of PharmacyUniversity of Wisconsin‐MadisonMadisonWI53705USA
| | - Jiayi Li
- Department of Biomedical EngineeringUniversity of Wisconsin‐MadisonMadisonWI53705USA
| | - Yanbo Feng
- Department of Biomedical EngineeringUniversity of Wisconsin‐MadisonMadisonWI53705USA
| | - Ryan L. Clark
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Hunter Hefti
- Department of Biomedical EngineeringUniversity of Wisconsin‐MadisonMadisonWI53705USA
| | - Jonathan Schrope
- School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWI53726USA
| | - Ophelia S. Venturelli
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWI53706USA
- Department of Chemical and Biological EngineeringUniversity of Wisconsin‐MadisonMadisonWI53706USA
- Department of BacteriologyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - David J. Beebe
- Carbone Cancer CenterUniversity of Wisconsin‐MadisonMadisonWI53705USA
- Department of Biomedical EngineeringUniversity of Wisconsin‐MadisonMadisonWI53705USA
- Department of Pathology and Laboratory MedicineUniversity of Wisconsin‐MadisonMadisonWI53705USA
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26
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Xi Y, Huang Y, Li Y, Huang Y, Yan J, Shi Z. The effects of dietary protein and fiber levels on growth performance, gout occurrence, intestinal microbial communities, and immunoregulation in the gut-kidney axis of goslings. Poult Sci 2022; 101:101780. [PMID: 35325834 PMCID: PMC8938869 DOI: 10.1016/j.psj.2022.101780] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/29/2022] [Accepted: 02/05/2022] [Indexed: 02/06/2023] Open
Abstract
The current study evaluated the effects of dietary protein and fiber levels on growth performance, gout occurrence, intestinal microbial communities, and immunoregulation in the gut-kidney axis of goslings. A completely randomized 2 × 3 factorial design was adopted with 2 CP levels (180 [18CP] and 220 [22CP] g/kg) and 3 crude fiber (CF) levels (30 [low CF], 50 [mid CF], and 70 [high CF] g/kg). The high CP or low CF diets predisposed the goslings to gout. The high protein diets worsened renal function; serum concentrations of UA and Cr as well as XOD activity in 9-day-old goslings fed 22% CP diets were significantly increased. Although CF levels from 3 to 7% did not directly affect kidney health, increasing CF levels might accelerate the increase of probiotics in the cecum of goslings and withhold maleficent bacteria, alleviating the gut dysbiosis caused by high protein diets. An analysis of the cecal microbiota via 16Sr RNA sequencing revealed that the abundance of Enterococcus in the 22CP group was higher than that in the 18CP group but decreased with increasing CF levels on d 9. The abundance of Lactobacillus increased with increasing CF levels. Additionally, higher serum LPS and proinflammatory cytokine concentrations and upregulated mRNA expression levels in the cecal, tonsil, and kidney tissues indicated that high-protein diets could activate the TLR4/MyD88/NFκB pathway and induce both intestinal and renal inflammation in young goslings. Serum LPS concentrations on d 9 were found to decrease with increasing CF, although altering dietary CF levels did not directly affect the serum immune indices of goslings. In conclusion, the high CP diet exerted a negative effect on gout occurrence, microbial communities, and immunoregulation in the gut-kidney axis of goslings, while appropriately increased dietary fiber levels helped maintain intestinal balance and reduced serum LPS concentration. We propose a diet of 18% CP paired with a 5% CF as the optimal combination for gosling feed.
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Berg JS, Ahmerkamp S, Pjevac P, Hausmann B, Milucka J, Kuypers MMM. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6517451. [PMID: 35094062 PMCID: PMC9075580 DOI: 10.1093/femsre/fuac006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 12/01/2022] Open
Abstract
Oxygen (O2) is the ultimate oxidant on Earth and its respiration confers such an energetic advantage that microorganisms have evolved the capacity to scavenge O2 down to nanomolar concentrations. The respiration of O2 at extremely low levels is proving to be common to diverse microbial taxa, including organisms formerly considered strict anaerobes. Motivated by recent advances in O2 sensing and DNA/RNA sequencing technologies, we performed a systematic review of environmental metatranscriptomes revealing that microbial respiration of O2 at nanomolar concentrations is ubiquitous and drives microbial activity in seemingly anoxic aquatic habitats. These habitats were key to the early evolution of life and are projected to become more prevalent in the near future due to anthropogenic-driven environmental change. Here, we summarize our current understanding of aerobic microbial respiration under apparent anoxia, including novel processes, their underlying biochemical pathways, the involved microorganisms, and their environmental importance and evolutionary origin.
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Affiliation(s)
- Jasmine S Berg
- Corrresponding author: Géopolis, Quartier Unil-Mouline, Université de Lausanne, 1015 Lausanne, Switzerland. E-mail:
| | - Soeren Ahmerkamp
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna 1090, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1090, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna 1090, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna 1090, Austria
| | - Jana Milucka
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 2359, Germany
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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: 80] [Impact Index Per Article: 26.7] [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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29
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Atashgahi S, Oosterkamp MJ, Peng P, Frank J, Kraft B, Hornung B, Schleheck D, Lücker S, Jetten MSM, Stams AJM, Smidt H. Proteogenomic analysis of Georgfuchsia toluolica revealed unexpected concurrent aerobic and anaerobic toluene degradation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:841-851. [PMID: 34374217 PMCID: PMC9290046 DOI: 10.1111/1758-2229.12996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Denitrifying Betaproteobacteria play a key role in the anaerobic degradation of monoaromatic hydrocarbons. We performed a multi-omics study to better understand the metabolism of the representative organism Georgfuchsia toluolica strain G5G6 known as a strict anaerobe coupling toluene oxidation with dissimilatory nitrate and Fe(III) reduction. Despite the genomic potential for degradation of different carbon sources, we did not find sugar or organic acid transporters, in line with the inability of strain G5G6 to use these substrates. Using a proteomics analysis, we detected proteins of fumarate-dependent toluene activation, membrane-bound nitrate reductase, and key components of the metal-reducing (Mtr) pathway under both nitrate- and Fe(III)-reducing conditions. High abundance of the multiheme cytochrome MtrC implied that a porin-cytochrome complex was used for respiratory Fe(III) reduction. Remarkably, strain G5G6 contains a full set of genes for aerobic toluene degradation, and we detected enzymes of aerobic toluene degradation under both nitrate- and Fe(III)-reducing conditions. We further detected an ATP-dependent benzoyl-CoA reductase, reactive oxygen species detoxification proteins, and cytochrome c oxidase indicating a facultative anaerobic lifestyle of strain G5G6. Correspondingly, we found diffusion through the septa a substantial source of oxygen in the cultures enabling concurrent aerobic and anaerobic toluene degradation by strain G5G6.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Department of Microbiology, IWWRRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Margreet J. Oosterkamp
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Sub‐department of Environmental TechnologyWageningen University & Research, Bornse weilanden 9Wageningen6708 DWThe Netherlands
| | - Peng Peng
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Department of Civil and Environmental EngineeringUniversity of Michigan, 1351 Beal AvenueAnn ArborMI48109‐2125USA
| | - Jeroen Frank
- Department of Microbiology, IWWRRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Beate Kraft
- Nordic Center for Earth EvolutionUniversity of Southern DenmarkOdenseDK‐5230Denmark
| | - Bastian Hornung
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy13288 Aix Marseille UniversitéMarseilleFrance
| | - David Schleheck
- Department of BiologyUniversity of KonstanzKonstanz78457Germany
| | - Sebastian Lücker
- Department of Microbiology, IWWRRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, IWWRRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Alfons J. M. Stams
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de GualtarBraga4710‐057Portugal
| | - Hauke Smidt
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
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Cryo-EM structure of mycobacterial cytochrome bd reveals two oxygen access channels. Nat Commun 2021; 12:4621. [PMID: 34330928 PMCID: PMC8324918 DOI: 10.1038/s41467-021-24924-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 07/14/2021] [Indexed: 12/21/2022] Open
Abstract
Cytochromes bd are ubiquitous amongst prokaryotes including many human-pathogenic bacteria. Such complexes are targets for the development of antimicrobial drugs. However, an understanding of the relationship between the structure and functional mechanisms of these oxidases is incomplete. Here, we have determined the 2.8 Å structure of Mycobacterium smegmatis cytochrome bd by single-particle cryo-electron microscopy. This bd oxidase consists of two subunits CydA and CydB, that adopt a pseudo two-fold symmetrical arrangement. The structural topology of its Q-loop domain, whose function is to bind the substrate, quinol, is significantly different compared to the C-terminal region reported for cytochromes bd from Geobacillus thermodenitrificans (G. th) and Escherichia coli (E. coli). In addition, we have identified two potential oxygen access channels in the structure and shown that similar tunnels also exist in G. th and E. coli cytochromes bd. This study provides insights to develop a framework for the rational design of antituberculosis compounds that block the oxygen access channels of this oxidase. Cytochromes bd oxidase (Cyt-bd) catalyzes the reduction of oxygen to water and is the terminal oxidase in the respiratory chain of prokaryotes. Here, the authors present the 2.8 Å cryo-EM structure of Mycobacterium smegmatis Cyt-bd and identify two potential oxygen access channels in the structure, which is of interest for the development of novel antituberculosis drugs.
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31
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Identification and optimization of quinolone-based inhibitors against cytochrome bd oxidase using an electrochemical assay. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Dank A, van Mastrigt O, Boeren S, Lillevang SK, Abee T, Smid EJ. Propionibacterium freudenreichii thrives in microaerobic conditions by complete oxidation of lactate to CO 2. Environ Microbiol 2021; 23:3116-3129. [PMID: 33955639 PMCID: PMC8360058 DOI: 10.1111/1462-2920.15532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 04/13/2021] [Indexed: 11/28/2022]
Abstract
In this study we show increased biomass formation for four species of food-grade propionic acid bacteria (Acidipropionibacterium acidipropionici, Acidipropionibacterium jensenii, Acidipropionibacterium thoenii and Propionibacterium freudenreichii) when exposed to oxygen, implicating functional respiratory systems. Using an optimal microaerobic condition, P. freudenreichii DSM 20271 consumed lactate to produce propionate and acetate initially. When lactate was depleted propionate was oxidized to acetate. We propose to name the switch from propionate production to consumption in microaerobic conditions the 'propionate switch'. When propionate was depleted the 'acetate switch' occurred, resulting in complete consumption of acetate. Both growth rate on lactate (0.100 versus 0.078 h-1 ) and biomass yield (20.5 versus 8.6 g* mol-1 lactate) increased compared to anaerobic conditions. Proteome analysis revealed that the abundance of proteins involved in the aerobic and anaerobic electron transport chains and major metabolic pathways did not significantly differ between anaerobic and microaerobic conditions. This implicates that P. freudenreichii is prepared for utilizing O2 when it comes available in anaerobic conditions. The ecological niche of propionic acid bacteria can conceivably be extended to environments with oxygen gradients from oxic to anoxic, so-called microoxic environments, as found in the rumen, gut and soils, where they can thrive by utilizing low concentrations of oxygen.
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Affiliation(s)
- Alexander Dank
- Laboratory of Food MicrobiologyWageningen University & Research, P.O. Box 17Wageningen6700AAThe Netherlands
| | - Oscar van Mastrigt
- Laboratory of Food MicrobiologyWageningen University & Research, P.O. Box 17Wageningen6700AAThe Netherlands
| | - Sjef Boeren
- Laboratory of BiochemistryWageningen University & ResearchWageningenThe Netherlands
| | - Søren K. Lillevang
- Arla Innovation Centre, Arla Foods, Agro Food Park 19Aarhus N8200Denmark
| | - Tjakko Abee
- Laboratory of Food MicrobiologyWageningen University & Research, P.O. Box 17Wageningen6700AAThe Netherlands
| | - Eddy J. Smid
- Laboratory of Food MicrobiologyWageningen University & Research, P.O. Box 17Wageningen6700AAThe Netherlands
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Borisov VB, Siletsky SA, Paiardini A, Hoogewijs D, Forte E, Giuffrè A, Poole RK. Bacterial Oxidases of the Cytochrome bd Family: Redox Enzymes of Unique Structure, Function, and Utility As Drug Targets. Antioxid Redox Signal 2021; 34:1280-1318. [PMID: 32924537 PMCID: PMC8112716 DOI: 10.1089/ars.2020.8039] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022]
Abstract
Significance: Cytochrome bd is a ubiquinol:oxygen oxidoreductase of many prokaryotic respiratory chains with a unique structure and functional characteristics. Its primary role is to couple the reduction of molecular oxygen, even at submicromolar concentrations, to water with the generation of a proton motive force used for adenosine triphosphate production. Cytochrome bd is found in many bacterial pathogens and, surprisingly, in bacteria formally denoted as anaerobes. It endows bacteria with resistance to various stressors and is a potential drug target. Recent Advances: We summarize recent advances in the biochemistry, structure, and physiological functions of cytochrome bd in the light of exciting new three-dimensional structures of the oxidase. The newly discovered roles of cytochrome bd in contributing to bacterial protection against hydrogen peroxide, nitric oxide, peroxynitrite, and hydrogen sulfide are assessed. Critical Issues: Fundamental questions remain regarding the precise delineation of electron flow within this multihaem oxidase and how the extraordinarily high affinity for oxygen is accomplished, while endowing bacteria with resistance to other small ligands. Future Directions: It is clear that cytochrome bd is unique in its ability to confer resistance to toxic small molecules, a property that is significant for understanding the propensity of pathogens to possess this oxidase. Since cytochrome bd is a uniquely bacterial enzyme, future research should focus on harnessing fundamental knowledge of its structure and function to the development of novel and effective antibacterial agents.
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Affiliation(s)
- Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Sergey A. Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | | | - David Hoogewijs
- Department of Medicine/Physiology, University of Fribourg, Fribourg, Switzerland
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Robert K. Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
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34
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Borisov VB, Siletsky SA, Nastasi MR, Forte E. ROS Defense Systems and Terminal Oxidases in Bacteria. Antioxidants (Basel) 2021; 10:antiox10060839. [PMID: 34073980 PMCID: PMC8225038 DOI: 10.3390/antiox10060839] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/07/2023] Open
Abstract
Reactive oxygen species (ROS) comprise the superoxide anion (O2•−), hydrogen peroxide (H2O2), hydroxyl radical (•OH), and singlet oxygen (1O2). ROS can damage a variety of macromolecules, including DNA, RNA, proteins, and lipids, and compromise cell viability. To prevent or reduce ROS-induced oxidative stress, bacteria utilize different ROS defense mechanisms, of which ROS scavenging enzymes, such as superoxide dismutases, catalases, and peroxidases, are the best characterized. Recently, evidence has been accumulating that some of the terminal oxidases in bacterial respiratory chains may also play a protective role against ROS. The present review covers this role of terminal oxidases in light of recent findings.
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Affiliation(s)
- Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia;
- Correspondence: (V.B.B.); (E.F.)
| | - Sergey A. Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia;
| | - Martina R. Nastasi
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy;
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy;
- Correspondence: (V.B.B.); (E.F.)
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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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Yang T, Chakraborty S, Mandal J, Mei X, Joe B. Microbiota and Metabolites as Factors Influencing Blood Pressure Regulation. Compr Physiol 2021; 11:1731-1757. [PMID: 33792901 DOI: 10.1002/cphy.c200009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The study of microbes has rapidly expanded in recent years due to a surge in our understanding that humans host a plethora of commensal microbes, which reside in their bodies and depending upon their composition, contribute to either normal physiology or pathophysiology. This article provides a general foundation for learning about host-commensal microbial interactions as an emerging area of research. The article is divided into two sections. The first section is dedicated to introducing commensal microbiota and its known effects on the host. The second section is on metabolites, which are biochemicals that the host and the microbes use for bi-directional communication with each other. Together, the sections review what is known about how microbes interact with the host to impact cardiovascular physiology, especially blood pressure regulation. © 2021 American Physiological Society. Compr Physiol 11:1731-1757, 2021.
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Affiliation(s)
- Tao Yang
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Saroj Chakraborty
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Juthika Mandal
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Xue Mei
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Bina Joe
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
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Wu Z, Nguyen D, Lam TYC, Zhuang H, Shrestha S, Raskin L, Khanal SK, Lee PH. Synergistic association between cytochrome bd-encoded Proteiniphilum and reactive oxygen species (ROS)-scavenging methanogens in microaerobic-anaerobic digestion of lignocellulosic biomass. WATER RESEARCH 2021; 190:116721. [PMID: 33326896 DOI: 10.1016/j.watres.2020.116721] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Intermittent (every other day) microaerobic [picomolar oxygen by oxidation-reduction potential (ORP) set at +25 mV above anaerobic baseline] digestion of lignocellulosic biomass showed higher digestibility and better stability at a high organic loading rate (OLR) of 5 g volatile solids (VS)/L/d than that under strict anaerobic conditions. However, the microbial mechanisms supporting the delicate balance under microaeration remain underexplored. On the basis of our previous findings that microbial communities in replicate experiments were dominated by strains of the genus Proteiniphilum but contained diverse taxa of methanogenic archaea, here we recovered related genomes and reconstructed the putative metabolic pathways using a genome-centric metagenomic approach. The highly enriched Proteiniphilum strains were identified as efficient cellulolytic facultative bacterium, which directly degraded lignocellulose to carbon dioxide, formate, and acetate via aerobic respiration and anaerobic fermentation, alternatively. Moreover, high oxygen affinity cytochromes, bd-type terminal oxidases, in Proteiniphilum strains were found to be closely associated with such picomolar oxygen conditions, which has long been overlooked in anaerobic digestion. Furthermore, hydrogenotrophic methanogenesis was the prevalent pathway for methane production while Methanosarcina, Methanobrevibacter, and Methanocorpusculum were the dominant methanogens in the replicate experiments. Importantly, the two functional groups, namely cellulolytic facultative Proteiniphilum strains and methanogens, encoded various antioxidant enzymes. Energy-dependent reactive oxygen species (ROS) scavengers (superoxide reductase (SOR) and rubrerythrin (rbr) were ubiquitously present in different methanogenic taxa in response to replicate-specific ORP levels (-470, -450 and -475 mV). Collectively, cytochrome bd oxidase and ROS defenders may play roles in improving the digestibility and stability observed in intermittent microaerobic digestion.
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Affiliation(s)
- Zhuoying Wu
- Department of Civil and Environmental Engineering, Imperial College, London, The United Kingdom
| | - Duc Nguyen
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Theo Y C Lam
- Department of Civil and Environmental Engineering, Imperial College, London, The United Kingdom; Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR
| | - Huichuan Zhuang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR
| | - Shilva Shrestha
- Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor, MI 48109-2125, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, 1351 Beal Avenue, 107 EWRE Building, Ann Arbor, MI 48109-2125, USA
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA.
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, Imperial College, London, The United Kingdom.
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38
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Bajeli S, Baid N, Kaur M, Pawar GP, Chaudhari VD, Kumar A. Terminal Respiratory Oxidases: A Targetables Vulnerability of Mycobacterial Bioenergetics? Front Cell Infect Microbiol 2020; 10:589318. [PMID: 33330134 PMCID: PMC7719681 DOI: 10.3389/fcimb.2020.589318] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
Recently, ATP synthase inhibitor Bedaquiline was approved for the treatment of multi-drug resistant tuberculosis emphasizing the importance of oxidative phosphorylation for the survival of mycobacteria. ATP synthesis is primarily dependent on the generation of proton motive force through the electron transport chain in mycobacteria. The mycobacterial electron transport chain utilizes two terminal oxidases for the reduction of oxygen, namely the bc1-aa3 supercomplex and the cytochrome bd oxidase. The bc1-aa3 supercomplex is an energy-efficient terminal oxidase that pumps out four vectoral protons, besides consuming four scalar protons during the transfer of electrons from menaquinone to molecular oxygen. In the past few years, several inhibitors of bc1-aa3 supercomplex have been developed, out of which, Q203 belonging to the class of imidazopyridine, has moved to clinical trials. Recently, the crystal structure of the mycobacterial cytochrome bc1-aa3 supercomplex was solved, providing details of the route of transfer of electrons from menaquinone to molecular oxygen. Besides providing insights into the molecular functioning, crystal structure is aiding in the targeted drug development. On the other hand, the second respiratory terminal oxidase of the mycobacterial respiratory chain, cytochrome bd oxidase, does not pump out the vectoral protons and is energetically less efficient. However, it can detoxify the reactive oxygen species and facilitate mycobacterial survival during a multitude of stresses. Quinolone derivatives (CK-2-63) and quinone derivative (Aurachin D) inhibit cytochrome bd oxidase. Notably, ablation of both the two terminal oxidases simultaneously through genetic methods or pharmacological inhibition leads to the rapid death of the mycobacterial cells. Thus, terminal oxidases have emerged as important drug targets. In this review, we have described the current understanding of the functioning of these two oxidases, their physiological relevance to mycobacteria, and their inhibitors. Besides these, we also describe the alternative terminal complexes that are used by mycobacteria to maintain energized membrane during hypoxia and anaerobic conditions.
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Affiliation(s)
- Sapna Bajeli
- Molecular Mycobacteriology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India
| | - Navin Baid
- Molecular Mycobacteriology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India
| | - Manjot Kaur
- Division of Medicinal Chemistry, Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India
| | - Ganesh P Pawar
- Division of Medicinal Chemistry, Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India
| | - Vinod D Chaudhari
- Division of Medicinal Chemistry, Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India
| | - Ashwani Kumar
- Molecular Mycobacteriology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India
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39
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García-Bayona L, Coyne MJ, Hantman N, Montero-Llopis P, Von SS, Ito T, Malamy MH, Basler M, Barquera B, Comstock LE. Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts. Proc Natl Acad Sci U S A 2020; 117:24484-24493. [PMID: 32938803 PMCID: PMC7533675 DOI: 10.1073/pnas.2009556117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mechanistic studies of anaerobic gut bacteria have been hindered by the lack of a fluorescent protein system to track and visualize proteins and dynamic cellular processes in actively growing bacteria. Although underappreciated, many gut "anaerobes" are able to respire using oxygen as the terminal electron acceptor. The oxygen continually released from gut epithelial cells creates an oxygen gradient from the mucus layer to the anaerobic lumen [L. Albenberg et al., Gastroenterology 147, 1055-1063.e8 (2014)], with oxygen available to bacteria growing at the mucus layer. Here, we show that Bacteroides species are metabolically and energetically robust and do not mount stress responses in the presence of 0.10 to 0.14% oxygen, defined as nanaerobic conditions [A. D. Baughn, M. H. Malamy, Nature 427, 441-444 (2004)]. Taking advantage of this metabolic capability, we show that nanaerobic growth provides sufficient oxygen for the maturation of oxygen-requiring fluorescent proteins in Bacteroides species. Type strains of four different Bacteroides species show bright GFP fluorescence when grown nanaerobically versus anaerobically. We compared four different red fluorescent proteins and found that mKate2 yields the highest red fluorescence intensity in our assay. We show that GFP-tagged proteins can be localized in nanaerobically growing bacteria. In addition, we used time-lapse fluorescence microscopy to image dynamic type VI secretion system processes in metabolically active Bacteroides fragilis The ability to visualize fluorescently labeled Bacteroides and fluorescently linked proteins in actively growing nanaerobic gut symbionts ushers in an age of imaging analyses not previously possible in these bacteria.
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Affiliation(s)
- Leonor García-Bayona
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Michael J Coyne
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Noam Hantman
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | | | - Salena S Von
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Takeshi Ito
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Michael H Malamy
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
| | - Marek Basler
- Biozentrum, University of Basel, CH 4056 Basel, Switzerland
| | - Blanca Barquera
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Laurie E Comstock
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115;
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40
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Yekani M, Baghi HB, Naghili B, Vahed SZ, Sóki J, Memar MY. To resist and persist: Important factors in the pathogenesis of Bacteroides fragilis. Microb Pathog 2020; 149:104506. [PMID: 32950639 DOI: 10.1016/j.micpath.2020.104506] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/15/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023]
Abstract
Bacteroides fragilis is a most frequent anaerobic pathogen isolated from human infections, particularly found in the abdominal cavity. Different factors contribute to the pathogenesis and persistence of B. fragilis at infection sites. The knowledge of the virulence factors can provide applicable information for finding alternative options for the antibiotic therapy and treatment of B. fragilis caused infections. Herein, a comprehensive review of the important B. fragilis virulence factors was prepared. In addition to B. fragilis toxin (BFT) and its potential role in the diarrhea and cancer development, some other important virulence factors and characteristics of B. fragilis are described including capsular polysaccharides, iron acquisition, resistance to antimicrobial agents, and survival during the prolonged oxidative stress, quorum sensing, and secretion systems.
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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
| | - Behrooz Naghili
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - József Sóki
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Szeged, Hungary.
| | - 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; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.
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41
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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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42
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Khazaei T, Williams RL, Bogatyrev SR, Doyle JC, Henry CS, Ismagilov RF. Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community. SCIENCE ADVANCES 2020; 6:eaba0353. [PMID: 32851161 PMCID: PMC7423363 DOI: 10.1126/sciadv.aba0353] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/26/2020] [Indexed: 05/20/2023]
Abstract
Major changes in the microbiome are associated with health and disease. Some microbiome states persist despite seemingly unfavorable conditions, such as the proliferation of aerobe-anaerobe communities in oxygen-exposed environments in wound infections or small intestinal bacterial overgrowth. Mechanisms underlying transitions into and persistence of these states remain unclear. Using two microbial taxa relevant to the human microbiome, we combine genome-scale mathematical modeling, bioreactor experiments, transcriptomics, and dynamical systems theory to show that multistability and hysteresis (MSH) is a mechanism describing the shift from an aerobe-dominated state to a resilient, paradoxically persistent aerobe-anaerobe state. We examine the impact of changing oxygen and nutrient regimes and identify changes in metabolism and gene expression that lead to MSH and associated multi-stable states. In such systems, conceptual causation-correlation connections break and MSH must be used for analysis. Using MSH to analyze microbiome dynamics will improve our conceptual understanding of stability of microbiome states and transitions between states.
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Affiliation(s)
- Tahmineh Khazaei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rory L. Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Said R. Bogatyrev
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - John C. Doyle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA
| | - Christopher S. Henry
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, USA
| | - Rustem F. Ismagilov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
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43
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Nobu MK, Narihiro T, Mei R, Kamagata Y, Lee PKH, Lee PH, McInerney MJ, Liu WT. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. MICROBIOME 2020; 8:111. [PMID: 32709258 PMCID: PMC7382037 DOI: 10.1186/s40168-020-00885-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/25/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H2 transfer between organotrophs and methanogens. However, many metabolic processes are thermodynamically sensitive to H2 accumulation and can be inhibited by H2 produced from co-occurring metabolisms. Strategies for driving thermodynamically competing metabolisms in methanogenic environments remain unexplored. RESULTS To uncover how anaerobes combat this H2 conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology-methanogenic bioreactors. Through analysis of 17 anaerobic digesters, we recovered 1343 high-quality metagenome-assembled genomes and corresponding gene expression profiles for uncultured lineages spanning 66 phyla and reconstructed their metabolic capacities. We discovered that diverse uncultured populations can drive H2-sensitive metabolisms through (i) metabolic coupling with concurrent H2-tolerant catabolism, (ii) forgoing H2 generation in favor of interspecies transfer of formate and electrons (cytochrome- and pili-mediated) to avoid thermodynamic conflict, and (iii) integration of low-concentration O2 metabolism as an ancillary thermodynamics-enhancing electron sink. Archaeal populations support these processes through unique methanogenic metabolisms-highly favorable H2 oxidation driven by methyl-reducing methanogenesis and tripartite uptake of formate, electrons, and acetate. CONCLUSION Integration of omics and eco-thermodynamics revealed overlooked behavior and interactions of uncultured organisms, including coupling favorable and unfavorable metabolisms, shifting from H2 to formate transfer, respiring low-concentration O2, performing direct interspecies electron transfer, and interacting with high H2-affinity methanogenesis. These findings shed light on how microorganisms overcome a critical obstacle in methanogenic carbon cycles we had hitherto disregarded and provide foundational insight into anaerobic microbial ecology. Video Abstract.
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Affiliation(s)
- Masaru K. Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Takashi Narihiro
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, HK Hong Kong
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, Imperial College, London, UK
| | - Michael J. McInerney
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 N. Mathews Ave, Urbana, IL 61801 USA
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44
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Gao Y, Liu Y, Ma F, Sun M, Mu G, Tuo Y. Global transcriptomic and proteomics analysis of Lactobacillus plantarum Y44 response to 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress. J Proteomics 2020; 226:103903. [PMID: 32682107 DOI: 10.1016/j.jprot.2020.103903] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/23/2020] [Accepted: 07/11/2020] [Indexed: 12/22/2022]
Abstract
Our previous study demonstrated that Lactobacillus plantarum Y44 exhibited antioxidant activity. However, the physiological characteristics of L. plantarum Y44 exposure to oxidative stress was not clear. In this research, the differentially expressed proteins and genes in L. plantarum Y44 under 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress at different concentrations were studied by using integrated transcriptomic and proteomic methods. Under 100 mM AAPH stress condition, 1139 differentially expressed genes (DEGs, 546 up-regulated and 593 down-regulated) and 329 differentially expressed proteins (DEPs, 127 up-regulated and 202 down-regulated) were observed. Under 200 mM AAPH stress condition, 1526 DEGs (751 up-regulated and 775 down-regulated) and 382 DEPs (139 up-regulated and 243 down-regulated) were observed. Overall, we found that L. plantarum Y44 fought against AAPH induced oxidative stress by up-regulating antioxidant enzymes and DNA repair proteins, such as ATP-dependent DNA helicase RuvA, adenine DNA glycosylase, single-strand DNA-binding protein SSB, DNA-binding ferritin-like protein DPS, thioredoxin reductase, protein-methionine-S-oxide reductase and glutathione peroxidase. Additionally, cell envelope composition of L. plantarum Y44 was highly remodeled by accelerating peptidoglycan and teichoic-acid (LTA) biosynthesis and modulating the fatty acids (FA) composition to achieve a higher ratio of unsaturated/saturated fatty acids (UFAs/SFAs) against AAPH stress. Moreover, metabolism processes including carbohydrate metabolism, amino acid biosynthesis, and nucleotide metabolism altered to respond to AAPH-induced damage. Altogether, our findings allow us to facilitate a better understanding of L. plantarum Y44 against oxidative stress. SIGNIFICANCE: This study represents an integrated proteomic and transcriptomic analysis of Lactobacillus plantarum Y44 response to 2,2-azobis(2-methylpropionamidine) dihydrochloride (AAPH) stress. Differentially expressed proteins and genes were identified between the proteome and transcriptome of L. plantarum Y44 under different AAPH stress. AAPH-induced response of L. plantarum Y44 appears to be primarily based on ROS scavenging, DNA repair, highly remodeled cell surface and specific metabolic processes. The knowledge about these proteomes and transcriptomes provides significant insights into the oxidative stress response of Lactobacillus plantarum.
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Affiliation(s)
- Yuan Gao
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China
| | - Yujun Liu
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China
| | - Fenglian Ma
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China
| | - Mengying Sun
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China
| | - Guangqing Mu
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China.
| | - Yanfeng Tuo
- School of food science and technology, Dalian Polytechnic University, Dalian 116034, China; Dalian probiotics function research key laboratory, Dalian Polytechnic University, Dalian 116034, China.
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45
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Suenaga M, Yokoyama Y, Fujii T, Yamada S, Yamaguchi J, Hayashi M, Asahara T, Nagino M, Kodera Y. Impact of Qualitative and Quantitative Biliary Contamination Status on the Incidence of Postoperative Infection Complications in Patients Undergoing Pancreatoduodenectomy. Ann Surg Oncol 2020; 28:560-569. [PMID: 32468346 DOI: 10.1245/s10434-020-08645-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Bacterial contamination status may differ under different biliary drainage conditions. The purpose of this study was to determine the impact of qualitative and quantitative biliary bacterial contamination on the incidence of infection complications in patients undergoing pancreatoduodenectomy. METHODS Patients undergoing pancreatoduodenectomy for periampullary diseases with different biliary drainage conditions, such as external drainage (ED), internal drainage (ID), and no drainage (ND), were included. Bile was collected intraoperatively, and biliary contamination status was qualified and quantified using bacterium-specific ribosomal RNA-targeted reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The impact of biliary contamination status on infection complications was analyzed. RESULTS A total of 152 patients were included (38 with ED, 40 with ID, and 74 with ND). The positive rate of microorganisms in bile was higher in the ID group (98%) compared with the ED group (82%, p = 0.021) and the ND group (65%, p < 0.001). The number of microorganisms detected in bile samples was higher in the ID group compared with the ED group (median 489,788 vs. 5375 bacteria/mL of bile, p < 0.001). With multivariate analysis, soft pancreas, intraoperative bleeding (> 600 mL), and biliary contamination by Atopobium cluster were identified as independent risk factors for infection complications. Biliary contamination by Atopobium cluster was significantly higher in the ID group compared with the other groups. CONCLUSIONS Biliary bacterial contamination is more frequently induced by ID than either ED or ND. In addition to the previously known risk factors, biliary contamination with Atopobium cluster may be one of the risk factors of infection complications following pancreatoduodenectomy.
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Affiliation(s)
- Masaya Suenaga
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukihiro Yokoyama
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tsutomu Fujii
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan. .,Department of Surgery and Science, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan.
| | - Suguru Yamada
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Junpei Yamaguchi
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masamichi Hayashi
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Masato Nagino
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
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Khademian M, Imlay JA. Do reactive oxygen species or does oxygen itself confer obligate anaerobiosis? The case of Bacteroides thetaiotaomicron. Mol Microbiol 2020; 114:333-347. [PMID: 32301184 DOI: 10.1111/mmi.14516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023]
Abstract
Bacteroides thetaiotaomicron was examined to determine whether its obligate anaerobiosis is imposed by endogenous reactive oxygen species or by molecular oxygen itself. Previous analyses established that aerated B. thetaiotaomicron loses some enzyme activities due to a high rate of endogenous superoxide formation. However, the present study establishes that another key step in central metabolism is poisoned by molecular oxygen itself. Pyruvate dissimilation was shown to depend upon two enzymes, pyruvate:formate lyase (PFL) and pyruvate:ferredoxin oxidoreductase (PFOR), that lose activity upon aeration. PFL is a glycyl-radical enzyme whose vulnerability to oxygen is already understood. The rate of PFOR damage was unaffected by the level of superoxide or peroxide, showing that molecular oxygen itself is the culprit. The cell cannot repair PFOR, which amplifies the impact of damage. The rates of PFOR and fumarase inactivation are similar, suggesting that superoxide dismutase is calibrated so the oxygen- and superoxide-sensitive enzymes are equally sensitive to aeration. The physiological purpose of PFL and PFOR is to degrade pyruvate without disrupting the redox balance, and they do so using catalytic mechanisms that are intrinsically vulnerable to oxygen. In this way, the anaerobic excellence and oxygen sensitivity of B. thetaiotaomicron are two sides of the same coin.
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Affiliation(s)
- Maryam Khademian
- Department of Microbiology, University of Illinois, Urbana, IL, USA
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, IL, USA
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Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice. Nat Microbiol 2020; 5:746-756. [PMID: 32152589 PMCID: PMC7426998 DOI: 10.1038/s41564-020-0683-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 02/03/2020] [Indexed: 12/11/2022]
Abstract
A complex microbiota inhabits various microenvironments of the gut, with some symbiotic bacteria having evolved traits to invade the epithelial mucus layer and reside deep within intestinal tissue of animals. Whether these distinct bacterial communities across gut biogeographies exhibit divergent behaviors remains largely unknown. Global transcriptomic analysis to investigate microbial physiology in specific mucosal niches has been hampered technically by overabundance of host RNA. Herein, we employed hybrid selection RNA sequencing (hsRNA-Seq) to enable detailed spatial transcriptomic profiling of a prominent human commensal as it colonizes the colonic lumen, mucus or epithelial tissue of mice. Compared to conventional RNA-Seq, hsRNA-Seq increased reads mapping to the Bacteroides fragilis genome by 48- and 154-fold in mucus and tissue, respectively, allowing for high fidelity comparisons across biogeographic sites. Near the epithelium, B. fragilis up-regulated numerous genes involved in protein synthesis, indicating that bacteria inhabiting the mucosal niche are metabolically active. Further, a specific sulfatase (BF3086) and glycosyl hydrolase (BF3134) were highly induced in mucus and tissue compared to bacteria in the lumen. In-frame deletion of these genes impaired in vitro growth on mucus as a carbon source, as well as mucosal colonization of mice. Mutants in either B. fragilis gene displayed a fitness defect in competing for colonization against bacterial challenge, revealing the importance of site-specific gene expression for robust host-microbial symbiosis. As a versatile tool, hsRNA-Seq can be deployed to explore the in vivo spatial physiology of numerous bacterial pathogens or commensals.
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48
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Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics. Syst Appl Microbiol 2020; 43:126065. [DOI: 10.1016/j.syapm.2020.126065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/20/2019] [Accepted: 01/16/2020] [Indexed: 11/19/2022]
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49
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Ito T, Gallegos R, Matano LM, Butler NL, Hantman N, Kaili M, Coyne MJ, Comstock LE, Malamy MH, Barquera B. Genetic and Biochemical Analysis of Anaerobic Respiration in Bacteroides fragilis and Its Importance In Vivo. mBio 2020; 11:e03238-19. [PMID: 32019804 PMCID: PMC7002350 DOI: 10.1128/mbio.03238-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 12/14/2022] Open
Abstract
In bacteria, the respiratory pathways that drive molecular transport and ATP synthesis include a variety of enzyme complexes that utilize different electron donors and acceptors. This property allows them to vary the efficiency of energy conservation and to generate different types of electrochemical gradients (H+ or Na+). We know little about the respiratory pathways in Bacteroides species, which are abundant in the human gut, and whether they have a simple or a branched pathway. Here, we combined genetics, enzyme activity measurements, and mammalian gut colonization assays to better understand the first committed step in respiration, the transfer of electrons from NADH to quinone. We found that a model gut Bacteroides species, Bacteroides fragilis, has all three types of putative NADH dehydrogenases that typically transfer electrons from the highly reducing molecule NADH to quinone. Analyses of NADH oxidation and quinone reduction in wild-type and deletion mutants showed that two of these enzymes, Na+-pumping NADH:quinone oxidoreductase (NQR) and NADH dehydrogenase II (NDH2), have NADH dehydrogenase activity, whereas H+-pumping NADH:ubiquinone oxidoreductase (NUO) does not. Under anaerobic conditions, NQR contributes more than 65% of the NADH:quinone oxidoreductase activity. When grown in rich medium, none of the single deletion mutants had a significant growth defect; however, the double Δnqr Δndh2 mutant, which lacked almost all NADH:quinone oxidoreductase activity, had a significantly increased doubling time. Despite unaltered in vitro growth, the single nqr deletion mutant was unable to competitively colonize the gnotobiotic mouse gut, confirming the importance of NQR to respiration in B. fragilis and the overall importance of respiration to this abundant gut symbiont.IMPORTANCEBacteroides species are abundant in the human intestine and provide numerous beneficial properties to their hosts. The ability of Bacteroides species to convert host and dietary glycans and polysaccharides to energy is paramount to their success in the human gut. We know a great deal about the molecules that these bacteria extract from the human gut but much less about how they convert those molecules into energy. Here, we show that B. fragilis has a complex respiratory pathway with two different enzymes that transfer electrons from NADH to quinone and a third enzyme complex that may use an electron donor other than NADH. Although fermentation has generally been believed to be the main mechanism of energy generation in Bacteroides, we found that a mutant lacking one of the NADH:quinone oxidoreductases was unable to compete with the wild type in the mammalian gut, revealing the importance of respiration to these abundant gut symbionts.
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Affiliation(s)
- Takeshi Ito
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Rene Gallegos
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Leigh M Matano
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicole L Butler
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Noam Hantman
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Matthew Kaili
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Michael J Coyne
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Laurie E Comstock
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael H Malamy
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Blanca Barquera
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
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50
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Pedraz L, Blanco‐Cabra N, Torrents E. Gradual adaptation of facultative anaerobic pathogens to microaerobic and anaerobic conditions. FASEB J 2019; 34:2912-2928. [DOI: 10.1096/fj.201902861r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Lucas Pedraz
- "Bacterial Infections: Antimicrobial Therapies” group Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Núria Blanco‐Cabra
- "Bacterial Infections: Antimicrobial Therapies” group Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Eduard Torrents
- "Bacterial Infections: Antimicrobial Therapies” group Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Barcelona Spain
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