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Pfister CA, Light SH, Bohannan B, Schmidt T, Martiny A, Hynson NA, Devkota S, David L, Whiteson K. Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes. mSystems 2022; 7:e0137421. [PMID: 35014872 PMCID: PMC8751383 DOI: 10.1128/msystems.01374-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 12/26/2022] Open
Abstract
Whether a microbe is free-living or associated with a host from across the tree of life, its existence depends on a limited number of elements and electron donors and acceptors. Yet divergent approaches have been used by investigators from different fields. The "environment first" research tradition emphasizes thermodynamics and biogeochemical principles, including the quantification of redox environments and elemental stoichiometry to identify transformations and thus an underlying microbe. The increasingly common "microbe first" research approach benefits from culturing and/or DNA sequencing methods to first identify a microbe and encoded metabolic functions. Here, the microbe itself serves as an indicator for environmental conditions and transformations. We illustrate the application of both approaches to the study of microbiomes and emphasize how both can reveal the selection of microbial metabolisms across diverse environments, anticipate alterations to microbiomes in host health, and understand the implications of a changing climate for microbial function.
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Affiliation(s)
- Catherine A. Pfister
- Department of Ecology & Evolution and The Microbiome Center, University of Chicago, Chicago, Illinois, USA
| | - Samuel H. Light
- Department of Microbiology & Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Brendan Bohannan
- Environmental Studies and Biology, University of Oregon, Eugene, Oregon, USA
| | - Thomas Schmidt
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam Martiny
- Earth System Science & Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - Nicole A. Hynson
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Suzanne Devkota
- Microbiome Research, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lawrence David
- Molecular Genetics & Microbiology, Duke University, Durham, North Carolina, USA
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
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Buret AG, Allain T, Motta JP, Wallace JL. Effects of Hydrogen Sulfide on the Microbiome: From Toxicity to Therapy. Antioxid Redox Signal 2022; 36:211-219. [PMID: 33691464 PMCID: PMC8861923 DOI: 10.1089/ars.2021.0004] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/13/2022]
Abstract
Significance: Hydrogen sulfide (H2S), an important regulator of physiology and health, helps resolve inflammation and promotes tissue repair in the gastrointestinal tract. Recent Advances: Gut microbiota live as a multispecies biofilm in close interaction with the upper mucus layer lining the epithelium. The relative abundance, spatial organization, and function of these microorganisms affect a broad range of health outcomes. This article provides a state-of-the-art review of our understanding of the cross talk between H2S, the gut microbiota, and health. H2S can have toxic or therapeutic effects, depending on its concentration and source. When produced at excessive concentrations by local microbiota, H2S may cause mucus disruption and inflammation and contribute to development of cancer. In contrast, low levels of endogenous or exogenous H2S directly stabilize mucus layers, prevent fragmentation and adherence of the microbiota biofilm to the epithelium, inhibit the release of invasive pathobionts, and help resolve inflammation and tissue injury. Although scarce, research findings suggest that dietary H2S obtained from plants or ingestion of the H2S precursor, L-cysteine, may also modulate the abundance and function of microbiota. Critical Issues: A critical issue is the lack of understanding of the metagenomic, transcriptomic, and proteomic alterations that characterize the interactions between H2S and gut microbiota to shape health outcomes. Future Directions: The ambivalent roles of H2S in the gut offer a fertile ground for research on such critical issues. The findings will improve our understanding of how H2S modulates the microbiota to affect body function and will help identify novel therapeutic strategies. Antioxid. Redox Signal. 36, 211-219.
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Affiliation(s)
- Andre G. Buret
- Host–Parasite Interactions Program, Inflammation Research Network, Biological Sciences, University of Calgary, Calgary, Canada
- Antibe Therapeutics, Inc., Toronto, Canada
| | - Thibault Allain
- Host–Parasite Interactions Program, Inflammation Research Network, Biological Sciences, University of Calgary, Calgary, Canada
| | - Jean-Paul Motta
- Institute of Digestive Health Research, IRSD, INSERM U1220, Toulouse, France
| | - John L. Wallace
- Host–Parasite Interactions Program, Inflammation Research Network, Biological Sciences, University of Calgary, Calgary, Canada
- Antibe Therapeutics, Inc., Toronto, Canada
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53
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Hu H, Shao W, Liu Q, Liu N, Wang Q, Xu J, Zhang X, Weng Z, Lu Q, Jiao L, Chen C, Sun H, Jiang Z, Zhang X, Gu A. Gut microbiota promotes cholesterol gallstone formation by modulating bile acid composition and biliary cholesterol secretion. Nat Commun 2022; 13:252. [PMID: 35017486 PMCID: PMC8752841 DOI: 10.1038/s41467-021-27758-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 12/03/2021] [Indexed: 12/11/2022] Open
Abstract
Cholesterol gallstone disease is a worldwide common disease. Cholesterol supersaturation in gallbladder bile is the prerequisite for its pathogenesis, while the mechanism is not completely understood. In this study, we find enrichment of gut microbiota (especially Desulfovibrionales) in patients with gallstone disease. Fecal transplantation of gut microbiota from gallstone patients to gallstone-resistant strain of mice can induce gallstone formation. Carrying Desulfovibrionales is associated with enhanced cecal secondary bile acids production and increase of bile acid hydrophobicity facilitating intestinal cholesterol absorption. Meanwhile, the metabolic product of Desulfovibrionales, H2S increase and is shown to induce hepatic FXR and inhibit CYP7A1 expression. Mice carrying Desulfovibrionales present induction of hepatic expression of cholesterol transporters Abcg5/g8 to promote biliary secretion of cholesterol as well. Our study demonstrates the role of gut microbiota, Desulfovibrionales, as an environmental regulator contributing to gallstone formation through its influence on bile acid and cholesterol metabolism. Metabolic conditions associated with alterations of the gut microbiome, such as obesity and diabetes, predispose to gallstone disease. Here the authors demonstrate that the gut microbiome, in particular the genus Desulfovibrionale, contribute to gallstone formation in mice.
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Affiliation(s)
- Hai Hu
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, Tongji University School of Medicine, Shanghai, China
| | - Wentao Shao
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, Tongji University School of Medicine, Shanghai, China.,State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu, China.,School of Instrument Science and Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Qian Liu
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu, China.,State Key Laboratory of Reproductive Medicine (Suzhou Center), Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Ning Liu
- School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Qihan Wang
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, Tongji University School of Medicine, Shanghai, China
| | - Jin Xu
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xin Zhang
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhenkun Weng
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.,Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Qifan Lu
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, Tongji University School of Medicine, Shanghai, China
| | - Long Jiao
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, Tongji University School of Medicine, Shanghai, China
| | - Chaobo Chen
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, Tongji University School of Medicine, Shanghai, China
| | - Haidong Sun
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, Tongji University School of Medicine, Shanghai, China
| | - Zhaoyan Jiang
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, Tongji University School of Medicine, Shanghai, China.
| | - Xiaoping Zhang
- Department of Institution of Interventional and Vascular Surgery, Tongji University School of Medicine, Shanghai, China.
| | - Aihua Gu
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China. .,Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu, China.
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54
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Lu Y, Peng B, Lin Y, Lin Q, Xia X, Zhong S, Luo L, Huang R. Spirulina polysaccharide induces the metabolic shifts and gut microbiota change of lung cancer in mice. Curr Res Food Sci 2022; 5:1313-1319. [PMID: 36065196 PMCID: PMC9440268 DOI: 10.1016/j.crfs.2022.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 02/07/2023] Open
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Deng WH, Lu Y, Liao RZ. Revealing the Mechanism of Isethionate Sulfite-Lyase by QM/MM Calculations. J Chem Inf Model 2021; 61:5871-5882. [PMID: 34806370 DOI: 10.1021/acs.jcim.1c00978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Isethionate sulfite-lyase (IseG) is a recently characterized glycyl radical enzyme (GRE) that catalyzes radical-mediated C-S bond cleavage of isethionate to produce acetaldehyde and sulfite. Herein, we use quantum mechanical/molecular mechanical (QM/MM) calculations to investigate the detailed catalytic reaction mechanism of IseG. Our calculations indicate that a previously proposed direct 1,2-elimination mechanism is disfavored. Instead, we suggest a new 1,2-migration mechanism for this enzymatic reaction: a key stepwise 1,2-SO3- radical migration occurs after the catalytically active cysteinyl radical grabs a hydrogen atom from isethionate, followed by hydrogen atom transfer from cysteine to a 1-hydroxylethane-1-sulfonate radical intermediate. Finally, the elimination of sulfite from 1-hydroxylethane-1-sulfonate to result in the final product is likely to occur outside the enzyme. Glu468 in the active site is found to help orient the substrate rather than grabbing a proton from the hydroxyl group of the substrate. Our findings help reveal the mechanisms of radical-mediated C-S bond cleavage of organosulfonates catalyzed by GREs and expand the understanding of radical-based enzymatic catalysis.
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Affiliation(s)
- Wen-Hao Deng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - You Lu
- Scientific Computing Department, UKRI STFC Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
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56
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Burrichter AG, Dörr S, Bergmann P, Haiß S, Keller A, Fournier C, Franchini P, Isono E, Schleheck D. Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia. BMC Microbiol 2021; 21:340. [PMID: 34903181 PMCID: PMC8667426 DOI: 10.1186/s12866-021-02386-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/08/2021] [Indexed: 11/15/2022] Open
Abstract
Background Bilophila wadsworthia, a strictly anaerobic, sulfite-reducing bacterium and common member of the human gut microbiota, has been associated with diseases such as appendicitis and colitis. It is specialized on organosulfonate respiration for energy conservation, i.e., utilization of dietary and host-derived organosulfonates, such as taurine (2-aminoethansulfonate), as sulfite donors for sulfite respiration, producing hydrogen sulfide (H2S), an important intestinal metabolite that may have beneficial as well as detrimental effects on the colonic environment. Its taurine desulfonation pathway involves the glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslAB), which cleaves isethionate (2-hydroxyethanesulfonate) into acetaldehyde and sulfite. Results We demonstrate that taurine metabolism in B. wadsworthia 3.1.6 involves bacterial microcompartments (BMCs). First, we confirmed taurine-inducible production of BMCs by proteomic, transcriptomic and ultra-thin sectioning and electron-microscopical analyses. Then, we isolated BMCs from taurine-grown cells by density-gradient ultracentrifugation and analyzed their composition by proteomics as well as by enzyme assays, which suggested that the GRE IslAB and acetaldehyde dehydrogenase are located inside of the BMCs. Finally, we are discussing the recycling of cofactors in the IslAB-BMCs and a potential shuttling of electrons across the BMC shell by a potential iron-sulfur (FeS) cluster-containing shell protein identified by sequence analysis. Conclusions We characterized a novel subclass of BMCs and broadened the spectrum of reactions known to take place enclosed in BMCs, which is of biotechnological interest. We also provided more details on the energy metabolism of the opportunistic pathobiont B. wadsworthia and on microbial H2S production in the human gut. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02386-w.
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Affiliation(s)
- Anna G Burrichter
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany. .,Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany.
| | - Stefanie Dörr
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paavo Bergmann
- Electron Microscopy Centre, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Sebastian Haiß
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Anja Keller
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | | | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Erika Isono
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
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57
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Naudhani M, Thakur K, Ni ZJ, Zhang JG, Wei ZJ. Formononetin reshapes the gut microbiota, prevents progression of obesity and improves host metabolism. Food Funct 2021; 12:12303-12324. [PMID: 34821251 DOI: 10.1039/d1fo02942h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Formononetin (FMNT) is an isoflavone that has been studied for its anti-hyperglycemic and anti-diabetic effects. However, the effect of FMNT on gut dysbiosis and metabolic complications associated with western-style diet consumption has not been reported yet. This study aimed to investigate how FMNT can reshape the gut microbiota at a specific dosage and ameliorate the symptoms of obesity-related metabolic disorders in both genders. Results indicate that FMNT at 60 mg per kg bodyweight dosage can effectively control body weight, hyperglycemia, and insulin resistance, leptin levels and improve HDL to LDL ratio. FMNT treatment suppressed Porphyromonadaceae (Uncultured Alistipes) and augmented maximum genera from families Lachnospiraceae and Clostridiacea, but at species level, formononetin increased Clostridium aldenense, Clostridiaceae unclassified, Eubacterium plexicaum; acetate and butyrate-producing bacteria. Moreover, formononetin regulated the expression of specific liver miRNA involved in obesity and down-regulated mRNA expression levels of pro-inflammatory cytokines IL-6, IL-22 and TNF-α. Additionally, FMNT maintained intestinal membrane integrity by regulating the expression of Muc-2 and occludin. Our findings indicate that FMNT could be a potential prebiotic that can effectively regulate the gut microbiota, improve host metabolism and systemic inflammation, and prevent deleterious effects of a western-style diet by elevating acetate lactate and lactate butyrate producers.
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Affiliation(s)
- Mahrukh Naudhani
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China. .,Department of Microbiology, Balochistan University of Information Technology Engineering and management sciences, Quetta 87300, Pakistan
| | - Kiran Thakur
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China. .,Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China.
| | - Zhi-Jing Ni
- Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China.
| | - Jian-Guo Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China. .,Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China.
| | - Zhao-Jun Wei
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China. .,Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China.
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58
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Dai Z, Wu Z, Zhu W, Wu G. Amino Acids in Microbial Metabolism and Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1354:127-143. [PMID: 34807440 DOI: 10.1007/978-3-030-85686-1_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Amino acids (AAs) not only serve as building blocks for protein synthesis in microorganisms but also play important roles in their metabolism, survival, inter-species crosstalk, and virulence. Different AAs have their distinct functions in microbes of the digestive tract and this in turn has important impacts on host nutrition and physiology. Deconjugation and re-conjugation of glycine- or taurine- conjugated bile acids in the process of their enterohepatic recycling is a good example of the bacterial adaptation to harsh gut niches, inter-kingdom cross-talk with AA metabolism, and cell signaling as the critical control point. It is also a big challenge for scientists to modulate the homeostasis of the pools of AAs and their metabolites in the digestive tract with the aim to improve nutrition and regulate AA metabolism related to anti-virulence reactions. Diversity of the metabolic pathways of AAs and their multi-functions in modulating bacterial growth and survival in the digestive tract should be taken into consideration in recommending nutrient requirements for animals. Thus, the concept of functional amino acids can guide not only microbiological studies but also nutritional and physiological investigations. Cutting edge discoveries in this research area will help to better understand the mechanisms responsible for host-microbe interactions and develop new strategies for improving the nutrition, health, and well-being of both animals and humans.
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Affiliation(s)
- Zhaolai Dai
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Zhenlong Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Weiyun Zhu
- National Center for International Research On Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Guoyao Wu
- Department of Animal Science, Texas A&M University, College Station, 77843, TX, USA
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Rescuing activity of oxygen-damaged pyruvate formate-lyase by a spare part protein. J Biol Chem 2021; 297:101423. [PMID: 34801558 PMCID: PMC8683613 DOI: 10.1016/j.jbc.2021.101423] [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] [Received: 07/25/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) that converts pyruvate and coenzyme A into acetyl-CoA and formate in a reaction that is crucial to the primary metabolism of many anaerobic bacteria. The glycyl radical cofactor, which is posttranslationally installed by a radical S-adenosyl-L-methionine (SAM) activase, is a simple and effective catalyst, but is also susceptible to oxidative damage in microaerobic environments. Such damage occurs at the glycyl radical cofactor, resulting in cleaved PFL (cPFL). Bacteria have evolved a spare part protein termed YfiD that can be used to repair cPFL. Previously, we obtained a structure of YfiD by NMR spectroscopy and found that the N-terminus of YfiD was disordered and that the C-terminus of YfiD duplicates the structure of the C-terminus of PFL, including a β-strand that is not removed by the oxygen-induced cleavage. We also showed that cPFL is highly susceptible to proteolysis, suggesting that YfiD rescue of cPFL competes with protein degradation. Here, we probe the mechanism by which YfiD can bind and restore activity to cPFL through enzymatic and spectroscopic studies. Our data show that the disordered N-terminal region of YfiD is important for YfiD glycyl radical installation but not for catalysis, and that the duplicate β-strand does not need to be cleaved from cPFL for YfiD to bind. In fact, truncation of this PFL region prevents YfiD rescue. Collectively our data suggest the molecular mechanisms by which YfiD activation is precluded both when PFL is not damaged and when it is highly damaged.
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Hong Y, Sheng L, Zhong J, Tao X, Zhu W, Ma J, Yan J, Zhao A, Zheng X, Wu G, Li B, Han B, Ding K, Zheng N, Jia W, Li H. Desulfovibrio vulgaris, a potent acetic acid-producing bacterium, attenuates nonalcoholic fatty liver disease in mice. Gut Microbes 2021; 13:1-20. [PMID: 34125646 PMCID: PMC8205104 DOI: 10.1080/19490976.2021.1930874] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The emerging evidence supports the use of prebiotics like herb-derived polysaccharides for treating nonalcoholic fatty liver disease (NAFLD) by modulating gut microbiome. The present study was initiated on the microbiota-dependent anti-NAFLD effect of Astragalus polysaccharides (APS) extracted from Astragalus mongholicus Bunge in high-fat diet (HFD)-fed mice. However, the exact mechanisms underlying the beneficial effects of APS on NAFLD formation remain poorly understood.Co-housing experiment was used to assess the microbiota dependent anti-NAFLD effect of APS. Then, targeted metabolomics and metagenomics were adopted for determining short-chain fatty acids (SCFAs) and bacteria that were specifically enriched by APS. Further in vitro experiment was carried out to test the capacity of SCFAs-producing of identified bacterium. Finally, the anti-NAFLD efficacy of identified bacterium was tested in HFD-fed mice.Our results first demonstrated the anti-NAFLD effect of APS in HFD-fed mice and the contribution of gut microbiota. Moreover, our results indicated that SCFAs, predominantly acetic acid were elevated in APS-supplemented mice and ex vivo experiment. Metagenomics revealed that D. vulgaris from Desulfovibrio genus was not only enriched by APS, but also a potent generator of acetic acid, which showed significant anti-NAFLD effects in HFD-fed mice. In addition, D. vulgaris modulated the hepatic gene expression pattern of lipids metabolism, particularly suppressed hepatic fatty acid synthase (FASN) and CD36 protein expression.Our results demonstrate that APS enriched D. vulgaris is effective on attenuating hepatic steatosis possibly through producing acetic acid, and modulation on hepatic lipids metabolism in mice. Further studies are warranted to explore the long-term impacts of D. vulgaris on host metabolism and the underlying mechanism.
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Affiliation(s)
- Ying Hong
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China,CONTACT Ningning Zheng Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lili Sheng
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jing Zhong
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Huzhou, China
| | - Xin Tao
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Weize Zhu
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Junli Ma
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Juan Yan
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Aihua Zhao
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xiaojiao Zheng
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Gaosong Wu
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bingbing Li
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering; Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Liu’an, China
| | - Kan Ding
- Glycochemistry and Glycobiology Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ningning Zheng
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Jia
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China,School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China,Wei Jia School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Houkai Li
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Houkai Li Functional Metabolomic and Gut Microbiome Laboratory, Institute for Interdisciplinary Medicine Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
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McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
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Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
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62
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Buckel W. Energy Conservation in Fermentations of Anaerobic Bacteria. Front Microbiol 2021; 12:703525. [PMID: 34589068 PMCID: PMC8473912 DOI: 10.3389/fmicb.2021.703525] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/30/2021] [Indexed: 02/04/2023] Open
Abstract
Anaerobic bacteria ferment carbohydrates and amino acids to obtain energy for growth. Due to the absence of oxygen and other inorganic electron acceptors, the substrate of a fermentation has to serve as electron donor as well as acceptor, which results in low free energies as compared to that of aerobic oxidations. Until about 10 years ago, anaerobes were thought to exclusively use substrate level phosphorylation (SLP), by which only part of the available energy could be conserved. Therefore, anaerobes were regarded as unproductive and inefficient energy conservers. The discovery of electrochemical Na+ gradients generated by biotin-dependent decarboxylations or by reduction of NAD+ with ferredoxin changed this view. Reduced ferredoxin is provided by oxidative decarboxylation of 2-oxoacids and the recently discovered flavin based electron bifurcation (FBEB). In this review, the two different fermentation pathways of glutamate to ammonia, CO2, acetate, butyrate and H2 via 3-methylaspartate or via 2-hydroxyglutarate by members of the Firmicutes are discussed as prototypical examples in which all processes characteristic for fermentations occur. Though the fermentations proceed on two entirely different pathways, the maximum theoretical amount of ATP is conserved in each pathway. The occurrence of the 3-methylaspartate pathway in clostridia from soil and the 2-hydroxyglutarate pathway in the human microbiome of the large intestine is traced back to the oxygen-sensitivity of the radical enzymes. The coenzyme B12-dependent glutamate mutase in the 3-methylaspartate pathway tolerates oxygen, whereas 2-hydroxyglutaryl-CoA dehydratase is extremely oxygen-sensitive and can only survive in the gut, where the combustion of butyrate produced by the microbiome consumes the oxygen and provides a strict anaerobic environment. Examples of coenzyme B12-dependent eliminases are given, which in the gut are replaced by simpler extremely oxygen sensitive glycyl radical enzymes.
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Affiliation(s)
- Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität Marburg, Marburg, Germany
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Mao L, Zhang Y, Tian J, Sang M, Zhang G, Zhou Y, Wang P. Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China. Front Microbiol 2021; 12:728479. [PMID: 34650532 PMCID: PMC8506127 DOI: 10.3389/fmicb.2021.728479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/27/2021] [Indexed: 01/14/2023] Open
Abstract
Gastrointestinal dysfunction plays an important role in the occurrence and development of Parkinson's disease (PD). This study investigates the composition of the gut microbiome using shotgun metagenomic sequencing in PD patients in central China. Fecal samples from 39 PD patients (PD group) and the corresponding 39 healthy spouses of the patients (SP) were collected for shotgun metagenomics sequencing. Results showed a significantly altered microbial composition in the PD patients. Bilophila wadsworthia enrichment was found in the gut microbiome of PD patients, which has not been reported in previous studies. The random forest (RF) model, which identifies differences in microbiomes, reliably discriminated patients with PD from controls; the area under the receiver operating characteristic curve was 0.803. Further analysis of the microbiome and clinical symptoms showed that Klebsiella and Parasutterella were positively correlated with the duration and severity of PD, whereas hydrogen-generating Prevotella was negatively correlated with disease severity. The Cluster of Orthologous Groups of protein database, the KEGG Orthology database, and the carbohydrate-active enzymes of gene-category analysis showed that branched-chain amino acid-related proteins were significantly increased, and GH43 was significantly reduced in the PD group. Functional analysis of the metagenome confirmed differences in microbiome metabolism in the PD group related to short-chain fatty acid precursor metabolism.
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Affiliation(s)
- Liangwei Mao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Biological Resources, School of Life Sciences, Hubei University, Wuhan, China
| | - Yu Zhang
- Hubei Clinical Research Center of Parkinson’s Disease, Xiangyang No. 1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Jing Tian
- Hubei Clinical Research Center of Parkinson’s Disease, Xiangyang No. 1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Ming Sang
- Hubei Clinical Research Center of Parkinson’s Disease, Xiangyang No. 1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Biological Resources, School of Life Sciences, Hubei University, Wuhan, China
| | - Yuling Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Biological Resources, School of Life Sciences, Hubei University, Wuhan, China
| | - Puqing Wang
- Hubei Clinical Research Center of Parkinson’s Disease, Xiangyang No. 1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
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64
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Wei J, Zhang C, Zhang Y, Zhang W, Doherty M, Yang T, Zhai G, Obotiba AD, Lyu H, Zeng C, Lei G. Association Between Gut Microbiota and Symptomatic Hand Osteoarthritis: Data From the Xiangya Osteoarthritis Study. Arthritis Rheumatol 2021; 73:1656-1662. [PMID: 33760399 PMCID: PMC8457181 DOI: 10.1002/art.41729] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/09/2021] [Indexed: 12/14/2022]
Abstract
Objective Systemic inflammatory factors have been implicated in symptomatic hand osteoarthritis (OA). Gut microbiome dysbiosis promotes systemic inflammation. The aim of this study was to examine the association between the gut microbiome and the presence of symptomatic hand OA in a population‐based study. Methods Study participants were subjects of the Xiangya Osteoarthritis Study, a community‐based observational study conducted in the Hunan Province of China. Symptomatic hand OA was defined as the presence of both symptoms and radiographic OA in the same hand. The gut microbiome was analyzed using 16S ribosomal RNA gene sequencing in stool samples. We examined the relation of α‐diversity, β‐diversity, relative abundance of taxa, and potential bacterial functional pathways to symptomatic hand OA. Results A total of 1,388 participants (mean age 61.3 years, 57.4% women) were included in the study, of whom 72 had symptomatic hand OA (prevalence of symptomatic hand OA 5.2%). Beta‐diversity of the gut microbiome, but not α‐diversity, was significantly associated with the presence of symptomatic hand OA (P = 0.003). Higher relative abundance of the genera Bilophila and Desulfovibrio as well as lower relative abundance of the genus Roseburia was associated with symptomatic hand OA. Most functional pathways (i.e., those annotated in the KEGG Ortholog hierarchy) that were observed to be altered in participants with symptomatic hand OA belonged to the amino acid, carbohydrate, and lipid metabolic pathways. Conclusion This large, population‐based study provides the first evidence that alterations in the composition of the gut microbiome were observed among study participants who had symptomatic hand OA, and a low relative abundance of Roseburia but high relative abundance of Bilophila and Desulfovibrio at the genus level were associated with prevalent symptomatic hand OA. These findings may help investigators understand the role of the microbiome in the development of symptomatic hand OA and could contribute to potential translational opportunities.
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Affiliation(s)
- Jie Wei
- Health Management Center, Xiangya Hospital, Central South University, Changsha, China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqing Zhang
- Division of Rheumatology, Allergy, and Immunology, Department of Medicine, Massachusetts General Hospital, and the Mongan Institute, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Weiya Zhang
- Academic Rheumatology, Clinical Sciences Building, University of Nottingham, City Hospital, Nottingham, and Arthritis Research UK Pain Centre, Nottingham, UK
| | - Michael Doherty
- Academic Rheumatology, Clinical Sciences Building, University of Nottingham, City Hospital, Nottingham, and Arthritis Research UK Pain Centre, Nottingham, UK
| | - Tuo Yang
- Health Management Center, Xiangya Hospital, Central South University, Changsha, China, Academic Rheumatology, Clinical Sciences Building, University of Nottingham, City Hospital, Nottingham, UK, and Arthritis Research UK Pain Centre, Nottingham, UK
| | - Guangju Zhai
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Abasiama D Obotiba
- Academic Rheumatology, Clinical Sciences Building, University of Nottingham, City Hospital, Nottingham, and Arthritis Research UK Pain Centre, Nottingham, UK
| | - Houchen Lyu
- Department of Orthopedics, General Hospital of Chinese PLA, Beijing, and Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Chao Zeng
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, and Hunan Key Laboratory of Joint Degeneration and Injury, Changsha, China
| | - Guanghua Lei
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, and Hunan Key Laboratory of Joint Degeneration and Injury, Changsha, China
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The Role of H 2S in the Gastrointestinal Tract and Microbiota. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1315:67-98. [PMID: 34302689 DOI: 10.1007/978-981-16-0991-6_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The pathways and mechanisms of the production of H2S in the gastrointestinal tract are briefly described, including endogenous H2S produced by the organism and H2S from microorganisms in the gastrointestinal tract. In addition, the physiological regulatory functions of H2S on gastrointestinal motility, sensation, secretion and absorption, endocrine system, proliferation and differentiation of stem cells, and the possible mechanisms involved are introduced. In view of the complexity of biosynthesis, physiological roles, and the mechanism of H2S, this chapter focuses on the interactions and dynamic balance among H2S, gastrointestinal microorganisms, and the host. Finally, we focus on some clinical gastrointestinal diseases, such as inflammatory bowel disease, colorectal cancer, functional gastrointestinal disease, which might occur or develop when the above balance is broken. Pharmacological regulation of H2S or the intestinal microorganisms related to H2S might provide new therapeutic approaches for some gastrointestinal diseases.
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66
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Heinken A, Basile A, Hertel J, Thinnes C, Thiele I. Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine. Annu Rev Microbiol 2021; 75:199-222. [PMID: 34314593 DOI: 10.1146/annurev-micro-060221-012134] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human microbiome plays an important role in human health and disease. Meta-omics analyses provide indispensable data for linking changes in microbiome composition and function to disease etiology. Yet, the lack of a mechanistic understanding of, e.g., microbiome-metabolome links hampers the translation of these findings into effective, novel therapeutics. Here, we propose metabolic modeling of microbial communities through constraint-based reconstruction and analysis (COBRA) as a complementary approach to meta-omics analyses. First, we highlight the importance of microbial metabolism in cardiometabolic diseases, inflammatory bowel disease, colorectal cancer, Alzheimer disease, and Parkinson disease. Next, we demonstrate that microbial community modeling can stratify patients and controls, mechanistically link microbes with fecal metabolites altered in disease, and identify host pathways affected by the microbiome. Finally, we outline our vision for COBRA modeling combined with meta-omics analyses and multivariate statistical analyses to inform and guide clinical trials, yield testable hypotheses, and ultimately propose novel dietary and therapeutic interventions. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Almut Heinken
- School of Medicine, National University of Ireland, Galway, H91 TK33, Ireland;
| | - Arianna Basile
- Department of Biology, University of Padua, Padua 35121, Italy
| | - Johannes Hertel
- School of Medicine, National University of Ireland, Galway, H91 TK33, Ireland; .,Department of Psychiatry and Psychotherapy, University of Greifswald, 17489 Greifswald, Germany
| | - Cyrille Thinnes
- School of Medicine, National University of Ireland, Galway, H91 TK33, Ireland;
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, H91 TK33, Ireland; .,Division of Microbiology, National University of Ireland, Galway, H91 TK33, Ireland.,APC Microbiome Ireland, University College Cork, Cork, T12 K8AF, Ireland
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67
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Discovery and mining of enzymes from the human gut microbiome. Trends Biotechnol 2021; 40:240-254. [PMID: 34304905 DOI: 10.1016/j.tibtech.2021.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022]
Abstract
Advances in technological and bioinformatics approaches have led to the generation of a plethora of human gut metagenomic datasets. Metabolomics has also provided substantial data regarding the small metabolites produced and modified by the microbiota. Comparatively, the microbial enzymes mediating the transformation of metabolites have not been intensively investigated. Here, we discuss the recent efforts and technologies used for discovering and mining enzymes from the human gut microbiota. The wealth of knowledge on metabolites, reactions, genome sequences, and structures of proteins, may drive the development of strategies for enzyme mining. Ongoing efforts to annotate gut microbiota enzymes will explain catalytic mechanisms that may guide the clinical applications of the gut microbiome for diagnostic and therapeutic purposes.
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68
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Tomasova L, Grman M, Ondrias K, Ufnal M. The impact of gut microbiota metabolites on cellular bioenergetics and cardiometabolic health. Nutr Metab (Lond) 2021; 18:72. [PMID: 34266472 PMCID: PMC8281717 DOI: 10.1186/s12986-021-00598-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/02/2021] [Indexed: 12/20/2022] Open
Abstract
Recent research demonstrates a reciprocal relationship between gut microbiota-derived metabolites and the host in controlling the energy homeostasis in mammals. On the one hand, to thrive, gut bacteria exploit nutrients digested by the host. On the other hand, the host utilizes numerous products of gut bacteria metabolism as a substrate for ATP production in the colon. Finally, bacterial metabolites seep from the gut into the bloodstream and interfere with the host’s cellular bioenergetics machinery. Notably, there is an association between alterations in microbiota composition and the development of metabolic diseases and their cardiovascular complications. Some metabolites, like short-chain fatty acids and trimethylamine, are considered markers of cardiometabolic health. Others, like hydrogen sulfide and nitrite, demonstrate antihypertensive properties. Scientific databases were searched for pre-clinical and clinical studies to summarize current knowledge on the role of gut microbiota metabolites in the regulation of mammalian bioenergetics and discuss their potential involvement in the development of cardiometabolic disorders. Overall, the available data demonstrates that gut bacteria products affect physiological and pathological processes controlling energy and vascular homeostasis. Thus, the modulation of microbiota-derived metabolites may represent a new approach for treating obesity, hypertension and type 2 diabetes.
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Affiliation(s)
- Lenka Tomasova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovak Republic.
| | - Marian Grman
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Karol Ondrias
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Marcin Ufnal
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, 02-091, Warsaw, Poland.
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Abstract
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The genomic era has dramatically changed how we discover and investigate
microbial biochemistry. In particular, the exponential expansion in
the number of sequenced microbial genomes provides investigators with
a vast wealth of sequence data to exploit for the discovery of biochemical
functions and mechanisms, as well as novel enzymes and metabolites.
In contrast to early biochemical work, which was largely characterized
by “forward” approaches that proceed from biomass to
enzyme to gene, the availability of genome sequences enables the discovery
of new microbial metabolic activities, enzymes, and metabolites by
“reverse” approaches that originate with genetic information
or by approaches that incorporate features of both forward and reverse
methodologies. In the genomic era, the canonical organization of microbial
genomes into gene clusters presents a singular opportunity for the
utilization of genomic data. Specifically, genomic context (information
gleaned from the genes surrounding a gene of interest in the chromosome)
is a powerful tool for chemical discovery in microbial systems because
of the functional and/or physiological relationship that usually exists
between genes found within a gene cluster. This means that the investigator
can use this inferred link to generate hypotheses about the functions
of individual genes in the cluster or even the function of the entire
cluster itself. Here, we discuss how analysis of genomic context in
combination with a mechanistic understanding of enzymes can facilitate
numerous facets of microbial biochemical research including the identification
of biosynthetic gene clusters, the discovery of important and novel
enzymes, the elucidation of natural product structures, and the identification
of new metabolic pathways. We highlight work from our laboratory using
genomic context to discover and study biosynthetic pathways that produce
natural products, including the cylindrocyclophanes, nitrogen–nitrogen
bond-containing metabolites, and the gut microbial genotoxin colibactin.
Although use of genomic context is most commonly associated with studies
of natural product biosynthesis, we also show that it can be applied
to the study of primary metabolism. We illustrate this with examples
from our work studying the members of the glycyl radical enzyme superfamily
involved in choline and 4-hydroxyproline degradation in the human
gut. Looking forward, we envision increased opportunities to use such
information, with the combination of biochemical knowledge and computational
tools poised to fuel a new revolution in our ability to connect genes
and their biochemical functions. In particular, we note a need for
methods that computationally formalize the functional association
between genes when such associations are not obvious from manual gene
annotations. Such tools will drastically augment the feasibility and
scope of gene cluster analysis and accelerate the discovery of new
microbial enzymes, metabolites, and metabolic processes.
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Affiliation(s)
- Duncan J. Kountz
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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70
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Kirst H, Kerfeld CA. Clues to the function of bacterial microcompartments from ancillary genes. Biochem Soc Trans 2021; 49:1085-1098. [PMID: 34196367 PMCID: PMC8517908 DOI: 10.1042/bst20200632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 01/14/2023]
Abstract
Bacterial microcompartments (BMCs) are prokaryotic organelles. Their bounding membrane is a selectively permeable protein shell, encapsulating enzymes of specialized metabolic pathways. While the function of a BMC is dictated by the encapsulated enzymes which vary with the type of the BMC, the shell is formed by conserved protein building blocks. The genes necessary to form a BMC are typically organized in a locus; they encode the shell proteins, encapsulated enzymes as well as ancillary proteins that integrate the BMC function into the cell's metabolism. Among these are transcriptional regulators which usually found at the beginning or end of a locus, and transmembrane proteins that presumably function to conduct the BMC substrate into the cell. Here, we describe the types of transcriptional regulators and permeases found in association with BMC loci, using a recently collected data set of more than 7000 BMC loci distributed over 45 bacterial phyla, including newly discovered BMC loci. We summarize the known BMC regulation mechanisms, and highlight how much remains to be uncovered. We also show how analysis of these ancillary proteins can inform hypotheses about BMC function; by examining the ligand-binding domain of the regulator and the transporter, we propose that nucleotides are the likely substrate for an enigmatic uncharacterized BMC of unknown function.
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Affiliation(s)
- Henning Kirst
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, U.S.A
| | - Cheryl A Kerfeld
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, U.S.A
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, U.S.A
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, U.S.A
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71
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Walker A, Schmitt-Kopplin P. The role of fecal sulfur metabolome in inflammatory bowel diseases. Int J Med Microbiol 2021; 311:151513. [PMID: 34147944 DOI: 10.1016/j.ijmm.2021.151513] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 04/22/2021] [Accepted: 05/17/2021] [Indexed: 12/17/2022] Open
Abstract
Sulfur metabolism and sulfur-containing metabolites play an important role in the human digestive system, and sulfur compounds and pathways are associated with inflammatory bowel diseases (IBD). In fact, cysteine metabolism results in the production of taurine and sulfate, and gut microbes catabolize them into hydrogen sulfide, a signaling molecule with various biological functions. Besides metabolites originating from sulfur metabolism, several other sulfur-containing metabolites of different classes were detected in human feces, consisting of non-volatile and volatile compounds. Sulfated steroids and bile acids such as taurine-conjugated bile acids are the major classes along with sulfur amino acids and sulfur-containing peptides. Indeed, sulfur-containing metabolites were described in stool samples from healthy subjects, patients suffering from colorectal cancer or IBD. In metabolomics-driven studies, around 50 known sulfur-containing metabolites were linked to IBD. Taurine, taurocholic acid, taurochenodeoxycholic acid, methionine, methanethiol and hydrogen sulfide were regularly reported in IBD studies, and most of them were elevated in stool samples from IBD patients. We summarized from this review that there is strong interplay between perturbed gut microbiota in IBD, and the consistently higher abundance of sulfur-containing metabolites, which potentially represent substrates for sulfidogenic bacteria such as Bilophila or Escherichia and promote their growth. These bacteria might shift their metabolism towards the degradation of taurine and cysteine and therefore to a higher hydrogen sulfide production.
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Affiliation(s)
- Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany; ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany; Chair of Analytical Food Chemistry, Technical University of Munich, Freising, Germany
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72
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Fang Q, Liu N, Zheng B, Guo F, Zeng X, Huang X, Ouyang D. Roles of Gut Microbial Metabolites in Diabetic Kidney Disease. Front Endocrinol (Lausanne) 2021; 12:636175. [PMID: 34093430 PMCID: PMC8173181 DOI: 10.3389/fendo.2021.636175] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Diabetes is a highly prevalent metabolic disease that has emerged as a global challenge due to its increasing prevalence and lack of sustainable treatment. Diabetic kidney disease (DKD), which is one of the most frequent and severe microvascular complications of diabetes, is difficult to treat with contemporary glucose-lowering medications. The gut microbiota plays an important role in human health and disease, and its metabolites have both beneficial and harmful effects on vital physiological processes. In this review, we summarize the current findings regarding the role of gut microbial metabolites in the development and progression of DKD, which will help us better understand the possible mechanisms of DKD and explore potential therapeutic approaches for DKD.
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Affiliation(s)
- Qing Fang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| | - Na Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| | - Binjie Zheng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| | - Fei Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| | - Xiangchang Zeng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| | - Xinyi Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
| | - Dongsheng Ouyang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd., Changsha, China
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73
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Abstract
Sulfonates include diverse natural products and anthropogenic chemicals and are widespread in the environment. Many bacteria can degrade sulfonates and obtain sulfur, carbon, and energy for growth, playing important roles in the biogeochemical sulfur cycle. Cleavage of the inert sulfonate C-S bond involves a variety of enzymes, cofactors, and oxygen-dependent and oxygen-independent catalytic mechanisms. Sulfonate degradation by strictly anaerobic bacteria was recently found to involve C-S bond cleavage through O2-sensitive free radical chemistry, catalyzed by glycyl radical enzymes (GREs). The associated discoveries of new enzymes and metabolic pathways for sulfonate metabolism in diverse anaerobic bacteria have enriched our understanding of sulfonate chemistry in the anaerobic biosphere. An anaerobic environment of particular interest is the human gut microbiome, where sulfonate degradation by sulfate- and sulfite-reducing bacteria (SSRB) produces H2S, a process linked to certain chronic diseases and conditions.
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Affiliation(s)
- Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology; and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China;
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74
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Hanson BT, Dimitri Kits K, Löffler J, Burrichter AG, Fiedler A, Denger K, Frommeyer B, Herbold CW, Rattei T, Karcher N, Segata N, Schleheck D, Loy A. Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut. ISME JOURNAL 2021; 15:2779-2791. [PMID: 33790426 PMCID: PMC8397734 DOI: 10.1038/s41396-021-00968-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/01/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
Responses of the microbiota to diet are highly personalized but mechanistically not well understood because many metabolic capabilities and interactions of human gut microorganisms are unknown. Here we show that sulfoquinovose (SQ), a sulfonated monosaccharide omnipresent in green vegetables, is a selective yet relevant substrate for few but ubiquitous bacteria in the human gut. In human feces and in defined co-culture, Eubacterium rectale and Bilophila wadsworthia used recently identified pathways to cooperatively catabolize SQ with 2,3-dihydroxypropane-1-sulfonate as a transient intermediate to hydrogen sulfide (H2S), a key intestinal metabolite with disparate effects on host health. SQ-degradation capability is encoded in almost half of E. rectale genomes but otherwise sparsely distributed among microbial species in the human intestine. However, re-analysis of fecal metatranscriptome datasets of four human cohorts showed that SQ degradation (mostly from E. rectale and Faecalibacterium prausnitzii) and H2S production (mostly from B. wadsworthia) pathways were expressed abundantly across various health states, demonstrating that these microbial functions are core attributes of the human gut. The discovery of green-diet-derived SQ as an exclusive microbial nutrient and an additional source of H2S in the human gut highlights the role of individual dietary compounds and organosulfur metabolism on microbial activity and has implications for precision editing of the gut microbiota by dietary and prebiotic interventions.
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Affiliation(s)
- Buck T Hanson
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,FFoQSI GmbH, Austrian Competence Centre for Feed and Food Quality Safety & Innovation, Tulln, Austria
| | - K Dimitri Kits
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Jessica Löffler
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anna G Burrichter
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | | | - Karin Denger
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Benjamin Frommeyer
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Craig W Herbold
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Nicola Segata
- CIBIO Department, University of Trento, Trento, Italy
| | - David Schleheck
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria. .,Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
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75
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Dawson CD, Irwin SM, Backman LRF, Le C, Wang JX, Vennelakanti V, Yang Z, Kulik HJ, Drennan CL, Balskus EP. Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase. Cell Chem Biol 2021; 28:1333-1346.e7. [PMID: 33773110 PMCID: PMC8473560 DOI: 10.1016/j.chembiol.2021.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 02/04/2021] [Accepted: 03/03/2021] [Indexed: 01/07/2023]
Abstract
Desulfonation of isethionate by the bacterial glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslA) generates sulfite, a substrate for respiration that in turn produces the disease-associated metabolite hydrogen sulfide. Here, we present a 2.7 Å resolution X-ray structure of wild-type IslA from Bilophila wadsworthia with isethionate bound. In comparison with other GREs, alternate positioning of the active site β strands allows for distinct residue positions to contribute to substrate binding. These structural differences, combined with sequence variations, create a highly tailored active site for the binding of the negatively charged isethionate substrate. Through the kinetic analysis of 14 IslA variants and computational analyses, we probe the mechanism by which radical chemistry is used for C-S bond cleavage. This work further elucidates the structural basis of chemistry within the GRE superfamily and will inform structure-based inhibitor design of IsIA and thus of microbial hydrogen sulfide production.
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Affiliation(s)
- Christopher D Dawson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephania M Irwin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Lindsey R F Backman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chip Le
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Jennifer X Wang
- Harvard Center for Mass Spectrometry, Faculty of Arts and Sciences Division of Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Vyshnavi Vennelakanti
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Catherine L Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02139, USA.
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76
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Effect of Duyun Compound Green Tea on Gut Microbiota Diversity in High-Fat-Diet-Induced Mice Revealed by Illumina High-Throughput Sequencing. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:8832554. [PMID: 33628318 PMCID: PMC7886516 DOI: 10.1155/2021/8832554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 01/19/2021] [Accepted: 01/30/2021] [Indexed: 11/17/2022]
Abstract
Intake of a high-fat diet (HFD) is closely related to disorders of the intestinal microbiota, which plays a key role in the pathogenesis of obesity. Duyun compound green tea, an ancient Chinese drink, is widely consumed to reduce weight, although the mechanism is not clear. In this study, 50 mice were randomly divided into 5 groups: normal control group (CK), HFD model control group (NK), positive control group with medicine (YK), low-dose compound tea group (DL), and high-dose compound tea group (DH). After 4 weeks of intervention, the feces of mice were taken under sterile conditions and evaluated using Illumina high-throughput sequencing technology. The results showed that the diversity of intestinal microbiota was the highest in the CK group, the lowest in the NK group, and relatively increased in the compound tea treatment group. Second, there were differences in intestinal microbiota in each group, among which the beneficial bacteria in the intestinal tract of the CK group were higher than those in the other groups, while the beneficial bacteria in each compound tea treatment group were more abundant than those in the NK group, in which harmful bacteria in the intestinal tract were found to be the highest. These results suggest that compounds in tea may be able to attenuate imbalances of intestinal microbiota induced by poor diet, acting as a therapeutic agent in obesity or other diseases associated with gut dysbiosis.
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77
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Stacy A, Andrade-Oliveira V, McCulloch JA, Hild B, Oh JH, Perez-Chaparro PJ, Sim CK, Lim AI, Link VM, Enamorado M, Trinchieri G, Segre JA, Rehermann B, Belkaid Y. Infection trains the host for microbiota-enhanced resistance to pathogens. Cell 2021; 184:615-627.e17. [PMID: 33453153 PMCID: PMC8786454 DOI: 10.1016/j.cell.2020.12.011] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 11/19/2020] [Accepted: 12/08/2020] [Indexed: 01/13/2023]
Abstract
The microbiota shields the host against infections in a process known as colonization resistance. How infections themselves shape this fundamental process remains largely unknown. Here, we show that gut microbiota from previously infected hosts display enhanced resistance to infection. This long-term functional remodeling is associated with altered bile acid metabolism leading to the expansion of taxa that utilize the sulfonic acid taurine. Notably, supplying exogenous taurine alone is sufficient to induce this alteration in microbiota function and enhance resistance. Mechanistically, taurine potentiates the microbiota's production of sulfide, an inhibitor of cellular respiration, which is key to host invasion by numerous pathogens. As such, pharmaceutical sequestration of sulfide perturbs the microbiota's composition and promotes pathogen invasion. Together, this work reveals a process by which the host, triggered by infection, can deploy taurine as a nutrient to nourish and train the microbiota, promoting its resistance to subsequent infection.
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Affiliation(s)
- Apollo Stacy
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Vinicius Andrade-Oliveira
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John A McCulloch
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benedikt Hild
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ji Hoon Oh
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - P Juliana Perez-Chaparro
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Choon K Sim
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ai Ing Lim
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michel Enamorado
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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78
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Wolf PG, Devendran S, Doden HL, Ly LK, Moore T, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Kakiyama G, Kashyap P, McCracken VJ, Gaskins HR, Gillevet PM, Ridlon JM. Berberine alters gut microbial function through modulation of bile acids. BMC Microbiol 2021; 21:24. [PMID: 33430766 PMCID: PMC7798349 DOI: 10.1186/s12866-020-02020-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Berberine (BBR) is a plant-based nutraceutical that has been used for millennia to treat diarrheal infections and in contemporary medicine to improve patient lipid profiles. Reduction in lipids, particularly cholesterol, is achieved partly through up-regulation of bile acid synthesis and excretion into the gastrointestinal tract (GI). The efficacy of BBR is also thought to be dependent on structural and functional alterations of the gut microbiome. However, knowledge of the effects of BBR on gut microbiome communities is currently lacking. Distinguishing indirect effects of BBR on bacteria through altered bile acid profiles is particularly important in understanding how dietary nutraceuticals alter the microbiome. RESULTS Germfree mice were colonized with a defined minimal gut bacterial consortium capable of functional bile acid metabolism (Bacteroides vulgatus, Bacteroides uniformis, Parabacteroides distasonis, Bilophila wadsworthia, Clostridium hylemonae, Clostridium hiranonis, Blautia producta; B4PC2). Multi-omics (bile acid metabolomics, 16S rDNA sequencing, cecal metatranscriptomics) were performed in order to provide a simple in vivo model from which to identify network-based correlations between bile acids and bacterial transcripts in the presence and absence of dietary BBR. Significant alterations in network topology and connectivity in function were observed, despite similarity in gut microbial alpha diversity (P = 0.30) and beta-diversity (P = 0.123) between control and BBR treatment. BBR increased cecal bile acid concentrations, (P < 0.05), most notably deoxycholic acid (DCA) (P < 0.001). Overall, analysis of transcriptomes and correlation networks indicates both bacterial species-specific responses to BBR, as well as functional commonalities among species, such as up-regulation of Na+/H+ antiporter, cell wall synthesis/repair, carbohydrate metabolism and amino acid metabolism. Bile acid concentrations in the GI tract increased significantly during BBR treatment and developed extensive correlation networks with expressed genes in the B4PC2 community. CONCLUSIONS This work has important implications for interpreting the effects of BBR on structure and function of the complex gut microbiome, which may lead to targeted pharmaceutical interventions aimed to achieve the positive physiological effects previously observed with BBR supplementation.
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Affiliation(s)
- Patricia G Wolf
- Institute for Health Research and Policy, University of Illinois Chicago, Chicago, IL, USA
- Cancer Education and Career Development Program, University of Illinois, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Saravanan Devendran
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Structural and Computational Biology Research Unit, European Molecular Biology Laboratory, Heidelburg, Germany
| | - Heidi L Doden
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Lindsey K Ly
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Tyler Moore
- Center for Microbiome Analysis, George Mason University, Manassas, VA, USA
| | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, 152-0011, Japan
| | - Hiroshi Nittono
- Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, 152-0011, Japan
| | - Tsuyoshi Murai
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - Takao Kurosawa
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - George E Chlipala
- University of Illinois Chicago Research Resources Center, University of Illinois Chicago, Chicago, IL, USA
| | - Stefan J Green
- University of Illinois Chicago Research Resources Center, University of Illinois Chicago, Chicago, IL, USA
| | - Genta Kakiyama
- Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Purna Kashyap
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Vance J McCracken
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA
| | - H Rex Gaskins
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center of Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Patrick M Gillevet
- Structural and Computational Biology Research Unit, European Molecular Biology Laboratory, Heidelburg, Germany
| | - Jason M Ridlon
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center of Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.
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79
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Zallot R, Oberg N, Gerlt JA. Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools. Curr Opin Biotechnol 2021; 69:77-90. [PMID: 33418450 DOI: 10.1016/j.copbio.2020.12.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/08/2020] [Accepted: 12/08/2020] [Indexed: 12/11/2022]
Abstract
The continuing expansion of protein and genome sequence databases is an opportunity to identify novel enzymes with biotechnological applications. Whether applied to enzymology, chemical biology, systems biology, and microbiology, database mining must be 'user-friendly' so that experimentalists can devise focused strategies to discover the in vitro activities and in vivo functions of uncharacterized enzymes. We developed a suite of genomic enzymology tools (https://efi.igb.illinois.edu/) to (1) generate sequence similarity networks (SSNs) for exploration of sequence-function space in protein families (EFI-EST) and (2) provide genome context for members of protein families (EFI-GNT). Integrated analysis of this complementary information allows to generate testable hypotheses about new functions. After a brief overview of EFI-EST and EFI-GNT, we describe applications that illustrate their use.
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Affiliation(s)
- Remi Zallot
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States; Institute of Life Sciences, Swansea University Medical School, Swansea SA2 8PP, Wales, United Kingdom
| | - Nils Oberg
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - John A Gerlt
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States; Departments of Biochemistry and Chemistry, University of Illinois, Urbana, Illinois 61801, United States.
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80
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Choudhry H. The Microbiome and Its Implications in Cancer Immunotherapy. Molecules 2021; 26:E206. [PMID: 33401586 PMCID: PMC7795182 DOI: 10.3390/molecules26010206] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer is responsible for ~18 million deaths globally each year, representing a major cause of death. Several types of therapy strategies such as radiotherapy, chemotherapy and more recently immunotherapy, have been implemented in treating various types of cancer. Microbes have recently been found to be both directly and indirectly involved in cancer progression and regulation, and studies have provided novel and clear insights into the microbiome-mediated emergence of cancers. Scientists around the globe are striving hard to identify and characterize these microbes and the underlying mechanisms by which they promote or suppress various kinds of cancer. Microbes may influence immunotherapy by blocking various cell cycle checkpoints and the production of certain metabolites. Hence, there is an urgent need to better understand the role of these microbes in the promotion and suppression of cancer. The identification of microbes may help in the development of future diagnostic tools to cure cancers possibly associated with the microbiome. This review mainly focuses on various microbes and their association with different types of cancer, responses to immunotherapeutic modulation, physiological responses, and prebiotic and postbiotic effects.
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Affiliation(s)
- Hani Choudhry
- Department of Biochemistry, Faculty of Sciences, Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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81
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Zhao X, Zhang Z, Wang Y, Qian K, Qin H, Wan H, Wang S, Zhu Z, Yang S, Jiang N, Zhang Y, Bai Y, Deng H, Yu B. Association of Antibiotic Alterations in Gut Microbiota With Decreased Osseointegration of an Intramedullary Nail in Mice With and Without Osteomyelitis. Front Endocrinol (Lausanne) 2021; 12:774257. [PMID: 34956085 PMCID: PMC8696274 DOI: 10.3389/fendo.2021.774257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/18/2021] [Indexed: 12/18/2022] Open
Abstract
Treatment of osteomyelitis requires prolonged antibiotic therapy which significantly alters the gut microbiota. While the influences on bone mass and microstructure have been extensively studied, it is poorly understood what impact the changes in gut microbiota may have on the host response to osseointegration around an intramedullary nail implanted. Here, we explored the influence of gut microbiota on the bone osseointegration process around an implant under two conditions: implantation of an intramedullary nail in the bone marrow cavity and chronic osteomyelitis (CO) induced by Staphylococcus aureus infection. Body weight, hepatorenal functions, serum levels of proinflammatory cytokines were monitored. The composition of gut microbiota was assessed via 16S rRNA sequencing, and the bone condition was analyzed via micro-computed tomography, hematoxylin and eosin staining, Safranin O-fast green and Goldner's trichrome staining. Osteoblastogenesis and osteoclastogenesis were assessed by detecting tartrate-resistant acid phosphatase and osterix expression. We found that perturbation of gut microbiota (increase in Proteobacteria and decrease in Bacteroidetes) associated with delayed osseointegration and increased levels of proinflammatory cytokines in the serum (p<0.05), lower bone mass (p<0.05), deficient endochondral ossification and bone formation, reduced osteoblastogenesis (p<0.05) and enhanced osteoclastogenesis (p<0.001). Survival rates (p=0.002) and bacterial loads (p=0.0363) in bone differed significantly between the CO and antibiotic-treated CO mice, but cytokines levels, bone mineral density, and bone formation did not differ, likely because of the severely damaged bone structure. In summary, antibiotic treatment perturbed the gut microbiota and significantly interfered with the bone osseointegration around the nail by increasing proinflammatory cytokine levels in circulation, inhibiting osteoblastogenesis, enhancing osteoclastogenesis, and thus leading to higher pathogen colonization as well as higher mortality postinfection. This report of ours is the first to demonstrate antibiotic-induced alterations in the gut microbiota affect bone osseointegration, helping us understand the role of gut microbiota disorders in osteoblastogenesis and osteoclastogenesis following implant insertion with or without infection.
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Affiliation(s)
- Xingqi Zhao
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou, China & Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhaohui Zhang
- Department of Gastroenterology, Huizhou Municipal Central Hospital, Huizhou, China
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province & Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Gastroenterology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Yiran Wang
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou, China & Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Gastroenterology, Huizhou Municipal Central Hospital, Huizhou, China
| | - Kai Qian
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province & Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hanjun Qin
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou, China & Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haoyang Wan
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou, China & Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shihao Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province & Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhengwen Zhu
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province & Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Siqi Yang
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province & Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Nan Jiang
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou, China & Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yifang Zhang
- Editorial Office, Chinese Journal of Orthpopaedic Trauma, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yang Bai
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province & Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Yang Bai, ; Huimin Deng, ; Bin Yu,
| | - Huimin Deng
- Department of Gastroenterology, Huizhou Municipal Central Hospital, Huizhou, China
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province & Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Yang Bai, ; Huimin Deng, ; Bin Yu,
| | - Bin Yu
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou, China & Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Yang Bai, ; Huimin Deng, ; Bin Yu,
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82
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Li GH, Huang SJ, Li X, Liu XS, Du QL. Response of gut microbiota to serum metabolome changes in intrahepatic cholestasis of pregnant patients. World J Gastroenterol 2020; 26:7338-7351. [PMID: 33362388 PMCID: PMC7739160 DOI: 10.3748/wjg.v26.i46.7338] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/09/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Intrahepatic cholestasis in pregnancy (ICP) is the most common liver disease during pregnancy, and its exact etiology and course of progression are still poorly understood.
AIM To investigate the link between the gut microbiota and serum metabolome in ICP patients.
METHODS In this study, a total of 30 patients were recruited, including 15 patients with ICP (disease group) and 15 healthy pregnant patients (healthy group). The serum nontarget metabolomes from both groups were determined. Amplification of the 16S rRNA V3-V4 region was performed using fecal samples from the disease and healthy groups. By comparing the differences in the microbiota and metabolite compositions between the two groups, the relationship between the gut microbiota and serum metabolites was also investigated.
RESULTS The Kyoto Encyclopedia of Genes and Genomes analysis results showed that the primary bile acid biosynthesis, bile secretion and taurine and hypotaurine metabolism pathways were enriched in the ICP patients compared with the healthy controls. In addition, some pathways related to protein metabolism were also enriched in the ICP patients. The principal coordination analysis results showed that there was a distinct difference in the gut microbiota composition (beta diversity) between the ICP patients and healthy controls. At the phylum level, we observed that the relative abundance of Firmicutes was higher in the healthy group, while Bacteroidetes were enriched in the disease group. At the genus level, most of the bacteria depleted in ICP are able to produce short-chain fatty acids (e.g., Faecalibacterium, Blautia and Eubacterium hallii), while the bacteria enriched in ICP are associated with bile acid metabolism (e.g., Parabacteroides and Bilophila). Our results also showed that specific genera were associated with the serum metabolome.
CONCLUSION Our study showed that the serum metabolome was altered in ICP patients compared to healthy controls, with significant differences in the bile, taurine and hypotaurine metabolite pathways. Alterations in the metabolization of these pathways may lead to disturbances in the gut microbiota, which may further affect the course of progression of ICP.
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Affiliation(s)
- Guo-Hua Li
- Department of Reproductive Immunology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 200040, China
| | - Shi-Jia Huang
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 200040, China
| | - Xiang Li
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 200040, China
| | - Xiao-Song Liu
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 200040, China
| | - Qiao-Ling Du
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 200040, China
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83
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New structural insights into bacterial sulfoacetaldehyde and taurine metabolism. Biochem J 2020; 477:1367-1371. [PMID: 32322897 DOI: 10.1042/bcj20200079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/17/2023]
Abstract
In last year's issue 4 of Biochemical Journal, Zhou et al. (Biochem J. 476, 733-746) kinetically and structurally characterized the reductase IsfD from Klebsiella oxytoca that catalyzes the reversible reduction in sulfoacetaldehyde to the corresponding alcohol isethionate. This is a key step in detoxification of the carbonyl intermediate formed in bacterial nitrogen assimilation from the α-aminoalkanesulfonic acid taurine. In 2019, the work on sulfoacetaldehyde reductase IsfD was the exciting start to a quite remarkable series of articles dealing with structural elucidation of proteins involved in taurine metabolism as well as the discovery of novel degradation pathways in bacteria.
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84
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Ducarmon QR, Hoogerwerf MA, Janse JJ, Geelen AR, Koopman JPR, Zwittink RD, Goeman JJ, Kuijper EJ, Roestenberg M. Dynamics of the bacterial gut microbiota during controlled human infection with Necator americanus larvae. Gut Microbes 2020; 12:1-15. [PMID: 33222610 PMCID: PMC7714523 DOI: 10.1080/19490976.2020.1840764] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Hookworms are soil-transmitted helminths that use immune-evasive strategies to persist in the human duodenum where they are responsible for anemia and protein loss. Given their location and immune regulatory effects, hookworms likely impact the bacterial microbiota. However, microbiota studies struggle to deconvolute the effect of hookworms from confounders such as coinfections and malnutrition. We thus used an experimental human hookworm infection model to explore temporal changes in the gut microbiota before and during hookworm infection. Volunteers were dermally exposed to cumulative dosages of 50, 100 or 150 L3 Necator americanus larvae. Fecal samples were collected for microbiota profiling through 16S rRNA gene amplicon sequencing at weeks zero, four, eight, fourteen and twenty. During the acute infection phase (trial week zero to eight) no changes in bacterial diversity were detected. During the established infection phase (trial week eight to twenty), bacterial richness (Chao1, p = .0174) increased significantly over all volunteers. No relation was found between larval dosage and diversity, stability or relative abundance of individual bacterial taxa. GI symptoms were associated with an unstable microbiota during the first eight weeks and rapid recovery at week twenty. Barnesiella, amongst other taxa, was more abundant in volunteers with more GI symptoms throughout the study. In conclusion, this study showed that clinical GI symptoms following N. americanus infection are associated with temporary microbiota instability and relative abundance of specific bacterial taxa. These results suggest a possible role of hookworm-induced enteritis on microbiota stability.
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Affiliation(s)
- Q. R. Ducarmon
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands,Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands,CONTACT Meta Roestenberg Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands; Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - M. A. Hoogerwerf
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - J. J. Janse
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - A. R. Geelen
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands,Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - J. P. R. Koopman
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - R. D. Zwittink
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands,Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - J. J. Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| | - E. J. Kuijper
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands,Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - M. Roestenberg
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands,Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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85
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Abstract
Cardiovascular disease (CVD) has been linked to animal-based diets, which are a major source of trimethylamine (TMA), a precursor of the proatherogenic compound trimethylamine-N-oxide (TMAO). Human gut bacteria in the genus Bilophila have genomic signatures for genetic code expansion that could enable them to metabolize both TMA and its precursors without production of TMAO. We uncovered evidence that the Bilophila demethylation pathway is actively transcribed in gut microbiomes and that animal-based diets cause Bilophila to rapidly increase in abundance. CVD occurrence and Bilophila abundance in humans were significantly negatively correlated. These data lead us to propose that Bilophila, which is commonly regarded as a pathobiont, may play a role in mitigating cardiovascular disease. Human gut microbiomes have been shown to affect the development of a myriad of disease states, but mechanistic connections between diet, health, and microbiota have been challenging to establish. The hypothesis that Bilophila reduces cardiovascular disease by circumventing TMAO production offers a clearly defined mechanism with a potential human health impact, but investigations of Bilophila cell biology and ecology will be needed to fully evaluate these ideas.IMPORTANCE Links between trimethylamine-N-oxide (TMAO) and cardiovascular disease (CVD) have focused attention on mechanisms by which animal-based diets have negative health consequences. In a meta-analysis of data from foundational gut microbiome studies, we found evidence that specialized bacteria have and express a metabolic pathway that circumvents TMAO production and is often misannotated because it relies on genetic code expansion. This naturally occurring mechanism for TMAO attenuation is negatively correlated with CVD. Ultimately, these findings point to new avenues of research that could increase microbiome-informed understanding of human health and hint at potential biomedical applications in which specialized bacteria are used to curtail CVD development.
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86
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Haange SB, Groeger N, Froment J, Rausch T, Burkhardt W, Gonnermann S, Braune A, Blaut M, von Bergen M, Rolle-Kampczyk U. Multiplexed Quantitative Assessment of the Fate of Taurine and Sulfoquinovose in the Intestinal Microbiome. Metabolites 2020; 10:E430. [PMID: 33114761 PMCID: PMC7692227 DOI: 10.3390/metabo10110430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/13/2020] [Accepted: 10/23/2020] [Indexed: 12/25/2022] Open
Abstract
(1) Introduction: Sulfonates, which can be diet- or host-derived, are a class of compounds detected in the gut, are involved in host-microbiome interactions and have several health effects. Our aim was to develop a method to quantify five of the sulfonates in the intestine and apply it in a simplified human microbiome model. These were taurine, its metabolic precursor cysteate and one of its degradation products isethionate, as well as sulfoquinovose and one of its most relevant degradation products 2,3-dihydroxy-1-propanesulfonate. (2) Methods: An extraction and sample preparation method was developed, without the need for derivatization. To detect and quantify the extracted sulfonates, a multiplexed LC-MS/MS-MRM method was established. (3) Results: The accuracy and precision of the method were within GLP-accepted parameters (www.ema.europa.eu). To apply this method in a pilot study, we spiked either taurine or sulfoquinovose into an in vitro simplified human microbiota model with and without Bilophila wadsworthia, a known sulfonate utilizer. The results revealed that only the culture with B. wadsworthia was able to degrade taurine, with isethionate as an intermediate. After spiking the communities with sulfoquinovose, the results revealed that the simplified human microbiome model was able to degrade sulfoquinovose to 2,3-dihydroxypropane-1-sulfonate, which was probably catalyzed by Escherichia coli. In the community with B. wadsworthia, the 2,3-dihydroxypropane-1-sulfonate produced was further degraded by B. wadsworthia to sulfide. (4) Conclusions: We successfully developed a method for sulfonate quantification and applied it in a first pilot study.
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Affiliation(s)
- Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (N.G.); (J.F.); (M.v.B.)
| | - Nicole Groeger
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (N.G.); (J.F.); (M.v.B.)
| | - Jean Froment
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (N.G.); (J.F.); (M.v.B.)
| | - Theresa Rausch
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (T.R.); (W.B.); (S.G.); (A.B.); (M.B.)
| | - Wiebke Burkhardt
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (T.R.); (W.B.); (S.G.); (A.B.); (M.B.)
| | - Svenja Gonnermann
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (T.R.); (W.B.); (S.G.); (A.B.); (M.B.)
| | - Annett Braune
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (T.R.); (W.B.); (S.G.); (A.B.); (M.B.)
| | - Michael Blaut
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (T.R.); (W.B.); (S.G.); (A.B.); (M.B.)
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (N.G.); (J.F.); (M.v.B.)
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, 04103 Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (N.G.); (J.F.); (M.v.B.)
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87
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Zhou C, Zhou X, Wen Z, Liu L, Yang Z, Yang L, Li P, Guo X, Mei X. Compound Fu brick tea modifies the intestinal microbiome composition in high-fat diet-induced obesity mice. Food Sci Nutr 2020; 8:5508-5520. [PMID: 33133553 PMCID: PMC7590332 DOI: 10.1002/fsn3.1850] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/17/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022] Open
Abstract
Compound Fu Brick Tea (CFBT), which is from Duyun city in China, is a traditional Chinese dark tea, Fu Brick Tea, mixed with six herbal medicine. It is consumed by local people for reducing weight, but the mechanism is not clear. The disorder of intestinal microbiome caused by long-term high-fat diet (HFD) is one of the inducements of obesity and related metabolic syndrome. In this study, mice were fed with HFD to establish a high-fat model. Fifty mice were randomly divided into six groups: normal control (CK), HFD model control (NK), positive control with medicine (YK), CFBT groups with low, middle, and high dose (FL, FM, FH). The V3-V4 DNA region of fecal microbiome from mouse intestine was sequenced. The results showed that the diversity of intestinal microflora was highest in CK and lowest in NK. Compared with CK, the dominant bacterium Firmicutes was increased and Bacteroidetes decreased at phylum level in NK. Compared with NK, the abundance of microbiome in CFBT groups was significantly higher and the composition was changed: Muribaculaceae, Bacteroidaceae, and Prevotellaceae increased and Lachnospiraceae decreased in CFBT groups at family level, while at the genus level, Bacteroides increased and Lactobacillus decreased. These results conclude that CFBT can increase the abundance of intestinal microbiome in mice, promote the growth of beneficial bacteria and reduce the number of pathogenic bacteria, and restore the imbalance of intestinal microbiome caused by poor diet.
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Affiliation(s)
- Caibi Zhou
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
| | - Xiaolu Zhou
- College of Horticulture and Landscape ArchitectureHunan Agricultural UniversityChangshaChina
| | - Zhirui Wen
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
| | - Liming Liu
- College of Horticulture and Landscape ArchitectureHunan Agricultural UniversityChangshaChina
| | - Zaibo Yang
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
| | - Lu Yang
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
| | - Ping Li
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
| | - Xiying Guo
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
| | - Xin Mei
- College of Biological Science and AgricultureQiannan Normal University for NationalitiesDuyunChina
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88
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Frommeyer B, Fiedler AW, Oehler SR, Hanson BT, Loy A, Franchini P, Spiteller D, Schleheck D. Environmental and Intestinal Phylum Firmicutes Bacteria Metabolize the Plant Sugar Sulfoquinovose via a 6-Deoxy-6-sulfofructose Transaldolase Pathway. iScience 2020; 23:101510. [PMID: 32919372 PMCID: PMC7491151 DOI: 10.1016/j.isci.2020.101510] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/04/2020] [Accepted: 08/25/2020] [Indexed: 01/22/2023] Open
Abstract
Bacterial degradation of the sugar sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) produced by plants, algae, and cyanobacteria, is an important component of the biogeochemical carbon and sulfur cycles. Here, we reveal a third biochemical pathway for primary SQ degradation in an aerobic Bacillus aryabhattai strain. An isomerase converts SQ to 6-deoxy-6-sulfofructose (SF). A novel transaldolase enzyme cleaves the SF to 3-sulfolactaldehyde (SLA), while the non-sulfonated C3-(glycerone)-moiety is transferred to an acceptor molecule, glyceraldehyde phosphate (GAP), yielding fructose-6-phosphate (F6P). Intestinal anaerobic bacteria such as Enterococcus gilvus, Clostridium symbiosum, and Eubacterium rectale strains also express transaldolase pathway gene clusters during fermentative growth with SQ. The now three known biochemical strategies for SQ catabolism reflect adaptations to the aerobic or anaerobic lifestyle of the different bacteria. The occurrence of these pathways in intestinal (family) Enterobacteriaceae and (phylum) Firmicutes strains further highlights a potential importance of metabolism of green-diet SQ by gut microbial communities to, ultimately, hydrogen sulfide.
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Affiliation(s)
- Benjamin Frommeyer
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | | | | | - Buck T. Hanson
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Wien, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Wien, Austria
| | - Paolo Franchini
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Dieter Spiteller
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
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89
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Walsh BJC, Giedroc DP. H 2S and reactive sulfur signaling at the host-bacterial pathogen interface. J Biol Chem 2020; 295:13150-13168. [PMID: 32699012 PMCID: PMC7504917 DOI: 10.1074/jbc.rev120.011304] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial pathogens that cause invasive disease in the vertebrate host must adapt to host efforts to cripple their viability. Major host insults are reactive oxygen and reactive nitrogen species as well as cellular stress induced by antibiotics. Hydrogen sulfide (H2S) is emerging as an important player in cytoprotection against these stressors, which may well be attributed to downstream more oxidized sulfur species termed reactive sulfur species (RSS). In this review, we summarize recent work that suggests that H2S/RSS impacts bacterial survival in infected cells and animals. We discuss the mechanisms of biogenesis and clearance of RSS in the context of a bacterial H2S/RSS homeostasis model and the bacterial transcriptional regulatory proteins that act as "sensors" of cellular RSS that maintain H2S/RSS homeostasis. In addition, we cover fluorescence imaging- and MS-based approaches used to detect and quantify RSS in bacterial cells. Last, we discuss proteome persulfidation (S-sulfuration) as a potential mediator of H2S/RSS signaling in bacteria in the context of the writer-reader-eraser paradigm, and progress toward ascribing regulatory significance to this widespread post-translational modification.
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Affiliation(s)
- Brenna J C Walsh
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA.
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90
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Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate. Proc Natl Acad Sci U S A 2020; 117:15599-15608. [PMID: 32571930 DOI: 10.1073/pnas.2003434117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
2(S)-dihydroxypropanesulfonate (DHPS) is a microbial degradation product of 6-deoxy-6-sulfo-d-glucopyranose (sulfoquinovose), a component of plant sulfolipid with an estimated annual production of 1010 tons. DHPS is also at millimolar levels in highly abundant marine phytoplankton. Its degradation and sulfur recycling by microbes, thus, play important roles in the biogeochemical sulfur cycle. However, DHPS degradative pathways in the anaerobic biosphere are not well understood. Here, we report the discovery and characterization of two O2-sensitive glycyl radical enzymes that use distinct mechanisms for DHPS degradation. DHPS-sulfolyase (HpsG) in sulfate- and sulfite-reducing bacteria catalyzes C-S cleavage to release sulfite for use as a terminal electron acceptor in respiration, producing H2S. DHPS-dehydratase (HpfG), in fermenting bacteria, catalyzes C-O cleavage to generate 3-sulfopropionaldehyde, subsequently reduced by the NADH-dependent sulfopropionaldehyde reductase (HpfD). Both enzymes are present in bacteria from diverse environments including human gut, suggesting the contribution of enzymatic radical chemistry to sulfur flux in various anaerobic niches.
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91
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Jian C, Luukkonen P, Sädevirta S, Yki-Järvinen H, Salonen A. Impact of short-term overfeeding of saturated or unsaturated fat or sugars on the gut microbiota in relation to liver fat in obese and overweight adults. Clin Nutr 2020; 40:207-216. [PMID: 32536582 DOI: 10.1016/j.clnu.2020.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUNDS & AIMS Intestinal microbiota may be causally involved in the pathogenesis of non-alcoholic fatty liver disease (NAFLD). We aimed to study the effect of short-term overfeeding on human gut microbiota in relation to baseline and overfeeding-induced liver steatosis. We also asked whether the baseline microbiota composition is associated to the overfeeding-induced increase in liver fat. METHODS In a randomized trial, 38 overweight and obese subjects were assigned to consume an excess of 1000 kcal/day of diets rich in either saturated fat, unsaturated fat, or simple sugars for 3 weeks. Fasting blood samples and 1H-MR spectroscopy were used for extensive clinical phenotyping as previously reported (PMID: 29844096). Fecal samples were collected for the analysis of the gut microbiota using 16S rRNA amplicon sequencing, imputed metagenomics and qPCR. Microbiota results were correlated with dietary intakes and clinical measurements before and during overfeeding. RESULTS The overall community structure of the microbiota remained highly stable and personalized during overfeeding based on between-sample Bray-Curtis dissimilarity, but the relative abundances of individual taxa were altered in a diet-specific manner: overfeeding saturated fat increased Proteobacteria, while unsaturated fat increased butyrate producers. Sugar overfeeding increased Lactococcus and Escherichia coli. Imputed functions of the gut microbiota were not affected by overfeeding. Several taxa affected by overfeeding significantly correlated with the changes in host metabolic markers. The baseline levels of proteobacterial family Desulfovibrionaceae, and especially genus Bilophila, were significantly associated to overfeeding-induced liver fat increase independently of the diet arm. In general, limited overlap was observed between the overfeeding-induced microbiota changes and the liver fat-associated microbiota features at baseline. CONCLUSIONS Our work indicates that the human gut microbiota is resilient to short-term overfeeding on community level, but specific taxa are altered on diet composition-dependent manner. Generalizable microbiota signatures directly associated with liver steatosis could not be identified. Instead, the carriage of Bilophila was identified as a potential novel risk factor for diet-induced liver steatosis in humans. Clinical trial registry number: NCT02133144 listed on NIH website: ClinicalTrials.gov.
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Affiliation(s)
- Ching Jian
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Panu Luukkonen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland; Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Sanja Sädevirta
- Minerva Foundation Institute for Medical Research, Helsinki, Finland; Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Hannele Yki-Järvinen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland; Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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92
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Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HR. The ' in vivo lifestyle' of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice. Gut Microbes 2020; 11:381-404. [PMID: 31177942 PMCID: PMC7524365 DOI: 10.1080/19490976.2019.1618173] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The formation of secondary bile acids by gut microbes is a current topic of considerable biomedical interest. However, a detailed understanding of the biology of anaerobic bacteria in the genus Clostridium that are capable of generating secondary bile acids is lacking. We therefore sought to determine the transcriptional responses of two prominent secondary bile acid producing bacteria, Clostridium hylemonae and Clostridium hiranonis to bile salts (in vitro) and the cecal environment of gnotobiotic mice. The genomes of C. hylemonae DSM 15053 and C. hiranonis DSM 13275 were closed, and found to encode 3,647 genes (3,584 protein-coding) and 2,363 predicted genes (of which 2,239 are protein-coding), respectively, and 1,035 orthologs were shared between C. hylemonae and C. hiranonis. RNA-Seq analysis was performed in growth medium alone, and in the presence of cholic acid (CA) and deoxycholic acid (DCA). Growth with CA resulted in differential expression (>0.58 log2FC; FDR < 0.05) of 197 genes in C. hiranonis and 118 genes in C. hylemonae. The bile acid-inducible operons (bai) from each organism were highly upregulated in the presence of CA but not DCA. We then colonized germ-free mice with human gut bacterial isolates capable of metabolizing taurine-conjugated bile acids. This consortium included bile salt hydrolase-expressing Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Parabacteroides distasonis DSM 20701, as well as taurine-respiring Bilophila wadsworthia DSM 11045, and deoxycholic/lithocholic acid generating Clostridium hylemonae DSM 15053 and Clostridium hiranonis DSM 13275. Butyrate and iso-bile acid-forming Blautia producta ATCC 27340 was also included. The Bacteroidetes made up 84.71% of 16S rDNA cecal reads, B. wadsworthia, constituted 14.7%, and the clostridia made up <.75% of 16S rDNA cecal reads. Bile acid metabolomics of the cecum, serum, and liver indicate that the synthetic community were capable of functional bile salt deconjugation, oxidation/isomerization, and 7α-dehydroxylation of bile acids. Cecal metatranscriptome analysis revealed expression of genes involved in metabolism of taurine-conjugated bile acids. The in vivo transcriptomes of C. hylemonae and C. hiranonis suggest fermentation of simple sugars and utilization of amino acids glycine and proline as electron acceptors. Genes predicted to be involved in trimethylamine (TMA) formation were also expressed.
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Affiliation(s)
- Jason M. Ridlon
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA,CONTACT Jason M. Ridlon, Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology
| | - Saravanan Devendran
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - João Mp Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Heidi Doden
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Patricia G. Wolf
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gabriel V. Pereira
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lindsey Ly
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alyssa Volland
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, Japan
| | | | - Tsuyoshi Murai
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
| | - Takao Kurosawa
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
| | - George E. Chlipala
- UIC Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Stefan J. Green
- UIC Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Alvaro G. Hernandez
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J. Fields
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christy L. Wright
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Genta Kakiyama
- Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Isaac Cann
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Purna Kashyap
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA,Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Vance McCracken
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA,Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA
| | - H. Rex Gaskins
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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93
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Watson KM, Gaulke CA, Tsikitis VL. Understanding the microbiome: a primer on the role of the microbiome in colorectal neoplasia. Ann Gastroenterol 2020; 33:223-236. [PMID: 32382225 PMCID: PMC7196612 DOI: 10.20524/aog.2020.0467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/24/2020] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer is a leading cause of cancer-related death internationally, with mounting evidence pointing to the role of the microbiome in adenoma and cancer development. This article aims to provide clinicians with a foundation for understanding the field of research into the microbiome. We also illustrate the various ways in which the microbiota have been linked to colorectal cancer, with a specific focus on microbiota with identified virulence factors, and also on the ways that byproducts of microbiota metabolism may result in oncogenesis. We also review strategies for manipulating the microbiome for therapeutic effects.
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Affiliation(s)
- Katherine M. Watson
- Department of Surgery, Oregon Health & Science University, Portland, OR (Katherine M. Watson, Vassiliki Liana Tsikitis)
| | | | - Vassiliki Liana Tsikitis
- Department of Surgery, Oregon Health & Science University, Portland, OR (Katherine M. Watson, Vassiliki Liana Tsikitis)
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94
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Krisko TI, Nicholls HT, Bare CJ, Holman CD, Putzel GG, Jansen RS, Sun N, Rhee KY, Banks AS, Cohen DE. Dissociation of Adaptive Thermogenesis from Glucose Homeostasis in Microbiome-Deficient Mice. Cell Metab 2020; 31:592-604.e9. [PMID: 32084379 PMCID: PMC7888548 DOI: 10.1016/j.cmet.2020.01.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 11/18/2019] [Accepted: 01/24/2020] [Indexed: 01/16/2023]
Abstract
Recent studies suggest that a key mechanism whereby the gut microbiome influences energy balance and glucose homeostasis is through the recruitment of brown and beige adipocytes, primary mediators of the adaptive thermogenic response. To test this, we assessed energy expenditure and glucose metabolism in two complementary mouse models of gut microbial deficiency, which were exposed to a broad range of thermal and dietary stresses. Neither ablation of the gut microbiome, nor the substantial microbial perturbations induced by cold ambient temperatures, influenced energy expenditure during cold exposure or high-fat feeding. Nevertheless, we demonstrated a critical role for gut microbial metabolism in maintaining euglycemia through the production of amino acid metabolites that optimized hepatic TCA (tricarboxylic acid) cycle fluxes in support of gluconeogenesis. These results distinguish the dispensability of the gut microbiome for the regulation of energy expenditure from its critical contribution to the maintenance of glucose homeostasis.
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Affiliation(s)
- Tibor I Krisko
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Hayley T Nicholls
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Curtis J Bare
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Corey D Holman
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Gregory G Putzel
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medical College, New York, NY 10021, USA
| | - Robert S Jansen
- Division of Infectious Diseases, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Natalie Sun
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Alexander S Banks
- Division of Endocrinology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - David E Cohen
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA.
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95
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Rodrigues AV, Tantillo DJ, Mukhopadhyay A, Keasling JD, Beller HR. Insight into the Mechanism of Phenylacetate Decarboxylase (PhdB), a Toluene-Producing Glycyl Radical Enzyme. Chembiochem 2020; 21:663-671. [PMID: 31512343 PMCID: PMC7079210 DOI: 10.1002/cbic.201900560] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Indexed: 01/14/2023]
Abstract
We recently reported the discovery of phenylacetate decarboxylase (PhdB), representing one of only ten glycyl-radical-enzyme reaction types known, and a promising biotechnological tool for first-time biochemical synthesis of toluene from renewable resources. Here, we used experimental and computational data to evaluate the plausibility of three candidate PhdB mechanisms, involving either attack at the phenylacetate methylene carbon or carboxyl group [via H-atom abstraction from COOH or single-electron oxidation of COO- (Kolbe-type decarboxylation)]. In vitro experimental data included assays with F-labeled phenylacetate, kinetic studies, and tests with site-directed PhdB mutants; computational data involved estimation of reaction energetics using density functional theory (DFT). The DFT results indicated that all three mechanisms are thermodynamically challenging (beyond the range of many known enzymes in terms of endergonicity or activation energy barrier), reflecting the formidable demands on PhdB for catalysis of this reaction. Evidence that PhdB was able to bind α,α-difluorophenylacetate but was unable to catalyze its decarboxylation supported the enzyme's abstraction of a methylene H atom. Diminished activity of H327A and Y691F mutants was consistent with proposed proton donor roles for His327 and Tyr691. Collectively, these and other data most strongly support PhdB attack at the methylene carbon.
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Affiliation(s)
- Andria V. Rodrigues
- Joint BioEnergy Institute (JBEI)5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems and EngineeringLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
| | - Dean J. Tantillo
- Department of ChemistryUniversity of California1 Shields AvenueDavisCA95616USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute (JBEI)5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems and EngineeringLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
| | - Jay D. Keasling
- Joint BioEnergy Institute (JBEI)5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems and EngineeringLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Department of BioengineeringUniversity of California306 Stanley HallBerkeleyCA94720USA
- Department of Chemical and Biomolecular EngineeringUniversity of California201 Gilman HallBerkeleyCA94720USA
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkBuilding 220, Kemitorvet2800Kgs. LyngbyDenmark
| | - Harry R. Beller
- Joint BioEnergy Institute (JBEI)5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems and EngineeringLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
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96
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Maini Rekdal V, Nol Bernadino P, Luescher MU, Kiamehr S, Le C, Bisanz JE, Turnbaugh PJ, Bess EN, Balskus EP. A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols. eLife 2020; 9:e50845. [PMID: 32067637 PMCID: PMC7028382 DOI: 10.7554/elife.50845] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022] Open
Abstract
Catechol dehydroxylation is a central chemical transformation in the gut microbial metabolism of plant- and host-derived small molecules. However, the molecular basis for this transformation and its distribution among gut microorganisms are poorly understood. Here, we characterize a molybdenum-dependent enzyme from the human gut bacterium Eggerthella lenta that dehydroxylates catecholamine neurotransmitters. Our findings suggest that this activity enables E. lenta to use dopamine as an electron acceptor. We also identify candidate dehydroxylases that metabolize additional host- and plant-derived catechols. These dehydroxylases belong to a distinct group of largely uncharacterized molybdenum-dependent enzymes that likely mediate primary and secondary metabolism in multiple environments. Finally, we observe catechol dehydroxylation in the gut microbiotas of diverse mammals, confirming the presence of this chemistry in habitats beyond the human gut. These results suggest that the chemical strategies that mediate metabolism and interactions in the human gut are relevant to a broad range of species and habitats.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Paola Nol Bernadino
- Department of Chemistry and Molecular BiologyUniversity of California, IrvineIrvineUnited States
- Department of Chemistry and Molecular BiochemistryUniversity of California, IrvineIrvineUnited States
| | - Michael U Luescher
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Sina Kiamehr
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Chip Le
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Jordan E Bisanz
- Department of Microbiology and ImmunologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Peter J Turnbaugh
- Department of Microbiology and ImmunologyUniversity of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Elizabeth N Bess
- Department of Chemistry and Molecular BiologyUniversity of California, IrvineIrvineUnited States
- Department of Chemistry and Molecular BiochemistryUniversity of California, IrvineIrvineUnited States
| | - Emily P Balskus
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
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97
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Sharma M, Abayakoon P, Lingford JP, Epa R, John A, Jin Y, Goddard-Borger ED, Davies GJ, Williams SJ. Dynamic Structural Changes Accompany the Production of Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04427] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Palika Abayakoon
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne, Parkville, Victoria 3010, Australia
| | - James P. Lingford
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ruwan Epa
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alan John
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yi Jin
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Ethan D. Goddard-Borger
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne, Parkville, Victoria 3010, Australia
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98
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Leite GGS, Weitsman S, Parodi G, Celly S, Sedighi R, Sanchez M, Morales W, Villanueva-Millan MJ, Barlow GM, Mathur R, Lo SK, Jamil LH, Paski S, Rezaie A, Pimentel M. Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study. Dig Dis Sci 2020; 65:2595-2604. [PMID: 32140945 PMCID: PMC7419378 DOI: 10.1007/s10620-020-06173-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/24/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Most gut microbiome studies have been performed using stool samples. However, the small intestine is of central importance to digestion, nutrient absorption, and immune function, and characterizing its microbial populations is essential for elucidating their roles in human health and disease. AIMS To characterize the microbial populations of different small intestinal segments and contrast these to the stool microbiome. METHODS Male and female subjects undergoing esophagogastroduodenoscopy without colon preparation were prospectively recruited. Luminal aspirates were obtained from the duodenum, jejunum, and farthest distance reached. A subset also provided stool samples. 16S rRNA sequencing was performed and analyses were carried out using CLC Genomics Workbench. RESULTS 16S rRNA sequencing identified differences in more than 2000 operational taxonomic units between the small intestinal and stool microbiomes. Firmicutes and Proteobacteria were the most abundant phyla in the small intestine, and Bacteroidetes were less abundant. In the small intestine, phylum Firmicutes was primarily represented by lactic acid bacteria, including families Streptococcaceae, Lactobacillaceae, and Carnobacteriaceae, and Proteobacteria was represented by families Neisseriaceae, Pasteurellaceae, and Enterobacteriaceae. The duodenal and FD microbial signatures were markedly different from each other, but there were overlaps between duodenal and jejunal and between jejunal and FD microbial signatures. In stool, Firmicutes were represented by families Ruminococcaceae, Lachnospiraceae, Christensenellaceae, and Proteobacteria by class Deltaproteobacteria. CONCLUSIONS The small bowel microbiome is markedly different from that in stool and also varies between segments. These findings may be important in determining how compositional changes in small intestinal microbiota contribute to human disease states.
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Affiliation(s)
- Gabriela G S Leite
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 240E, Los Angeles, CA, 90048, USA
| | - Stacy Weitsman
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 240E, Los Angeles, CA, 90048, USA
| | - Gonzalo Parodi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 240E, Los Angeles, CA, 90048, USA
| | - Shreya Celly
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 240E, Los Angeles, CA, 90048, USA
| | - Rashin Sedighi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 240E, Los Angeles, CA, 90048, USA
| | - Maritza Sanchez
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 240E, Los Angeles, CA, 90048, USA
| | - Walter Morales
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 240E, Los Angeles, CA, 90048, USA
| | - Maria Jesus Villanueva-Millan
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 240E, Los Angeles, CA, 90048, USA
| | - Gillian M Barlow
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 240E, Los Angeles, CA, 90048, USA
| | - Ruchi Mathur
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 240E, Los Angeles, CA, 90048, USA
- Division of Endocrinology, Diabetes, and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Simon K Lo
- Pancreatic and Biliary Diseases Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Laith H Jamil
- Interventional Endoscopy Service, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shirley Paski
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ali Rezaie
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 240E, Los Angeles, CA, 90048, USA
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, 8730 Alden Drive, Suite 240E, Los Angeles, CA, 90048, USA.
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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99
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Zallot R, Oberg N, Gerlt JA. The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways. Biochemistry 2019; 58:4169-4182. [PMID: 31553576 DOI: 10.1021/acs.biochem.9b00735] [Citation(s) in RCA: 417] [Impact Index Per Article: 83.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The assignment of functions to uncharacterized proteins discovered in genome projects requires easily accessible tools and computational resources for large-scale, user-friendly leveraging of the protein, genome, and metagenome databases by experimentalists. This article describes the web resource developed by the Enzyme Function Initiative (EFI; accessed at https://efi.igb.illinois.edu/ ) that provides "genomic enzymology" tools ("web tools") for (1) generating sequence similarity networks (SSNs) for protein families (EFI-EST); (2) analyzing and visualizing genome context of the proteins in clusters in SSNs (in genome neighborhood networks, GNNs, and genome neighborhood diagrams, GNDs) (EFI-GNT); and (3) prioritizing uncharacterized SSN clusters for functional assignment based on metagenome abundance (chemically guided functional profiling, CGFP) (EFI-CGFP). The SSNs generated by EFI-EST are used as the input for EFI-GNT and EFI-CGFP, enabling easy transfer of information among the tools. The networks are visualized and analyzed using Cytoscape, a widely used desktop application; GNDs and CGFP heatmaps summarizing metagenome abundance are viewed within the tools. We provide a detailed example of the integrated use of the tools with an analysis of glycyl radical enzyme superfamily (IPR004184) found in the human gut microbiome. This analysis demonstrates that (1) SwissProt annotations are not always correct, (2) large-scale genome context analyses allow the prediction of novel metabolic pathways, and (3) metagenome abundance can be used to identify/prioritize uncharacterized proteins for functional investigation.
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100
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A gene cluster for taurine sulfur assimilation in an anaerobic human gut bacterium. Biochem J 2019; 476:2271-2279. [DOI: 10.1042/bcj20190486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/17/2022]
Abstract
AbstractAminoethylsulfonate (taurine) is widespread in the environment and highly abundant in the human body. Taurine and other aliphatic sulfonates serve as sulfur sources for diverse aerobic bacteria, which carry out cleavage of the inert sulfonate C–S bond through various O2-dependent mechanisms. Taurine also serves as a sulfur source for certain strict anaerobic fermenting bacteria. However, the mechanism of C–S cleavage by these bacteria has long been a mystery. Here we report the biochemical characterization of an anaerobic pathway for taurine sulfur assimilation in a strain of Clostridium butyricum from the human gut. In this pathway, taurine is first converted to hydroxyethylsulfonate (isethionate), followed by C–S cleavage by the O2-sensitive isethionate sulfo-lyase IseG, recently identified in sulfate- and sulfite-reducing bacteria. Homologs of the enzymes described in this study have a sporadic distribution in diverse strict and facultative anaerobic bacteria, from both the environment and the taurine-rich human gut, and may enable sulfonate sulfur acquisition in certain nutrient limiting conditions.
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