1
|
Romero-Rodríguez A, Ruíz-Villafán B, Sánchez S, Paredes-Sabja D. Is there a role for intestinal sporobiota in the antimicrobial resistance crisis? Microbiol Res 2024; 288:127870. [PMID: 39173554 DOI: 10.1016/j.micres.2024.127870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/23/2024] [Accepted: 08/06/2024] [Indexed: 08/24/2024]
Abstract
Antimicrobial resistance (AMR) is a complex issue requiring specific, multi-sectoral measures to slow its spread. When people are exposed to antimicrobial agents, it can cause resistant bacteria to increase. This means that the use, misuse, and excessive use of antimicrobial agents exert selective pressure on bacteria, which can lead to the development of "silent" reservoirs of antimicrobial resistance genes. These genes can later be mobilized into pathogenic bacteria and contribute to the spread of AMR. Many socioeconomic and environmental factors influence the transmission and dissemination of resistance genes, such as the quality of healthcare systems, water sanitation, hygiene infrastructure, and pollution. The sporobiota is an essential part of the gut microbiota that plays a role in maintaining gut homeostasis. However, because spores are highly transmissible and can spread easily, they can be a vector for AMR. The sporobiota resistome, particularly the mobile resistome, is important for tracking, managing, and limiting the spread of antimicrobial resistance genes among pathogenic and commensal bacterial species.
Collapse
Affiliation(s)
- A Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Ciudad de México 04510, Mexico.
| | - B Ruíz-Villafán
- Laboratorio de Microbiología Industrial. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - S Sánchez
- Laboratorio de Microbiología Industrial. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - D Paredes-Sabja
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| |
Collapse
|
2
|
Vico-Oton E, Volet C, Jacquemin N, Dong Y, Hapfelmeier S, Meibom KL, Bernier-Latmani R. Strain-dependent induction of primary bile acid 7-dehydroxylation by cholic acid. BMC Microbiol 2024; 24:286. [PMID: 39090543 PMCID: PMC11293179 DOI: 10.1186/s12866-024-03433-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Bile acids (BAs) are steroid-derived molecules with important roles in digestion, the maintenance of host metabolism, and immunomodulation. Primary BAs are synthesized by the host, while secondary BAs are produced by the gut microbiome through transformation of the former. The regulation of microbial production of secondary BAs is not well understood, particularly the production of 7-dehydroxylated BAs, which are the most potent agonists for host BA receptors. The 7-dehydroxylation of cholic acid (CA) is well established and is linked to the expression of a bile acid-inducible (bai) operon responsible for this process. However, little to no 7-dehydroxylation has been reported for other host-derived BAs (e.g., chenodeoxycholic acid, CDCA or ursodeoxycholic acid, UDCA). RESULTS Here, we demonstrate that the 7-dehydroxylation of CDCA and UDCA by the human isolate Clostridium scindens is induced when CA is present, suggesting that CA-dependent transcriptional regulation is required for substantial 7-dehydroxylation of these primary BAs. This is supported by the finding that UDCA alone does not promote expression of bai genes. CDCA upregulates expression of the bai genes but the expression is greater when CA is present. In contrast, the murine isolate Extibacter muris exhibits a distinct response; CA did not induce significant 7-dehydroxylation of primary BAs, whereas BA 7-dehydroxylation was promoted upon addition of germ-free mouse cecal content in vitro. However, E. muris was found to 7-dehydroxylate in vivo. CONCLUSIONS The distinct expression responses amongst strains indicate that bai genes are regulated differently. CA promoted bai operon gene expression and the 7-dehydroxylating activity in C. scindens strains. Conversely, the in vitro activity of E. muris was promoted only after the addition of cecal content and the isolate did not alter bai gene expression in response to CA. The accessory gene baiJ was only upregulated in the C. scindens ATCC 35704 strain, implying mechanistic differences amongst isolates. Interestingly, the human-derived C. scindens strains were also capable of 7-dehydroxylating murine bile acids (muricholic acids) to a limited extent. This study shows novel 7-dehydroxylation activity in vitro resulting from the presence of CA and suggests distinct bai gene expression across bacterial species.
Collapse
Affiliation(s)
- Eduard Vico-Oton
- Environmental Microbiology Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Colin Volet
- Environmental Microbiology Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Jacquemin
- Environmental Microbiology Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Yuan Dong
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Karin Lederballe Meibom
- Environmental Microbiology Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- EPFL ENAC IIE EML CH A1 375 (Bâtiment CH), Station 6, CH-1015, Lausanne, Switzerland.
| |
Collapse
|
3
|
Wei X, Yao C, He X, Li J, Wang Y, Wang C, Chen Q, Ma X, Guo DA. Biotransformation of chenodeoxycholic acid by human intestinal fungi and the agonistic effects on FXR. PHYTOCHEMISTRY 2024; 224:114162. [PMID: 38797255 DOI: 10.1016/j.phytochem.2024.114162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Bile acids play a vital role in modulating host metabolism, with chenodeoxycholic acid (CDCA) standing out as a primary bile acid that naturally activates farnesoid X receptor (FXR). In this study, we investigated the microbial transformations of CDCA by seven human intestinal fungal species. Our findings revealed that hydroxylation and dehydrogenation were the most prevalent metabolic pathways. Incubation of CDCA with Rhizopus microspores (PT2906) afforded eight undescribed compounds (6-13) alongside five known analogs (1-5) which were elucidated by HRESI-MS and NMR data. Notably, compounds 8, 12 and 13 exhibited an inhibitory effect on FXR in contrast to the FXR activation observed with CDCA in vitro assays. This study shone a light on the diverse transformations of CDCA by intestinal fungi, unveiling potential modulators of FXR activity with implications for host metabolism.
Collapse
Affiliation(s)
- Xuemei Wei
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Changliang Yao
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xin He
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jiayuan Li
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yulu Wang
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chao Wang
- College of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Qinhua Chen
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Xiaochi Ma
- College of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, 116044, China.
| | - De-An Guo
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
| |
Collapse
|
4
|
Yang X, Xu Y, Li J, Ran X, Gu Z, Song L, Zhang L, Wen L, Ji G, Wang R. Bile acid-gut microbiota imbalance in cholestasis and its long-term effect in mice. mSystems 2024; 9:e0012724. [PMID: 38934542 PMCID: PMC11265269 DOI: 10.1128/msystems.00127-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Cholestasis is a common morbid state that may occur in different phases; however, a comprehensive evaluation of the long-term effect post-recovery is still lacking. In the hepatic cholestasis mouse model, which was induced by a temporary complete blockage of the bile duct, the stasis of bile acids and liver damage typically recovered within a short period. However, we found that the temporary hepatic cholestasis had a long-term effect on gut microbiota dysbiosis, including overgrowth of small intestinal bacteria, decreased diversity of the gut microbiota, and an overall imbalance in its composition accompanied by an elevated inflammation level. Additionally, we observed an increase in Escherichia-Shigella (represented by ASV136078), rich in virulence factors, in both small and large intestines following cholestasis. To confirm the causal role of dysregulated gut microbiota in promoting hepatic inflammation and injury, we conducted gut microbiota transplantation into germ-free mice. We found that recipient mice transplanted with feces from cholestasis mice exhibited liver inflammation, damage, and accumulation of hepatic bile acids. In conclusion, our study demonstrates that cholestasis disrupts the overall load and structural composition of the gut microbiota in mice, and these adverse effects persist after recovery from cholestatic liver injury. This finding suggests the importance of monitoring the structural composition of the gut microbiota in patients with cholestasis and during their recovery. IMPORTANCE Our pre-clinical study using a mouse model of cholestasis underscores that cholestasis not only disrupts the equilibrium and structural configuration of the gut microbiota but also emphasizes the persistence of these adverse effects even after bile stasis restoration. This suggests the need of monitoring and initiating interventions for gut microbiota structural restoration in patients with cholestasis during and after recovery. We believe that our study contributes to novel and better understanding of the intricate interplay among bile acid homeostasis, gut microbiota, and cholestasis-associated complications. Our pre-clinical findings may provide implications for the clinical management of patients with cholestasis.
Collapse
Affiliation(s)
- Xin Yang
- Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Yuesong Xu
- Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jie Li
- Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ximing Ran
- Department of Biostatistics and Bioinformatics, Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Zhihao Gu
- School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, China
| | - Linfeng Song
- General Medicine, Medical school, Kunming University of Science and Technology, Kunming, China
| | - Lei Zhang
- Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Li Wen
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Guang Ji
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ruirui Wang
- Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| |
Collapse
|
5
|
Li XJ, Fang C, Zhao RH, Zou L, Miao H, Zhao YY. Bile acid metabolism in health and ageing-related diseases. Biochem Pharmacol 2024; 225:116313. [PMID: 38788963 DOI: 10.1016/j.bcp.2024.116313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Bile acids (BAs) have surpassed their traditional roles as lipid solubilizers and regulators of BA homeostasis to emerge as important signalling molecules. Recent research has revealed a connection between microbial dysbiosis and metabolism disruption of BAs, which in turn impacts ageing-related diseases. The human BAs pool is primarily composed of primary BAs and their conjugates, with a smaller proportion consisting of secondary BAs. These different BAs exert complex effects on health and ageing-related diseases through several key nuclear receptors, such as farnesoid X receptor and Takeda G protein-coupled receptor 5. However, the underlying molecular mechanisms of these effects are still debated. Therefore, the modulation of signalling pathways by regulating synthesis and composition of BAs represents an interesting and novel direction for potential therapies of ageing-related diseases. This review provides an overview of synthesis and transportion of BAs in the healthy body, emphasizing its dependence on microbial community metabolic capacity. Additionally, the review also explores how ageing and ageing-related diseases affect metabolism and composition of BAs. Understanding BA metabolism network and the impact of their nuclear receptors, such as farnesoid X receptor and G protein-coupled receptor 5 agonists, paves the way for developing therapeutic agents for targeting BA metabolism in various ageing-related diseases, such as metabolic disorder, hepatic injury, cardiovascular disease, renal damage and neurodegenerative disease.
Collapse
Affiliation(s)
- Xiao-Jun Li
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China; Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, Southern Medical University, No.13, Shi Liu Gang Road, Haizhu District, Guangzhou, Guangdong 510315, China
| | - Chu Fang
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China
| | - Rui-Hua Zhao
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China
| | - Liang Zou
- School of Food and Bioengineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, Sichuan 610106, China
| | - Hua Miao
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China.
| | - Ying-Yong Zhao
- School of Pharmacy, Zhejiang Chinese Medical University, No. 548 Binwen Road, Hangzhou, Zhejiang 310053, China; National Key Laboratory of Kidney Diseases, First Medical Center of Chinese PLA General Hospital, No. 28 Fuxing Road, Beijing 100853, China.
| |
Collapse
|
6
|
Baumeister T, Proaño-Vasco A, Metwaly A, Kleigrewe K, Kuznetsov A, Schömig L, Borgmann M, Khiat M, Anand A, Böttcher K, Haller D, Dunkel A, Somoza V, Reiter S, Meng C, Thimme R, Schmid RM, Patil DT, Burgermeister E, Huang Y, Sun Y, Wang HH, Wang TC, Abrams JA, Quante M. Microbiota metabolized Bile Acids accelerate Gastroesophageal Adenocarcinoma via FXR inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598405. [PMID: 38915718 PMCID: PMC11195123 DOI: 10.1101/2024.06.11.598405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Background The incidence of Barrett esophagus (BE) and Gastroesophageal Adenocarcinoma (GEAC) correlates with obesity and a diet rich in fat. Bile acids (BA) support fat digestion and undergo microbial metabolization in the gut. The farnesoid X receptor (FXR) is an important modulator of the BA homeostasis. The capacity of inhibiting cancer-related processes when activated, make FXR an appealing therapeutic target. In this work, we assess the role of diet on the microbiota-BA axis and evaluate the role of FXR in disease progression. Results Here we show that high fat diet (HFD) accelerated tumorigenesis in L2-IL1B mice (BE- and GEAC- mouse model) while increasing BA levels and enriching gut microbiota that convert primary to secondary BA. While upregulated in BE, expression of FXR was downregulated in GEAC in mice and humans. In L2-IL1B mice, FXR knockout enhanced the dysplastic phenotype and increased Lgr5 progenitor cell numbers. Treatment of murine organoids and L2-IL1B mice with the FXR agonist obeticholic acid (OCA) deacelerated GEAC progression. Conclusion We provide a novel concept of GEAC carcinogenesis being accelerated via the diet-microbiome-metabolome axis and FXR inhibition on progenitor cells. Further, FXR activation protected with OCA ameliorated the phenotype in vitro and in vivo, suggesting that FXR agonists have potential as differentiation therapy in GEAC prevention.
Collapse
Affiliation(s)
- Theresa Baumeister
- Klinik für Innere Medizin II, Universitätsklinikum Freiburg; Germany
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich; Germany
| | - Andrea Proaño-Vasco
- Klinik für Innere Medizin II, Universitätsklinikum Freiburg; Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg; Germany
- Faculty of Biology, University of Freiburg; Germany
| | - Amira Metwaly
- Chair of Nutrition and Immunology; Technical University of Munich; Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich; Germany
| | - Alexander Kuznetsov
- Klinik für Innere Medizin II, Universitätsklinikum Freiburg; Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg; Germany
- Faculty of Biology, University of Freiburg; Germany
| | - Linus Schömig
- Klinik für Innere Medizin II, Universitätsklinikum Freiburg; Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg; Germany
- Faculty of Biology, University of Freiburg; Germany
| | - Martin Borgmann
- Klinik für Innere Medizin II, Universitätsklinikum Freiburg; Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg; Germany
- Faculty of Biology, University of Freiburg; Germany
| | - Mohammed Khiat
- Klinik für Innere Medizin II, Universitätsklinikum Freiburg; Germany
| | - Akanksha Anand
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich; Germany
| | - Katrin Böttcher
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich; Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology; Technical University of Munich; Germany
| | - Andreas Dunkel
- Leibniz-Institute for Food Systems Biology, Technical University of Munich; Germany
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich; Germany
| | - Veronika Somoza
- Leibniz-Institute for Food Systems Biology, Technical University of Munich; Germany
| | - Sinah Reiter
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich; Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich; Germany
| | - Robert Thimme
- Klinik für Innere Medizin II, Universitätsklinikum Freiburg; Germany
| | - Roland M. Schmid
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich; Germany
| | - Deepa T. Patil
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, USA
| | - Elke Burgermeister
- Dept. of Internal Medicine II, Medical Faculty Mannheim, Heidelberg University; Germany
| | - Yiming Huang
- Systems & Synthetic Biology, Columbia University Medical Center; New York, NY, USA
| | - Yiwei Sun
- Systems & Synthetic Biology, Columbia University Medical Center; New York, NY, USA
| | - Harris H. Wang
- Systems & Synthetic Biology, Columbia University Medical Center; New York, NY, USA
| | - Timothy C. Wang
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Julian A. Abrams
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Michael Quante
- Klinik für Innere Medizin II, Universitätsklinikum Freiburg; Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg; Germany
| |
Collapse
|
7
|
Wahlström A, Brumbaugh A, Sjöland W, Olsson L, Wu H, Henricsson M, Lundqvist A, Makki K, Hazen SL, Bergström G, Marschall HU, Fischbach MA, Bäckhed F. Production of deoxycholic acid by low-abundant microbial species is associated with impaired glucose metabolism. Nat Commun 2024; 15:4276. [PMID: 38769296 PMCID: PMC11106306 DOI: 10.1038/s41467-024-48543-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
Alterations in gut microbiota composition are suggested to contribute to cardiometabolic diseases, in part by producing bioactive molecules. Some of the metabolites are produced by very low abundant bacterial taxa, which largely have been neglected due to limits of detection. However, the concentration of microbially produced metabolites from these taxa can still reach high levels and have substantial impact on host physiology. To explore this concept, we focused on the generation of secondary bile acids by 7α-dehydroxylating bacteria and demonstrated that addition of a very low abundant bacteria to a community can change the metabolic output dramatically. We show that Clostridium scindens converts cholic acid into the secondary bile acid deoxycholic acid (DCA) very efficiently even though the abundance of C. scindens is low, but still detectable by digital droplet PCR. We also show that colonization of germ-free female mice with a community containing C. scindens induces DCA production and affects host metabolism. Finally, we show that DCA correlates with impaired glucose metabolism and a worsened lipid profile in individuals with type 2 diabetes, which implies that this metabolic pathway may contribute to the development of cardiometabolic disease.
Collapse
Affiliation(s)
- Annika Wahlström
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ariel Brumbaugh
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Wilhelm Sjöland
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lisa Olsson
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hao Wu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Fudan Microbiome Center, and Department of Bariatric and Metabolic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Marcus Henricsson
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Annika Lundqvist
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kassem Makki
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Stanley L Hazen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, OH, USA
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Göran Bergström
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden
| | - Hanns-Ulrich Marschall
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Michael A Fischbach
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- ChEM-H Institute, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Fredrik Bäckhed
- Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
8
|
Liu S, Li W, Chen J, Li M, Geng Y, Liu Y, Wu W. The footprint of gut microbiota in gallbladder cancer: a mechanistic review. Front Cell Infect Microbiol 2024; 14:1374238. [PMID: 38774627 PMCID: PMC11106419 DOI: 10.3389/fcimb.2024.1374238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Gallbladder cancer (GBC) is the most common malignant tumor of the biliary system with the worst prognosis. Even after radical surgery, the majority of patients with GBC have difficulty achieving a clinical cure. The risk of tumor recurrence remains more than 65%, and the overall 5-year survival rate is less than 5%. The gut microbiota refers to a variety of microorganisms living in the human intestine, including bacteria, viruses and fungi, which profoundly affect the host state of general health, disease and even cancer. Over the past few decades, substantial evidence has supported that gut microbiota plays a critical role in promoting the progression of GBC. In this review, we summarize the functions, molecular mechanisms and recent advances of the intestinal microbiota in GBC. We focus on the driving role of bacteria in pivotal pathways, such as virulence factors, metabolites derived from intestinal bacteria, chronic inflammatory responses and ecological niche remodeling. Additionally, we emphasize the high level of correlation between viruses and fungi, especially EBV and Candida spp., with GBC. In general, this review not only provides a solid theoretical basis for the close relationship between gut microbiota and GBC but also highlights more potential research directions for further research in the future.
Collapse
Affiliation(s)
- Shujie Liu
- Joint Program of Nanchang University and Queen Mary University of London, Jiangxi Medical College of Nanchang University, Nanchang, Jiangxi, China
| | - Weijian Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Jun Chen
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Maolan Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Yajun Geng
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Yingbin Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| | - Wenguang Wu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Shanghai, China
| |
Collapse
|
9
|
Garrigues Q, Mugnier A, Chastant S, Sicard F, Martin JC, Svilar L, Castex M, Ramis-Vidal MG, Rovere N, Michaud L, David P, Mansalier E, Rodiles A, Mila H, Apper E. The supplementation of female dogs with live yeast Saccharomyces cerevisiae var. boulardii CNCM I-1079 acts as gut stabilizer at whelping and modulates immunometabolic phenotype of the puppies. Front Nutr 2024; 11:1366256. [PMID: 38680531 PMCID: PMC11048480 DOI: 10.3389/fnut.2024.1366256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024] Open
Abstract
Time around parturition is a stressful period for both bitches and their puppies. The use of probiotics has been proposed, e.g., in pigs, to improve health status of sows, their reproductive performances and in turn, the health and performance of their progeny. The objective of the present study was to evaluate the impact, on both dams and puppies, of a supplementation of bitches with the live yeast Saccharomyces cerevisiae var. boulardii CNCM I-1079 (SB-1079) during the second part of the gestation and the lactation period. A total of 36 bitches of medium and large-sized breeds were enrolled. They were divided into two groups, one of which received 1.3 × 109 colony forming units of live yeast per day. At dam's level, SB-1079 yeast shaped a different microbiota structure between the two groups just after whelping, impacted alpha diversity and some plasma metabolites related to energy metabolism. Regarding reproductive performances, SB-1079 improved gross energy of the colostrum (1.4 vs. 1.2 kcal of ME/g) as well as the concentration of protein in milk at Day 7 after parturition (10.4 vs. 7.6%). SB-1079 also reduced the odds of having low birth weight in the litter. At puppy's level, a modulation of immunometabolic phenotype is suggested by the observation of increased growth rates during the early pediatric period (i.e., between 21 and 56 days of life, 225 vs. 190%) and a decrease of the IL-8:IL-10 ratio after vaccination against rabies (4.2 vs. 16.9). Our findings suggest that SB-1079 supplementation during gestation and lactation has the potential to enhance health of bitches and in turn health of puppies through maternal programming.
Collapse
Affiliation(s)
| | | | | | - Flavie Sicard
- Aix-Marseille Université, C2VN, INRAE, INSERM, Marseille, France
- CriBioM, Aix Marseille Université, Marseille, France
| | | | - Ljubica Svilar
- Aix-Marseille Université, C2VN, INRAE, INSERM, Marseille, France
- CriBioM, Aix Marseille Université, Marseille, France
| | | | - Manuel Guillermo Ramis-Vidal
- Department of Animal Production, Faculty of Veterinary Medicine, University of Murcia, Murcia, Spain
- Instituo Murciano de Investigación en Biomedicina (IMIB), Murcia, Spain
| | - Nicoletta Rovere
- Department of HASFS, VESPA, University of Veterinary, Milan, Italy
| | | | - Pauline David
- NeoCare, ENVT, Université de Toulouse, Toulouse, France
| | | | | | - Hanna Mila
- NeoCare, ENVT, Université de Toulouse, Toulouse, France
| | | |
Collapse
|
10
|
Wang H, Kim R, Wang Y, Furtado KL, Sims CE, Tamayo R, Allbritton NL. In vitro co-culture of Clostridium scindens with primary human colonic epithelium protects the epithelium against Staphylococcus aureus. Front Bioeng Biotechnol 2024; 12:1382389. [PMID: 38681959 PMCID: PMC11045926 DOI: 10.3389/fbioe.2024.1382389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/28/2024] [Indexed: 05/01/2024] Open
Abstract
A complex and dynamic network of interactions exists between human gastrointestinal epithelium and intestinal microbiota. Therefore, comprehending intestinal microbe-epithelial cell interactions is critical for the understanding and treatment of intestinal diseases. Primary human colonic epithelial cells derived from a healthy human donor were co-cultured with Clostridium scindens (C. scindens), a probiotic obligate anaerobe; Staphylococcus aureus (S. aureus), a facultative anaerobe and intestinal pathogen; or both bacterial species in tandem. The co-culture hanging basket platform used for these experiments possessed walls of controlled oxygen (O2) permeability to support the formation of an O2 gradient across the intestinal epithelium using cellular O2 consumption, resulting in an anaerobic luminal and aerobic basal compartment. Both the colonic epithelial cells and C. scindens remained viable over 48 h during co-culture. In contrast, co-culture with S. aureus elicited significant damage to colonic epithelial cells within 24 h. To explore the influence of the intestinal pathogen on the epithelium in the presence of the probiotic bacteria, colonic epithelial cells were inoculated sequentially with the two bacterial species. Under these conditions, C. scindens was capable of repressing the production of S. aureus enterotoxin. Surprisingly, although C. scindens converted cholic acid to secondary bile acids in the luminal medium, the growth of S. aureus was not significantly inhibited. Nevertheless, this combination of probiotic and pathogenic bacteria was found to benefit the survival of the colonic epithelial cells compared with co-culture of the epithelial cells with S. aureus alone. This platform thus provides an easy-to-use and low-cost tool to study the interaction between intestinal bacteria and colonic cells in vitro to better understand the interplay of intestinal microbiota with human colonic epithelium.
Collapse
Affiliation(s)
- Hao Wang
- Department of Bioengineering, University of Washington, Seattle, WA, United States
| | - Raehyun Kim
- Department of Bioengineering, University of Washington, Seattle, WA, United States
- Department of Biological and Chemical Engineering, Hongik University, Sejong, Republic of Korea
| | - Yuli Wang
- Department of Bioengineering, University of Washington, Seattle, WA, United States
| | - Kathleen L. Furtado
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - Christopher E. Sims
- Department of Bioengineering, University of Washington, Seattle, WA, United States
- Department of Medicine/Division of Rheumatology, University of Washington, Seattle, WA, United States
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA, United States
| |
Collapse
|
11
|
Liu W, Li Z, Ze X, Deng C, Xu S, Ye F. Multispecies probiotics complex improves bile acids and gut microbiota metabolism status in an in vitro fermentation model. Front Microbiol 2024; 15:1314528. [PMID: 38444809 PMCID: PMC10913090 DOI: 10.3389/fmicb.2024.1314528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
The consumption of probiotics has been extensively employed for the management or prevention of gastrointestinal disorders by modifying the gut microbiota and changing metabolites. Nevertheless, the probiotic-mediated regulation of host metabolism through the metabolism of bile acids (BAs) remains inadequately comprehended. The gut-liver axis has received more attention in recent years due to its association with BA metabolism. The objective of this research was to examine the changes in BAs and gut microbiota using an in vitro fermentation model. The metabolism and regulation of gut microbiota by commercial probiotics complex containing various species such as Lactobacillus, Bifidobacterium, and Streptococcus were investigated. The findings indicated that the probiotic strains had produced diverse metabolic profiles of BAs. The probiotics mixture demonstrated the greatest capacity for Bile salt hydrolase (BSH) deconjugation and 7α-dehydroxylation, leading to a significant elevation in the concentrations of Chenodeoxycholic acid, Deoxycholic acidcholic acid, and hyocholic acid in humans. In addition, the probiotic mixtures have the potential to regulate the microbiome of the human intestines, resulting in a reduction of isobutyric acid, isovaleric acid, hydrogen sulfide, and ammonia. The probiotics complex intervention group showed a significant increase in the quantities of Lactobacillus and Bifidobacterium strains, in comparison to the control group. Hence, the use of probiotics complex to alter gut bacteria and enhance the conversion of BAs could be a promising approach to mitigate metabolic disorders in individuals.
Collapse
Affiliation(s)
- Wei Liu
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhongxia Li
- BYHEALTH Institute of Nutrition and Health, Guangzhou, China
| | - Xiaolei Ze
- BYHEALTH Institute of Nutrition and Health, Guangzhou, China
| | - Chaoming Deng
- BYHEALTH Institute of Nutrition and Health, Guangzhou, China
| | - Shunfu Xu
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Ye
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| |
Collapse
|
12
|
Guo Y, Shen K, Zhang X, Huang H. In vitro characterization of alternative l-threonate and d-erythronate catabolic pathways. Biochem Biophys Res Commun 2024; 695:149440. [PMID: 38157628 DOI: 10.1016/j.bbrc.2023.149440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
l-threonate is the metabolite of vitamin C, while d-erythronate is the metabolite of N-acetyl-d-glucosamine, the nutritional supplement for joint health. They are widely distributed in the environment and human biofluids. Nevertheless, the catabolisms of l-threonate and d-erythronate are sparsely reported. Here we explored the functional diversity of an acid sugar kinase family (Pfam families PF07005-PF17042), and discovered a novel 2-oxo-tetronate kinase. The conserved genome neighborhood of the 2-oxo-tetronate kinase encodes members of class-II fructose-bisphosphate aldolase family (F_bP_aldolase, PF01116) and a dehydrogenase family (PF03446-PF14833). Instructed by this analysis, we experimentally verified that these enzymes are capable of degrading l-threonate into dihydroxyacetone phosphate (DHAP) in Arthrobacter sp. ZBG10, Clostridium scindens ATCC 35704, and Pseudonocardia dioxanivorans ATCC 55486. Meanwhile, a convergent catabolic pathway for d-erythronate was characterized in P. dioxanivorans ATCC 55486. Moreover, the phylogenetic distribution analysis indicates that the biological range of the identified l-threonate and d-erythronate catabolic pathways appears to extend mostly to members of the Actinomycetota, Cyanobacteriota, Bacillota, Pseudomonadota, and Bacteroidota phyla.
Collapse
Affiliation(s)
- Yibo Guo
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Ke Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xinshuai Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Hua Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| |
Collapse
|
13
|
Su C, Wang J, Luo H, Chen J, Lin F, Mo J, Xiong F, Zha L. Gut Microbiota Plays Essential Roles in Soyasaponin's Preventive Bioactivities against Steatohepatitis in the Methionine and Choline Deficient (MCD) Diet-Induced Non-Alcoholic Steatohepatitis (NASH) Mice. Mol Nutr Food Res 2024; 68:e2300561. [PMID: 38234006 DOI: 10.1002/mnfr.202300561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/24/2023] [Indexed: 01/19/2024]
Abstract
SCOPE Gut microbiota (GM) is involved in nonalcoholic steatohepatitis (NASH) development. Phytochemicals soyasaponins can prevent NASH possibly by modulating GM. This study aims to investigate the preventive bioactivities of soyasaponin monomers (SS-A1 and SS-Bb) against NASH and explores the mechanisms by targeting GM. METHODS AND RESULTS Male C57BL/6 mice are fed with methionine and choline deficient (MCD) diet containing SS-A1 , SS-Bb, or not for 16 weeks. Antibiotics-treated pseudo germ-free (PGF) mice are fed with MCD diet containing SS-A1 , SS-Bb, or not for 8 weeks. GM is determined by 16S rRNA amplicon sequencing. Bile acids (BAs) are measured by UPLC-MS/MS. In NASH mice, SS-A1 and SS-Bb alleviate steatohepatitis and fibrosis, reduce ALT, AST, and LPS in serum, decrease TNF-α, IL-6, α-SMA, triglycerides, and cholesterol in liver. SS-A1 and SS-Bb decrease Firmicutes, Erysipelotrichaceae, unidentified-Clostridiales, Eggerthellaceae, Atopobiaceae, Aerococcus, Jeotgalicoccus, Gemella, Rikenella, increase Proteobacteria, Verrucomicrobia, Akkermansiaceae, Romboutsia, and Roseburia. SS-A1 and SS-Bb alter BAs composition in liver, serum, and feces, activate farnesoid X receptor (FXR) in liver and ileum, increase occludin and ZO-1 in intestine. However, GM clearance abrogates the preventive bioactivities of SS-A1 and SS-Bb against NASH. CONCLUSION GM plays essential roles in soyasaponin's preventive bioactivities against steatohepatitis in MCD diet-induced NASH mice.
Collapse
Affiliation(s)
- Chuhong Su
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, National Medical Products Administration (NMPA), Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong, 510515, P. R. China
| | - Jiexian Wang
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, National Medical Products Administration (NMPA), Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong, 510515, P. R. China
| | - Huiyu Luo
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, National Medical Products Administration (NMPA), Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong, 510515, P. R. China
| | - Junbin Chen
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, National Medical Products Administration (NMPA), Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong, 510515, P. R. China
| | - Fengjuan Lin
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, National Medical Products Administration (NMPA), Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong, 510515, P. R. China
| | - Jiaqi Mo
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, National Medical Products Administration (NMPA), Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong, 510515, P. R. China
| | - Fei Xiong
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, National Medical Products Administration (NMPA), Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong, 510515, P. R. China
- Department of Clinical Nutrition, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510280, P. R. China
| | - Longying Zha
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, National Medical Products Administration (NMPA), Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong, 510515, P. R. China
| |
Collapse
|
14
|
Sung CH, Marsilio S, Pilla R, Wu YA, Cavasin JP, Hong MP, Suchodolski JS. Temporal Variability of the Dominant Fecal Microbiota in Healthy Adult Cats. Vet Sci 2024; 11:31. [PMID: 38250937 PMCID: PMC10819787 DOI: 10.3390/vetsci11010031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
While shifts in gut microbiota have been studied in diseased states, the temporal variability of the microbiome in cats has not been widely studied. This study investigated the temporal variability of the feline dysbiosis index (DI) and the abundance of core bacterial groups in healthy adult cats. The secondary aim was to evaluate the relationship between the fecal abundance of Clostridium hiranonis and the fecal concentrations of unconjugated bile acids. A total of 142 fecal samples collected from 17 healthy cats were prospectively included: nine cats with weekly collection over 3 weeks (at least four time points), five cats with monthly collection over 2 months (three time points), and three cats with additional collections for up to 10 months. The DI remained stable within the reference intervals over two months for all cats (Friedman test, p > 0.2), and 100% of the DI values (n = 142) collected throughout the study period remained within the RI. While some temporal individual variation was observed for individual taxa, the magnitude was minimal compared to cats with chronic enteropathy and antibiotic exposure. Additionally, the abundance of Clostridium hiranonis was significantly correlated with the percentage of fecal primary bile acids, supporting its role as a bile acid converter in cats.
Collapse
Affiliation(s)
- Chi-Hsuan Sung
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Sina Marsilio
- UC Davis School of Veterinary Medicine, Department of Veterinary Medicine and Epidemiology, University of California, Davis, CA 95616, USA
| | - Rachel Pilla
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Yu-An Wu
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Joao Pedro Cavasin
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Min-Pyo Hong
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| |
Collapse
|
15
|
Correa Lopes B, Chen CC, Sung CH, Ishii PE, Medina LFDC, Gaschen FP, Suchodolski JS, Pilla R. Correlation between Peptacetobacter hiranonis, the baiCD Gene, and Secondary Bile Acids in Dogs. Animals (Basel) 2024; 14:216. [PMID: 38254385 PMCID: PMC10812727 DOI: 10.3390/ani14020216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/15/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Bile acid metabolism is a key pathway modulated by intestinal microbiota. Peptacetobacter (Clostridium) hiranonis has been described as the main species responsible for the conversion of primary into secondary fecal unconjugated bile acids (fUBA) in dogs. This multi-step biochemical pathway is encoded by the bile acid-inducible (bai) operon. We aimed to assess the correlation between P. hiranonis abundance, the abundance of one specific gene of the bai operon (baiCD), and secondary fUBA concentrations. In this retrospective study, 133 fecal samples were analyzed from 24 dogs. The abundances of P. hiranonis and baiCD were determined using qPCR. The concentration of fUBA was measured by gas chromatography-mass spectrometry. The baiCD abundance exhibited a strong positive correlation with secondary fUBA (ρ = 0.7377, 95% CI (0.6461, 0.8084), p < 0.0001). Similarly, there was a strong correlation between P. hiranonis and secondary fUBA (ρ = 0.6658, 95% CI (0.5555, 0.7532), p < 0.0001). Animals displaying conversion of fUBA and lacking P. hiranonis were not observed. These results suggest P. hiranonis is the main converter of primary to secondary bile acids in dogs.
Collapse
Affiliation(s)
- Bruna Correa Lopes
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| | - Chih-Chun Chen
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| | - Chi-Hsuan Sung
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| | - Patricia Eri Ishii
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| | - Luis Fernando da Costa Medina
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| | - Frederic P. Gaschen
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| | - Rachel Pilla
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77840, USA; (C.-C.C.); (C.-H.S.); (P.E.I.); (L.F.d.C.M.); (J.S.S.); (R.P.)
| |
Collapse
|
16
|
Calton CM, Carothers K, Ramamurthy S, Jagadish N, Phanindra B, Garcia A, Viswanathan VK, Halpern MD. Clostridium scindens exacerbates experimental necrotizing enterocolitis via upregulation of the apical sodium-dependent bile acid transporter. Am J Physiol Gastrointest Liver Physiol 2024; 326:G25-G37. [PMID: 37933481 PMCID: PMC11208032 DOI: 10.1152/ajpgi.00102.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/19/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Abstract
Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in premature infants. Evidence indicates that bile acid homeostasis is disrupted during NEC: ileal bile acid levels are elevated in animals with experimental NEC, as is expression of the apical sodium-dependent bile acid transporter (Asbt). In addition, bile acids, which are synthesized in the liver, are extensively modified by the gut microbiome, including via the conversion of primary bile acids to more cytotoxic secondary forms. We hypothesized that the addition of bile acid-modifying bacteria would increase susceptibility to NEC in a neonatal rat model of the disease. The secondary bile acid-producing species Clostridium scindens exacerbated both incidence and severity of NEC. C. scindens upregulated the bile acid transporter Asbt and increased levels of intraenterocyte bile acids. Treatment with C. scindens also altered bile acid profiles and increased hydrophobicity of the ileal intracellular bile acid pool. The ability of C. scindens to enhance NEC requires bile acids, as pharmacological sequestration of ileal bile acids protects animals from developing disease. These findings indicate that bile acid-modifying bacteria can contribute to NEC pathology and provide additional evidence for the role of bile acids in the pathophysiology of experimental NEC.NEW & NOTEWORTHY Necrotizing enterocolitis (NEC), a life-threatening gastrointestinal emergency in premature infants, is characterized by dysregulation of bile acid homeostasis. We demonstrate that administering the secondary bile acid-producing bacterium Clostridium scindens enhances NEC in a neonatal rat model of the disease. C. scindens-enhanced NEC is dependent on bile acids and driven by upregulation of the ileal bile acid transporter Asbt. This is the first report of bile acid-modifying bacteria exacerbating experimental NEC pathology.
Collapse
Affiliation(s)
- Christine M Calton
- Department of Pediatrics and Steele Children's Research Center, University of Arizona, Tucson, Arizona, United States
| | - Katelyn Carothers
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States
| | - Shylaja Ramamurthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States
| | - Neha Jagadish
- Department of Pediatrics and Steele Children's Research Center, University of Arizona, Tucson, Arizona, United States
| | - Bhumika Phanindra
- Department of Pediatrics and Steele Children's Research Center, University of Arizona, Tucson, Arizona, United States
| | - Anett Garcia
- Department of Pediatrics and Steele Children's Research Center, University of Arizona, Tucson, Arizona, United States
| | - V K Viswanathan
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States
| | - Melissa D Halpern
- Department of Pediatrics and Steele Children's Research Center, University of Arizona, Tucson, Arizona, United States
| |
Collapse
|
17
|
Meibom KL, Marion S, Volet C, Nass T, Vico-Oton E, Menin L, Bernier-Latmani R. BaiJ and BaiB are key enzymes in the chenodeoxycholic acid 7α-dehydroxylation pathway in the gut microbe Clostridium scindens ATCC 35704. Gut Microbes 2024; 16:2323233. [PMID: 38465624 PMCID: PMC10936602 DOI: 10.1080/19490976.2024.2323233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/21/2024] [Indexed: 03/12/2024] Open
Abstract
Bile acid transformation is a common gut microbiome activity that produces secondary bile acids, some of which are important for human health. One such process, 7α-dehydroxylation, converts the primary bile acids, cholic acid and chenodeoxycholic acid, to deoxycholic acid and lithocholic acid, respectively. This transformation requires a number of enzymes, generally encoded in a bile acid-inducible (bai) operon and consists of multiple steps. Some 7α-dehydroxylating bacteria also harbor additional genes that encode enzymes with potential roles in this pathway, but little is known about their functions. Here, we purified 11 enzymes originating either from the bai operon or encoded at other locations in the genome of Clostridium scindens strain ATCC 35704. Enzyme activity was probed in vitro under anoxic conditions to characterize the biochemical pathway of chenodeoxycholic acid 7α-dehydroxylation. We found that more than one combination of enzymes can support the process and that a set of five enzymes, including BaiJ that is encoded outside the bai operon, is sufficient to achieve the transformation. We found that BaiJ, an oxidoreductase, exhibits an activity that is not harbored by the homologous enzyme from another C. scindens strain. Furthermore, ligation of bile acids to coenzyme A (CoA) was shown to impact the product of the transformation. These results point to differences in the 7α-dehydroxylation pathway among microorganisms and the crucial role of CoA ligation in the process.
Collapse
Affiliation(s)
- Karin Lederballe Meibom
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Solenne Marion
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Colin Volet
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Théo Nass
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Eduard Vico-Oton
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laure Menin
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| |
Collapse
|
18
|
Manchester AC, Chow L, Wheat W, Dow S. Modulation of In Vitro Macrophage Responses via Primary and Secondary Bile Acids in Dogs. Animals (Basel) 2023; 13:3714. [PMID: 38067065 PMCID: PMC10705343 DOI: 10.3390/ani13233714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 04/07/2024] Open
Abstract
Bile acids (BA) are important metabolites secreted into the intestinal lumen and impacted by luminal microbes and dietary intake. Prior studies in humans and rodents have shown that BAs are immunologically active and that primary and secondary BAs have distinct immune properties. Therefore, the composition of the gut BA pool may influence GI inflammatory responses. The current study investigated the relative immune modulatory properties of primary (cholic acid, CA) and secondary BAs (lithocholic acid, LCA) by assessing their effects on canine macrophage cytokine secretion and BA receptor (TGR5) expression. In addition, RNA sequencing was used to further interrogate how CA and LCA differentially modulated macrophage responses to LPS (lipopolysaccharide). We found that exposure to either CA or LCA influenced LPS-induced cytokine production via macrophages similarly, with suppression of TNF-α secretion and enhancement of IL-10 secretion. Neither BA altered the expression of the BA receptor TGR5. Transcriptomic analysis revealed that CA activated inflammatory signaling pathways in macrophages involving type II interferon signaling and the aryl hydrocarbon receptor, whereas LCA activated pathways related to nitric oxide signaling and cell cycle regulation. Thus, we concluded that both primary and secondary BAs are active modulators of macrophage responses in dogs, with differential and shared effects evident with sequencing analysis.
Collapse
Affiliation(s)
- Alison C. Manchester
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA (S.D.)
| | - Lyndah Chow
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA (S.D.)
| | - William Wheat
- Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Steven Dow
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA (S.D.)
| |
Collapse
|
19
|
Araj-Khodaei M, Ayati MH, Azizi Zeinalhajlou A, Novinbahador T, Yousefi M, Shiri M, Mahmoodpoor A, Shamekh A, Namazi N, Sanaie S. Berberine-induced glucagon-like peptide-1 and its mechanism for controlling type 2 diabetes mellitus: a comprehensive pathway review. Arch Physiol Biochem 2023:1-8. [PMID: 37921026 DOI: 10.1080/13813455.2023.2258559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/05/2023] [Indexed: 11/04/2023]
Abstract
Introduction: A growing number of studies have thus far showed the association between type 2 diabetes mellitus (DM) and the intestinal microbiome homoeostasis. As reported, the gut microflora can be significantly different in patients with type 2 DM (T2DM) compared to those in healthy individuals.Methods: The authors collected the relevant articles published until 2022 and these are carefully selected from three scientific databases based on keywords.Discussion: This review highlights research on the anti-diabetic properties of berberine (BBR)-induced glucagon-like peptide-1 (GLP-1), as a glucose-lowering factor and a balance regulator in the microbial flora of the intestines, which plays an important role in adjusting the signalling pathways affecting insulin secretion.Results: Considering the anti-diabetic characteristics of the BBR-induced GLP-1, BBR makes a promising complementary treatment for reducing the clinical symptoms of DM by reducing the hyperglycaemia. Berberin might be a safe and effective drug for T2DM with little or no adverse effects.HighlightsBerberine induces GLP-1 insulin secretion by PLC2 pathway in the intestinalBerberine-induced GLP-1 decreases mitochondrial stress and relocates cytochrome c out of the mitochondria.Berberine induces GLP-1 secretion in the intestine by altering the bacterial profile, thus could possibly lighten diabetes symptomsBerberine-induced SCFA production, SCFA causes GLP-1 secretion from the intestinal L-Cell.Preventing mitochondrial damage, reducing adipose tissue fat, and reducing oxidative stress are thus among the results of BBR-induced GLP-1.The lower costs of BBR, and its limited side effects and higher availability, make it a promising supplementary medicine for DM.
Collapse
Affiliation(s)
| | - Mohammad Hossein Ayati
- Department of Traditional Medicine, School of Persian Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Integrative Medicine in Aging, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Akbar Azizi Zeinalhajlou
- Department of Geriatric Health, Faculty of Health Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tannaz Novinbahador
- Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
- Physical Medicine and Rehabilitation Research Center, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahdi Shiri
- Department of Pharmacology, School of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Ata Mahmoodpoor
- Department of Anesthesiology and Critical Care Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Shamekh
- Student Research Committee, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazli Namazi
- Research Center for Integrative Medicine in Aging, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
- Diabetes Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sarvin Sanaie
- Research Center of Psychiatry and Behavioral Sciences, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
20
|
Kister B, Viehof A, Rolle-Kampczyk U, Schwentker A, Treichel NS, Jennings SA, Wirtz TH, Blank LM, Hornef MW, von Bergen M, Clavel T, Kuepfer L. A physiologically based model of bile acid metabolism in mice. iScience 2023; 26:107922. [PMID: 37817939 PMCID: PMC10561051 DOI: 10.1016/j.isci.2023.107922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/04/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
Bile acid (BA) metabolism is a complex system that includes a wide variety of primary and secondary, as well as conjugated and unconjugated BAs that undergo continuous enterohepatic circulation (EHC). Alterations in both composition and dynamics of BAs have been associated with various diseases. However, a mechanistic understanding of the relationship between altered BA metabolism and related diseases is lacking. Computational modeling may support functional analyses of the physiological processes involved in the EHC of BAs along the gut-liver axis. In this study, we developed a physiologically based model of murine BA metabolism describing synthesis, hepatic and microbial transformations, systemic distribution, excretion, and EHC of BAs at the whole-body level. For model development, BA metabolism of specific pathogen-free (SPF) mice was characterized in vivo by measuring BA levels and composition in various organs, expression of transporters along the gut, and cecal microbiota composition. We found significantly different BA levels between male and female mice that could only be explained by adjusted expression of the hepatic enzymes and transporters in the model. Of note, this finding was in agreement with experimental observations. The model for SPF mice could also describe equivalent experimental data in germ-free mice by specifically switching off microbial activity in the intestine. The here presented model can therefore facilitate and guide functional analyses of BA metabolism in mice, e.g., the effect of pathophysiological alterations on BA metabolism and translation of results from mouse studies to a clinically relevant context through cross-species extrapolation.
Collapse
Affiliation(s)
- Bastian Kister
- Institute for Systems Medicine with Focus on Organ Interaction, University Hospital RWTH Aachen, Aachen, Germany
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Alina Viehof
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Annika Schwentker
- Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Nicole Simone Treichel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Susan A.V. Jennings
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Theresa H. Wirtz
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Mathias W. Hornef
- Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Leipzig, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Lars Kuepfer
- Institute for Systems Medicine with Focus on Organ Interaction, University Hospital RWTH Aachen, Aachen, Germany
| |
Collapse
|
21
|
Mandal RK, Schmidt NW. Mechanistic insights into the interaction between the host gut microbiome and malaria. PLoS Pathog 2023; 19:e1011665. [PMID: 37824458 PMCID: PMC10569623 DOI: 10.1371/journal.ppat.1011665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
Malaria is a devastating infectious disease and significant global health burden caused by the bite of a Plasmodium-infected female Anopheles mosquito. Gut microbiota was recently discovered as a risk factor of severe malaria. This review entails the recent advances on the impact of gut microbiota composition on malaria severity and consequence of malaria infection on gut microbiota in mammalian hosts. Additionally, this review provides mechanistic insight into interactions that might occur between gut microbiota and host immunity which in turn can modulate malaria severity. Finally, approaches to modulate gut microbiota composition are discussed. We anticipate this review will facilitate novel hypotheses to move the malaria-gut microbiome field forward.
Collapse
Affiliation(s)
- Rabindra K. Mandal
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indiana, United States of America
| | - Nathan W. Schmidt
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indiana, United States of America
| |
Collapse
|
22
|
Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA. Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome. Cell 2023; 186:2839-2852.e21. [PMID: 37352836 PMCID: PMC10299816 DOI: 10.1016/j.cell.2023.05.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 04/10/2023] [Accepted: 05/26/2023] [Indexed: 06/25/2023]
Abstract
The gut microbiome is complex, raising questions about the role of individual strains in the community. Here, we address this question by constructing variants of a complex defined community in which we eliminate strains that occupy the bile acid 7α-dehydroxylation niche. Omitting Clostridium scindens (Cs) and Clostridium hylemonae (Ch) eliminates secondary bile acid production and reshapes the community in a highly specific manner: eight strains change in relative abundance by >100-fold. In single-strain dropout communities, Cs and Ch reach the same relative abundance and dehydroxylate bile acids to a similar extent. However, Clostridium sporogenes increases >1,000-fold in the ΔCs but not ΔCh dropout, reshaping the pool of microbiome-derived phenylalanine metabolites. Thus, strains that are functionally redundant within a niche can have widely varying impacts outside the niche, and a strain swap can ripple through the community in an unpredictable manner, resulting in a large impact on an unrelated community-level phenotype.
Collapse
Affiliation(s)
- Min Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Lucas J Osborn
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sunit Jain
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Xiandong Meng
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Allison Weakley
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jia Yan
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - William J Massey
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Venkateshwari Varadharajan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Anthony Horak
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Rakhee Banerjee
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Daniela S Allende
- Department of Anatomical Pathology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - E Ricky Chan
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Adeline M Hajjar
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zeneng Wang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Alejandra Dimas
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Aishan Zhao
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Kazuki Nagashima
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Alice G Cheng
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Steven Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Stanley L Hazen
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - J Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Michael A Fischbach
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| |
Collapse
|
23
|
Nowicki C, Ray L, Engen P, Madrigrano A, Witt T, Lad T, Cobleigh M, Mutlu EA. Comparison of gut microbiome composition in colonic biopsies, endoscopically-collected and at-home-collected stool samples. Front Microbiol 2023; 14:1148097. [PMID: 37323911 PMCID: PMC10264612 DOI: 10.3389/fmicb.2023.1148097] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Aim The goal of this study is to compare microbiome composition in three different sample types in women, namely stool brought from home vs. solid stool samples obtained at the time of an unprepped sigmoidoscopy vs. biopsies of the colonic mucosa at the time of an unprepped sigmoidoscopy, using alpha- and beta-diversity metrics following bacterial 16S rRNA sequencing. The findings may have relevance to health and disease states in which bacterial metabolism has a significant impact on molecules/metabolites that are recirculated between the gut lumen and mucosa and systemic circulation, such as estrogens (as in breast cancer) or bile acids. Methods Concomitant at-home-collected stool, endoscopically-collected stool, and colonic biopsy samples were collected from 48 subjects (24 breast cancer, 24 control.) After 16S rRNA sequencing, an amplicon sequence variant (ASV) based approach was used to analyze the data. Alpha diversity metrics (Chao1, Pielou's Evenness, Faith PD, Shannon, and Simpson) and beta diversity metrics (Bray-Curtis, Weighted and Unweighted Unifrac) were calculated. LEfSe was used to analyze differences in the abundance of various taxa between sample types. Results Alpha and beta diversity metrics were significantly different between the three sample types. Biopsy samples were different than stool samples in all metrics. The highest variation in microbiome diversity was noted in the colonic biopsy samples. At-home and endoscopically-collected stool showed more similarities in count-based and weighted beta diversity metrics. There were significant differences in rare taxa and phylogenetically-diverse taxa between the two types of stool samples. Generally, there were higher levels of Proteobacteria in biopsy samples, with significantly more Actinobacteria and Firmicutes in stool (all p < 0.001, q-value < 0.05). Overall, there was a significantly higher relative abundance of Lachnospiraceae and Ruminococcaceae in stool samples (at-home collected and endoscopically-collected) and higher abundances of Tisserellaceae in biopsy samples (all p < 0.001, q-value < 0.05). Conclusion Our data shows that different sampling methods can impact results when looking at the composition of the gut microbiome using ASV-based approaches.
Collapse
Affiliation(s)
- Christina Nowicki
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
| | - Lucille Ray
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
| | - Philip Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Andrea Madrigrano
- Department of Surgery, Rush Medical College, Rush University Medical Center, Chicago, IL, United States
| | - Thomas Witt
- Department of Surgery, Rush Medical College, Rush University Medical Center, Chicago, IL, United States
| | - Thomas Lad
- Department of Oncology, Cook County Health and Hospital Systems, Chicago, IL, United States
| | - Melody Cobleigh
- Department of Internal Medicine, Division of Hematology, Oncology, and Cell Therapy, Rush University Medical Center, Chicago, IL, United States
| | - Ece A. Mutlu
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
| |
Collapse
|
24
|
Su X, Gao Y, Yang R. Gut microbiota derived bile acid metabolites maintain the homeostasis of gut and systemic immunity. Front Immunol 2023; 14:1127743. [PMID: 37256134 PMCID: PMC10225537 DOI: 10.3389/fimmu.2023.1127743] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/07/2023] [Indexed: 06/01/2023] Open
Abstract
Bile acids (BAs) as cholesterol-derived molecules play an essential role in some physiological processes such as nutrient absorption, glucose homeostasis and regulation of energy expenditure. They are synthesized in the liver as primary BAs such as cholic acid (CA), chenodeoxycholic acid (CDCA) and conjugated forms. A variety of secondary BAs such as deoxycholic acid (DCA) and lithocholic acid (LCA) and their derivatives is synthesized in the intestine through the involvement of various microorganisms. In addition to essential physiological functions, BAs and their metabolites are also involved in the differentiation and functions of innate and adaptive immune cells such as macrophages (Macs), dendritic cells (DCs), myeloid derived suppressive cells (MDSCs), regulatory T cells (Treg), Breg cells, T helper (Th)17 cells, CD4 Th1 and Th2 cells, CD8 cells, B cells and NKT cells. Dysregulation of the BAs and their metabolites also affects development of some diseases such as inflammatory bowel diseases. We here summarize recent advances in how BAs and their metabolites maintain gut and systemic homeostasis, including the metabolism of the BAs and their derivatives, the role of BAs and their metabolites in the differentiation and function of immune cells, and the effects of BAs and their metabolites on immune-associated disorders.
Collapse
Affiliation(s)
- Xiaomin Su
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Yunhuan Gao
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Rongcun Yang
- Translational Medicine Institute, Affiliated Tianjin Union Medical Center of Nankai University, Nankai University, Tianjin, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Immunology, Nankai University School of Medicine, Nankai University, Tianjin, China
| |
Collapse
|
25
|
Development of the Anaerobic Microbiome in the Infant Gut. Pediatr Infect Dis J 2023:00006454-990000000-00384. [PMID: 36917032 DOI: 10.1097/inf.0000000000003905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Ninety-five percent of gut microbiota are anaerobes and vary according to age and diet. Complex carbohydrates in human milk enhance the growth of Bifidobacterium and Bacteroides in the first year. Complex carbohydrates in solid foods enhance the growth of Bacteroides and Clostridium in the second year. Short-chain fatty acids produced by Akkermansia and Faecalibacterium may reduce obesity, diabetes and IBD.
Collapse
|
26
|
Cheng JKJ, Unnikrishnan M. Clostridioides difficile infection: traversing host-pathogen interactions in the gut. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36848200 DOI: 10.1099/mic.0.001306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
C. difficile is the primary cause for nosocomial infective diarrhoea. For a successful infection, C. difficile must navigate between resident gut bacteria and the harsh host environment. The perturbation of the intestinal microbiota by broad-spectrum antibiotics alters the composition and the geography of the gut microbiota, deterring colonization resistance, and enabling C. difficile to colonize. This review will discuss how C. difficile interacts with and exploits the microbiota and the host epithelium to infect and persist. We provide an overview of C. difficile virulence factors and their interactions with the gut to aid adhesion, cause epithelial damage and mediate persistence. Finally, we document the host responses to C. difficile, describing the immune cells and host pathways that are associated and triggered during C. difficile infection.
Collapse
Affiliation(s)
- Jeffrey K J Cheng
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| |
Collapse
|
27
|
Gillard J, Leclercq IA. Biological tuners to reshape the bile acid pool for therapeutic purposes in non-alcoholic fatty liver disease. Clin Sci (Lond) 2023; 137:65-85. [PMID: 36601783 PMCID: PMC9816373 DOI: 10.1042/cs20220697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023]
Abstract
Bile acids synthesized within the hepatocytes are transformed by gut microorganisms and reabsorbed into the portal circulation. During their enterohepatic cycling, bile acids act as signaling molecules by interacting with receptors to regulate pathways involved in many physiological processes. The bile acid pool, composed of a variety of bile acid species, has been shown to be altered in diseases, hence contributing to disease pathogenesis. Thus, understanding the changes in bile acid pool size and composition in pathological processes will help to elaborate effective pharmacological treatments. Five crucial steps along the enterohepatic cycle shape the bile acid pool size and composition, offering five possible targets for therapeutic intervention. In this review, we provide an insight on the strategies to modulate the bile acid pool, and then we discuss the potential benefits in non-alcoholic fatty liver disease.
Collapse
Affiliation(s)
- Justine Gillard
- Laboratory of Hepato‐Gastroenterology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Isabelle A. Leclercq
- Laboratory of Hepato‐Gastroenterology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| |
Collapse
|
28
|
Shen Y, Wu SD, Chen Y, Li XY, Zhu Q, Nakayama K, Zhang WQ, Weng CZ, Zhang J, Wang HK, Wu J, Jiang W. Alterations in gut microbiome and metabolomics in chronic hepatitis B infection-associated liver disease and their impact on peripheral immune response. Gut Microbes 2023; 15:2155018. [PMID: 36519342 PMCID: PMC9757487 DOI: 10.1080/19490976.2022.2155018] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Gut dysbiosis has been reported in chronic hepatitis B (CHB) infection, however its role in CHB progression and antiviral treatment remains to be clarified. Herein, the present study aimed to characterize gut microbiota (GM) in patients with chronic hepatitis B virus infection-associated liver diseases (HBV-CLD) by combining microbiome with metabolome analyses and to evaluate their effects on peripheral immunity. Fecal samples from HBV-CLD patients (n = 64) and healthy controls (n = 17) were collected for 16s rRNA sequencing. Fecal metabolomics was measured with untargeted liquid chromatography-mass spectrometry in subgroups of 58 subjects. Lineage changes of peripheral blood mononuclear cells (PBMCs) were determined upon exposure to bacterial extracts (BE) from HBV-CLD patients. Integrated analyses of microbiome with metabolome revealed a remarkable shift of gut microbiota and metabolites in HBV-CLD patients, and disease progression and antiviral treatment were found to be two main contributing factors for the shift. Concordant decreases in Turicibacter with 4-hydroxyretinoic acid were detected to be inversely correlated with serum AST levels through host-microbiota-metabolite interaction analysis in cirrhotic patients. Moreover, depletion of E.hallii group with elevated choline was restored in patients with 5-year antiviral treatment. PBMC exposure to BE from non-cirrhotic patients enhanced expansion of T helper 17 cells; however, BE from cirrhotics attenuated T helper 1 cell count. CHB progression and antiviral treatment are two main factors contributing to the compositional shift in microbiome and metabolome of HBV-CLD patients. Peripheral immunity might be an intermediate link in gut microbe-host interplay underlying CHB pathogenesis.
Collapse
Affiliation(s)
- Yue Shen
- Department of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China,Shanghai Institute of Liver Diseases, Fudan University Shanghai Medical College, Shanghai, China
| | - Sheng-Di Wu
- Department of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China,Shanghai Institute of Liver Diseases, Fudan University Shanghai Medical College, Shanghai, China,Department of Gastroenterology& Hepatology, Zhongshan Hospital Xiamen Branch of Fudan University, Xiamen, China
| | - Yao Chen
- Department of Emergency Medicine, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Xin-Yue Li
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, China
| | - Qin Zhu
- Department of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China,Shanghai Institute of Liver Diseases, Fudan University Shanghai Medical College, Shanghai, China
| | - Kiyoko Nakayama
- Department of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China,Shanghai Institute of Liver Diseases, Fudan University Shanghai Medical College, Shanghai, China
| | - Wan-Qin Zhang
- Department of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China,Shanghai Institute of Liver Diseases, Fudan University Shanghai Medical College, Shanghai, China
| | - Cheng-Zhao Weng
- Department of Gastroenterology& Hepatology, Zhongshan Hospital Xiamen Branch of Fudan University, Xiamen, China
| | - Jun Zhang
- Department of Gastroenterology& Hepatology, Zhongshan Hospital Xiamen Branch of Fudan University, Xiamen, China
| | - Hai-Kun Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Jian Wu
- Department of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China,Shanghai Institute of Liver Diseases, Fudan University Shanghai Medical College, Shanghai, China,Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, China,Jian Wu Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology, Fudan University School of Basic Medical Sciences, 138 Yixue Yuan Road, P. O. Box 228, Shanghai, China
| | - Wei Jiang
- Department of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China,Shanghai Institute of Liver Diseases, Fudan University Shanghai Medical College, Shanghai, China,Department of Gastroenterology& Hepatology, Zhongshan Hospital Xiamen Branch of Fudan University, Xiamen, China,CONTACT Wei Jiang Department of Gastroenterology & Hepatology Zhongshan Hospital of Fudan University, Zhongshan Hospital Xiamen Branch of Fudan University,180 Fenglin Road, Shanghai, China
| |
Collapse
|
29
|
Ramsay TG, Arfken AM, Summers KL. Enteroendocrine peptides, growth, and the microbiome during the porcine weaning transition. Anim Microbiome 2022; 4:56. [DOI: 10.1186/s42523-022-00206-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 09/28/2022] [Indexed: 11/19/2022] Open
Abstract
Abstract
Background
Growth rate in pigs can be affected by numerous factors that also affect feeding behavior and the microbiome. Recent studies report some communication between the microbiome and the enteroendocrine system. The present study examined if changes in the piglet microbiome between birth and during the weaning transition can be correlated either positively or negatively with growth rate and plasma concentrations of enteroendocrine peptides.
Results
During the post-weaning transition, a 49% reduction in average daily gain was observed at day 24 (P < 0.05) relative to day 21. Pigs recovered by day 28 with body weight and average daily gain increases of 17% and 175%, respectively relative to day 24 and the highest rate of gain was measured at day 35 (462 g/day). The time interval between day 21–24 had the highest number of correlations (n = 25) between the relative abundance differences in taxa over time and corresponding percent weight gain. Amplicon sequence variants with the greatest correlation with percent weight gain between day 21–24 belonged to families Prevotellaceae NK3B31 (ρ = 0.65, P < 0.001), Veillonellaceae (ρ = 0.63, P < 0.001) and Rikenellaceae RC9 (ρ = 0.62, P < 0.001). Seven taxa were positively correlated with percent weight gain between day 24–28. Eight taxa were positively correlated with percent weight gain between day 28–35, of which four were Clostridia. Only Lactobacillus reuteri was positively correlated across both day 24–28 and day 28–35 analyses. Insulin-like growth factor 1 (IGF-1; R2 = 0.61, P < 0.001), glucose-dependent insulinotropic polypeptide (GIP; R2 = 0.20, P < 0.001), glucagon-like peptide 1 (GLP-1; R2 = 0.51, P < 0.001), and glucagon-like peptide 2 (GLP-2; R2 = 0.21, P < 0.001) were significantly associated with the piglet fecal community NMDS, while serotonin showed no significant association (R2 = 0.03, P = 0.15). Higher concentrations of GLP-1 and GLP-2 characterized day 1 fecal communities, while GIP levels had the strongest relationship primarily with samples ordinated with the day 21 cluster.
Conclusions
Demonstration of an association of certain taxa with individual gut peptides at specific ages suggests the potential for the microbiome to elicit changes in the gut enteroendocrine system during early postnatal development in the pig.
Collapse
|
30
|
Li JY, Gillilland M, Lee AA, Wu X, Zhou SY, Owyang C. Secondary bile acids mediate high-fat diet-induced upregulation of R-spondin 3 and intestinal epithelial proliferation. JCI Insight 2022; 7:e148309. [PMID: 36099053 PMCID: PMC9675439 DOI: 10.1172/jci.insight.148309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
A high-fat diet (HFD) contributes to the increased incidence of colorectal cancer, but the mechanisms are unclear. We found that R-spondin 3 (Rspo3), a ligand for leucine-rich, repeat-containing GPCR 4 and 5 (LGR4 and LGR5), was the main subtype of R-spondins and was produced by myofibroblasts beneath the crypts in the intestine. HFD upregulated colonic Rspo3, LGR4, LGR5, and β-catenin gene expression in specific pathogen-free rodents, but not in germ-free mice, and the upregulations were prevented by the bile acid (BA) binder cholestyramine or antibiotic treatment, indicating mediation by both BA and gut microbiota. Cholestyramine or antibiotic treatments prevented HFD-induced enrichment of members of the Lachnospiraceae and Rumincoccaceae, which can transform primary BA into secondary BA. Oral administration of deoxycholic acid (DCA), or inoculation of a combination of the BA deconjugator Lactobacillus plantarum and 7α-dehydroxylase-containing Clostridium scindens with an HFD to germ-free mice increased serum DCA and colonic Rspo3 mRNA levels, indicating that formation of secondary BA by gut microbiota is responsible for HFD-induced upregulation of Rspo3. In primary myofibroblasts, DCA increased Rspo3 mRNA via TGR5. Finally, we showed that cholestyramine or conditional deletion of Rspo3 prevented HFD- or DCA-induced intestinal proliferation. We conclude that secondary BA is responsible for HFD-induced upregulation of Rspo3, which, in turn, mediates HFD-induced intestinal epithelial proliferation.
Collapse
|
31
|
Distinct colon mucosa microbiomes associated with tubular adenomas and serrated polyps. NPJ Biofilms Microbiomes 2022; 8:69. [PMID: 36038569 PMCID: PMC9424272 DOI: 10.1038/s41522-022-00328-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
Colorectal cancer is the second most deadly and third most common cancer in the world. Its development is heterogenous, with multiple mechanisms of carcinogenesis. Two distinct mechanisms include the adenoma-carcinoma sequence and the serrated pathway. The gut microbiome has been identified as a key player in the adenoma-carcinoma sequence, but its role in serrated carcinogenesis is less clear. In this study, we characterized the gut microbiome of 140 polyp-free and polyp-bearing individuals using colon mucosa and fecal samples to determine if microbiome composition was associated with each of the two key pathways. We discovered significant differences between the microbiomes of colon mucosa and fecal samples, with sample type explaining 10–15% of the variation observed in the microbiome. Multiple mucosal brushings were collected from each individual to investigate whether the gut microbiome differed between polyp and healthy intestinal tissue, but no differences were found. Mucosal aspirate sampling revealed that the microbiomes of individuals with tubular adenomas and serrated polyps were significantly different from each other and polyp-free individuals, explaining 1–4% of the variance in the microbiome. Microbiome composition also enabled the accurate prediction of subject polyp types using Random Forest, which produced an area under curve values of 0.87–0.99. By directly sampling the colon mucosa and distinguishing between the different developmental pathways of colorectal cancer, our study helps characterize potential mechanistic targets for serrated carcinogenesis. This research also provides insight into multiple microbiome sampling strategies by assessing each method’s practicality and effect on microbial community composition.
Collapse
|
32
|
Sheng W, Ji G, Zhang L. The Effect of Lithocholic Acid on the Gut-Liver Axis. Front Pharmacol 2022; 13:910493. [PMID: 35873546 PMCID: PMC9301130 DOI: 10.3389/fphar.2022.910493] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
Lithocholic acid (LCA) is a monohydroxy bile acid produced by intestinal flora, which has been found to be associated with a variety of hepatic and intestinal diseases. LCA is previously considered to be toxic, however, recent studies revealed that LCA and its derivatives may exert anti-inflammatory and anti-tumor effects under certain conditions. LCA goes through enterohepatic circulation along with other bile acids, here, we mainly discuss the effects of LCA on the gut-liver axis, including the regulation of gut microbiota, intestinal barrier, and relevant nuclear receptors (VDR, PXR) and G protein-coupled receptor five in related diseases. In addition, we also find that some natural ingredients are involved in regulating the detoxification and excretion of LCA, and the interaction with LCA also mediates its own biological activity.
Collapse
|
33
|
Kean IRL, Wagner J, Wijeyesekera A, De Goffau M, Thurston S, Clark JA, White DK, Ridout J, Agrawal S, Kayani R, O'Donnell R, Ramnarayan P, Peters MJ, Klein N, Holmes E, Parkhill J, Baker S, Pathan N. Profiling gut microbiota and bile acid metabolism in critically ill children. Sci Rep 2022; 12:10432. [PMID: 35729169 PMCID: PMC9213539 DOI: 10.1038/s41598-022-13640-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/26/2022] [Indexed: 11/08/2022] Open
Abstract
Broad-spectrum antimicrobial use during the treatment of critical illness influences gastrointestinal fermentation endpoints, host immune response and metabolic activity including the conversion of primary to secondary bile acids. We previously observed reduced fermentation capacity in the faecal microbiota of critically ill children upon hospital admission. Here, we further explore the timecourse of the relationship between the microbiome and bile acid profile in faecal samples collected from critically ill children. The microbiome was assayed by sequencing of the 16S rRNA gene, and faecal water bile acids were measured by liquid chromatography mass spectrometry. In comparison to admission faecal samples, members of the Lachnospiraceae recovered during the late-acute phase (days 8-10) of hospitalisation. Patients with infections had a lower proportion of Lachnospiraceae in their gut microbiota than controls and patients with primary admitting diagnoses. Keystone species linked to ecological recovery were observed to decline with the length of PICU admission. These species were further suppressed in patients with systemic infection, respiratory failure, and undergoing surgery. Bile acid composition recovers quickly after intervention for critical illness which may be aided by the compositional shift in Lachnospiraceae. Our findings suggest gut microbiota recovery can be readily assessed via measurement of faecal bile acids.
Collapse
Affiliation(s)
| | - Joseph Wagner
- The Peter Doherty Institute for Infection and Immunity, Melbourne Health, Melbourne, Australia
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Anisha Wijeyesekera
- Department of Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
| | - Marcus De Goffau
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Thurston
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - John A Clark
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Deborah K White
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Jenna Ridout
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
- EACH, Milton, Cambridge, United Kingdom
| | - Shruti Agrawal
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Riaz Kayani
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Roddy O'Donnell
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Padmanabhan Ramnarayan
- Paediatric Intensive Care Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- St Mary's Hospital, London, United Kingdom
| | - Mark J Peters
- Paediatric Intensive Care Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Nigel Klein
- Paediatric Intensive Care Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Elaine Holmes
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Julian Parkhill
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nazima Pathan
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| |
Collapse
|
34
|
Kelly J, Al-Rammahi M, Daly K, Flanagan PK, Urs A, Cohen MC, di Stefano G, Bijvelds MJC, Sheppard DN, de Jonge HR, Seidler UE, Shirazi-Beechey SP. Alterations of mucosa-attached microbiome and epithelial cell numbers in the cystic fibrosis small intestine with implications for intestinal disease. Sci Rep 2022; 12:6593. [PMID: 35449374 PMCID: PMC9023491 DOI: 10.1038/s41598-022-10328-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/04/2022] [Indexed: 02/07/2023] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Defective CFTR leads to accumulation of dehydrated viscous mucus within the small intestine, luminal acidification and altered intestinal motility, resulting in blockage. These changes promote gut microbial dysbiosis, adversely influencing the normal proliferation and differentiation of intestinal epithelial cells. Using Illumina 16S rRNA gene sequencing and immunohistochemistry, we assessed changes in mucosa-attached microbiome and epithelial cell profile in the small intestine of CF mice and a CF patient compared to wild-type mice and non-CF humans. We found increased abundance of pro-inflammatory Escherichia and depletion of beneficial secondary bile-acid producing bacteria in the ileal mucosa-attached microbiome of CFTR-null mice. The ileal mucosa in a CF patient was dominated by a non-aeruginosa Pseudomonas species and lacked numerous beneficial anti-inflammatory and short-chain fatty acid-producing bacteria. In the ileum of both CF mice and a CF patient, the number of absorptive enterocytes, Paneth and glucagon-like peptide 1 and 2 secreting L-type enteroendocrine cells were decreased, whereas stem and goblet cell numbers were increased. These changes in mucosa-attached microbiome and epithelial cell profile suggest that microbiota-host interactions may contribute to intestinal CF disease development with implications for therapy.
Collapse
Affiliation(s)
- Jennifer Kelly
- Department of Infection Biology and Microbiomes, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Miran Al-Rammahi
- Department of Infection Biology and Microbiomes, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.,Department of Physiology, Biochemistry and Pharmacology, College of Veterinary Medicine, University of Al-Qadisiyah, Al Diwaniyah, 58002, Iraq
| | - Kristian Daly
- Department of Infection Biology and Microbiomes, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Paul K Flanagan
- Arrowe Park University Teaching Hospital NHS Trust, Wirral, CH49 5PE, UK.,Gastrointestinal and Liver Services, Aintree University Hospital, Lower Lane, Liverpool, Merseyside, L9 7AL, UK
| | - Arun Urs
- Sheffield Children's Hospital NHS Trust, Western Bank, Sheffield, S10 2TH, UK
| | - Marta C Cohen
- Histopathology Department, Sheffield Children's Hospital NHS Trust, Western Bank, Sheffield, S10 2TH, UK
| | - Gabriella di Stefano
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625, Hannover, Germany
| | - Marcel J C Bijvelds
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - David N Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK
| | - Hugo R de Jonge
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Ursula E Seidler
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625, Hannover, Germany
| | - Soraya P Shirazi-Beechey
- Department of Infection Biology and Microbiomes, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
| |
Collapse
|
35
|
Sangaraju D, Katavolos P, Liang X, Chou C, Zabka TS, Dean B, Maher J. Establishment of baseline profiles of 50 bile acids in preclinical toxicity species: A comprehensive assessment of translational differences and study design considerations for biomarker development. Toxicol Appl Pharmacol 2022; 443:116008. [DOI: 10.1016/j.taap.2022.116008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022]
|
36
|
Affiliation(s)
- Alessia Perino
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kristina Schoonjans
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| |
Collapse
|
37
|
Kobayashi N, Abe K, Akagi S, Kitamura M, Shiraishi Y, Yamaguchi A, Yutani M, Amatsu S, Matsumura T, Nomura N, Ozaki N, Obana N, Fujinaga Y. Membrane Vesicles Derived From Clostridium botulinum and Related Clostridial Species Induce Innate Immune Responses via MyD88/TRIF Signaling in vitro. Front Microbiol 2022; 13:720308. [PMID: 35185840 PMCID: PMC8851338 DOI: 10.3389/fmicb.2022.720308] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 01/10/2022] [Indexed: 11/21/2022] Open
Abstract
Clostridium botulinum produces botulinum neurotoxin complexes that cause botulism. Previous studies elucidated the molecular pathogenesis of botulinum neurotoxin complexes; however, it currently remains unclear whether other components of the bacterium affect host cells. Recent studies provided insights into the role of bacterial membrane vesicles (MVs) produced by some bacterial species in host immunity and pathology. We herein examined and compared the cellular effects of MVs isolated from four strains of C. botulinum with those of closely related Clostridium sporogenes and two strains of the symbiont Clostridium scindens. MVs derived from all strains induced inflammatory cytokine expression in intestinal epithelial and macrophage cell lines. Cytokine expression was dependent on myeloid differentiation primary response (MyD) 88 and TIR-domain-containing adapter-inducing interferon-β (TRIF), essential adaptors for toll-like receptors (TLRs), and TLR1/2/4. The inhibition of actin polymerization impeded the uptake of MVs in RAW264.7 cells, however, did not reduce the induction of cytokine expression. On the other hand, the inhibition of dynamin or phosphatidylinositol-3 kinase (PI3K) suppressed the induction of cytokine expression by MVs, suggesting the importance of these factors downstream of TLR signaling. MVs also induced expression of Reg3 family antimicrobial peptides via MyD88/TRIF signaling in primary cultured mouse small intestinal epithelial cells (IECs). The present results indicate that MVs from C. botulinum and related clostridial species induce host innate immune responses.
Collapse
Affiliation(s)
- Nobuhide Kobayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kimihiro Abe
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Sachiyo Akagi
- Department of Bacteriology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Mayu Kitamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yoshitake Shiraishi
- Department of Functional Anatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Aki Yamaguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Masahiro Yutani
- Department of Bacteriology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Sho Amatsu
- Department of Forensic Medicine and Pathology, Graduate School of Medical Sciences, Kanazawa, Japan
| | - Takuhiro Matsumura
- Department of Bacteriology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, Ibaraki, Japan
| | - Noriyuki Ozaki
- Department of Functional Anatomy, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Nozomu Obana
- Microbiology Research Center for Sustainability, University of Tsukuba, Ibaraki, Japan.,Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yukako Fujinaga
- Department of Bacteriology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| |
Collapse
|
38
|
Liu L, Zhang J, Cheng Y, Zhu M, Xiao Z, Ruan G, Wei Y. Gut microbiota: A new target for T2DM prevention and treatment. Front Endocrinol (Lausanne) 2022; 13:958218. [PMID: 36034447 PMCID: PMC9402911 DOI: 10.3389/fendo.2022.958218] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/22/2022] [Indexed: 12/12/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM), one of the fastest growing metabolic diseases, has been characterized by metabolic disorders including hyperglycemia, hyperlipidemia and insulin resistance (IR). In recent years, T2DM has become the fastest growing metabolic disease in the world. Studies have indicated that patients with T2DM are often associated with intestinal flora disorders and dysfunction involving multiple organs. Metabolites of the intestinal flora, such as bile acids (BAs), short-chain fatty acids (SCFAs) and amino acids (AAs)may influence to some extent the decreased insulin sensitivity associated with T2DM dysfunction and regulate metabolic as well as immune homeostasis. In this paper, we review the changes in the gut flora in T2DM and the mechanisms by which the gut microbiota modulates metabolites affecting T2DM, which may provide a basis for the early identification of T2DM-susceptible individuals and guide targeted interventions. Finally, we also highlight gut microecological therapeutic strategies focused on shaping the gut flora to inform the improvement of T2DM progression.
Collapse
Affiliation(s)
- Lulu Liu
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Plastic and Cosmetic Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jiheng Zhang
- Department of Plastic and Cosmetic Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yi Cheng
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Meng Zhu
- Department of Plastic and Cosmetic Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Zhifeng Xiao
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Guangcong Ruan
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Yanling Wei, ; Guangcong Ruan,
| | - Yanling Wei
- Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Yanling Wei, ; Guangcong Ruan,
| |
Collapse
|
39
|
So SY, Savidge TC. Gut feelings: the microbiota-gut-brain axis on steroids. Am J Physiol Gastrointest Liver Physiol 2022; 322:G1-G20. [PMID: 34730020 PMCID: PMC8698538 DOI: 10.1152/ajpgi.00294.2021] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 01/31/2023]
Abstract
The intricate connection between central and enteric nervous systems is well established with emerging evidence linking gut microbiota function as a significant new contributor to gut-brain axis signaling. Several microbial signals contribute to altered gut-brain communications, with steroids representing an important biological class that impacts central and enteric nervous system function. Neuroactive steroids contribute pathologically to neurological disorders, including dementia and depression, by modulating the activity of neuroreceptors. However, limited information is available on the influence of neuroactive steroids on the enteric nervous system and gastrointestinal function. In this review, we outline how steroids can modulate enteric nervous system function by focusing on their influence on different receptors that are present in the intestine in health and disease. We also highlight the potential role of the gut microbiota in modulating neuroactive steroid signaling along the gut-brain axis.
Collapse
Affiliation(s)
- Sik Yu So
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Tor C Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
| |
Collapse
|
40
|
Blake SJ, James J, Ryan FJ, Caparros-Martin J, Eden GL, Tee YC, Salamon JR, Benson SC, Tumes DJ, Sribnaia A, Stevens NE, Finnie JW, Kobayashi H, White DL, Wesselingh SL, O’Gara F, Lynn MA, Lynn DJ. The immunotoxicity, but not anti-tumor efficacy, of anti-CD40 and anti-CD137 immunotherapies is dependent on the gut microbiota. Cell Rep Med 2021; 2:100464. [PMID: 35028606 PMCID: PMC8714857 DOI: 10.1016/j.xcrm.2021.100464] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 02/06/2023]
Abstract
Immune agonist antibodies (IAAs) are promising immunotherapies that target co-stimulatory receptors to induce potent anti-tumor immune responses, particularly when combined with checkpoint inhibitors. Unfortunately, their clinical translation is hampered by serious dose-limiting, immune-mediated toxicities, including high-grade and sometimes fatal liver damage, cytokine release syndrome (CRS), and colitis. We show that the immunotoxicity, induced by the IAAs anti-CD40 and anti-CD137, is dependent on the gut microbiota. Germ-free or antibiotic-treated mice have significantly reduced colitis, CRS, and liver damage following IAA treatment compared with conventional mice or germ-free mice recolonized via fecal microbiota transplant. MyD88 signaling is required for IAA-induced CRS and for anti-CD137-induced, but not anti-CD40-induced, liver damage. Importantly, antibiotic treatment does not impair IAA anti-tumor efficacy, alone or in combination with anti-PD1. Our results suggest that microbiota-targeted therapies could overcome the toxicity induced by IAAs without impairing their anti-tumor activity.
Collapse
Affiliation(s)
- Stephen J. Blake
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Jane James
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5000, Australia
| | - Feargal J. Ryan
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Jose Caparros-Martin
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
- Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Georgina L. Eden
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Yee C. Tee
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5000, Australia
| | - John R. Salamon
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5000, Australia
| | - Saoirse C. Benson
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5000, Australia
| | - Damon J. Tumes
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Anastasia Sribnaia
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Natalie E. Stevens
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - John W. Finnie
- Adelaide Medical School, University of Adelaide and SA Pathology, Adelaide, SA 5000, Australia
| | - Hiroki Kobayashi
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- School of Medicine, The University of Adelaide, Adelaide, SA, Australia
| | - Deborah L. White
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- School of Medicine, The University of Adelaide, Adelaide, SA, Australia
| | - Steve L. Wesselingh
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5000, Australia
| | - Fergal O’Gara
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
- Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
- BIOMERIT Research Centre, University College Cork, Cork, Ireland
| | - Miriam A. Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - David J. Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5000, Australia
| |
Collapse
|
41
|
So SY, Wu Q, Leung KS, Kundi ZM, Savidge TC, El-Nezami H. Yeast β-glucan reduces obesity-associated Bilophila abundance and modulates bile acid metabolism in healthy and high-fat diet mouse models. Am J Physiol Gastrointest Liver Physiol 2021; 321:G639-G655. [PMID: 34643089 DOI: 10.1152/ajpgi.00226.2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/20/2021] [Accepted: 10/09/2021] [Indexed: 01/31/2023]
Abstract
Emerging evidence links dietary fiber with altered gut microbiota composition and bile acid signaling in maintaining metabolic health. Yeast β-glucan (Y-BG) is a dietary supplement known for its immunomodulatory effect, yet its impact on the gut microbiota and bile acid composition remains unclear. This study investigated whether dietary forms of Y-BG modulate these gut-derived signals. We performed 4-wk dietary supplementation in healthy mice to evaluate the effects of different fiber composition (soluble vs. particulate Y-BG) and dose (0.1% vs. 2%). We found that 2% particulate Y-BG induced robust gut microbiota community shifts with elevated liver Cyp7a1 mRNA abundance and bile acid synthesis. These diet-induced responses were notably different when compared with the prebiotic inulin, and included a marked reduction in fecal Bilophila abundance which we demonstrated as translatable to obesity in population-scale American Gut and TwinsUK clinical cohorts. This prompted us to test whether 2% Y-BG maintained metabolic health in mice fed 60% HFD over 13 wk. Y-BG consistently altered the gut microbiota composition and reduced Bilophila abundance, with trends observed in improvement of metabolic phenotype. Notably, Y-BG improved insulin sensitization and this was associated with enhanced ileal Glpr1r mRNA accumulation and reduced Bilophila abundance. Collectively, our results demonstrate that Y-BG modulates gut microbiota community composition and bile acid signaling, but the dietary regime needs to be optimized to facilitate clinical improvement in metabolic phenotype in an aggressive high-fat diet animal model.NEW & NOTEWORTHY The study shows that dietary Y-BG supplementation modulated gut microbiota, bile acid metabolism and associated signaling pathways. Y-BG significantly reduced Bilophila abundance which is associated with obesity in human cohorts. Correlation analysis confirmed functional interactions between bile acid composition, gut microbiota, and metabolic phenotype, although clinical benefit did not reach significance in an aggressive obesity model. Gut microbiota and bile acids correlated with metabolic parameters, indicating future potential of dietary Y-BG modulation of metabolic pathways.
Collapse
Affiliation(s)
- Sik Yu So
- School of Biological Sciences, Faculty of Science, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam, Hong Kong
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Qinglong Wu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Kin Sum Leung
- School of Biological Sciences, Faculty of Science, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam, Hong Kong
| | - Zuzanna Maria Kundi
- School of Biological Sciences, Faculty of Science, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam, Hong Kong
| | - Tor C Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Hani El-Nezami
- School of Biological Sciences, Faculty of Science, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam, Hong Kong
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| |
Collapse
|
42
|
Xia D, Yang L, Cui J, Li Y, Jiang X, Meca G, Wang S, Feng Y, Zhao Y, Qin J, Zhu Y, Ye H, Wang W. Combined Analysis of the Effects of Exposure to Blue Light in Ducks Reveals a Reduction in Cholesterol Accumulation Through Changes in Methionine Metabolism and the Intestinal Microbiota. Front Nutr 2021; 8:737059. [PMID: 34901103 PMCID: PMC8656972 DOI: 10.3389/fnut.2021.737059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/18/2021] [Indexed: 11/21/2022] Open
Abstract
Monochromatic light is widely used in industry, medical treatment, and animal husbandry. Green-blue light has been found to stimulate the proliferation of satellite cells and the results of studies on the effects of blue light on poultry vary widely. It would be worthwhile to study the effect of blue light on poultry growth and how exposure to blue light affects metabolism and the intestinal microbiota. In this study, we irradiated Cherry Valley ducks with 460 nm wavelength light (blue light) for 3 weeks to explore the effects of blue light in comparison to those of white light (combined wavelength light) on animal growth and development. Our results showed that, under exposure to blue light, the body weight and average daily feed intake of ducks were decreased, but the leg muscle and relative length of the intestine were increased. Exposure to blue light chiefly enhanced the anti-inflammatory and antioxidant capacities of the animal and decreased lipid levels in serum and liver. Metabolomic analysis revealed that blue light heightened cysteine and methionine metabolism, and increased serum taurine and primary bile acid levels, as well as up-regulating the metabolites L-carnitine and glutamine. Treatment with blue light significantly increased the beta diversity of intestinal microbiota and the relative abundances of bile acid hydrolase-producing bacteria, especially Alistipes. These changes promote the synthesis of secondary bile acids to further enhance lipid metabolism in the host, thereby reducing cholesterol accumulation in ducks. These results should help us better understand the effects of exposure to blue light on metabolite levels and the intestinal microbiota, and suggest that it may be possible to use colored light to control the development of livestock and poultry.
Collapse
Affiliation(s)
- Daiyang Xia
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Lin Yang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jiajie Cui
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yu Li
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xianzhi Jiang
- Microbiome Research Center, Moon (Guangzhou) Biotech Co. Ltd., Guangzhou, China
| | - Giuseppe Meca
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Valencia, Spain
| | | | - Yan Feng
- Guangdong Haida Group Co. Ltd., Guangzhou, China
| | - Yujie Zhao
- Gold Coin Feedmill (Dong Guan) Co. Ltd., Dongguan, China
| | | | - Yongwen Zhu
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Hui Ye
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wence Wang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, China
| |
Collapse
|
43
|
Yan Q, Zhang S, Li S, Wang G, Zhang A, Jin T, Zhang Y, Lv Q, Xiao M, Sun Y, Li X, Cui S, Li R, Ma X, Wang C, Tian X, Duan X, Xin Y, Mao X, Ma Y. Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients. Front Microbiol 2021; 12:739621. [PMID: 34790179 PMCID: PMC8591784 DOI: 10.3389/fmicb.2021.739621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 10/07/2021] [Indexed: 12/18/2022] Open
Abstract
The microbes in human bile are closely related to gallbladder health and other potential disorders. Although the bile microbial community has been investigated by recent studies using amplicon or metagenomic sequencing technologies, the genomic information of the microbial species resident in bile is rarely reported. Herein, we isolated 138 bacterial colonies from the fresh bile specimens of four cholecystitis patients using a culturome approach and genomically characterized 35 non-redundant strains using whole-genome shotgun sequencing. The bile bacterial isolates spanned 3 classes, 6 orders, 10 families, and 14 genera, of which the members of Enterococcus, Escherichia-Shigella, Lysinibacillus, and Enterobacter frequently appeared. Genomic analysis identified three species, including Providencia sp. D135, Psychrobacter sp. D093, and Vibrio sp. D074, which are not represented in existing reference genome databases. Based on the genome data, the functional capacity between bile and gut isolates was compared. The bile strains encoded 5,488 KEGG orthologs, of which 4.9% were specific to the gut strains, including the enzymes involved in biofilm formation, two-component systems, and quorum-sensing pathways. A total of 472 antibiotic resistance genes (ARGs) were identified from the bile genomes including multidrug resistance proteins (42.6%), fluoroquinolone resistance proteins (12.3%), aminoglycoside resistance proteins (9.1%), and β-lactamase (7.2%). Moreover, in vitro experiments showed that some bile bacteria have the capabilities for bile salt deconjugation or biotransformation (of primary bile acids into secondary bile acids). Although the physiological or pathological significance of these bacteria needs further exploration, our works expanded knowledge about the genome, diversity, and function of human bile bacteria.
Collapse
Affiliation(s)
- Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China.,Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Siyi Zhang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China.,Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Taiyang Jin
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan, China
| | - Manchun Xiao
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yuanyuan Sun
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xiang Li
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Song Cui
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Rui Li
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xiaochi Ma
- College of Pharmacy, Dalian Medical University, Dalian, China
| | - Chao Wang
- College of Pharmacy, Dalian Medical University, Dalian, China
| | - Xiangge Tian
- College of Pharmacy, Dalian Medical University, Dalian, China
| | - Xiaohui Duan
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Yi Xin
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xianhai Mao
- Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Yufang Ma
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| |
Collapse
|
44
|
Song I, Gotoh Y, Ogura Y, Hayashi T, Fukiya S, Yokota A. Comparative Genomic and Physiological Analysis against Clostridium scindens Reveals Eubacterium sp. c-25 as an Atypical Deoxycholic Acid Producer of the Human Gut Microbiota. Microorganisms 2021; 9:microorganisms9112254. [PMID: 34835380 PMCID: PMC8623032 DOI: 10.3390/microorganisms9112254] [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: 09/24/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 12/27/2022] Open
Abstract
The human gut houses bile acid 7α-dehydroxylating bacteria that produce secondary bile acids such as deoxycholic acid (DCA) from host-derived bile acids through enzymes encoded by the bai operon. While recent metagenomic studies suggest that these bacteria are highly diverse and abundant, very few DCA producers have been identified. Here, we investigated the physiology and determined the complete genome sequence of Eubacterium sp. c-25, a DCA producer that was isolated from human feces in the 1980s. Culture experiments showed a preference for neutral to slightly alkaline pH in both growth and DCA production. Genomic analyses revealed that c-25 is phylogenetically distinct from known DCA producers and possesses a multi-cluster arrangement of predicted bile-acid inducible (bai) genes that is considerably different from the typical bai operon structure. This arrangement is also found in other intestinal bacterial species, possibly indicative of unconfirmed 7α-dehydroxylation capabilities. Functionality of the predicted bai genes was supported by the induced expression of baiB, baiCD, and baiH in the presence of cholic acid substrate. Taken together, Eubacterium sp. c-25 is an atypical DCA producer with a novel bai gene cluster structure that may represent an unexplored genotype of DCA producers in the human gut.
Collapse
Affiliation(s)
- Isaiah Song
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (I.S.); (A.Y.)
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (Y.G.); (T.H.)
| | - Yoshitoshi Ogura
- Department of Infectious Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan;
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (Y.G.); (T.H.)
| | - Satoru Fukiya
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (I.S.); (A.Y.)
- Correspondence: ; Tel.: +81-11-706-2501
| | - Atsushi Yokota
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (I.S.); (A.Y.)
| |
Collapse
|
45
|
Choudhuri S, Klaassen CD. MOLECULAR REGULATION OF BILE ACID HOMEOSTASIS. Drug Metab Dispos 2021; 50:425-455. [PMID: 34686523 DOI: 10.1124/dmd.121.000643] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/20/2021] [Indexed: 11/22/2022] Open
Abstract
Bile acids have been known for decades to aid in the digestion and absorption of dietary fats and fat-soluble vitamins in the intestine. The development of gene knockout mice models and transgenic humanized mouse models have helped us understand other function of bile acids, such as their role in modulating fat, glucose, and energy metabolism, and in the molecular regulation of the synthesis, transport, and homeostasis of bile acids. The G-protein coupled receptor TGR5 regulates the bile acid induced alterations of intermediary metabolism, while the nuclear receptor FXR regulates bile acid synthesis and homeostasis. However, this review indicates that unidentified factors in addition to FXR must exist to aid in the regulation of bile acid synthesis and homeostasis. Significance Statement This review captures the present understanding of bile acid synthesis, the role of bile acid transporters in the enterohepatic circulation of bile acids, the role of the nuclear receptor FXR on the regulation of bile acid synthesis and bile acid transporters, and the importance of bile acids in activating GPCR signaling via TGR5 to modify intermediary metabolism. This information is useful for developing drugs for the treatment of various hepatic and intestinal diseases, as well as the metabolic syndrome.
Collapse
Affiliation(s)
| | - Curtis D Klaassen
- Environmental & Occupational Health Sciences, Univ Washington, United States
| |
Collapse
|
46
|
Intestinal hypoxia-inducible factor 2α regulates lactate levels to shape the gut microbiome and alter thermogenesis. Cell Metab 2021; 33:1988-2003.e7. [PMID: 34329568 DOI: 10.1016/j.cmet.2021.07.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/12/2021] [Accepted: 07/07/2021] [Indexed: 12/17/2022]
Abstract
Accumulating evidence suggests that the gut microbiota regulates obesity through metabolite-host interactions. However, the mechanisms underlying such interactions have been unclear. Here, we found that intestinal hypoxia-inducible factor 2α (HIF-2α) positively regulates gut lactate by controlling the expression of intestinal Ldha. Intestine-specific HIF-2α ablation in mice resulted in lower lactate levels, and less Bacteroides vulgatus and greater Ruminococcus torques abundance, respectively. Together, these changes resulted in elevated taurine-conjugated cholic acid (TCA) and deoxycholic acid (DCA) levels and activation of the adipose G-protein-coupled bile acid receptor, GPBAR1 (TGR5). This activation upregulated expression of uncoupling protein (UCP) 1 and mitochondrial creatine kinase (CKMT) 2, resulting in elevation of white adipose tissue thermogenesis. Administration of TCA and DCA mirrored these phenotypes, and colonization with B. vulgatus and R. torques inhibited and induced thermogenesis, respectively. This work deepens our understanding of how host genes regulate the microbiome and provides novel strategies for alleviating obesity.
Collapse
|
47
|
Thompson RS, Gaffney M, Hopkins S, Kelley T, Gonzalez A, Bowers SJ, Vitaterna MH, Turek FW, Foxx CL, Lowry CA, Vargas F, Dorrestein PC, Wright KP, Knight R, Fleshner M. Ruminiclostridium 5, Parabacteroides distasonis, and bile acid profile are modulated by prebiotic diet and associate with facilitated sleep/clock realignment after chronic disruption of rhythms. Brain Behav Immun 2021; 97:150-166. [PMID: 34242738 DOI: 10.1016/j.bbi.2021.07.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 12/12/2022] Open
Abstract
Chronic disruption of rhythms (CDR) impacts sleep and can result in circadian misalignment of physiological systems which, in turn, is associated with increased disease risk. Exposure to repeated or severe stressors also disturbs sleep and diurnal rhythms. Prebiotic nutrients produce favorable changes in gut microbial ecology, the gut metabolome, and reduce several negative impacts of acute severe stressor exposure, including disturbed sleep, core body temperature rhythmicity, and gut microbial dysbiosis. In light of previous compelling evidence that prebiotic diet broadly reduces negative impacts of acute, severe stressors, we hypothesize that prebiotic diet will also effectively mitigate the negative impacts of chronic disruption of circadian rhythms on physiology and sleep/wake behavior. Male, Sprague Dawley rats were fed diets enriched in prebiotic substrates or calorically matched control chow. After 5 weeks on diet, rats were exposed to CDR (12 h light/dark reversal, weekly for 8 weeks) or remained on undisturbed normal light/dark cycles (NLD). Sleep EEG, core body temperature, and locomotor activity were recorded via biotelemetry in freely moving rats. Fecal samples were collected on experimental days -33, 0 (day of onset of CDR), and 42. Taxonomic identification and relative abundances of gut microbes were measured in fecal samples using 16S rRNA gene sequencing and shotgun metagenomics. Fecal primary, bacterially modified secondary, and conjugated bile acids were measured using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Prebiotic diet produced rapid and stable increases in the relative abundances of Parabacteroides distasonis and Ruminiclostridium 5. Shotgun metagenomics analyses confirmed reliable increases in relative abundances of Parabacteroides distasonis and Clostridium leptum, a member of the Ruminiclostridium genus. Prebiotic diet also modified fecal bile acid profiles; and based on correlational and step-wise regression analyses, Parabacteroides distasonis and Ruminiclostridium 5 were positively associated with each other and negatively associated with secondary and conjugated bile acids. Prebiotic diet, but not CDR, impacted beta diversity. Measures of alpha diversity evenness were decreased by CDR and prebiotic diet prevented that effect. Rats exposed to CDR while eating prebiotic, compared to control diet, more quickly realigned NREM sleep and core body temperature (ClockLab) diurnal rhythms to the altered light/dark cycle. Finally, both cholic acid and Ruminiclostridium 5 prior to CDR were associated with time to realign CBT rhythms to the new light/dark cycle after CDR; whereas both Ruminiclostridium 5 and taurocholic acid prior to CDR were associated with NREM sleep recovery after CDR. These results support our hypothesis and suggest that ingestion of prebiotic substrates is an effective strategy to increase the relative abundance of health promoting microbes, alter the fecal bile acid profile, and facilitate the recovery and realignment of sleep and diurnal rhythms after circadian disruption.
Collapse
Affiliation(s)
- Robert S Thompson
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA; Center for Neuroscience, University of Colorado at Boulder, Boulder, CO, USA.
| | - Michelle Gaffney
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA; Center for Neuroscience, University of Colorado at Boulder, Boulder, CO, USA
| | - Shelby Hopkins
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA
| | - Tel Kelley
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Samuel J Bowers
- Department of Neurobiology, Northwestern University, Center for Sleep and Circadian Biology, Evanston, IL, USA
| | - Martha Hotz Vitaterna
- Department of Neurobiology, Northwestern University, Center for Sleep and Circadian Biology, Evanston, IL, USA
| | - Fred W Turek
- Department of Neurobiology, Northwestern University, Center for Sleep and Circadian Biology, Evanston, IL, USA
| | - Christine L Foxx
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA
| | - Christopher A Lowry
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA; Center for Neuroscience, University of Colorado at Boulder, Boulder, CO, USA
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, CA, USA
| | - Kenneth P Wright
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA; Center for Neuroscience, University of Colorado at Boulder, Boulder, CO, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Monika Fleshner
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA; Center for Neuroscience, University of Colorado at Boulder, Boulder, CO, USA.
| |
Collapse
|
48
|
Lucas LN, Barrett K, Kerby RL, Zhang Q, Cattaneo LE, Stevenson D, Rey FE, Amador-Noguez D. Dominant Bacterial Phyla from the Human Gut Show Widespread Ability To Transform and Conjugate Bile Acids. mSystems 2021; 6:e0080521. [PMID: 34463573 DOI: 10.1128/msystems.00805-21] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022] Open
Abstract
Gut bacteria influence human physiology by chemically modifying host-synthesized primary bile acids. These modified bile acids, known as secondary bile acids, can act as signaling molecules that modulate host lipid, glucose, and energy metabolism and affect gut microbiota composition via selective antimicrobial properties. However, knowledge regarding the bile acid-transforming capabilities of individual gut microbes remains limited. To help address this knowledge gap, we screened 72 bacterial isolates, spanning seven major phyla commonly found in the human gut, for their ability to chemically modify unconjugated bile acids. We found that 43 isolates, representing 41 species, were capable of in vitro modification of one or more of the three most abundant unconjugated bile acids in humans: cholic acid, chenodeoxycholic acid, and deoxycholic acid. Of these, 32 species have not been previously described as bile acid transformers. The most prevalent bile acid transformations detected were oxidation of 3α-, 7α-, or 12α-hydroxyl groups on the steroid core, a reaction catalyzed by hydroxysteroid dehydrogenases. In addition, we found 7α-dehydroxylation activity to be distributed across various bacterial genera, and we observed several other complex bile acid transformations. Finally, our screen revealed widespread bacterial conjugation of primary and secondary bile acids to glycine, a process that was thought to only occur in the liver, and to 15 other amino acids, resulting in the discovery of 44 novel microbially conjugated bile acids. IMPORTANCE Our current knowledge regarding microbial bile acid transformations comes primarily from biochemical studies on a relatively small number of species or from bioinformatic predictions that rely on homology to known bile acid-transforming enzyme sequences. Therefore, much remains to be learned regarding the variety of bile acid transformations and their representation across gut microbial species. By carrying out a systematic investigation of bacterial species commonly found in the human intestinal tract, this study helps better define the gut bacteria that impact composition of the bile acid pool, which has implications in the context of metabolic disorders and cancers of the digestive tract. Our results greatly expand upon the list of bacterial species known to perform different types of bile acid transformations. This knowledge will be vital for assessing the causal connections between the microbiome, bile acid pool composition, and human health.
Collapse
Affiliation(s)
- L N Lucas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - K Barrett
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - R L Kerby
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Q Zhang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - L E Cattaneo
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - D Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - F E Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - D Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
49
|
Hassouneh SAD, Loftus M, Yooseph S. Linking Inflammatory Bowel Disease Symptoms to Changes in the Gut Microbiome Structure and Function. Front Microbiol 2021; 12:673632. [PMID: 34349736 PMCID: PMC8326577 DOI: 10.3389/fmicb.2021.673632] [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: 02/28/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease of the gastrointestinal tract that is often characterized by abdominal pain, rectal bleeding, inflammation, and weight loss. Many studies have posited that the gut microbiome may play an integral role in the onset and exacerbation of IBD. Here, we present a novel computational analysis of a previously published IBD dataset. This dataset consists of shotgun sequence data generated from fecal samples collected from individuals with IBD and an internal control group. Utilizing multiple external controls, together with appropriate techniques to handle the compositionality aspect of sequence data, our computational framework can identify and corroborate differences in the taxonomic profiles, bacterial association networks, and functional capacity within the IBD gut microbiome. Our analysis identified 42 bacterial species that are differentially abundant between IBD and every control group (one internal control and two external controls) with at least a twofold difference. Of the 42 species, 34 were significantly elevated in IBD, relative to every other control. These 34 species were still present in the control groups and appear to play important roles, according to network centrality and degree, in all bacterial association networks. Many of the species elevated in IBD have been implicated in modulating the immune response, mucin degradation, antibiotic resistance, and inflammation. We also identified elevated relative abundances of protein families related to signal transduction, sporulation and germination, and polysaccharide degradation as well as decreased relative abundance of protein families related to menaquinone and ubiquinone biosynthesis. Finally, we identified differences in functional capacities between IBD and healthy controls, and subsequently linked the changes in the functional capacity to previously published clinical research and to symptoms that commonly occur in IBD.
Collapse
Affiliation(s)
- Sayf Al-Deen Hassouneh
- Burnett School of Biomedical Sciences, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, United States
| | - Mark Loftus
- Burnett School of Biomedical Sciences, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, United States
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, United States
| |
Collapse
|
50
|
Wen J, Mercado GP, Volland A, Doden HL, Lickwar CR, Crooks T, Kakiyama G, Kelly C, Cocchiaro JL, Ridlon JM, Rawls JF. Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine. SCIENCE ADVANCES 2021; 7:eabg1371. [PMID: 34301599 PMCID: PMC8302129 DOI: 10.1126/sciadv.abg1371] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/07/2021] [Indexed: 05/02/2023]
Abstract
Bile salt synthesis, secretion into the intestinal lumen, and resorption in the ileum occur in all vertebrate classes. In mammals, bile salt composition is determined by host and microbial enzymes, affecting signaling through the bile salt-binding transcription factor farnesoid X receptor (Fxr). However, these processes in other vertebrate classes remain poorly understood. We show that key components of hepatic bile salt synthesis and ileal transport pathways are conserved and under control of Fxr in zebrafish. Zebrafish bile salts consist primarily of a C27 bile alcohol and a C24 bile acid that undergo multiple microbial modifications including bile acid deconjugation that augments Fxr activity. Using single-cell RNA sequencing, we provide a cellular atlas of the zebrafish intestinal epithelium and uncover roles for Fxr in transcriptional and differentiation programs in ileal and other cell types. These results establish zebrafish as a nonmammalian vertebrate model for studying bile salt metabolism and Fxr signaling.
Collapse
Affiliation(s)
- Jia Wen
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Gilberto Padilla Mercado
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Alyssa Volland
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Heidi L Doden
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Colin R Lickwar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Taylor Crooks
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Genta Kakiyama
- Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Cecelia Kelly
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Jordan L Cocchiaro
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Jason M Ridlon
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, 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 of Illinois, Urbana, IL, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA.
| |
Collapse
|