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Camilleri M. Pouchitis: Is It Time to Think Beyond the Inflammation in the Pouch? Gastroenterology 2024:S0016-5085(24)04997-7. [PMID: 39007794 DOI: 10.1053/j.gastro.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/02/2024] [Accepted: 05/04/2024] [Indexed: 07/16/2024]
Affiliation(s)
- Michael Camilleri
- Clinical Enteric Neuroscience Translational and Epidemiological Research, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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2
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Santiago P, Quinn KP, Chen J, Friton JJ, Rypstra CR, Kashyap PC, Raffals LE. Altered Bile Acid and Pouch Microbiota Composition in Patients With Chronic Pouchitis. Inflamm Bowel Dis 2024; 30:1062-1070. [PMID: 38037191 PMCID: PMC11219471 DOI: 10.1093/ibd/izad288] [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: 03/17/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Patients with ulcerative colitis and total abdominal proctocolectomy with ileal pouch-anal anastomosis have a 50% risk of pouchitis and a 5% to 10% risk of chronic pouchitis. AIMS The goal of the study was to compare pouch microbiota and stool bile acid composition in patients with chronic pouchitis, chronic pouchitis and primary sclerosing cholangitis, and normal pouch. METHODS Patients with ulcerative colitis and ileal pouch-anal anastomosis were recruited from March 20, 2014, to August 6, 2019, and categorized into normal pouch, chronic pouchitis, and chronic pouchitis/primary sclerosing cholangitis groups. Stool samples were subjected to bile acid quantification and 16S rRNA gene sequencing. Statistical comparisons of absolute bile acid abundance and pouch microbiota α-diversity, β-diversity, and taxa abundance were performed among the patient groups. RESULTS A total of 51 samples were analyzed. Both α-diversity (P = .01, species richness) and β-diversity (P = .001) significantly differed among groups. Lithocholic acid was significantly lower in patients with chronic pouchitis/primary sclerosing cholangitis than in those with chronic pouchitis (P = .01) or normal pouch (P = .03). Decreased α-diversity was associated with an increased primary to secondary bile acid ratio (P = .002), which was also associated with changes in β-diversity (P = .006). CONCLUSIONS Pouch microbiota α- and β-diversity differed among patients with normal pouch, chronic pouchitis, and chronic pouchitis/primary sclerosing cholangitis. Lithocholic acid level and primary to secondary bile acid ratio were highly associated with pouch microbiota richness, structure, and composition. These findings emphasize the associations between pouch microbiota and bile acid composition in dysbiosis and altered metabolism, suggesting that secondary bile acids are decreased in chronic pouchitis.
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Affiliation(s)
- Priscila Santiago
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, United States
| | - Kevin P Quinn
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, United States
| | - Jun Chen
- Division of Computational Biology, Mayo Clinic, Rochester, United States
| | - Jessica J Friton
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, United States
| | - Chad R Rypstra
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, United States
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, United States
| | - Laura E Raffals
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, United States
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3
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Alenzi M, Schildkraut T, Hartley I, Badiani S, Ding NS, Rao V, Segal JP. The aetiology of pouchitis in patients with inflammatory bowel disease. Therap Adv Gastroenterol 2024; 17:17562848241249449. [PMID: 38812704 PMCID: PMC11135114 DOI: 10.1177/17562848241249449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 04/08/2024] [Indexed: 05/31/2024] Open
Abstract
Restorative proctocolectomy with ileal pouch-anal anastomosis is a treatment option for patients with refractory ulcerative colitis. Pouchitis is the most common complication, representing a spectrum of diseases ranging from acute antibiotic-responsive type to chronic antibiotic-refractory. Early accurate diagnosis using a combined assessment of symptoms, endoscopy and histology is important for both treatment and prognostication. Most patients respond well to antibiotic therapy; however, management of chronic antibiotic-refractory pouchitis remains a challenge, and treatment options are based on small studies. Pouchitis is thought to be driven by the interaction between genetics, the immune system and the environment but as yet a causal relationship has yet to be identified. Further longitudinal assessment of the pouch integrating new technologies may help us understand the factors driving pouchitis. This review outlines the currently understood risk factors and aetiology of pouchitis.
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Affiliation(s)
- Maram Alenzi
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Tamar Schildkraut
- Department of Gastroenterology, St Vincent’s Hospital, Melbourne, VIC, Australia
| | - Imogen Hartley
- Department of Gastroenterology, St Vincent’s Hospital, Melbourne, VIC, Australia
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Sarit Badiani
- Department of Surgery, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Nik Sheng Ding
- Department of Gastroenterology, St Vincent’s Hospital, Melbourne, VIC, Australia
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Vikram Rao
- Department of General Medicine, Western Health, Footscray, VIC, Australia
| | - Jonathan P. Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, VIC, Australia
- Department of Medicine, University of Melbourne, Parkville, VIC, Australia
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4
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Zhang M, Shi Z, Wu C, Yang F, Su T, Jing X, Shi J, Ren H, Jiang L, Jiang Y, Zhang C, Zhou W, Zhou Y, Wu K, Zheng S, Zhong X, Wu L, Gu W, Hong J, Wang J, Ning G, Liu R, Zhong H, Zhou W, Wang W. Cushing Syndrome Is Associated With Gut Microbial Dysbiosis and Cortisol-Degrading Bacteria. J Clin Endocrinol Metab 2024; 109:1474-1484. [PMID: 38157274 DOI: 10.1210/clinem/dgad766] [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: 08/29/2023] [Revised: 11/28/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
CONTEXT Cushing syndrome (CS) is a severe endocrine disease characterized by excessive secretion of cortisol with multiple metabolic disorders. While gut microbial dysbiosis plays a vital role in metabolic disorders, the role of gut microbiota in CS remains unclear. OBJECTIVE The objective of this work is to examine the alteration of gut microbiota in patients with CS. METHODS We performed shotgun metagenomic sequencing of fecal samples from 78 patients with CS and 78 healthy controls matched for age and body mass index. Furthermore, we verify the cortisol degradation capacity of Ruminococcus gnavus in vitro and identify the potential metabolite by LC-MC/MS. RESULTS We observed significant differences in microbial composition between CS and controls in both sexes, with CS showing reduced Bacteroidetes (Bacteroides vulgatus) and elevated Firmicutes (Erysipelotrichaceae_bacterium_6_1_45) and Proteobacteria (Enterobacter cloacae). Despite distinct causes of hypercortisolism in ACTH-dependent and ACTH-independent CS, we found no significant differences in metabolic profiles or gut microbiota between the 2 subgroups. Furthermore, we identified a group of gut species, including R. gnavus, that were positively correlated with cortisol levels in CS. These bacteria were found to harbor cortisol-degrading desAB genes and were consistently enriched in CS. Moreover, we demonstrated the efficient capacity of R. gnavus to degrade cortisol to 11-oxygenated androgens in vitro. CONCLUSION This study provides evidence of gut microbial dysbiosis in patients with CS and identifies a group of CS-enriched bacteria capable of degrading cortisol. These findings highlight the potential role of gut microbiota in regulating host steroid hormone levels, and consequently host health.
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Affiliation(s)
- Minchun Zhang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhun Shi
- BGI Research, Shenzhen 518083, China
| | - Chao Wu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | | | - Tingwei Su
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaohuan Jing
- China National GeneBank, BGI Research, Shenzhen 518120, China
| | - Juan Shi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | | | - Lei Jiang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yiran Jiang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Cui Zhang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wenzhong Zhou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yijing Zhou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Kui Wu
- BGI Research, Shenzhen 518083, China
| | - Sichang Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xu Zhong
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Luming Wu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Weiqiong Gu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jie Hong
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiqiu Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ruixin Liu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | | | - Weiwei Zhou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Weiqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
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5
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Hong J, Fu T, Liu W, Du Y, Bu J, Wei G, Yu M, Lin Y, Min C, Lin D. An Update on the Role and Potential Molecules in Relation to Ruminococcus gnavus in Inflammatory Bowel Disease, Obesity and Diabetes Mellitus. Diabetes Metab Syndr Obes 2024; 17:1235-1248. [PMID: 38496006 PMCID: PMC10942254 DOI: 10.2147/dmso.s456173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/27/2024] [Indexed: 03/19/2024] Open
Abstract
Ruminococcus gnavus (R. gnavus) is a gram-positive anaerobe commonly resides in the human gut microbiota. The advent of metagenomics has linked R. gnavus with various diseases, including inflammatory bowel disease (IBD), obesity, and diabetes mellitus (DM), which has become a growing area of investigation. The initial focus of research primarily centered on assessing the abundance of R. gnavus and its potential association with disease presentation, taking into account variations in sample size, sequencing and analysis methods. However, recent investigations have shifted towards elucidating the underlying mechanistic pathways through which R. gnavus may contribute to disease manifestation. In this comprehensive review, we aim to provide an updated synthesis of the current literature on R. gnavus in the context of IBD, obesity, and DM. We critically analyze relevant studies and summarize the potential molecular mediators implicated in the association between R. gnavus and these diseases. Across numerous studies, various molecules such as methylation-controlled J (MCJ), glucopolysaccharides, ursodeoxycholic acid (UDCA), interleukin(IL)-10, IL-17, and capric acid have been proposed as potential contributors to the link between R. gnavus and IBD. Similarly, in the realm of obesity, molecules such as hydrogen peroxide, butyrate, and UDCA have been suggested as potential mediators, while glycine ursodeoxycholic acid (GUDCA) has been implicated in the connection between R. gnavus and DM. Furthermore, it is imperative to emphasize the necessity for additional studies to evaluate the potential efficacy of targeting pathways associated with R. gnavus as a viable strategy for managing these diseases. These findings have significantly expanded our understanding of the functional role of R. gnavus in the context of IBD, obesity, and DM. This review aims to offer updated insights into the role and potential mechanisms of R. gnavus, as well as potential strategies for the treatment of these diseases.
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Affiliation(s)
- Jinni Hong
- Department of Traditional Chinese Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, People’s Republic of China
- Guangdong Provincial Institute of Geriatric, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Tingting Fu
- Department of Traditional Chinese Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, People’s Republic of China
- Guangdong Provincial Institute of Geriatric, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Weizhen Liu
- Department of Traditional Chinese Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, People’s Republic of China
- Guangdong Provincial Institute of Geriatric, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Yu Du
- Department of Traditional Chinese Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, People’s Republic of China
- Guangdong Provincial Institute of Geriatric, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Junmin Bu
- Department of Traditional Chinese Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, People’s Republic of China
- Guangdong Provincial Institute of Geriatric, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Guojian Wei
- Department of Traditional Chinese Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, People’s Republic of China
- Guangdong Provincial Institute of Geriatric, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Miao Yu
- Department of Traditional Chinese Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, People’s Republic of China
- Guangdong Provincial Institute of Geriatric, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Yanshan Lin
- Department of Traditional Chinese Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, People’s Republic of China
- Guangdong Provincial Institute of Geriatric, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Cunyun Min
- Department of Traditional Chinese Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, People’s Republic of China
- Guangdong Provincial Institute of Geriatric, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Datao Lin
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, People’s Republic of China
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6
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Fiebig A, Schnizlein MK, Pena-Rivera S, Trigodet F, Dubey AA, Hennessy MK, Basu A, Pott S, Dalal S, Rubin D, Sogin ML, Eren AM, Chang EB, Crosson S. Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. mBio 2024; 15:e0283023. [PMID: 38063424 PMCID: PMC10790697 DOI: 10.1128/mbio.02830-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 12/19/2023] Open
Abstract
IMPORTANCE The Gram-negative bacterium Bacteroides fragilis is a common member of the human gut microbiota that colonizes multiple host niches and can influence human physiology through a variety of mechanisms. Identification of genes that enable B. fragilis to grow across a range of host environments has been impeded in part by the relatively limited genetic tractability of this species. We have developed a high-throughput genetic resource for a B. fragilis strain isolated from a UC pouchitis patient. Bile acids limit microbial growth and are altered in abundance in UC pouches, where B. fragilis often blooms. Using this resource, we uncovered pathways and processes that impact B. fragilis fitness in bile and that may contribute to population expansions during bouts of gut inflammation.
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Affiliation(s)
- Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Matthew K. Schnizlein
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Selymar Pena-Rivera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Florian Trigodet
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Abhishek Anil Dubey
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Miette K. Hennessy
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Anindita Basu
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sebastian Pott
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sushila Dalal
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - David Rubin
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - A. Murat Eren
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Eugene B. Chang
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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7
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Hartikainen AK, Khan I, Karjalainen EK, Renkonen-Sinisalo L, Arkkila P, Jalanka J, Lepistö AH, Satokari R. Microbiota and mucosal gene expression of fecal microbiota transplantation or placebo treated patients with chronic pouchitis. Gut Microbes 2024; 16:2295445. [PMID: 38214604 PMCID: PMC10793679 DOI: 10.1080/19490976.2023.2295445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024] Open
Abstract
Altered microbiota and impaired host immune function have been linked to the pathogenesis of pouchitis. We used 16S rRNA gene sequencing and RNA sequencing data from a previous randomized clinical trial (RCT) on fecal microbiota transplantation (FMT) therapy in 26 chronic pouchitis patients with one-year follow-up. We analyzed changes in both luminal and mucosal microbiota composition, as well as in host mucosal gene expression to gain insights into the host-microbiota interactions possibly underlying clinical outcomes of the patients. Antibiotic type and pattern of use were significant drivers of the luminal microbiota at baseline. Differential gene expression analysis indicated transition from ileal to colonic gene expression in the pouch, and upregulation in inflammation- and immune system-related pathways in the pouch. At 4 weeks, the non-relapsed FMT patients had a lower microbiota dissimilarity to the donor than the non-relapsed placebo patients (p = .02). While two FMT-treated patients showed a shift toward the donor's microbiota during the one-year follow-up, the overall FMT microbiota modulation effect was low. Patient's luminal and mucosal microbiota profiles were unstable in both FMT and placebo groups. Expression of the chemokine receptor CXCR4 was downregulated at 52 weeks compared to the baseline in the non-relapsed patients in both FMT and placebo groups. Microbiota modulation by FMT seems to be low in this patient group. The microbiota composition or alterations did not explain the relapse status of the patients. Some evidence for remission-related host gene expression pattern was found; specifically, CXCR4 expression may have a role in sustained remission.
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Affiliation(s)
- Anna K. Hartikainen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Imran Khan
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Essi K. Karjalainen
- Department of Gastrointestinal Surgery, Helsinki University Hospital, Helsinki, Finland
| | - Laura Renkonen-Sinisalo
- Department of Gastrointestinal Surgery, Helsinki University Hospital, Helsinki, Finland
- Genome-Scale Biology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Perttu Arkkila
- Department of Gastroenterology, Helsinki University Hospital, Helsinki, Finland
- Department of Medicine, University of Helsinki, Helsinki, Finland
| | - Jonna Jalanka
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna H. Lepistö
- Department of Gastrointestinal Surgery, Helsinki University Hospital, Helsinki, Finland
- Genome-Scale Biology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Reetta Satokari
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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8
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Jia XM, Wu BX, Chen BD, Li KT, Liu YD, Xu Y, Wang J, Zhang X. Compositional and functional aberrance of the gut microbiota in treatment-naïve patients with primary Sjögren's syndrome. J Autoimmun 2023; 141:103050. [PMID: 37120327 DOI: 10.1016/j.jaut.2023.103050] [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] [Indexed: 05/01/2023]
Abstract
OBJECTIVES To investigate the compositional and functional characteristics of the gut microbiota in primary Sjögren's syndrome (pSS) and compare them with those in systemic lupus erythematosus (SLE). METHODS Stool samples from 78 treatment-naïve pSS patients and 78 matched healthy controls were detected by shotgun metagenomic sequencing and compared with those from 49 treatment-naïve SLE patients. The virulence loads and mimotopes of the gut microbiota were also assessed by sequence alignment. RESULTS The gut microbiota of treatment-naïve pSS patients had lower richness and evenness and showed a different community distribution than that of healthy controls. The microbial species enriched in the pSS-associated gut microbiota included Lactobacillus salivarius, Bacteroides fragilis, Ruminococcus gnavus, Clostridium bartlettii, Clostridium bolteae, Veillonella parvula, and Streptococcus parasanguinis. Lactobacillus salivarius was the most discriminating species in the pSS patients, especially in those with interstitial lung disease (ILD). Among the differentiating microbial pathways, the superpathway of l-phenylalanine biosynthesis was also further enriched in pSS complicated with ILD. There were more virulence genes carried by the gut microbiota in pSS patients, most of which encoded peritrichous flagella, fimbriae, or curli fimbriae, three types of bacterial surface organelles involved in bacterial colonization and invasion. Five microbial peptides with the potential to mimic pSS-related autoepitopes were also enriched in the pSS gut. SLE and pSS shared significant gut microbial traits, including community distribution, altered microbial taxonomy and pathways, and enriched virulence genes. However, Ruminococcus torques was depleted in pSS patients but enriched in SLE patients compared to healthy controls. CONCLUSIONS The gut microbiota in treatment-naïve pSS patients was disturbed and shared significant similarity with that in SLE patients.
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Affiliation(s)
- Xin-Miao Jia
- Medical Research Center, Peking Union Medical College Hospital; Department of Rheumatology, Beijing Hospital, National Center of Gerontology; Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Bing-Xuan Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China; Department of Rheumatology and Immunology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Bei-di Chen
- Department of Rheumatology and Immunology, Peking University Third Hospital, Beijing, 100191, China
| | - Ke-Tian Li
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yu-Dong Liu
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yue Xu
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jun Wang
- CAS Key Laboratory for Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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9
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Fiebig A, Schnizlein MK, Pena-Rivera S, Trigodet F, Dubey AA, Hennessy M, Basu A, Pott S, Dalal S, Rubin D, Sogin ML, Murat Eren A, Chang EB, Crosson S. Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540287. [PMID: 37214927 PMCID: PMC10197588 DOI: 10.1101/2023.05.11.540287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bacteroides fragilis comprises 1-5% of the gut microbiota in healthy humans but can expand to >50% of the population in ulcerative colitis (UC) patients experiencing inflammation. The mechanisms underlying such microbial blooms are poorly understood, but the gut of UC patients has physicochemical features that differ from healthy patients and likely impact microbial physiology. For example, levels of the secondary bile acid deoxycholate (DC) are highly reduced in the ileoanal J-pouch of UC colectomy patients. We isolated a B. fragilis strain from a UC patient with pouch inflammation (i.e. pouchitis) and developed it as a genetic model system to identify genes and pathways that are regulated by DC and that impact B. fragilis fitness in DC and crude bile. Treatment of B. fragilis with a physiologically relevant concentration of DC reduced cell growth and remodeled transcription of one-quarter of the genome. DC strongly induced expression of chaperones and select transcriptional regulators and efflux systems and downregulated protein synthesis genes. Using a barcoded collection of ≈50,000 unique insertional mutants, we further defined B. fragilis genes that contribute to fitness in media containing DC or crude bile. Genes impacting cell envelope functions including cardiolipin synthesis, cell surface glycosylation, and systems implicated in sodium-dependent bioenergetics were major bile acid fitness factors. As expected, there was limited overlap between transcriptionally regulated genes and genes that impacted fitness in bile when disrupted. Our study provides a genome-scale view of a B. fragilis bile response and genetic determinants of its fitness in DC and crude bile.
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Affiliation(s)
- Aretha Fiebig
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Matthew K. Schnizlein
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Selymar Pena-Rivera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Florian Trigodet
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Abhishek Anil Dubey
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Miette Hennessy
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Anindita Basu
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sushila Dalal
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - David Rubin
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - A. Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
| | - Eugene B. Chang
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sean Crosson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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10
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O'Shea D, Picoraro JA. De Novo Crohn's Disease in the Pediatric Pouch. Inflamm Bowel Dis 2023:izad231. [PMID: 37815461 DOI: 10.1093/ibd/izad231] [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: 09/11/2023] [Indexed: 10/11/2023]
Abstract
Children who undergo ileal pouch anal anastomosis (IPAA) surgery for refractory ulcerative colitis (UC) may ultimately develop a Crohn's disease (CD) phenotype. This de novo CD is open to broad interpretation and misattribution, and its manifestation in children is poorly understood. The surgically altered environment of the ileal pouch is at risk of a spectrum of ileal pouch disorders, which have limited description in children. In this issue of Inflammatory Bowel Diseases, a multicenter, retrospective study of children with UC who underwent IPAA and developed de novo CD highlights the challenges and opportunities of ileal pouch characterization in children.
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Affiliation(s)
- Delia O'Shea
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Columbia University Irving Medical Center, NewYork-Presbyterian Hospital, New York, NY, USA
| | - Joseph A Picoraro
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Columbia University Irving Medical Center, NewYork-Presbyterian Hospital, New York, NY, USA
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11
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Martinelli M, Romeo E, Caldaro T, Dimakou K, Papadopoulou A, Matar M, Assa A, Dipasquale V, Romano C, Aloi M, Alvisi P, Röser D, Kolho KL, Afzal N, Ledder O, Cohen S, Bronsky J, Escher JC, Brueckner A, Shamir R, Staiano A, Miele E. De Novo Crohn's Disease in Children With Ulcerative Colitis Undergoing Ileal Pouch-Anal Anastomosis: A Multicenter, Retrospective Study From the Pediatric IBD Porto Group of the ESPGHAN. Inflamm Bowel Dis 2023:izad199. [PMID: 37816230 DOI: 10.1093/ibd/izad199] [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: 03/30/2023] [Indexed: 10/12/2023]
Abstract
BACKGROUND AND AIMS We sought to define the prevalence and to characterize possible predictive factors of Crohn's disease (CD) occurring in children with ulcerative colitis (UC) after ileal pouch-anal anastomosis (IPAA). METHODS This was a multicenter, retrospective study including 15 centers of the Porto IBD group of the European Society for Pediatric Gastroenterology, Hepatology and Nutrition. Children with a confirmed diagnosis of UC undergoing colectomy with IPAA and a minimal follow up of 6 months were identified. The following data were collected: demographic data; endoscopic and histologic data; disease activity; laboratory exams; therapeutic history; indication for surgery, type, and timing; and IPAA functional outcomes and complications. In de novo CD cases, time of diagnosis, phenotype, location, and therapies were gathered. RESULTS We identified 111 UC children undergoing IPAA from January 2008 to June 2018 (median age at colectomy: 13 years; age range: 1-18 years; female/male: 59/52). The median time from diagnosis to colectomy was 16 (range, 0-202) months. At the last follow-up, 40 (36%) of 111 children developed pouchitis. The criteria for de novo CD were met in 19(17.1%) of 111 children with a 25-month median (range, 3-61 months). At last follow-up, 12 (63.1%) of 19 were treated with biologics and in 5 (26.3%) of 19 children, the pouch was replaced with definitive ileostomy. In a multivariable logistic regression model, decreased preoperative body mass index z scores (odds ratio, 2.2; 95% confidence interval, 1.1-4.4; P = .01) resulted as the only variable associated with CD development. CONCLUSIONS Children with UC undergoing IPAA carry a high risk of developing subsequent CD. De novo CD cases showed decreased preoperative body mass index z scores, identifying a poor nutritional status as a possible predictive factor.
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Affiliation(s)
- Massimo Martinelli
- Section of Pediatrics, Department of Translational Medical Science, University of Naples Federico II, Naples, Italy
| | - Erminia Romeo
- Digestive Endoscopy and Surgery Unit, Bambino Gesu Children's Hospital-IRCCS, Rome, Italy
| | - Tamara Caldaro
- Digestive Endoscopy and Surgery Unit, Bambino Gesu Children's Hospital-IRCCS, Rome, Italy
| | - Konstantina Dimakou
- Division of Gastroenterology and Hepatology, First Department of Pediatrics, Children's Hospital Agia Sofia, University of Athens, Athens, Greece
| | - Alexandra Papadopoulou
- Division of Gastroenterology and Hepatology, First Department of Pediatrics, Children's Hospital Agia Sofia, University of Athens, Athens, Greece
| | - Manar Matar
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Sackler Faculty of Medicine, Tel-Aviv University, Petah-Tikva, Israel
| | - Amit Assa
- Juliet Keidan institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, Hebrew University, Jerusalem, Israel
| | - Valeria Dipasquale
- Pediatric Gastroenterology and Cystic Fibrosis Unit, University of Messina, Messina, Italy
| | - Claudio Romano
- Pediatric Gastroenterology and Cystic Fibrosis Unit, University of Messina, Messina, Italy
| | - Marina Aloi
- Pediatric Gastroenterology Unit, Department of Women's and Children's Health, Sapienza University, Rome, Italy
| | - Patrizia Alvisi
- Pediatric Gastroenterology Unit, Maggiore Hospital, Bologna, Italy
| | - Dennis Röser
- Department of Paediatrics, Hvidovre University Hospital, Copenhagen, Denmark
| | - Kaija Leena Kolho
- Children's Hospital, University of Helsinki and HUS Helsinki, Finland
| | - Nadeem Afzal
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, United Kingdom
- University of Portsmouth, Portsmouth, United Kingdom
| | - Oren Ledder
- Juliet Keidan institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, Hebrew University, Jerusalem, Israel
| | - Schlomi Cohen
- Pediatric Gastroenterology Institute, Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jiri Bronsky
- Department of Paediatrics, University Hospital Motol, Prague, Czech Republic
| | - Johanna C Escher
- Department of Pediatric Gastroenterology, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Annecarin Brueckner
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, Ludwig Maximilians University, Munich, Germany
| | - Raanan Shamir
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Sackler Faculty of Medicine, Tel-Aviv University, Petah-Tikva, Israel
| | - Annamaria Staiano
- Section of Pediatrics, Department of Translational Medical Science, University of Naples Federico II, Naples, Italy
| | - Erasmo Miele
- Section of Pediatrics, Department of Translational Medical Science, University of Naples Federico II, Naples, Italy
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12
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Hu M, Zhu J, Peng G, Lu W, Wang H, Xie Z. IMOVNN: incomplete multi-omics data integration variational neural networks for gut microbiome disease prediction and biomarker identification. Brief Bioinform 2023; 24:bbad394. [PMID: 37930027 DOI: 10.1093/bib/bbad394] [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: 04/21/2023] [Revised: 09/03/2023] [Accepted: 10/14/2023] [Indexed: 11/07/2023] Open
Abstract
The gut microbiome has been regarded as one of the fundamental determinants regulating human health, and multi-omics data profiling has been increasingly utilized to bolster the deep understanding of this complex system. However, stemming from cost or other constraints, the integration of multi-omics often suffers from incomplete views, which poses a great challenge for the comprehensive analysis. In this work, a novel deep model named Incomplete Multi-Omics Variational Neural Networks (IMOVNN) is proposed for incomplete data integration, disease prediction application and biomarker identification. Benefiting from the information bottleneck and the marginal-to-joint distribution integration mechanism, the IMOVNN can learn the marginal latent representation of each individual omics and the joint latent representation for better disease prediction. Moreover, owing to the feature-selective layer predicated upon the concrete distribution, the model is interpretable and can identify the most relevant features. Experiments on inflammatory bowel disease multi-omics datasets demonstrate that our method outperforms several state-of-the-art methods for disease prediction. In addition, IMOVNN has identified significant biomarkers from multi-omics data sources.
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Affiliation(s)
- Mingyi Hu
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China
| | - Jinlin Zhu
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | | | - Wenwei Lu
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hongchao Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Zhenping Xie
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China
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13
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Crost EH, Coletto E, Bell A, Juge N. Ruminococcus gnavus: friend or foe for human health. FEMS Microbiol Rev 2023; 47:fuad014. [PMID: 37015876 PMCID: PMC10112845 DOI: 10.1093/femsre/fuad014] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 02/06/2023] [Accepted: 04/03/2023] [Indexed: 04/06/2023] Open
Abstract
Ruminococcus gnavus was first identified in 1974 as a strict anaerobe in the gut of healthy individuals, and for several decades, its study has been limited to specific enzymes or bacteriocins. With the advent of metagenomics, R. gnavus has been associated both positively and negatively with an increasing number of intestinal and extraintestinal diseases from inflammatory bowel diseases to neurological disorders. This prompted renewed interest in understanding the adaptation mechanisms of R. gnavus to the gut, and the molecular mediators affecting its association with health and disease. From ca. 250 publications citing R. gnavus since 1990, 94% were published in the last 10 years. In this review, we describe the biological characterization of R. gnavus, its occurrence in the infant and adult gut microbiota and the factors influencing its colonization of the gastrointestinal tract; we also discuss the current state of our knowledge on its role in host health and disease. We highlight gaps in knowledge and discuss the hypothesis that differential health outcomes associated with R. gnavus in the gut are strain and niche specific.
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Affiliation(s)
- Emmanuelle H Crost
- Quadram Institute Bioscience, Rosalind Franklin Road, Colney, Norwich NR4 7UQ, United Kingdom
| | - Erika Coletto
- Quadram Institute Bioscience, Rosalind Franklin Road, Colney, Norwich NR4 7UQ, United Kingdom
| | - Andrew Bell
- Quadram Institute Bioscience, Rosalind Franklin Road, Colney, Norwich NR4 7UQ, United Kingdom
| | - Nathalie Juge
- Quadram Institute Bioscience, Rosalind Franklin Road, Colney, Norwich NR4 7UQ, United Kingdom
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14
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Li N, Xu S, Zhang S, Zhu Q, Meng X, An W, Fu B, Zhong M, Yang Y, Lin Z, Liu X, Xia J, Wang J, You T, Yan C, Tang H, Zhuang G, Peng Z. MSI2 deficiency in ILC3s attenuates DSS-induced colitis by affecting the intestinal microbiota. Front Immunol 2023; 13:963379. [PMID: 36713428 PMCID: PMC9877450 DOI: 10.3389/fimmu.2022.963379] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Background The etiology and pathogenesis of inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), are generally believed to be related to immune dysfunction and intestinal microbiota disorder. However, the exact mechanism is not yet fully understood. The pathological changes associated with dextran sodium sulfate (DSS)-induced colitis are similar to those in human UC. As a subgroup of the innate immune system, group 3 innate lymphoid cells (ILC3s) are widely distributed in the lamina propria of the intestinal mucosa, and their function can be regulated by a variety of molecules. Musashi2 (MSI2) is a type of evolutionarily conserved RNA-binding protein that maintains the function of various tissue stem cells and is essential for postintestinal epithelial regeneration. The effect of MSI2 deficiency in ILC3s on IBD has not been reported. Thus, mice with conditional MSI2 knockout in ILC3s were used to construct a DSS-induced colitis model and explore its effects on the pathogenesis of IBD and the species, quantity and function of the intestinal microbiota. Methods Msi2flox/flox mice (Msi2fl/fl ) and Msi2flox/floxRorcCre mice (Msi2ΔRorc ) were induced by DSS to establish the IBD model. The severity of colitis was evaluated by five measurements: body weight percentage, disease activity index, colon shortening degree, histopathological score and routine blood examination. The species, quantity and function of the intestinal microbiota were characterized by high-throughput 16S rRNA gene sequencing of DNA extracted from fecal samples. Results MSI2 was knocked out in the ILC3s of Msi2ΔRorc mice. The Msi2ΔRorc mice exhibited reductions in body weight loss, the disease activity index, degree of colon shortening, tissue histopathological score and immune cells in the peripheral blood compared to those of Msi2fl/fl mice after DSS administration. The 16S rRNA sequencing results showed that the diversity of the intestinal microbiota in DSS-treated Msi2ΔRorc mice changed, with the abundance of Firmicutes increasing and that of Bacteroidetes decreasing. The linear discriminant analysis effect size (LEfSe) approach revealed that Lactobacillaceae could be the key bacteria in the Msi2ΔRorc mouse during the improvement of colitis. Using PICRUST2 to predict the function of the intestinal microbiota, it was found that the functions of differential bacteria inferred by modeling were mainly enriched in infectious diseases, immune system and metabolic functions. Conclusions MSI2 deficiency in ILC3s attenuated DSS-induced colonic inflammation in mice and affected intestinal microbiota diversity, composition, and function, with Lactobacillaceae belonging to the phylum Firmicutes possibly representing the key bacteria. This finding could contribute to our understanding of the pathogenesis of IBD and provide new insights for its clinical diagnosis and treatment.
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Affiliation(s)
- Nengneng Li
- Department of Organ Transplantation, Xiang’an Hospital, Xiamen University, Xiamen, Fujian, China,Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Shiquan Xu
- Department of Organ Transplantation, Xiang’an Hospital, Xiamen University, Xiamen, Fujian, China,Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Shuaishuai Zhang
- Department of Organ Transplantation, Xiang’an Hospital, Xiamen University, Xiamen, Fujian, China,Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Qiang Zhu
- Department of Organ Transplantation, Xiang’an Hospital, Xiamen University, Xiamen, Fujian, China,Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Xiaole Meng
- Department of Organ Transplantation, Xiang’an Hospital, Xiamen University, Xiamen, Fujian, China,Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Wenbin An
- Department of Organ Transplantation, Xiang’an Hospital, Xiamen University, Xiamen, Fujian, China,Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Baoqing Fu
- Department of Organ Transplantation, Xiang’an Hospital, Xiamen University, Xiamen, Fujian, China,Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China,Department of Laboratory Medicine, Xiang’an Hospital, Xiamen University, Xiamen, Fujian, China
| | - Mengya Zhong
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yan Yang
- Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Zeyang Lin
- Department of Pathology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
| | - Xueni Liu
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junjie Xia
- Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Jie Wang
- Department of Organ Transplantation, Xiang’an Hospital, Xiamen University, Xiamen, Fujian, China,Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Tingting You
- Department of Organ Transplantation, Xiang’an Hospital, Xiamen University, Xiamen, Fujian, China,Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Changxiu Yan
- Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Huamei Tang
- Department of Pathology, Xiang’an Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China,*Correspondence: Zhihai Peng, ; Guohong Zhuang, ; Huamei Tang,
| | - Guohong Zhuang
- Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China,*Correspondence: Zhihai Peng, ; Guohong Zhuang, ; Huamei Tang,
| | - Zhihai Peng
- Department of Organ Transplantation, Xiang’an Hospital, Xiamen University, Xiamen, Fujian, China,Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China,Organ Transplantation Clinical Medical Center of Xiamen University, Xiamen, Fujian, China,*Correspondence: Zhihai Peng, ; Guohong Zhuang, ; Huamei Tang,
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15
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Jia XM, Wu BX, Chen BD, Li KT, Liu YD, Xu Y, Wang J, Zhang X. Compositional and functional aberrance of the gut microbiota in treatment naïve patients with primary Sjögren's syndrome. J Autoimmun 2022; 134:102958. [PMID: 36455385 DOI: 10.1016/j.jaut.2022.102958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/20/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To investigate the compositional and functional characteristics of the gut microbiota in primary Sjögren's syndrome (pSS) and compare them with those in systemic lupus erythematosus (SLE). METHODS Stool samples from 78 treatment naïve pSS patients and 78 matched healthy controls were detected by shotgun metagenomic sequencing and compared with those from 49 treatment naïve SLE patients. The virulence loads and mimotopes of the gut microbiota were also assessed by sequence alignment. RESULTS The gut microbiota of treatment naïve pSS patients had lower richness and evenness and showed a different community distribution than that of healthy controls. The microbial species enriched in the pSS-associated gut microbiota included Lactobacillus salivarius, Bacteroides fragilis, Ruminococcus gnavus, Clostridium bartlettii, Clostridium bolteae, Veillonella parvula, and Streptococcus parasanguinis. Lactobacillus salivarius was the most discriminating species in the pSS patients, especially in those with interstitial lung disease (ILD). Among the differentiating microbial pathways, the superpathway of l-phenylalanine biosynthesis was also further enriched in pSS complicated with ILD. There were more virulence genes carried by the gut microbiota in pSS patients, most of which encoded peritrichous flagella, fimbriae, or curli fimbriae, three types of bacterial surface organelles involved in bacterial colonization and invasion. Five microbial peptides with the potential to mimic pSS-related autoepitopes were also enriched in the pSS gut. SLE and pSS shared significant gut microbial traits, including the community distribution, altered microbial taxonomy and pathways, and enriched virulence genes. However, Ruminococcus torques was depleted in pSS patients but enriched in SLE patients compared to that in healthy controls. CONCLUSIONS The gut microbiota in treatment naïve pSS patients was disturbed and shared significant similarity with that in SLE patients.
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Affiliation(s)
- Xin-Miao Jia
- Medical Research Center, Peking Union Medical College Hospital; Department of Rheumatology, Beijing Hospital, National Center of Gerontology; Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Bing-Xuan Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China; Department of Rheumatology and Immunology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Bei-di Chen
- Department of Rheumatology and Immunology, Peking University Third Hospital, Beijing, 100191, China
| | - Ke-Tian Li
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yu-Dong Liu
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yue Xu
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jun Wang
- CAS Key Laboratory for Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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16
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Rosso AD, Aguilera P, Quesada S, Mascardi F, Mascuka SN, Cimolai MC, Cerezo J, Spiazzi R, Conlon C, Milano C, Iraola GM, Penas-Steinhardt A, Belforte FS. Comprehensive Phenotyping in Inflammatory Bowel Disease: Search for Biomarker Algorithms in the Transkingdom Interactions Context. Microorganisms 2022; 10:microorganisms10112190. [PMID: 36363782 PMCID: PMC9698371 DOI: 10.3390/microorganisms10112190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Inflammatory bowel disease (IBD) is the most common form of intestinal inflammation associated with a dysregulated immune system response to the commensal microbiota in a genetically susceptible host. IBD includes ulcerative colitis (UC) and Crohn’s disease (CD), both of which are remarkably heterogeneous in their clinical presentation and response to treatment. This translates into a notable diagnostic challenge, especially in underdeveloped countries where IBD is on the rise and access to diagnosis or treatment is not always accessible for chronic diseases. The present work characterized, for the first time in our region, epigenetic biomarkers and gut microbial profiles associated with UC and CD patients in the Buenos Aires Metropolitan area and revealed differences between non-IBD controls and IBD patients. General metabolic functions associated with the gut microbiota, as well as core microorganisms within groups, were also analyzed. Additionally, the gut microbiota analysis was integrated with relevant clinical, biochemical and epigenetic markers considered in the follow-up of patients with IBD, with the aim of generating more powerful diagnostic tools to discriminate phenotypes. Overall, our study provides new insights into data analysis algorithms to promote comprehensive phenotyping tools using quantitative and qualitative analysis in a transkingdom interactions network context.
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Affiliation(s)
- Ayelén D. Rosso
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
| | - Pablo Aguilera
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - Sofía Quesada
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - Florencia Mascardi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de Buenos Aires (HIBA), Ciudad Autónoma de Buenos Aires C1199, Argentina
| | - Sebastian N. Mascuka
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
| | - María C. Cimolai
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
| | - Jimena Cerezo
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Renata Spiazzi
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Carolina Conlon
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Claudia Milano
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Gregorio M. Iraola
- Laboratorio de Genómica Microbiana, Institut Pasteur Montevideo, Montevideo 11400, Uruguay
- Centro de Biología Integrativa, Universidad Mayor, Santiago 7510041, Chile
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridgeshire CB10 1SA, UK
| | - Alberto Penas-Steinhardt
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto Universitario de Ciencias de la Salud, Fundación H.A. Barceló, Ciudad Autónoma de Buenos Aires 1127, Argentina
| | - Fiorella S. Belforte
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Correspondence: ; Tel.: +54-91153114059
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17
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Dubinsky V, Reshef L, Rabinowitz K, Wasserberg N, Dotan I, Gophna U. Escherichia coli Strains from Patients with Inflammatory Bowel Diseases have Disease-specific Genomic Adaptations. J Crohns Colitis 2022; 16:1584-1597. [PMID: 35560165 DOI: 10.1093/ecco-jcc/jjac071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIMS Escherichia coli is over-abundant in the gut microbiome of patients with inflammatory bowel disease [IBD]. Here, we aimed to identify IBD-specific genomic functions of diverse E. coli lineages. METHODS We investigated E. coli genomes from patients with ulcerative colitis [UC], Crohn's disease [CD] or a pouch, and healthy subjects. The majority of genomes were reconstructed from metagenomic samples, including newly sequenced faecal metagenomes. Clinical metadata were collected. Functional analysis at the gene and mutation level were performed and integrated with IBD phenotypes and biomarkers. RESULTS Overall, 530 E. coli genomes were analysed. The E. coli B2 lineage was more prevalent in UC compared with other IBD phenotypes. Genomic metabolic capacities varied across E. coli lineages and IBD phenotypes. Host mucin utilisation enzymes were present in a single lineage and depleted in patients with a pouch, whereas those involved in inulin hydrolysis were enriched in patients with a pouch. E. coli strains from patients with UC were twice as likely to encode the genotoxic molecule colibactin than strains from patients with CD or a pouch. Strikingly, patients with a pouch showed the highest inferred E. coli growth rates, even in the presence of antibiotics. Faecal calprotectin did not correlate with the relative abundance of E. coli. Finally, we identified multiple IBD-specific non-synonymous mutations in E. coli genes encoding for bacterial cell envelope components. CONCLUSIONS Comparative genomics indicates that E. coli is a commensal species adapted to the overactive mucosal immune milieu in IBD, rather than causing it. Our results reveal mutations that may lead to attenuated antigenicity in some E. coli strains.
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Affiliation(s)
- Vadim Dubinsky
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Leah Reshef
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Keren Rabinowitz
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Nir Wasserberg
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel.,Colorectal Unit, Division of Surgery, Rabin Medical Center, Petah-Tikva, Israel
| | - Iris Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Uri Gophna
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
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18
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Godny L, Reshef L, Sharar Fischler T, Elial-Fatal S, Pfeffer-Gik T, Raykhel B, Rabinowitz K, Levi-Barda A, Perets TT, Barkan R, Goren I, Ollech JE, Yanai H, Gophna U, Dotan I. Increasing adherence to the Mediterranean diet and lifestyle is associated with reduced fecal calprotectin and intra-individual changes in microbial composition of healthy subjects. Gut Microbes 2022; 14:2120749. [PMID: 36226673 PMCID: PMC9578447 DOI: 10.1080/19490976.2022.2120749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Mediterranean diet (MED) is associated with the modification of gut microbial composition. In this pilot study, we investigate the feasibility of a microbiota-targeted MED-based lifestyle intervention in healthy subjects. MED intervention integrating dietary counseling, a supporting mobile application, and daily physical activity measurement using step trackers was prospectively applied for 4 weeks. Blood and fecal samples were collected at baseline, after the 4-week intervention, and at 6 and 12 months. Blood counts, inflammatory markers, microbial and eukaryotic composition were analyzed. Dietary adherence was assessed using daily questionnaires. All 20 healthy participants (females 65%, median age 37), completed the 4-week intervention. Adherence to MED increased from 15.6 ± 4.1 (baseline) to 23.2 ± 3.6 points (4 weeks), p < .01, reflected by increased dietary fiber and decreased saturated fat intake (both p < .05). MED intervention modestly reduced fecal calprotectin, white blood cell, neutrophil, and lymphocyte counts, within the normal ranges (P < .05). Levels of butyrate producers including Faecalibacterium and Lachnospira were positively correlated with adherence to MED and the number of daily steps. Bacterial composition was associated with plant-based food intake, while fungal composition with animal-based food as well as olive oil and sweets. Increasing adherence to MED correlated with increased absolute abundances of multiple beneficial gut symbionts. Therefore, increasing adherence to MED is associated with reduction of fecal calprotectin and beneficial microbial alterations in healthy subjects. Microbiota targeted lifestyle interventions may be used to modify the intestinal ecosystem with potential implications for microbiome-mediated diseases.
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Affiliation(s)
- L. Godny
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - L. Reshef
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - T. Sharar Fischler
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - S. Elial-Fatal
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - T. Pfeffer-Gik
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - B. Raykhel
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - K. Rabinowitz
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - A. Levi-Barda
- Biobank, Department of Pathology, Rabin Medical Center, Petah Tikva, Israel
| | - TT. Perets
- Gastroenterology Laboratory, Division of Gastroenterology, Rabin Medical Center, Petah Tikva, Israel,Adelson School of Medicine, Ariel University, Ariel, Israel
| | - R. Barkan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - I. Goren
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Department of inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Ohio, USA
| | - JE. Ollech
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - H. Yanai
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - U. Gophna
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - I. Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,CONTACT I. Dotan Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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19
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Metwaly A, Reitmeier S, Haller D. Microbiome risk profiles as biomarkers for inflammatory and metabolic disorders. Nat Rev Gastroenterol Hepatol 2022; 19:383-397. [PMID: 35190727 DOI: 10.1038/s41575-022-00581-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 12/12/2022]
Abstract
The intestine harbours a complex array of microorganisms collectively known as the gut microbiota. The past two decades have witnessed increasing interest in studying the gut microbiota in health and disease, largely driven by rapid innovation in high-throughput multi-omics technologies. As a result, microbial dysbiosis has been linked to many human pathologies, including type 2 diabetes mellitus and inflammatory bowel disease. Integrated analyses of multi-omics data, including metagenomics and metabolomics along with measurements of host response and cataloguing of bacterial isolates, have identified many bacteria and bacterial products that are correlated with disease. Nevertheless, insight into the mechanisms through which microbes affect intestinal health requires going beyond correlation to causation. Current understanding of the contribution of the gut microbiota to disease causality remains limited, largely owing to the heterogeneity of microbial community structures, interindividual differences in disease evolution and incomplete understanding of the mechanisms that integrate microbiota-derived signals into host signalling pathways. In this Review, we provide a broad insight into the microbiome signatures linked to inflammatory and metabolic disorders, discuss outstanding challenges in this field and propose applications of multi-omics technologies that could lead to an improved mechanistic understanding of microorganism-host interactions.
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Affiliation(s)
- Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Sandra Reitmeier
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany. .,ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany.
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20
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Fliss Isakov N, Kornblum J, Zemel M, Cohen NA, Hirsch A, Maharshak N. The Effect of the Crohn's Disease Exclusion Diet on Patients With Pouch Inflammation: An Interventional Pilot Study. Clin Gastroenterol Hepatol 2022; 21:1654-1656.e3. [PMID: 35447313 DOI: 10.1016/j.cgh.2022.03.049] [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] [Received: 01/23/2022] [Revised: 03/14/2022] [Accepted: 03/28/2022] [Indexed: 02/07/2023]
Abstract
Restorative proctocolectomy with ileal pouch-anal anastomosis is the surgical treatment of choice for patients with ulcerative colitis.1 Unfortunately, pouch inflammation (ie, pouchitis) is reported in up to 72% of pouch patients.1,2.
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Affiliation(s)
- Naomi Fliss Isakov
- Sackler School of Medicine, Tel Aviv University, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel.
| | - Jasmine Kornblum
- Sackler School of Medicine, Tel Aviv University, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Meir Zemel
- Sackler School of Medicine, Tel Aviv University, Department of Surgery, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Nathaniel Aviv Cohen
- Sackler School of Medicine, Tel Aviv University, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Ayal Hirsch
- Sackler School of Medicine, Tel Aviv University, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Nitsan Maharshak
- Sackler School of Medicine, Tel Aviv University, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv, Israel
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21
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Si J, Lee G, You HJ, Joo SK, Lee DH, Ku BJ, Park S, Kim W, Ko G. Gut microbiome signatures distinguish type 2 diabetes mellitus from non-alcoholic fatty liver disease. Comput Struct Biotechnol J 2021; 19:5920-5930. [PMID: 34849196 PMCID: PMC8591343 DOI: 10.1016/j.csbj.2021.10.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 02/08/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is closely associated with type 2 diabetes mellitus (T2D), and these two metabolic diseases demonstrate bidirectional influences. The identification of microbiome profiles that are specific to liver injury or impaired glucose metabolism may assist understanding of the role of the gut microbiota in the relationship between NAFLD and T2D. Here, we studied a biopsy-proven Asian NAFLD cohort (n = 329; 187 participants with NAFLD, 101 with NAFLD and T2D, and 41 with neither) and identified Enterobacter, Romboutsia, and Clostridium sensu stricto as the principal taxa associated with the severity of NAFLD and T2D, whereas Ruminococcus and Megamonas were specific to NAFLD. In particular, the taxa that were associated with both severe liver pathology and T2D were also significantly associated with markers of diabetes, such as fasting blood glucose and Hb1Ac. Enterotype analysis demonstrated that participants with NAFLD had a significantly higher proportion of Bacteroides and a lower proportion of Ruminococcus than a Korean healthy twin cohort (n = 756). However, T2D could not be clearly distinguished from NAFLD. Analysis of an independent T2D cohort (n = 185) permitted us to validate the T2D-specific bacterial signature identified in the NAFLD cohort. Functional inference analysis revealed that endotoxin biosynthesis pathways were significantly enriched in participants with NAFLD and T2D, compared with those with NAFLD alone. These findings may assist with the development of effective therapeutic approaches for metabolic diseases that are associated with specific bacterial signatures.
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Key Words
- ALT, alanine aminotransferase
- BMI, body mass index
- Biomarker
- Enterotype
- FBS, fasting blood sugar
- FDR, false discovery rate
- FLI, fatty liver index
- Gut microbiome
- HbA1c, glycosylated hemoglobin
- LDL, low-density lipoprotein
- LPS, lipopolysaccharide
- MaAsLin2, microbiome multivariable association with linear models 2
- NAFL, non-alcoholic fatty liver
- NAFLD, non-alcoholic fatty liver disease
- NASH, non-alcoholic steatohepatitis
- NASH-CRN, non-alcoholic steatohepatitis clinical research network
- Non-alcoholic fatty liver disease (NAFLD)
- PICRUSt2, phylogenetic investigation of communities by reconstruction of unobserved states 2
- T2D, type 2 diabetes mellitus
- Type 2 diabetes mellitus
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Affiliation(s)
- Jiyeon Si
- Medical Science Research Institute, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Giljae Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyun Ju You
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Health and Environment, Seoul National University, Seoul 08826, Republic of Korea
| | - Sae Kyung Joo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul 07061, Republic of Korea
| | - Dong Hyeon Lee
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul 07061, Republic of Korea
| | - Bon Jeong Ku
- Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
| | - Seoyeon Park
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
| | - Won Kim
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Seoul National University College of Medicine, Seoul Metropolitan Government Boramae Medical Center, Seoul 07061, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
- Center for Human and Environmental Microbiome, Institute of Health and Environment, Seoul National University, Seoul 08826, Republic of Korea
- KoBioLabs, Inc., Seoul 08826, Republic of Korea
- Bio-MAX/N-Bio, Seoul National University, Seoul 08826, Republic of Korea
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