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Teige ES, Sortvik U, Lied GA. A Systematic Review: Fecal Bacterial Profile in Patients with Irritable Bowel Syndrome Analyzed with the GA-Map Dysbiosis Test Based on the 16S rRNA Gene of Bacterial Species or Groups. Clin Exp Gastroenterol 2024; 17:109-120. [PMID: 38646157 PMCID: PMC11032674 DOI: 10.2147/ceg.s451675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/20/2024] [Indexed: 04/23/2024] Open
Abstract
Purpose The diagnosis of irritable bowel syndrome (IBS) is based on symptom-based criteria due to lack of reliable disease-specific biomarkers. Gut microbiota is perturbed in IBS and when comparing different methods used to analyze gut microbiota, the results might be obscured. Therefore, in this systematic review we aimed to investigate the profile of fecal bacterial markers and dysbiosis index (DI) in patients with IBS and IBS subgroups compared to healthy controls (HCs) conducted by the same method (GA-map Dysbiosis Test based on16S rRNA sequencing). Material and Method We searched PubMed, EMBASE (Ovid) and Cochrane Library for case-control studies comparing fecal gut microbiota analyzed with the GA-map® Dysbiosis Test (Oslo, Norway) in patients with IBS and HCs. Our outcomes were the difference in fecal bacterial markers and DI in patients with IBS and IBS subgroups compared to HCs. Results The search identified 28 citations; five articles were included. Most studies evaluated fecal bacterial markers and DI in patients with diarrhea-predominant IBS (IBS-D). Results of fecal bacteria profile in IBS and IBS subgroups compared to HCs are inconsistent, however, two studies showed increased levels of Ruminococcus gnavus in IBS-D compared to HCs and results of DI indicated IBS and IBS subgroups (especially IBS-D) having higher DI compared to HCs. Conclusion This systematic review revealed inconsistent findings in respect to differences in bacterial markers between IBS and IBS subgroups with HCs in studies using the GA-map Dysbiosis Test based on 16S rRNA sequencing. However, the test is quite novel, and few studies have used the method so far. More research comparing fecal microbiota profile differences in IBS and IBS subgroups compared to HCs utilizing the same method of analysis is needed to give us further insight into the gut bacteria profile in IBS and the clinical consequences of intestinal dysbiosis.
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Affiliation(s)
- Erica Sande Teige
- Centre for Nutrition, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Urd Sortvik
- Centre for Nutrition, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Gülen Arslan Lied
- Centre for Nutrition, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Section of Gastroenterology, Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Hong J, Fu T, Liu W, Du Y, Bu J, Wei G, Yu M, Lin Y, Min C, Lin D. Specific Alternation of Gut Microbiota and the Role of Ruminococcus gnavus in the Development of Diabetic Nephropathy. J Microbiol Biotechnol 2024; 34:547-561. [PMID: 38346799 PMCID: PMC11016775 DOI: 10.4014/jmb.2310.10028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 04/17/2024]
Abstract
In this study, we aim to investigate the precise alterations in the gut microbiota during the onset and advancement of diabetic nephropathy (DN) and examine the impact of Ruminococcus gnavus (R. gnavus) on DN. Eight-week-old male KK-Ay mice were administered antibiotic cocktails for a duration of two weeks, followed by oral administration of R. gnavus for an additional eight weeks. Our study revealed significant changes in the gut microbiota during both the initiation and progression of DN. Specifically, we observed a notable increase in the abundance of Clostridia at the class level, higher levels of Lachnospirales and Oscillospirales at the order level, and a marked decrease in Clostridia_UCG-014 in DN group. Additionally, there was a significant increase in the abundance of Lachnospiraceae, Oscillospiraceae, and Ruminococcaceae at the family level. Moreover, oral administration of R. gnavus effectively aggravated kidney pathology in DN mice, accompanied by elevated levels of urea nitrogen (UN), creatinine (Cr), and urine protein. Furthermore, R. gnavus administration resulted in down-regulation of tight junction proteins such as Claudin-1, Occludin, and ZO-1, as well as increased levels of uremic toxins in urine and serum samples. Additionally, our study demonstrated that orally administered R. gnavus up-regulated the expression of inflammatory factors, including nucleotide-binding oligomerization domain-like receptor pyrin domain-containing protein 3 (NLRP3) and Interleukin (IL)-6. These changes indicated the involvement of the gut-kidney axis in DN, and R. gnavus may worsen diabetic nephropathy by affecting uremic toxin levels and promoting inflammation in DN.
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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, 510080, P.R. China
- Guangdong Provincial Institute of Geriatric, Guangzhou, 510080, P.R. China
| | - Tingting Fu
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
- Guangdong Provincial Institute of Geriatric, Guangzhou, 510080, P.R. China
| | - Weizhen Liu
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
- Guangdong Provincial Institute of Geriatric, Guangzhou, 510080, P.R. China
| | - Yu Du
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
- Guangdong Provincial Institute of Geriatric, Guangzhou, 510080, P.R. China
| | - Junmin Bu
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
- Guangdong Provincial Institute of Geriatric, Guangzhou, 510080, P.R. China
| | - Guojian Wei
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
- Guangdong Provincial Institute of Geriatric, Guangzhou, 510080, P.R. China
| | - Miao Yu
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
- Guangdong Provincial Institute of Geriatric, Guangzhou, 510080, P.R. China
| | - Yanshan Lin
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
- Guangdong Provincial Institute of Geriatric, Guangzhou, 510080, P.R. China
| | - Cunyun Min
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
- Guangdong Provincial Institute of Geriatric, Guangzhou, 510080, P.R. China
| | - Datao Lin
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, P.R. China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Watanabe N, Watari T, Otsuka Y, Hosokawa N, Yamagata K, Fujioka M. Clinical and microbiological characteristics of Ruminococcus gnavus bacteremia and intra-abdominal infection. Anaerobe 2024; 85:102818. [PMID: 38211774 DOI: 10.1016/j.anaerobe.2024.102818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/13/2024]
Abstract
OBJECTIVES Ruminococcus gnavus is a rare human pathogen, and clinical data on R. gnavus infection are insufficient. This retrospective study aimed to investigate the clinical characteristics of R. gnavus infections. METHODS This study included 13 cases of bacteremia and three cases of non-bacteremia infections caused by R. gnavus. We evaluated the patient data, infection source, clinical outcomes, and antimicrobial susceptibility of R. gnavus isolates for these cases. RESULTS The median age of patients was 75 years (range 47-95), and eight patients were female. Twelve cases were presumed to have an intra-abdominal infection source, and the remaining four cases had an unknown infection source. The most common underlying conditions were immunosuppression (seven cases), solid tumors (seven cases), and history of gastrointestinal surgery (five cases). Thirteen patients exhibited gastrointestinal problems (dysfunction, bleeding, intra-abdominal infection, or inflammation). Multiple pathogens were observed in six cases, and fatal outcomes were recorded in three cases. Antimicrobial susceptibility data were available for eight isolates, all of which exhibited low minimum inhibitory concentrations to penicillin (≤0.03 μg/mL), ampicillin-sulbactam (≤0.5 μg/mL), piperacillin-tazobactam (≤4 μg/mL), and metronidazole (≤0.5-1 μg/mL). CONCLUSION Ruminococcus gnavus is frequently associated with an intra-abdominal infection source, and treatment strategies should consider the possibility of multiple pathogens.
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Affiliation(s)
- Naoki Watanabe
- Department of Clinical Laboratory, Kameda Medical Center, Higashi-cho 929, Kamogawa, Chiba, Japan; Graduate School of Health Sciences, Hirosaki University, Hon-cho 66-1, Hirosaki, Aomori, Japan.
| | - Tomohisa Watari
- Department of Clinical Laboratory, Kameda Medical Center, Higashi-cho 929, Kamogawa, Chiba, Japan.
| | - Yoshihito Otsuka
- Department of Clinical Laboratory, Kameda Medical Center, Higashi-cho 929, Kamogawa, Chiba, Japan.
| | - Naoto Hosokawa
- Department of Infectious Diseases, Kameda Medical Center, Higashi-cho 929, Kamogawa, Chiba, Japan.
| | - Kazufumi Yamagata
- Graduate School of Health Sciences, Hirosaki University, Hon-cho 66-1, Hirosaki, Aomori, Japan.
| | - Miyuki Fujioka
- Graduate School of Health Sciences, Hirosaki University, Hon-cho 66-1, Hirosaki, Aomori, Japan.
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Li W, Jiang J, Yin X, Zhang Y, Zou X, Sun M, Jia J, Ma B, Xu J. Mediation of Regional Cerebral Blood Flow in the Relationship between Specific Gut Microbiota and Cognition in Vascular Cognitive Impairment. J Alzheimers Dis 2024; 97:435-445. [PMID: 38108351 DOI: 10.3233/jad-230709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
BACKGROUND Gut microbiota could affect the onset and development of vascular cognitive impairment (VCI) through modulating metabolic and immune pathways. However, the vascular mechanisms involved remain unclear. OBJECTIVE To investigate the gut microbiota associated with VCI and examine the mediating effects of regional cerebral blood flow (CBF) to explore potential therapeutic targets for VCI. METHODS This prospective study enrolled patients with VCI (n = 16) and healthy controls (n = 18) from the Chinese Imaging, Biomarkers, and Lifestyle study between January 1 and June 30, 2022. The gut microbiota composition and diversity were determined by 16 S ribosomal RNA gene sequencing. The association between gut microbiota and Montreal Cognitive Assessment (MoCA) scores was determined using Spearman's correlation analysis. Regional CBF was calculated using pseudo-continuous arterial spin labeling. The mediating effects of regional CBF on the relationship between specific gut microbiota and cognition in VCI were investigated using mediation analysis. RESULTS Compared to healthy controls, patients with VCI had significantly greater abundance of Bifidobacterium, Veillonella, R uminococcus gnavus , Fusobacterium, and Erysipelatoclostridium and smaller abundance of Collinsella. The abundance of Ruminococcus gnavus was negatively associated with MoCA scores in patients with VCI, with the CBF in the left hypothalamus, right hypothalamus, and left amygdala accounting for 63.96%, 48.22%, and 36.51%, respectively, of this association after adjusting for confounders. CONCLUSIONS Ruminococcus gnavus is associated with cognition in VCI, which is strongly mediated by CBF in the bilateral hypothalamus and left amygdala. These findings highlight the potential regulatory roles of nutrition and metabolism-related areas of the brain in VCI.
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Affiliation(s)
- Wenyi Li
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jiwei Jiang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | | | - Yuan Zhang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Xinying Zou
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Mengfan Sun
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jianjun Jia
- Department of Geriatric Neurology, The Second Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Baiping Ma
- Beijing Institute of Radiation Medicine, Beijing, China
| | - Jun Xu
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
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Amarnani A, Silverman GJ. Understanding the roles of the microbiome in autoimmune rheumatic diseases. Rheumatol Immunol Res 2023; 4:177-187. [PMID: 38125641 PMCID: PMC10729600 DOI: 10.2478/rir-2023-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/06/2023] [Indexed: 12/23/2023]
Abstract
The gut microbiome represents a potential promising therapeutic target for autoimmune diseases. This review summarizes the current knowledge on the links between the gut microbiome and several autoimmune rheumatic diseases including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) spondyloarthropathies (SpA), Sjogren's syndrome (SS), and systemic sclerosis (SSc). Evidence from studies of RA and SLE patients suggests that alterations in the gut microbiome composition and function contribute to disease development and progression through increased gut permeability, with microbes and microbial metabolites driving an excessive systemic activation of the immune system. Also, there is growing evidence that gut dysbiosis and subsequent immune cell activation may contribute to disease pathogenesis in SpA and SS. For SSc, there are fewer, but these are still informative, reports on alterations in the gut microbiome. In general, the complex interplay between the microbiome and the immune system is still not fully understood. Here we discuss the current knowledge of the link between the gut microbiome and autoimmune rheumatic diseases, highlighting potentially fertile areas for future research and make considerations on the potential benefits of strategies that restore gut microbiome homeostasis.
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Affiliation(s)
- Abhimanyu Amarnani
- Department of Medicine, NYU Grossman School of Medicine, New York, NYUSA
| | - Gregg J. Silverman
- Department of Medicine, NYU Grossman School of Medicine, New York, NYUSA
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Teramoto Y, Akagawa S, Hori SI, Tsuji S, Higasa K, Kaneko K. Dysbiosis of the gut microbiota as a susceptibility factor for Kawasaki disease. Front Immunol 2023; 14:1268453. [PMID: 38022552 PMCID: PMC10644744 DOI: 10.3389/fimmu.2023.1268453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Gut microbial imbalance (dysbiosis) has been reported in patients with acute Kawasaki disease (KD). However, no studies have analyzed the gut microbiota while focusing on susceptibility to KD. This study aimed to evaluate whether dysbiosis elevates susceptibility to KD by assessing children with a history of KD. Methods Fecal DNA was extracted from 26 children with a history of KD approximately 1 year prior (KD group, 12 boys; median age, 32.5 months; median time from onset, 11.5 months) and 57 age-matched healthy controls (HC group, 35 boys; median age, 36.0 months). 16S rRNA gene analysis was conducted with the Illumina Miseq instrument. Sequence reads were analyzed using QIIME2. Results For alpha diversity, Faith's phylogenetic diversity was significantly higher in the KD group. Regarding beta diversity, the two groups formed significantly different clusters based on Bray-Curtis dissimilarity. Comparing microbial composition at the genus level, the KD and HC groups were significantly different in the abundance of two genera with abundance over 1% after Benjamini-Hochberg false discovery rate correction for multiple comparisons. Compared with the HC group, the KD group had higher relative abundance of Ruminococcus gnavus group and lower relative abundance of Blautia. Discussion and conclusion Ruminococcus gnavus group reportedly includes pro-inflammatory bacteria. In contrast, Blautia suppresses inflammation via butyrate production. In the predictive functional analysis, the proportion of gut microbiota involved in several pathways was lower in the KD group. Therefore, dysbiosis characterized by distinct microbial diversity and decreased abundance of Blautia in parallel with increased abundance of Ruminococcus gnavus group might be a susceptibility factor for KD.
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Affiliation(s)
- Yoshiki Teramoto
- Department of Pediatrics, Kansai Medical University, Hirakata, Osaka, Japan
| | - Shohei Akagawa
- Department of Pediatrics, Kansai Medical University, Hirakata, Osaka, Japan
| | - Shin-ichiro Hori
- Department of Pediatrics, Kansai Medical University, Hirakata, Osaka, Japan
| | - Shoji Tsuji
- Department of Pediatrics, Kansai Medical University, Hirakata, Osaka, Japan
| | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Hirakata, Osaka, Japan
| | - Kazunari Kaneko
- Department of Pediatrics, Kansai Medical University, Hirakata, Osaka, Japan
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Pöysti S, Silojärvi S, Brodnicki TC, Catterall T, Liu X, Mackin L, Luster AD, Kay TWH, Christen U, Thomas HE, Hänninen A. Gut dysbiosis promotes islet-autoimmunity by increasing T-cell attraction in islets via CXCL10 chemokine. J Autoimmun 2023; 140:103090. [PMID: 37572540 DOI: 10.1016/j.jaut.2023.103090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 08/14/2023]
Abstract
CXCL10 is an IFNγ-inducible chemokine implicated in the pathogenesis of type 1 diabetes. T-cells attracted to pancreatic islets produce IFNγ, but it is unclear what attracts the first IFNγ -producing T-cells in islets. Gut dysbiosis following administration of pathobionts induced CXCL10 expression in pancreatic islets of healthy non-diabetes-prone (C57BL/6) mice and depended on TLR4-signaling, and in non-obese diabetic (NOD) mice, gut dysbiosis induced also CXCR3 chemokine receptor in IGRP-reactive islet-specific T-cells in pancreatic lymph node. In amounts typical to low-grade endotoxemia, bacterial lipopolysaccharide induced CXCL10 production in isolated islets of wild type and RAG1 or IFNG-receptor-deficient but not type-I-IFN-receptor-deficient NOD mice, dissociating lipopolysaccharide-induced CXCL10 production from T-cells and IFNγ. Although mostly myeloid-cell dependent, also β-cells showed activation of innate immune signaling pathways and Cxcl10 expression in response to lipopolysaccharide indicating their independent sensitivity to dysbiosis. Thus, CXCL10 induction in response to low levels of lipopolysaccharide may allow islet-specific T-cells imprinted in pancreatic lymph node to enter in healthy islets independently of IFN-g, and thus link gut dysbiosis to early islet-autoimmunity via dysbiosis-associated low-grade endotoxemia.
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Affiliation(s)
- Sakari Pöysti
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Satu Silojärvi
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Tara Catterall
- St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Xin Liu
- St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Leanne Mackin
- St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Andrew D Luster
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Thomas W H Kay
- St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Urs Christen
- Klinikum der Goethe Universität Frankfurt, Frankfurt Am Main, Germany
| | - Helen E Thomas
- St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Arno Hänninen
- Institute of Biomedicine, University of Turku, Turku, Finland; Turku University Hospital Laboratory Division, Turku, Finland.
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Martínez de Victoria Carazo J, Vinuesa García D, Serrano-Conde Sánchez E, Peregrina Rivas JA, Ruíz Rodríguez AJ, Hernández Quero J. Ruminococcus gnavus bacteremia: Literature review and a case report associated with acute flare of ulcerative colitis in an immunocompromised patient. Anaerobe 2023; 82:102762. [PMID: 37481231 DOI: 10.1016/j.anaerobe.2023.102762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/24/2023]
Abstract
We present a case of bacteremia caused by Ruminococcus gnavus in an immunocompromised patient. R. gnavus is a Gram-positive strict anaerobe bacterium that forms chains. The bacteremia has been associated with an acute flare of ulcerative colitis. Anaerobic bacteremia is becoming increasingly frequent in patients with compromised gastrointestinal barrier. The role of the human microbiota and its alterations in the pathogenesis of immune-related diseases is an expanding area of interest. R. gnavus has been identified as a microorganism that may be responsible for the development of these diseases. The contribution of anaerobic bacteria to the pathogenesis of inflammatory bowel disease (IBD) is discussed, and cases reported up until 2023 were reviewed.
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Affiliation(s)
| | - David Vinuesa García
- Infectious Diseases Service, Hospital Universitario Clínico San Cecilio, Av. del Conocimiento, 18016, Granada, Spain
| | - Esther Serrano-Conde Sánchez
- Microbiology and Parasitology Service, Hospital Universitario Clínico San Cecilio, Av. del Conocimiento, 18016, Granada, Spain
| | - José Antonio Peregrina Rivas
- Infectious Diseases Service, Hospital Universitario Clínico San Cecilio, Av. del Conocimiento, 18016, Granada, Spain
| | - Antonio José Ruíz Rodríguez
- Gastroenterology and Hepatology Service, Hospital Universitario Clínico San Cecilio, Av. del Conocimiento, 18016, Granada, Spain
| | - José Hernández Quero
- Infectious Diseases Service, Hospital Universitario Clínico San Cecilio, Av. del Conocimiento, 18016, Granada, Spain
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Juge N. Microbe Profile: Ruminococcus gnavus: the yin and yang of human gut symbionts. Microbiology (Reading) 2023; 169. [PMID: 37622435 PMCID: PMC10482369 DOI: 10.1099/mic.0.001383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023]
Abstract
Graphical abstract
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Affiliation(s)
- Nathalie Juge
- Quadram Institute Bioscience, Food, Microbiome and Health Institute Strategic Programme, Norwich NR4 7UQ, UK
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11
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Abdugheni R, Liu C, Liu FL, Zhou N, Jiang CY, Liu Y, Li L, Li WJ, Liu SJ. Comparative genomics reveals extensive intra-species genetic divergence of the prevalent gut commensal Ruminococcus gnavus. Microb Genom 2023; 9:mgen001071. [PMID: 37486746 PMCID: PMC10438805 DOI: 10.1099/mgen.0.001071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Ruminococcus gnavus is prevalent in the intestines of humans and animals, and ambiguities have been reported regarding its relations with the development of diseases and host well-being. We postulate the ambiguities of its function in different cases may be attributed to strain-level variability of genomic features of R. gnavus. We performed comparative genomic and pathogenicity prediction analysis on 152 filtered high-quality genomes, including 4 genomes of strains isolated from healthy adults in this study. The mean G+C content of genomes of R. gnavus was 42.73±0.33 mol%, and the mean genome size was 3.46±0.34 Mbp. Genome-wide evolutionary analysis revealed R. gnavus genomes were divided into three major phylogenetic clusters. Pan-core genome analysis revealed that there was a total of 28 072 predicted genes, and the core genes, soft-core genes, shell genes and cloud genes accounted for 3.74 % (1051/28 072), 1.75 % (491/28 072), 9.88 % (2774/28 072) and 84.63 % (23 756/28 072) of the total genes, respectively. The small proportion of core genes reflected the wide divergence among R. gnavus strains. We found certain coding sequences with determined health benefits (such as vitamin production and arsenic detoxification), whilst some had an implication of health adversity (such as sulfide dehydrogenase subunits). The functions of the majority of core genes were unknown. The most widespread genes functioning in antibiotic resistance and virulence are tetO (tetracycline-resistance gene, present in 75 strains) and cps4J (capsular polysaccharide biosynthesis protein Cps4J encoding gene, detected in 3 genomes), respectively. Our results revealed genomic divergence and the existence of certain safety-relevant factors of R. gnavus. This study provides new insights for understanding the genomic features and health relevance of R. gnavus, and raises concerns regarding predicted prevalent pathogenicity and antibiotic resistance among most of the strains.
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Affiliation(s)
- Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266000, PR China
| | - Feng-Lan Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- College of Life Sciences, Hebei University, Baoding 071000, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266000, PR China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yonghong Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266000, PR China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center (EMRC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of the Chinese Academy of Sciences, Beijing 100049, PR China
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12
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Hioki T, Kataoka K, Mutoh Y. Ruminococcus gnavus bacteraemia showing morphological diversity on Gram staining: a case report and literature review. Access Microbiol 2023; 5:acmi000442. [PMID: 37424554 PMCID: PMC10323785 DOI: 10.1099/acmi.0.000442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/12/2022] [Indexed: 07/11/2023] Open
Abstract
Ruminococcus gnavus , a Gram-positive anaerobic coccus, is a common constituent of the human gut microbiota but rarely causes any disease in humans. Herein, we report a case of R. gnavus bacteraemia in an immunocompromised 73-year-old man with sigmoid colon perforation. R. gnavus is usually reported as Gram-positive diplococci or short chains on Gram staining; however, in our patient, a blood isolate showed Gram-positive cocci in long chains, and organisms from an anaerobic subculture showed morphological diversity. This case provides insight into the morphological diversity of R. gnavus , which might help with the recognition of these bacteria in the preliminary identification stage on Gram staining.
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Affiliation(s)
- Tatsuya Hioki
- Department of Clinical Laboratory, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Kensuke Kataoka
- Department of Respiratory Medicine and Allergy, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Yoshikazu Mutoh
- Department of Infectious Diseases, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
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13
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Wu X, Chen S, Yan Q, Yu F, Shao H, Zheng X, Zhang X. Gpr35 shapes gut microbial ecology to modulate hepatic steatosis. Pharmacol Res 2023; 189:106690. [PMID: 36758734 DOI: 10.1016/j.phrs.2023.106690] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/05/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
The gut microbiome is closely shaped by host genetic and dietary factors to regulate metabolic health and disease. However, the signaling mechanisms underlying such interactions have been largely unclear. Here we identify G protein-coupled receptor 35 (Gpr35) as a regulator of gut microbial ecology and the susceptibility to obesity and hepatic steatosis in mice. Both global and intestinal epithelia specific ablation of Gpr35 aggravated high-fat diet (HFD)-induced metabolic disturbance and hepatic steatosis in mice. Gpr35 deficiency induced a remarkable loss of goblet cells and an extensive remodeling of the gut microbiome, featuring enrichment of the Bacteroides and Ruminococcus genera. Antibiotics treatment and co-housing alleviated the metabolic disturbance markers in Gpr35 deficient mice. Spatiotemporal profiling and mono-colonization screening revealed that Ruminococcus gnavus synergized with HFD to promote hepatic steatosis possibly via tryptophan and phenylalanine pathway metabolites. Our results provide mechanistic insights into a genetic-diet-microbe interplay that dictates susceptibility to metabolic disorder.
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Affiliation(s)
- Xin Wu
- Department of Pharmacy, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, Jiangsu, China
| | - Shuobing Chen
- Department of Pharmacy, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, Jiangsu, China
| | - Qingyuan Yan
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, Jiangsu, China; Laboratory of Metabolic Regulation and Drug Target Discovery, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, Jiangsu, China
| | - Feng Yu
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China
| | - Hua Shao
- Department of Pharmacy, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China.
| | - Xiao Zheng
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, Jiangsu, China; Laboratory of Metabolic Regulation and Drug Target Discovery, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, Jiangsu, China.
| | - Xueli Zhang
- Department of Pharmacy, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China.
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14
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Dubinsky V, Dotan I, Gophna U. Strains Colonizing Different Intestinal Sites within an Individual Are Derived from a Single Founder Population. mBio 2023; 14:e0345622. [PMID: 36719226 DOI: 10.1128/mbio.03456-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Metagenomics has improved our understanding of commensal bacteria that colonize human intestines yet relies almost exclusively on fecal samples. Thus, spatial information about the niche range of these gut microbes and the level of specialized adaptation that they undergo has been inaccessible to fecal metagenomic studies. Here, we leveraged metagenomic data obtained through colonoscopy aspirates from three intestinal sites of healthy adults, and reconstructed metagenome-assembled genomes of several common gut bacteria to address intestinal site-specific evolution. We show that the genomes of bacterial strains at specific intestinal sites are clearly distinct yet are interrelated and are derived from a single founder strain colonizing multiple sites. We also reveal that within those intestinal sites, purifying selection is the dominant evolutionary force acting on Escherichia coli genomes within human hosts. Importantly, no site-specific adaptations at the level of accessory genes were detected, implying that these commensals are well-adapted to several host microniches and can therefore colonize multiple intestinal sites with high efficiency. Nevertheless, bacterial in situ growth rates differ markedly across different sections of the intestine. Metagenomics of aspirate samples can reveal unique strain- and intestinal tissue-specific genomic information. Such information may be critical for understanding bacterial contribution to gastrointestinal diseases, which involve only a part of the intestine, as is often the case in inflammatory bowel disease. IMPORTANCE By reconstructing bacterial genomes from samples taken from specific sites within the human intestines, via aspiration, we show that strains at specific intestinal sites are genetically distinct yet interrelated and are derived from a single founder population. Organ-specific metagenomic information represents a powerful tool to generate insights into gastrointestinal diseases, which involve only a part of the intestine, such as inflammatory bowel disease.
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15
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Buttimer C, Khokhlova EV, Stein L, Hueston CM, Govi B, Draper LA, Ross RP, Shkoporov AN, Hill C. Temperate bacteriophages infecting the mucin-degrading bacterium Ruminococcus gnavus from the human gut. Gut Microbes 2023; 15:2194794. [PMID: 36994608 PMCID: PMC10072058 DOI: 10.1080/19490976.2023.2194794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
Ruminococcus gnavus is a prevalent gut microbe reported to occur in higher abundance among individuals with inflammatory bowel disease (IBD). This study reports the isolation and characterization of six bacteriophages (phages) isolated from human fecal material and environmental samples that infect this species. Isolated phages have a siphovirus morphology, with genomes ranging between 36.5 and 37.8 kbp. Genome analysis indicates that the phages have a temperate lifestyle, which was confirmed by their ability to form lysogens on their host bacterial species. In contrast to the finding that phages lyse their host in liquid medium, results from a mouse trial indicate these phages can co-exist with the host bacterium in the gut without causing a significant reduction of R. gnavus. The bacterial counts in the feces of phage-treated mice did not significantly differ in the presence of phage. Furthermore, analysis of publicly available gut virome sequence data indicates a high abundance of these phages among individuals suffering from IBD. This work provides the first insight into how phages interact with R. gnavus in the human gut microbiome.
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Affiliation(s)
- Colin Buttimer
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | - Ekaterina V Khokhlova
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | - Lisa Stein
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | - Cara M Hueston
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | - Bianca Govi
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
| | | | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College, Cork, Ireland
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16
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Saralegui C, García-Durán C, Romeu E, Hernáez-Sánchez ML, Maruri A, Bastón-Paz N, Lamas A, Vicente S, Pérez-Ruiz E, Delgado I, Luna-Paredes C, Caballero JDD, Zamora J, Monteoliva L, Gil C, del Campo R. Statistical Evaluation of Metaproteomics and 16S rRNA Amplicon Sequencing Techniques for Study of Gut Microbiota Establishment in Infants with Cystic Fibrosis. Microbiol Spectr 2022; 10:e0146622. [PMID: 36255300 PMCID: PMC9784762 DOI: 10.1128/spectrum.01466-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/23/2022] [Indexed: 01/05/2023] Open
Abstract
Newborn screening for cystic fibrosis (CF) can identify affected but asymptomatic infants. The selection of omic technique for gut microbiota study is crucial due to both the small amount of feces available and the low microorganism load. Our aims were to compare the agreement between 16S rRNA amplicon sequencing and metaproteomics by a robust statistical analysis, including both presence and abundance of taxa, to describe the sequential establishment of the gut microbiota during the first year of life in a small size sample (8 infants and 28 fecal samples). The taxonomic assignations by the two techniques were similar, whereas certain discrepancies were observed in the abundance detection, mostly the lower predicted relative abundance of Bifidobacterium and the higher predicted relative abundance of certain Firmicutes and Proteobacteria by amplicon sequencing. During the first months of life, the CF gut microbiota is characterized by a significant enrichment of Ruminococcus gnavus, the expression of certain virulent bacterial traits, and the detection of human inflammation-related proteins. Metaproteomics provides information on composition and functionality, as well as data on host-microbiome interactions. Its strength is the identification and quantification of Actinobacteria and certain classes of Firmicutes, but alpha diversity indices are not comparable to those of amplicon sequencing. Both techniques detected an aberrant microbiota in our small cohort of infants with CF during their first year of life, dominated by the enrichment of R. gnavus within a human inflammatory environment. IMPORTANCE In recent years, some techniques have been incorporated for the study of microbial ecosystems, being 16S rRNA gene sequencing being the most widely used. Metaproteomics provides the advantage of identifying the interaction between microorganisms and human cells, but the available databases are less extensive as well as imprecise. Few studies compare the statistical differences between the two techniques to define the composition of an ecosystem. Our work shows that the two methods are comparable in terms of microorganism identification but provide different results in alpha diversity analysis. On the other hand, we have studied newborns with cystic fibrosis, for whom we have described the establishment of an intestinal ecosystem marked by the inflammatory response of the host and the enrichment of Ruminococcus gnavus.
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Affiliation(s)
- Claudia Saralegui
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Carmen García-Durán
- Departamento de Microbiología y Parasitología, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Eduardo Romeu
- Unidad de Proteómica, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Ainhize Maruri
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Natalia Bastón-Paz
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Adelaida Lamas
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Servicio de Pediatría, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Saioa Vicente
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Servicio de Pediatría, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Estela Pérez-Ruiz
- Unidad de Fibrosis Quística, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Isabel Delgado
- Unidad de Fibrosis Quística, Hospital Virgen del Rocío, Seville, Spain
| | - Carmen Luna-Paredes
- Sección de Neumología y Alergia Infantil, Unidad Multidisciplinar Fibrosis Quística, Hospital Doce de Octubre, Madrid, Spain
| | - Juan de Dios Caballero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Javier Zamora
- Unidad de Bioestadística, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria and CIBERESP, Madrid, Spain
| | - Lucía Monteoliva
- Departamento de Microbiología y Parasitología, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Unidad de Proteómica, Universidad Complutense de Madrid, Madrid, Spain
| | - Concepción Gil
- Departamento de Microbiología y Parasitología, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Unidad de Proteómica, Universidad Complutense de Madrid, Madrid, Spain
| | - Rosa del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Universidad Alfonso X El Sabio, Madrid, Spain
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17
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Terrisse S, Zitvogel L, Kroemer G. Effects of the intestinal microbiota on prostate cancer treatment by androgen deprivation therapy. Microb Cell 2022; 9:202-206. [PMID: 36483309 PMCID: PMC9714294 DOI: 10.15698/mic2022.12.787] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 08/27/2023]
Abstract
Prostate cancer (PC) can be kept in check by androgen deprivation therapy (ADT, usually with the androgen synthesis inhibitor abiraterone acetate or the androgen receptor antagonist such as enzalutamide) until the tumor evolves to castration-resistant prostate cancer (CRPC). The transition of hormone-sensitive PC (HSPC) to CPRC has been explained by cancer cell-intrinsic resistance mechanisms. Recent data indicate that this transition is also marked by cancer cell-extrinsic mechanisms such as the failure of ADT-induced PC immunosurveillance, which depends on the presence of immunostimulatory bacteria in the gut. Moreover, intestinal bacteria that degrade drugs used for ADT, as well as bacteria that produce androgens, can interfere with the efficacy of ADT. Thus, specific bacteria in the gut serve as a source of testosterone, which accelerates prostate cancer progression, and men with CRPC exhibit an increased abundance of such bacteria with androgenic functions. In conclusion, the response of PC to ADT is profoundly influenced by the composition of the microbiota with its immunostimulatory, immunosuppressive and directly ADT-subversive elements.
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Affiliation(s)
| | - Laurence Zitvogel
- INSERM U1015, Equipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
- University Paris Saclay, Gif-sur-Yvette, France
- Gustave Roussy, ClinicObiome, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Guido Kroemer
- Equipe labellisée par la Ligue contre le Cancer, Université de Paris Cité, Sorbonne Université, Institut Universitaire de France, Inserm U1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
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18
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Coletto E, Latousakis D, Pontifex MG, Crost EH, Vaux L, Perez Santamarina E, Goldson A, Brion A, Hajihosseini MK, Vauzour D, Savva GM, Juge N. The role of the mucin-glycan foraging Ruminococcus gnavus in the communication between the gut and the brain. Gut Microbes 2022; 14:2073784. [PMID: 35579971 PMCID: PMC9122312 DOI: 10.1080/19490976.2022.2073784] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Ruminococcus gnavus is a prevalent member of the human gut microbiota, which is over-represented in inflammatory bowel disease and neurological disorders. We previously showed that the ability of R. gnavus to forage on mucins is strain-dependent and associated with sialic acid metabolism. Here, we showed that mice monocolonized with R. gnavus ATCC 29149 (Rg-mice) display changes in major sialic acid derivatives in their cecum content, blood, and brain, which is accompanied by a significant decrease in the percentage of sialylated residues in intestinal mucins relative to germ-free (GF) mice. Changes in metabolites associated with brain function such as tryptamine, indolacetate, and trimethylamine N-oxide were also detected in the cecal content of Rg-mice when compared to GF mice. Next, we investigated the effect of R. gnavus monocolonization on hippocampus cell proliferation and behavior. We observed a significant decrease of PSA-NCAM immunoreactive granule cells in the dentate gyrus (DG) of Rg-mice as compared to GF mice and recruitment of phagocytic microglia in the vicinity. Behavioral assessments suggested an improvement of the spatial working memory in Rg-mice but no change in other cognitive functions. These results were also supported by a significant upregulation of genes involved in proliferation and neuroplasticity. Collectively, these data provide first insights into how R. gnavus metabolites may influence brain regulation and function through modulation of granule cell development and synaptic plasticity in the adult hippocampus. This work has implications for further understanding the mechanisms underpinning the role of R. gnavus in neurological disorders.
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Affiliation(s)
- Erika Coletto
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK
| | - Dimitrios Latousakis
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK
| | - Matthew G Pontifex
- Norwich Medical School, Biomedical Research Centre, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Emmanuelle H Crost
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK
| | - Laura Vaux
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK
| | - Estella Perez Santamarina
- Norwich Medical School, Biomedical Research Centre, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrew Goldson
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK
| | - Arlaine Brion
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK
| | - Mohammad K Hajihosseini
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - David Vauzour
- Norwich Medical School, Biomedical Research Centre, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - George M Savva
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK
| | - Nathalie Juge
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK
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19
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Bordugo A, Salvetti E, Rodella G, Piazza M, Dianin A, Amoruso A, Piacentini G, Pane M, Torriani S, Vitulo N, Felis GE. Assessing Gut Microbiota in an Infant with Congenital Propionic Acidemia before and after Probiotic Supplementation. Microorganisms 2021; 9:2599. [PMID: 34946200 DOI: 10.3390/microorganisms9122599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/25/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022] Open
Abstract
Propionic Acidemia (PA) is a rare inherited metabolic disorder caused by the enzymatic block of propionyl-CoA carboxylase with the consequent accumulation of propionic acid, which is toxic for the brain and cardiac cells. Since a considerable amount of propionate is produced by intestinal bacteria, interest arose in the attempt to reduce propionate-producing bacteria through a monthly antibiotic treatment of metronidazole. In the present study, we investigated the gut microbiota structure of an infant diagnosed at 4 days of life through Expanded Newborn Screening (NBS) and treated the child following international guidelines with a special low-protein diet, specific medications and strict biochemical monitoring. Microbiota composition was assessed during the first month of life, and the presence of Bacteroides fragilis, known to be associated with propionate production, was effectively decreased by metronidazole treatment. After five antibiotic therapy cycles, at 4 months of age, the infant was supplemented with a daily mixture of three bifidobacterial strains, known not to be propionate producers. The supplementation increased the population of bifidobacteria, with Bifidobacterium breve as the dominating species; Ruminococcus gnavus, an acetate and formate producer, was also identified. Metabarcoding analysis, compared with low coverage whole metagenome sequencing, proved to capture all the microbial biodiversity and could be the elected tool for fast and cost-effective monitoring protocols to be implemented in the follow up of rare metabolic disorders such as PA. Data obtained could be a possible starting point to set up tailored microbiota modification treatment studies in the attempt to improve the quality of life of people affected by propionic acidemia.
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20
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Maresca M, Alatou R, Pujol A, Nicoletti C, Perrier J, Giardina T, Simon G, Méjean V, Fons M. RadA, a MSCRAMM Adhesin of the Dominant Symbiote Ruminococcus gnavus E1, Binds Human Immunoglobulins and Intestinal Mucins. Biomolecules 2021; 11:1613. [PMID: 34827611 DOI: 10.3390/biom11111613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 01/10/2023] Open
Abstract
Adhesion to the digestive mucosa is considered a key factor for bacterial persistence within the gut. In this study, we show that Ruminococcus gnavus E1 can express the radA gene, which encodes an adhesin of the MSCRAMMs family, only when it colonizes the gut. The RadA N-terminal region contains an all-β bacterial Ig-like domain known to interact with collagens. We observed that it preferentially binds human immunoglobulins (IgA and IgG) and intestinal mucins. Using deglycosylated substrates, we also showed that the RadA N-terminal region recognizes two different types of motifs, the protein backbone of human IgG and the glycan structure of mucins. Finally, competition assays with lectins and free monosaccharides identified Galactose and N-Acetyl-Galactosamine motifs as specific targets for the binding of RadA to mucins and the surface of human epithelial cells.
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21
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Borowska MT, Drees C, Yarawsky AE, Viswanathan M, Ryan SM, Bunker JJ, Herr AB, Bendelac A, Adams EJ. The molecular characterization of antibody binding to a superantigen-like protein from a commensal microbe. Proc Natl Acad Sci U S A 2021; 118:e2023898118. [PMID: 34548394 PMCID: PMC8488583 DOI: 10.1073/pnas.2023898118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2021] [Indexed: 11/18/2022] Open
Abstract
Microorganisms have coevolved diverse mechanisms to impair host defenses. A major one, superantigens, can result in devastating effects on the immune system. While all known superantigens induce vast immune cell proliferation and come from opportunistic pathogens, recently, proteins with similar broad specificity to antibody variable (V) domain families were identified in a commensal microbiota. These proteins, identified in the human commensal Ruminococcus gnavus, are called immunoglobulin-binding protein (Ibp) A and B and have been shown to activate B cells in vitro expressing either human VH3 or murine VH5/6/7. Here, we provide molecular and functional studies revealing the basis of this Ibp/immunoglobulin (Ig) interaction. The crystal structure and biochemical assays of a truncated IbpA construct in complex with mouse VH5 antigen-binding fragment (Fab) shows a binding of Ig heavy chain framework residues to the Ibp Domain D and the C-terminal heavy chain binding domain (HCBD). We used targeted mutagenesis of contact residues and affinity measurements and performed studies of the Fab-IbpA complex to determine the stoichiometry between Ibp and VH domains, suggesting Ibp may serve to cluster full-length IgA antibodies in vivo. Furthermore, in vitro stimulation experiments indicate that binding of the Ibp HCBD alone is sufficient to activate responsive murine B cell receptors. The presence of these proteins in a commensal microbe suggest that binding a broad repertoire of immunoglobulins, particularly in the gut/microbiome environment, may provide an important function in the maintenance of host/microbiome homeostasis contrasting with the pathogenic role of structurally homologous superantigens expressed by pathogens.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Christoph Drees
- Department of Pathology, University of Chicago, Chicago, IL 60637
| | - Alexander E Yarawsky
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | | | - Sean M Ryan
- Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - Jeffrey J Bunker
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - Andrew B Herr
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Albert Bendelac
- Department of Pathology, University of Chicago, Chicago, IL 60637;
- Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - Erin J Adams
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637;
- Committee on Immunology, University of Chicago, Chicago, IL 60637
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22
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Henke MT, Brown EM, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J. Capsular polysaccharide correlates with immune response to the human gut microbe Ruminococcus gnavus. Proc Natl Acad Sci U S A 2021; 118:e2007595118. [PMID: 33972416 PMCID: PMC8157926 DOI: 10.1073/pnas.2007595118] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Active inflammatory bowel disease (IBD) often coincides with increases of Ruminococcus gnavus, a gut microbe found in nearly everyone. It was not known how, or if, this correlation contributed to disease. We investigated clinical isolates of R. gnavus to identify molecular mechanisms that would link R. gnavus to inflammation. Here, we show that only some isolates of R. gnavus produce a capsular polysaccharide that promotes a tolerogenic immune response, whereas isolates lacking functional capsule biosynthetic genes elicit robust proinflammatory responses in vitro. Germ-free mice colonized with an isolate of R. gnavus lacking a capsule show increased measures of gut inflammation compared to those colonized with an encapsulated isolate in vivo. These observations in the context of our earlier identification of an inflammatory cell-wall polysaccharide reveal how some strains of R. gnavus could drive the inflammatory responses that characterize IBD.
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Affiliation(s)
- Matthew T Henke
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Eric M Brown
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Chelsi D Cassilly
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Hera Vlamakis
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Ramnik J Xavier
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114
| | - Jon Clardy
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;
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23
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Yu S, Balasubramanian I, Laubitz D, Tong K, Bandyopadhyay S, Lin X, Flores J, Singh R, Liu Y, Macazana C, Zhao Y, Béguet-Crespel F, Patil K, Midura-Kiela MT, Wang D, Yap GS, Ferraris RP, Wei Z, Bonder EM, Häggblom MM, Zhang L, Douard V, Verzi MP, Cadwell K, Kiela PR, Gao N. Paneth Cell-Derived Lysozyme Defines the Composition of Mucolytic Microbiota and the Inflammatory Tone of the Intestine. Immunity 2021; 53:398-416.e8. [PMID: 32814028 DOI: 10.1016/j.immuni.2020.07.010] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 03/26/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023]
Abstract
Paneth cells are the primary source of C-type lysozyme, a β-1,4-N-acetylmuramoylhydrolase that enzymatically processes bacterial cell walls. Paneth cells are normally present in human cecum and ascending colon, but are rarely found in descending colon and rectum; Paneth cell metaplasia in this region and aberrant lysozyme production are hallmarks of inflammatory bowel disease (IBD) pathology. Here, we examined the impact of aberrant lysozyme production in colonic inflammation. Targeted disruption of Paneth cell lysozyme (Lyz1) protected mice from experimental colitis. Lyz1-deficiency diminished intestinal immune responses to bacterial molecular patterns and resulted in the expansion of lysozyme-sensitive mucolytic bacteria, including Ruminococcus gnavus, a Crohn's disease-associated pathobiont. Ectopic lysozyme production in colonic epithelium suppressed lysozyme-sensitive bacteria and exacerbated colitis. Transfer of R. gnavus into Lyz1-/- hosts elicited a type 2 immune response, causing epithelial reprograming and enhanced anti-colitogenic capacity. In contrast, in lysozyme-intact hosts, processed R. gnavus drove pro-inflammatory responses. Thus, Paneth cell lysozyme balances intestinal anti- and pro-inflammatory responses, with implications for IBD.
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Affiliation(s)
- Shiyan Yu
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | | | - Daniel Laubitz
- Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | - Kevin Tong
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | | | - Xiang Lin
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Juan Flores
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Rajbir Singh
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Yue Liu
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Carlos Macazana
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Yanlin Zhao
- Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Fabienne Béguet-Crespel
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Karuna Patil
- Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | | | - Daniel Wang
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - George S Yap
- Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Ronaldo P Ferraris
- Department of Pharmacology, Physiology and Neuroscience, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
| | - Lanjing Zhang
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA; Department of Pathology, Princeton Medical Center, Plainsboro, NJ, USA
| | - Veronique Douard
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Ken Cadwell
- Department of Microbiology and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Pawel R Kiela
- Department of Pediatrics, University of Arizona, Tucson, AZ, USA; Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
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24
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Veale R, Hughes C, Woolley I. A novel case of bilateral tubo-ovarian abscesses attributed to Ruminococcus gnavus without gastrointestinal involvement. Anaerobe 2020; 67:102312. [PMID: 33271361 DOI: 10.1016/j.anaerobe.2020.102312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 12/25/2022]
Abstract
Ruminococcus gnavus is a Gram-positive anaerobe and normal gut commensal in the human host. There have been a small number of reported cases of infections attributed to R. gnavus, and no cases of urogenital infections have previously been published. We describe here a case of bilateral tubo-ovarian abscesses (TOAs) which cultured a pure growth of R. gnavus in a young female with concurrent deep infiltrating endometriosis and evidence of pelvic inflammatory disease. This case provides an insight into the behaviour of R. gnavus as a coloniser of the human host and provides further incentive to investigate its potentially pathogenic role in inflammatory conditions such as pelvic inflammatory disease.
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Affiliation(s)
- Ruby Veale
- Monash Infectious Diseases, Monash Health, Clayton Rd, Clayton, Vic, 3168, Australia; School of Clinical Sciences, Monash University, Clayton Rd, Clayton, Vic, 3168, Australia.
| | - Carly Hughes
- Monash Infectious Diseases, Monash Health, Clayton Rd, Clayton, Vic, 3168, Australia; Department of Microbiology, Monash Pathology, Clayton Rd, Clayton, Vic, 3168, Australia
| | - Ian Woolley
- Monash Infectious Diseases, Monash Health, Clayton Rd, Clayton, Vic, 3168, Australia; School of Clinical Sciences, Monash University, Clayton Rd, Clayton, Vic, 3168, Australia
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25
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Gren C, Spiegelhauer MR, Rotbain EC, Ehmsen BK, Kampmann P, Andersen LP. Ruminococcus gnavus bacteraemia in a patient with multiple haematological malignancies. Access Microbiol 2020; 1:e000048. [PMID: 32974553 PMCID: PMC7470407 DOI: 10.1099/acmi.0.000048] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
We present a case of Ruminococcus gnavus sepsis in a woman suffering from multiple myeloma and myelodysplastic syndrome. R. gnavus, a Gram-positive coccus and a gut commensal, has been described in nine cases of infection in the literature, with most infections having occurred in patients with either gastrointestinal symptoms or prosthesis infections. In this case, R gnavus was identified by mass spectrometry, and showed susceptibility to penicillin, meropenem, tetracycline, metronidazole and clindamycin. The patient was successfully treated initially with intravenous piperacillin/tazobactam and metronidazole, and then switched to oral penicillin and metronidazole. The cause of infection is hypothesized to have been a shift in the gut microbiota towards an excess growth of R. gnavus caused by immunosuppression, and bacterial translocation across a vulnerable mucosal barrier due to prednisolone treatment and severe thrombocytopenia.
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Affiliation(s)
- Caroline Gren
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | | | | | | | - Peter Kampmann
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
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26
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Bell A, Severi E, Lee M, Monaco S, Latousakis D, Angulo J, Thomas GH, Naismith JH, Juge N. Uncovering a novel molecular mechanism for scavenging sialic acids in bacteria. J Biol Chem 2020; 295:13724-13736. [PMID: 32669363 PMCID: PMC7535918 DOI: 10.1074/jbc.ra120.014454] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
The human gut symbiont Ruminococcus gnavus scavenges host-derived N-acetylneuraminic acid (Neu5Ac) from mucins by converting it to 2,7-anhydro-Neu5Ac. We previously showed that 2,7-anhydro-Neu5Ac is transported into R. gnavus ATCC 29149 before being converted back to Neu5Ac for further metabolic processing. However, the molecular mechanism leading to the conversion of 2,7-anhydro-Neu5Ac to Neu5Ac remained elusive. Using 1D and 2D NMR, we elucidated the multistep enzymatic mechanism of the oxidoreductase (RgNanOx) that leads to the reversible conversion of 2,7-anhydro-Neu5Ac to Neu5Ac through formation of a 4-keto-2-deoxy-2,3-dehydro-N-acetylneuraminic acid intermediate and NAD+ regeneration. The crystal structure of RgNanOx in complex with the NAD+ cofactor showed a protein dimer with a Rossman fold. Guided by the RgNanOx structure, we identified catalytic residues by site-directed mutagenesis. Bioinformatics analyses revealed the presence of RgNanOx homologues across Gram-negative and Gram-positive bacterial species and co-occurrence with sialic acid transporters. We showed by electrospray ionization spray MS that the Escherichia coli homologue YjhC displayed activity against 2,7-anhydro-Neu5Ac and that E. coli could catabolize 2,7-anhydro-Neu5Ac. Differential scanning fluorimetry analyses confirmed the binding of YjhC to the substrates 2,7-anhydro-Neu5Ac and Neu5Ac, as well as to co-factors NAD and NADH. Finally, using E. coli mutants and complementation growth assays, we demonstrated that 2,7-anhydro-Neu5Ac catabolism in E. coli depended on YjhC and on the predicted sialic acid transporter YjhB. These results revealed the molecular mechanisms of 2,7-anhydro-Neu5Ac catabolism across bacterial species and a novel sialic acid transport and catabolism pathway in E. coli.
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Affiliation(s)
- Andrew Bell
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Micah Lee
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Dimitrios Latousakis
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom; Departamento de Química Orgánica, Universidad de Sevilla, Sevilla, Spain; Instituto de Investigaciones Químicas (CSIC-US), Sevilla, Spain
| | - Gavin H Thomas
- Department of Biology, University of York, York, United Kingdom
| | - James H Naismith
- Division of Structural Biology, University of Oxford, Headington, Oxford, United Kingdom
| | - Nathalie Juge
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom.
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27
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Jeffery IB, Das A, O'Herlihy E, Coughlan S, Cisek K, Moore M, Bradley F, Carty T, Pradhan M, Dwibedi C, Shanahan F, O'Toole PW. Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption. Gastroenterology 2020; 158:1016-1028.e8. [PMID: 31843589 DOI: 10.1053/j.gastro.2019.11.301] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 11/16/2019] [Accepted: 11/01/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Irritable bowel syndrome (IBS) is a heterogeneous disorder, but diagnoses and determination of subtypes are made based on symptoms. We profiled the fecal microbiomes of patients with and without IBS to identify biomarkers of this disorder. METHODS We collected fecal and urine samples from 80 patients with IBS (Rome IV criteria; 16-70 years old) and 65 matched individuals without IBS (control individuals), along with anthropometric, medical, and dietary information. Shotgun and 16S ribosomal RNA amplicon sequencing were performed on feces, whereas urine and fecal metabolites were analyzed by gas chromatography and liquid chromatography-mass spectrometry. Co-occurrence networks were generated based on significant Spearman correlations between data. Bile acid malabsorption (BAM) was identified in patients with diarrhea by retention of radiolabeled selenium-75 homocholic acid taurine. RESULTS Patients with IBS had significant differences in network connections between diet and fecal microbiomes compared with control individuals; these were accompanied by differences in fecal metabolomes. We did not find significant differences in fecal microbiota composition among patients with different IBS symptom subtypes. Fecal metabolome profiles could discriminate patients with IBS from control individuals. Urine metabolomes also differed significantly between patients with IBS and control individuals, but most discriminatory metabolites were related to diet or medications. Fecal metabolomes, but not microbiomes, could distinguish patients with IBS with vs those without BAM. CONCLUSIONS Despite the heterogeneity of IBS, patients have significant differences in urine and fecal metabolomes and fecal microbiome vs control individuals, independent of symptom-based subtypes of IBS. Fecal metabolome analysis can be used to distinguish patients with IBS with vs those without BAM. These findings might be used for developing microbe-based treatments for these disorders.
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Affiliation(s)
- Ian B Jeffery
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Anubhav Das
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Eileen O'Herlihy
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Simone Coughlan
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Katryna Cisek
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Michael Moore
- Department of Radiology, Cork University Hospital, Cork, Ireland
| | - Fintan Bradley
- Medical Physics Department, Cork University Hospital, Cork, Ireland
| | - Tom Carty
- Medical Physics Department, Cork University Hospital, Cork, Ireland
| | - Meenakshi Pradhan
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Chinmay Dwibedi
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - Fergus Shanahan
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland
| | - Paul W O'Toole
- 4D pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland; School of Microbiology, University College Cork, Ireland.
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28
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Abdellatif AM, Jensen Smith H, Harms RZ, Sarvetnick NE. Human Islet Response to Selected Type 1 Diabetes-Associated Bacteria: A Transcriptome-Based Study. Front Immunol 2019; 10:2623. [PMID: 31781116 PMCID: PMC6857727 DOI: 10.3389/fimmu.2019.02623] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022] Open
Abstract
Type 1 diabetes (T1D) is a chronic autoimmune disease that results from destruction of pancreatic β-cells. T1D subjects were recently shown to harbor distinct intestinal microbiome profiles. Based on these findings, the role of gut bacteria in T1D is being intensively investigated. The mechanism connecting intestinal microbial homeostasis with the development of T1D is unknown. Specific gut bacteria such as Bacteroides dorei (BD) and Ruminococcus gnavus (RG) show markedly increased abundance prior to the development of autoimmunity. One hypothesis is that these bacteria might traverse the damaged gut barrier, and their constituents elicit a response from human islets that causes metabolic abnormalities and inflammation. We have tested this hypothesis by exposing human islets to BD and RG in vitro, after which RNA-Seq analysis was performed. The bacteria altered expression of many islet genes. The commonly upregulated genes by these bacteria were cytokines, chemokines and enzymes, suggesting a significant effect of gut bacteria on islet antimicrobial and biosynthetic pathways. Additionally, each bacteria displayed a unique set of differentially expressed genes (DEGs). Ingenuity pathway analysis of DEGs revealed that top activated pathways and diseases included TREM1 signaling and inflammatory response, illustrating the ability of bacteria to induce islet inflammation. The increased levels of selected factors were confirmed using immunoblotting and ELISA methods. Our data demonstrate that islets produce a complex anti-bacterial response. The response includes both symbiotic and pathogenic aspects. Both oxidative damage and leukocyte recruitment factors were prominent, which could induce beta cell damage and subsequent autoimmunity.
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Affiliation(s)
- Ahmed M. Abdellatif
- Department of Surgery-Transplant, University of Nebraska Medical Center, Omaha, NE, United States
- Mary and Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, United States
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Heather Jensen Smith
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, United States
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE, United States
| | - Robert Z. Harms
- Department of Surgery-Transplant, University of Nebraska Medical Center, Omaha, NE, United States
- Mary and Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, United States
| | - Nora E. Sarvetnick
- Department of Surgery-Transplant, University of Nebraska Medical Center, Omaha, NE, United States
- Mary and Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, United States
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29
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Ribaldone DG, Caviglia GP, Abdulle A, Pellicano R, Ditto MC, Morino M, Fusaro E, Saracco GM, Bugianesi E, Astegiano M. Adalimumab Therapy Improves Intestinal Dysbiosis in Crohn's Disease. J Clin Med 2019; 8:jcm8101646. [PMID: 31601034 PMCID: PMC6832711 DOI: 10.3390/jcm8101646] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022] Open
Abstract
The response to treatment with biologic drugs, in patients with Crohn’s disease, could be associated with changes in gut microbiota composition. The aim of our study was to analyse the modification of microbiota during adalimumab therapy in patients with Crohn’s disease. We performed a prospective study in patients with Crohn’s disease analysing gut microbiota before start of adalimumab therapy (T0) and after six months of therapy (T1). Among the 20 included patients, the phylum Proteobacteria fell from 15.7 ± 3.5% at T0 to 10.3 ± 3.4% at T1 (p = 0.038). Furthermore, the trend in relation to therapeutic success was analysed. Regarding bacterial phyla, Proteobacteria decreased in patients in whom therapeutic success was obtained, passing from a value of 15.8% (± 4.6%) to 6.8 ± 3.1% (p = 0.049), while in non-responder patients, percentages did not change (T0 = 15.6 ± 5.7%, T1 = 16.8 ± 7.6%, p = 0.890). Regarding the Lachnospiraceae family, in patients with normalization of C reactive protein six 6 months of adalimumab therapy, it increased from 16.6 ± 3.1% at T0 to 23.9 ± 2.6% at T1 (p = 0.049). In conclusion, in patients who respond to Adalimumab therapy by decreasing inflammation, there is a trend of intestinal eubiosis being restored.
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Affiliation(s)
| | | | - Amina Abdulle
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy.
| | | | - Maria Chiara Ditto
- S.C. Reumatologia, Città della Salute e della Scienza di Torino, 10126 Turin, Italy.
| | - Mario Morino
- Department of Surgical Sciences, University of Turin, 10124 Turin, Italy.
| | - Enrico Fusaro
- S.C. Reumatologia, Città della Salute e della Scienza di Torino, 10126 Turin, Italy.
| | | | | | - Marco Astegiano
- Unit of Gastroenterology, Molinette Hospital, 10126 Turin, Italy.
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Tanaka M, Sanefuji M, Morokuma S, Yoden M, Momoda R, Sonomoto K, Ogawa M, Kato K, Nakayama J. The association between gut microbiota development and maturation of intestinal bile acid metabolism in the first 3 y of healthy Japanese infants. Gut Microbes 2019; 11:205-216. [PMID: 31550982 PMCID: PMC7053967 DOI: 10.1080/19490976.2019.1650997] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The gut microbial community greatly changes in early life, influencing infant health and subsequent host physiology, notably through its collective metabolism, including host-microbiota interplay of bile acid (BA) metabolism. However, little is known regarding how the development of the intestinal microbial community is associated with maturation of intestinal BA metabolism. To address this, we monitored the succession of gut bacterial community and its association with fecal BA profile in the first 3 y of ten healthy Japanese infants. The BA profiles were classified into four types, defined by high content of conjugated primary BA (Con type), unconjugated primary BA (chenodeoxycholic acid and cholic acid) (Pri type), ursodeoxycholic acid (Urs type), and deoxycholic and lithocholic acid (Sec type). Most subjects begun with Con type or Pri type profiles during lactation and eventually transited to Sec type through Urs type after the start of solid food intake. Con type and Pri type were associated with Enterobacteriaceae-dominant microbiota corresponding to the neonatal type or Bifidobacterium-dominant microbiota corresponding to lactation type, respectively. Urs type subjects were strongly associated with Ruminococcus gnavus colonization, mostly occurring between Pri type and Sec type. Sec type was associated with adult-type complex microbiota dominated by a variety of Firmicutes and Bacteroidetes species. Addressing the link of the common developmental passage of intestinal BA metabolism with infant's health and subsequent host physiology requires further study.
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Affiliation(s)
- Masaru Tanaka
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Masafumi Sanefuji
- Research Center for Environment and Developmental Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Seiichi Morokuma
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Misako Yoden
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Rie Momoda
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Kenji Sonomoto
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Masanobu Ogawa
- Research Center for Environment and Developmental Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kiyoko Kato
- Department of Obstetrics and Gynecology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jiro Nakayama
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan,CONTACT Jiro Nakayama Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
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Monestier M, Latousakis D, Bell A, Tribolo S, Tailford LE, Colquhoun IJ, Le Gall G, Yu H, Chen X, Rejzek M, Dedola S, Field RA, Juge N. Membrane-enclosed multienzyme (MEME) synthesis of 2,7-anhydro-sialic acid derivatives. Carbohydr Res 2017; 451:110-117. [PMID: 28851488 PMCID: PMC5667892 DOI: 10.1016/j.carres.2017.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 12/05/2022]
Abstract
Naturally occurring 2,7-anhydro-alpha-N-acetylneuraminic acid (2,7-anhydro-Neu5Ac) is a transglycosylation product of bacterial intramolecular trans-sialidases (IT-sialidases). A facile one-pot two-enzyme approach has been established for the synthesis of 2,7-anhydro-sialic acid derivatives including those containing different sialic acid forms such as Neu5Ac and N-glycolylneuraminic acid (Neu5Gc). The approach is based on the use of Ruminoccocus gnavus IT-sialidase for the release of 2,7-anhydro-sialic acid from glycoproteins, and the conversion of free sialic acid by a sialic acid aldolase. This synthetic method, which is based on a membrane-enclosed enzymatic synthesis, can be performed on a preparative scale. Using fetuin as a substrate, high-yield and cost-effective production of 2,7-anhydro-Neu5Ac was obtained to high-purity. This method was also applied to the synthesis of 2,7-anhydro-Neu5Gc. The membrane-enclosed multienzyme (MEME) strategy reported here provides an efficient approach to produce a variety of sialic acid derivatives.
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Affiliation(s)
- Marie Monestier
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Dimitrios Latousakis
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Andrew Bell
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Sandra Tribolo
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Louise E Tailford
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Ian J Colquhoun
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Gwenaelle Le Gall
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Hai Yu
- Department of Chemistry, University of California-Davis, Davis, CA 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California-Davis, Davis, CA 95616, USA
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Simone Dedola
- Iceni Diagnostic Ltd, The Innovation Centre, Norwich Research Park, Norwich NR4 7GJ, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; Iceni Diagnostic Ltd, The Innovation Centre, Norwich Research Park, Norwich NR4 7GJ, UK
| | - Nathalie Juge
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK.
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Crost EH, Tailford LE, Monestier M, Swarbreck D, Henrissat B, Crossman LC, Juge N. The mucin-degradation strategy of Ruminococcus gnavus: The importance of intramolecular trans-sialidases. Gut Microbes 2016; 7:302-312. [PMID: 27223845 PMCID: PMC4988440 DOI: 10.1080/19490976.2016.1186334] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/19/2016] [Accepted: 04/29/2016] [Indexed: 02/07/2023] Open
Abstract
We previously identified and characterized an intramolecular trans-sialidase (IT-sialidase) in the gut symbiont Ruminococcus gnavus ATCC 29149, which is associated to the ability of the strain to grow on mucins. In this work we have obtained and analyzed the draft genome sequence of another R. gnavus mucin-degrader, ATCC 35913, isolated from a healthy individual. Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans. R. gnavus ATCC 35913 also encodes a predicted IT-sialidase and harbors a Nan cluster dedicated to sialic acid utilization. We showed that the Nan cluster was upregulated when the strains were grown in presence of mucin. In addition we demonstrated that both R. gnavus strains were able to grow on 2,7-anyhydro-Neu5Ac, the IT-sialidase transglycosylation product, as a sole carbon source. Taken together these data further support the hypothesis that IT-sialidase expressing gut microbes, provide commensal bacteria such as R. gnavus with a nutritional competitive advantage, by accessing and transforming a source of nutrient to their own benefit.
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Affiliation(s)
- Emmanuelle H. Crost
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
| | - Louise E. Tailford
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
| | - Marie Monestier
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
| | - David Swarbreck
- The Genome Analysis Center, Norwich Research Park, Norwich, United Kingdom
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Université Aix-Marseille, CNRS UMR 7257, France
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lisa C. Crossman
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
- SequenceAnalysis.co.uk, NRP Innovation Center, Norwich, United Kingdom
| | - Nathalie Juge
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
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33
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Graziani F, Pujol A, Nicoletti C, Dou S, Maresca M, Giardina T, Fons M, Perrier J. Ruminococcus gnavus E1 modulates mucin expression and intestinal glycosylation. J Appl Microbiol 2016; 120:1403-17. [PMID: 26868655 DOI: 10.1111/jam.13095] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 01/15/2016] [Accepted: 02/07/2016] [Indexed: 12/16/2022]
Abstract
AIMS The molecular cross-talk between commensal bacteria and the gut play an important role in the maintenance of the intestinal homeostasis and general health. Here, we studied the impact of a major Gram-positive anaerobic bacterium of the human gut microbiota, that is, Ruminococcus gnavus on the glycosylation pattern and the production of intestinal mucus by the goblet cells. METHODS AND RESULTS Our results showed that R. gnavus E1 specifically increases the expression and the glycosylation level of the intestinal glyco-conjugates by goblet cells in the colonic mucosa of mono-associated mice with R. gnavus E1 as well as in human HT29-MTX cells. Such an effect was mediated through induction of the level of mRNA encoding for the major intestinal gel-forming mucin such as MUC2 and various glycosyltransferase enzymes. CONCLUSIONS This study demonstrates for the first time that R. gnavus E1 possess the ability to modulate the glycosylation profile of the glyco-conjugate molecules and mucus in goblet cells. SIGNIFICANCE AND IMPACT OF THE STUDY Furthermore, we demonstrated that R. gnavus E1 modified specifically the glycosylation pattern and MUC2 expression by means of a small soluble factor of peptidic nature (<3 kDa) and heat stable in the HT29-MTX cell.
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Affiliation(s)
- F Graziani
- iSm2 UMR 7313, CNRS, Centrale Marseille, Aix Marseille Université, Marseille, France
| | - A Pujol
- iSm2 UMR 7313, CNRS, Centrale Marseille, Aix Marseille Université, Marseille, France
| | - C Nicoletti
- iSm2 UMR 7313, CNRS, Centrale Marseille, Aix Marseille Université, Marseille, France
| | - S Dou
- UP 2012.10.120.EGEAL, Institut Polytechnique, La Salle Beauvais, France
| | - M Maresca
- iSm2 UMR 7313, CNRS, Centrale Marseille, Aix Marseille Université, Marseille, France
| | - T Giardina
- iSm2 UMR 7313, CNRS, Centrale Marseille, Aix Marseille Université, Marseille, France
| | - M Fons
- IMM UMR 7283, CNRS, Aix Marseille Université, Marseille, France
| | - J Perrier
- iSm2 UMR 7313, CNRS, Centrale Marseille, Aix Marseille Université, Marseille, France
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