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Acar C, Celik SK, Ozdemirel HO, Tuncdemir BE, Alan S, Mergen H. Composition of the colon microbiota in the individuals with inflammatory bowel disease and colon cancer. Folia Microbiol (Praha) 2024; 69:333-345. [PMID: 37344611 DOI: 10.1007/s12223-023-01072-w] [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] [Received: 09/21/2022] [Accepted: 06/15/2023] [Indexed: 06/23/2023]
Abstract
The human intestine is a habitat for microorganisms and, recently, the composition of the intestinal microbiota has been correlated with the etiology of diseases such as inflammations, sores, and tumors. Although many studies have been conducted to understand the composition of that microbiota, expanding these studies to more samples and different backgrounds will improve our knowledge. In this work, we showed the colon microbiota composition and diversity of healthy subjects, patients with inflammatory bowel disease (IBD), and colon cancer by metagenomic sequencing. Our results indicated that the relative abundance of prokaryotic and eukaryotic microbes differs between the healthy vs. tumor biopsies, tumor vs. IBD biopsies, and fresh vs. paraffin-embedded tumor biopsies. Fusobacterium, Escherichia-Shigella, and Streptococcus genera were relatively abundant in fresh tumor biopsies, while Pseudomonas was significantly elevated in IBD biopsies. Additionally, another opportunist pathogen Malasseziales was revealed as the most abundant fungal clade in IBD biopsies, especially in ulcerative colitis. We also found that, while the Basidiomycota:Ascomycota ratio was slightly lower in tumor biopsies compared to biopsies from healthy subjects, there was a significant increase in IBD biopsies. Our work will contribute to the known diversity of prokaryotic and eukaryotic microbes in the colon biopsies in patients with IBD and colon cancer.
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Affiliation(s)
- Ceren Acar
- Faculty of Science and Literature, Department of Molecular Biology and Genetics, Inonu University, Malatya, 44280, Turkey.
| | | | - H Ozgur Ozdemirel
- Faculty of Science, Department of Biology, Hacettepe University, Ankara, 06800, Turkey
| | - Beril Erdem Tuncdemir
- Faculty of Science, Department of Biology, Hacettepe University, Ankara, 06800, Turkey
| | - Saadet Alan
- Faculty of Medicine, Department of Medical Pathology, Inonu University, Malatya, 44000, Turkey
| | - Hatice Mergen
- Faculty of Science, Department of Biology, Hacettepe University, Ankara, 06800, Turkey
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Becker HE, Kameli N, Rustichelli A, Heijnens BA, Stassen FR, Penders J, Jonkers DM. In vitro mucin degradation and paracellular permeability by fecal water from Crohn's disease patients. Future Microbiol 2024; 19:335-347. [PMID: 38470403 DOI: 10.2217/fmb-2022-0265] [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] [Indexed: 03/13/2024] Open
Abstract
Aim: This study aimed to examine the impact of fecal water (FW) of active and remissive Crohn's disease (CD) patients on mucin degradation and epithelial barrier function. Methods: FW and bacterial membrane vesicles (MVs) were isolated from fresh fecal samples of six healthy controls (HCs) and 12 CD patients. Bacterial composition was determined by 16S rRNA gene amplicon sequencing. Results: In vitro FW-induced mucin degradation was higher in CD samples versus HC (p < 0.01), but not associated with specific bacterial genera. FW of three remissive samples decreased transepithelial electrical resistance in Caco-2 cells by 78-87% (p < 0.001). MVs did not induce barrier alterations. Conclusion: The higher mucin-degradation capacity of CD-derived FW might suggest contributions of microbial products to CD pathophysiology.
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Affiliation(s)
- Heike Ef Becker
- Department of Gastroenterology/Hepatology, Division of Internal Medicine, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
- Department of Medical Microbiology, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Nader Kameli
- Department of Medical Microbiology, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
- Department of Medical Microbiology, Faculty of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | | | - Britt Am Heijnens
- Department of Gastroenterology/Hepatology, Division of Internal Medicine, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Frank Rm Stassen
- Department of Medical Microbiology, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - John Penders
- Department of Medical Microbiology, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
- Department of Medical Microbiology, Caphri School for Public Health & Primary Care, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Daisy Mae Jonkers
- Department of Gastroenterology/Hepatology, Division of Internal Medicine, NUTRIM School of Nutrition & Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
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Kuenstner JT, Xu Q, Bull TJ, Foddai ACG, Grant IR, Naser SA, Potula R, Zhang P, Shafran I, Akhanli SE, Khaiboullina S, Kruzelock R. Cytokine expression in subjects with Mycobacterium avium ssp. paratuberculosis positive blood cultures and a meta-analysis of cytokine expression in Crohn's disease. Front Cell Infect Microbiol 2024; 14:1327969. [PMID: 38415011 PMCID: PMC10896875 DOI: 10.3389/fcimb.2024.1327969] [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: 10/25/2023] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Abstract
Objectives 1) Culture Mycobacterium avium ssp. paratuberculosis (MAP)from blood, 2) assess infection persistence, 3) determine Crohn's disease (CD) cytokine expression, 4) compare CD cytokine expression to tuberculosis, and 5) perform a meta-analysis of cytokine expression in CD. Methods The Temple University/Abilene Christian University (TU/ACU) study had a prospective case control design with 201 subjects including 61 CD patients and 140 non-CD controls. The culture methods included MGIT, TiKa and Pozzato broths, and were deemed MAP positive, if IS900 PCR positive. A phage amplification assay was also performed to detect MAP. Cytokine analysis of the TU/ACU samples was performed using Simple Plex cytokine reagents on the Ella ELISA system. Statistical analyses were done after log transformation using the R software package. The meta-analysis combined three studies. Results Most subjects had MAP positive blood cultures by one or more methods in 3 laboratories. In our cytokine study comparing CD to non-CD controls, IL-17, IFNγ and TNFα were significantly increased in CD, but IL-2, IL-5, IL-10 and GM-CSF were not increased. In the meta-analysis, IL-6, IL-8 and IL-12 were significantly increased in the CD patients. Conclusion Most subjects in our sample had MAP infection and 8 of 9 subjects remained MAP positive one year later indicating persistent infection. While not identical, cytokine expression patterns in MAP culture positive CD patients in the TU/ACU study showed similarities (increased IL-17, IFNγ and TNFα) to patterns of patients with Tuberculosis in other studies, indicating the possibilities of similar mechanisms of pathogen infection and potential strategies for treatment.
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Affiliation(s)
- J Todd Kuenstner
- Department of Biology, Abilene Christian University, Abilene, TX, United States
| | - Qiang Xu
- Department of Biology, Abilene Christian University, Abilene, TX, United States
| | - Tim J Bull
- Institute of Infection and Immunity, St. George's University of London, London, United Kingdom
| | - Antonio C G Foddai
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
| | - Irene R Grant
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Saleh A Naser
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, United States
| | - Raghava Potula
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | | | | | | | - Svetlana Khaiboullina
- Department of Microbiology and Immunology, University of Nevada, Reno, NV, United States
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Russell Kruzelock
- Department of Biology, Abilene Christian University, Abilene, TX, United States
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Bajaj A, Markandey M, Kedia S, Ahuja V. Gut bacteriome in inflammatory bowel disease: An update on recent advances. Indian J Gastroenterol 2024; 43:103-111. [PMID: 38374283 DOI: 10.1007/s12664-024-01541-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/21/2024]
Abstract
Inflammatory bowel diseases (IBD) are chronic inflammatory gut disorders, majorly classified as ulcerative colitis and Crohn's disease. The complex, multifactorial etiopathogenesis of IBD involves genetic predisposition, environmental cues, aberrant mucosal immune response and a disturbed gut microbiota. Epidemiological trends, studies in gnotobiotic mice models and genome-wide association studies, identifying genes involved in microbial handling, together mount evidence in support of the gut microbiota playing a pivotal role in IBD pathogenesis. Both Crohn's disease and ulcerative colitis are characterized by severe dysbiosis of the gut microbiome, marked by an expansion of detrimental taxa and concomitant depletion of beneficial members. IBD is characterized by reduction in abundances of bacterial genera involved in production of short-chain fatty acids, bio-transformations of bile acids and synthesis of indole-based tryptophan compounds such as Faecalibacterium, Ruminococcus, Coprococcus, Dorea, Parabacteroides, Eubacterium, Oscillibacter and Prevotella and elevation in members of phyla Proteobacteria and Actinobacteria. This imbalance not only results in exaggerated immune signaling towards the microbial antigens, but also results in an altered metabolomic milieu that triggers additional inflammatory cascades. The present review provides insights into the bacterial dysbiosis observed across different intestinal sites and their metabolomic imprints participating in IBD.
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Affiliation(s)
- Aditya Bajaj
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Manasvini Markandey
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Saurabh Kedia
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, 110 029, India.
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Abstract
There is abundant literature reporting about the use of antibiotics in inflammatory bowel disease (IBD), but their role in the management of IBD is not entirely clear. Diverse infectious organisms have been implicated in the pathogenesis of Crohn's disease. Also, infections are believed to be a trigger for flares of ulcerative colitis. The benefit of the routine use of antibiotics in IBD is equivocal. However, there are certain situations, where antibiotics have a clear role and evidence of benefit: perianal fistula, intra-abdominal abscesses in Crohn's disease, acute pouchitis and infection-related flares. However, there is a lack of supportive evidence for the routine use of antibiotics in all disease-related flares. Evidence indicates a lack of benefit of intravenous antibiotics in acute severe ulcerative colitis and only limited benefit in active ulcerative colitis. Limited evidence suggests the role of a combination of oral antibiotics in pediatric ulcerative colitis. Certain targeted antibiotic regimens have been used in IBD. In ulcerative colitis, limited evidence suggests the benefit of the use of an antibiotic cocktail directed against Fusobacterium varium. Therapy directed against Escherichia coli does not seem to have a benefit in inflammatory Crohn's disease. In Crohn's disease, antimycobacterial therapy may result in symptomatic improvement but no durable benefit. Antitubercular therapy (ATT), on the contrary, may result in fibrotic transformation, suggesting a need to avoid misdiagnosis and limit the duration of ATT in Crohn's disease. This review assesses the published literature with respect to antibiotic use and provides guidance to clinicians in appropriate antibiotic use in various situations in the setting of IBD.
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Affiliation(s)
- Daya K Jha
- Indian Navy, Visakhapatnam, 530 014, India
| | | | - Usha Dutta
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160 012, India
| | - Vishal Sharma
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160 012, India.
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Zeng W, Wu J, Xie H, Xu H, Liang D, He Q, Yang X, Liu C, Gong J, Zhang Q, Luo Z, Chen Y, He Z, Lan P. Enteral nutrition promotes the remission of colitis by gut bacteria-mediated histidine biosynthesis. EBioMedicine 2024; 100:104959. [PMID: 38215690 PMCID: PMC10827402 DOI: 10.1016/j.ebiom.2023.104959] [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: 06/27/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Exclusive enteral nutrition (EEN) is an important alternative strategy for patients with Crohn's disease (CD), and during this process, microbiota alterations have been observed. However, the underlying mechanisms by which EEN reduces intestinal inflammation are currently unclear. METHODS The therapeutic potential of enteral nutrition (EN) was assessed using various mouse models. Fecal full-length 16S rDNA sequencing analysis and several CD metagenome datasets were used to identify the candidate therapeutic bacteria Faecalibaculum rodentium (F. rodentium). Whole genome sequencing of F. rodentium and widely-targeted metabolome analysis of the supernatant showed that EN-induced F. rodentium accumulation protected against colitis via histidine biosynthesis. FINDINGS The therapeutic potential of EN therapy was observed in both dextran sulfate sodium (DSS)-induced colitis and Il10-/- spontaneous colitis mouse models. Accumulation of F. rodentium after EN therapy was determined using full-length 16S rDNA sequencing and verified with several metagenome datasets from patients with CD. Colonization of an isolated F. rodentium could reduce colitis in Il10-/- mice. Significant histidine enrichment was observed in the F. rodentium culture supernatant, and a series of histidine biosynthesis genes were observed in the F. rodentium genome. Engineered Escherichia coli Nissle 1917 (EcN), encoding the heterologous hisG of F. rodentium (EcN-hisG), which was a key driver of histidine biosynthesis in F. rodentium, was found to protect against colitis. INTERPRETATION This study suggests that EN-induced F. rodentium accumulation protects against colitis in mice via gut bacteria-mediated histidine biosynthesis. FUNDING A full list of funding bodies can be found in the Acknowledgements section.
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Affiliation(s)
- Wanyi Zeng
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Jinjie Wu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Hongyu Xie
- Department of Anesthesia, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Haoyang Xu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Dayi Liang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Qilang He
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China
| | - Xiaoya Yang
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China
| | - Chen Liu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Junli Gong
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Qiang Zhang
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China
| | - Zhanhao Luo
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Yuan Chen
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China
| | - Zhen He
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China.
| | - Ping Lan
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; State Key Laboratory of Oncology in South China, Guangzhou, Guangdong 510655, China.
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Geesala R, Recharla N, Zhang K, Johnson JC, Golovko G, Khanipov K, Brining DL, Shi XZ. Exclusive Enteral Nutrition Beneficially Modulates Gut Microbiome in a Preclinical Model of Crohn's-like Colitis. Nutrients 2024; 16:363. [PMID: 38337648 PMCID: PMC10857303 DOI: 10.3390/nu16030363] [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] [Received: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Exclusive enteral nutrition (EEN) is an established dietary treatment for Crohn's disease (CD) by alleviating inflammation and inducing remission. However, the mechanisms of action of EEN are incompletely understood. As CD is associated with gut microbiome dysbiosis, we investigated the effect of EEN on the microbiome in a rat model of CD-like colitis. The rat model of CD-like colitis was established by an intracolonic instillation of TNBS at 65 mg/kg in 250 µL of 40% ethanol. Sham control rats were instilled with saline. Rats were fed ad libitum with either regular pellet food or EEN treatment with a clear liquid diet (Ensure). Rats were euthanized at 7 days. Fecal pellets were collected from the distal colon for 16S rRNA sequencing analysis of gut microbiota. In addition, colon tissues were taken for histological and molecular analyses in all the groups of rats. EEN administration to TNBS-induced CD rats significantly improved the body weight change, inflammation scores, and disease activity index. The mRNA expression of IL-17A and interferon-γ was significantly increased in the colonic tissue in TNBS rats when fed with regular food. However, EEN treatment significantly attenuated the increase in IL-17A and interferon-γ in TNBS rats. Our 16S rRNA sequencing analysis found that gut microbiota diversity and compositions were significantly altered in TNBS rats, compared to controls. However, EEN treatment improved alpha diversity and increased certain beneficial bacteria such as Lactobacillus and Dubosiella and decreased bacteria such as Bacteroides and Enterorhabdus in CD-like rats, compared to CD-like rats with the regular pellet diet. In conclusion, EEN treatment increases the diversity of gut microbiota and the composition of certain beneficial bacteria. These effects may contribute to the reduced inflammation by EEN in the rat model of CD-like colitis.
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Affiliation(s)
- Ramasatyaveni Geesala
- Department of Internal Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (R.G.); (N.R.); (K.Z.); (J.C.J.)
| | - Neeraja Recharla
- Department of Internal Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (R.G.); (N.R.); (K.Z.); (J.C.J.)
| | - Ke Zhang
- Department of Internal Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (R.G.); (N.R.); (K.Z.); (J.C.J.)
| | - John C. Johnson
- Department of Internal Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (R.G.); (N.R.); (K.Z.); (J.C.J.)
| | - George Golovko
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (G.G.); (K.K.)
| | - Kamil Khanipov
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (G.G.); (K.K.)
| | - Douglas L. Brining
- Department of Microbiology & Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA;
| | - Xuan-Zheng Shi
- Department of Internal Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (R.G.); (N.R.); (K.Z.); (J.C.J.)
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K I, Y M, A N, D S, G G, R S, D G, V SN, O S, M F, S R, S O, J MG, A M. Cognitive behavioral and mindfulness with daily exercise intervention is associated with changes in intestinal microbial taxa and systemic inflammation in patients with Crohn's disease. Gut Microbes 2024; 16:2337269. [PMID: 38591914 PMCID: PMC11005811 DOI: 10.1080/19490976.2024.2337269] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory bowel disease associated with psychological distress and intestinal microbial changes. Here, we examined whether a 3-month period of Cognitive Behavioral and Mindfulness with Daily Exercise (COBMINDEX) intervention, which improves the wellbeing and inflammatory state of CD patients, may also affect their gut microbiome. Gut microbiota, circulating inflammatory markers and hormones were analyzed in 24 CD patients before (T1) and after 3 months of COBMINDEX (T2), and in 25 age- and sex-matched wait-list control patients at the corresponding time-points. Microbiota analysis examined relative taxonomical abundance, alpha and beta diversity, and microbiome correlations with inflammatory and psychological parameters. At T1, CD patients exhibited a characteristic microbial profile mainly constituted of Proteobacteria (17.71%), Firmicutes (65.56%), Actinobacteria (8.46%) and Bacteroidetes (6.24%). Baseline bacterial abundances showed significant correlations with psychological markers of distress and with IFNγ . Following COBMINDEX, no significant changes in alpha and beta diversity were observed between both study groups, though a trend change in beta diversity was noted. Significant changes occurred in the abundance of phyla, families and genera only among the COBMINDEX group. Furthermore, abundance of phyla, families and genera that were altered following COBMNIDEX, significantly correlated with levels of cytokines and psychological parameters. Our results demonstrated that a short-term intervention of COBMINDEX was associated with changes in microbial indices, some of which are linked to psychological manifestations and systemic inflammation in CD patients. Psychological interventions to reduce chronic stress, such as COBMINDEX, appear to be beneficial in mitigating the pathobiology of CD patients, and may thus provide a useful adjunct to pharmacological therapy.
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Affiliation(s)
- Ilan K
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The National Institute of Biotechnology in the Negev, School of Brain Sciences and Cognition, and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Motro Y
- MAGICAL Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben‐Gurion University of the Negev, Beer‐Sheva, Israel
| | - Nemirovsky A
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The National Institute of Biotechnology in the Negev, School of Brain Sciences and Cognition, and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Schwartz D
- Department of Gastroenterology and Hepatology, Soroka Medical Center, and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Goren G
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sergienko R
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Greenberg D
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Slonim-Nevo V
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sarid O
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Friger M
- Department of Epidemiology, Biostatistics and Community Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Regev S
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Odes S
- Department of Gastroenterology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Moran-Gilad J
- MAGICAL Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben‐Gurion University of the Negev, Beer‐Sheva, Israel
| | - Monsonego A
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The National Institute of Biotechnology in the Negev, School of Brain Sciences and Cognition, and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Smith CR, Miller AD. In situ hybridization to detect Escherichia coli in canine granulomatous colitis. J Vet Diagn Invest 2024; 36:142-145. [PMID: 37968864 PMCID: PMC10734575 DOI: 10.1177/10406387231213358] [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: 11/17/2023] Open
Abstract
Canine granulomatous colitis (histiocytic ulcerative colitis) is an uncommon disease, predominantly of young French Bulldogs and Boxer dogs, that manifests from a dysregulated immune response, primarily to adherent-invasive Escherichia coli (AIEC). In conjunction with histopathology and periodic acid-Schiff staining, the diagnosis of granulomatous colitis currently relies on fluorescence in situ hybridization (ISH) or immunohistochemistry to identify and localize AIEC organisms within macrophages in the mucosa and/or submucosa. We investigated the utility of ISH for E. coli using formalin-fixed, paraffin-embedded specimens collected from 29 cases of suspected granulomatous colitis. Most confirmed cases of granulomatous colitis were in French Bulldogs (12 of 20; 60%) and Boxers (3 of 20; 15%), and the mean age was 25 ± 6 mo with no sex predilection. E. coli ISH signal localized bacterial genetic material within the mucosa in 20 of 29 (69%) cases, supporting the diagnosis. ISH signal was limited to the lumen in 8 of 29 (28%) cases, which did not support the identification of these organisms as AIEC. The remaining case had no hybridization signal, and the diagnosis of granulomatous colitis was not supported. Our results revealed that ISH is a quick and specific detection method that can effectively confirm the diagnosis of canine granulomatous colitis.
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Affiliation(s)
- Carmen R. Smith
- Department of Population Medicine and Diagnostic Sciences, Section of Anatomic Pathology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Andrew D. Miller
- Department of Population Medicine and Diagnostic Sciences, Section of Anatomic Pathology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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10
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Pinto S, Benincà E, Galazzo G, Jonkers D, Penders J, Bogaards JA. Heterogeneous associations of gut microbiota with Crohn's disease activity. Gut Microbes 2024; 16:2292239. [PMID: 38105519 PMCID: PMC10730216 DOI: 10.1080/19490976.2023.2292239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023] Open
Abstract
The multi-factorial involvement of gut microbiota with Crohn's disease (CD) necessitates robust analysis to uncover possible associations with particular microbes. CD has been linked to specific bacteria, but reported associations vary widely across studies. This inconsistency may result from heterogeneous associations across individual patients, resulting in no apparent or only weak relationships with the means of bacterial abundances. We investigated the relationship between bacterial relative abundances and disease activity in a longitudinal cohort of CD patients (n = 57) and healthy controls (n = 15). We applied quantile regression, a statistical technique that allows investigation of possible relationships outside the mean response. We found several significant and mostly negative associations with CD, especially in lower quantiles of relative abundance on family or genus level. Associations found by quantile regression deviated from the mean response in relative abundances of Coriobacteriaceae, Pasteurellaceae, Peptostreptococcaceae, Prevotellaceae, and Ruminococcaceae. For the family Streptococcaceae we found a significant elevation in relative abundance for patients experiencing an exacerbation relative to those who remained without self-reported symptoms or measurable inflammation. Our analysis suggests that specific bacterial families are related to CD and exacerbation, but associations vary between patients due to heterogeneity in disease course, medication history, therapy response, gut microbiota composition and historical contingency. Our study underscores that microbial diversity is reduced in the gut of CD patients, but suggests that the process of diversity loss is rather irregular with respect to specific taxonomic groups. This novel insight may advance our ecological understanding of this complex disease.
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Affiliation(s)
- Susanne Pinto
- Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| | - Elisa Benincà
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Gianluca Galazzo
- School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, Netherlands
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, Maastricht UMC, Maastricht, Netherlands
| | - Daisy Jonkers
- School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, Netherlands
- Department of Gastroenterology-Hepatology, Maastricht UMC, Maastricht, Netherlands
| | - John Penders
- School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, Netherlands
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, Maastricht UMC, Maastricht, Netherlands
| | - Johannes A. Bogaards
- Epidemiology and Data Science, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Institute for Infection and Immunity (AII), Amsterdam UMC, Amsterdam, Netherlands
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11
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Iaquinto G, Aufiero VR, Mazzarella G, Lucariello A, Panico L, Melina R, Iaquinto S, De Luca A, Sellitto C. Pathogens in Crohn's Disease: The Role of Adherent Invasive Escherichia coli. Crit Rev Eukaryot Gene Expr 2024; 34:83-99. [PMID: 38305291 DOI: 10.1615/critreveukaryotgeneexpr.2023050088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
In Crohn's disease (CD), gut dysbiosis is marked by the prevalence of pathogenic bacterial species. Although several microbes have been reported as risk factors or causative agents of CD, it is not yet clear which is the real trigger of the disease. Thirty years ago, a new pathovar of Escherichia coli strain was isolated in the ileal mucosa of CD patients. This strain, called adherent invasive E. coli (AIEC), for its ability to invade the intestinal mucosa, could represent the causative agent of the disease. Several authors studied the mechanisms by which the AIEC penetrate and replicate within macrophages, and release inflammatory cytokines sustaining inflammation. In this review we will discuss about the role of AIEC in the pathogenesis of CD, the virulence factors mediating adhesion and invasion of AIEC in mucosal tissue, the environmental conditions improving AIEC survival and replication within macrophages. Finally, we will also give an overview of the new strategies developed to limit AIEC overgrowth.
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Affiliation(s)
- Gaetano Iaquinto
- Gastroenterology Division, S. Rita Hospital, Atripalda, Avellino, Italy
| | - Vera Rotondi Aufiero
- Institute of Food Sciences, CNR, Avellino, Italy and Department of Translational Medical Science and E.L.F.I.D, University "Federico II" Napoli, Italy
| | - Giuseppe Mazzarella
- Institute of Food Sciences, CNR, Avellino, Italy and Department of Translational Medical Science and E.L.F.I.D, University "Federico II" Napoli, Italy
| | - Angela Lucariello
- Department of Sport Sciences and Wellness, University of Naples "Parthenope," 80100, Naples, Italy
| | - Luigi Panico
- Pathological Anatomy and Histology Unit, Monaldi Hospital, Napoli, Italy
| | - Raffaele Melina
- Department of Gastroenterology, San G. Moscati Hospital, Avellino, Italy
| | | | - Antonio De Luca
- Department of Mental Health and Physics, Preventive Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy
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12
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Sheikh IA, Bianchi-Smak J, Laubitz D, Schiro G, Midura-Kiela MT, Besselsen DG, Vedantam G, Jarmakiewicz S, Filip R, Ghishan FK, Gao N, Kiela PR. Transplant of microbiota from Crohn's disease patients to germ-free mice results in colitis. Gut Microbes 2024; 16:2333483. [PMID: 38532703 PMCID: PMC10978031 DOI: 10.1080/19490976.2024.2333483] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Although the role of the intestinal microbiota in the pathogenesis of inflammatory bowel disease (IBD) is beyond debate, attempts to verify the causative role of IBD-associated dysbiosis have been limited to reports of promoting the disease in genetically susceptible mice or in chemically induced colitis. We aimed to further test the host response to fecal microbiome transplantation (FMT) from Crohn's disease patients on mucosal homeostasis in ex-germ-free (xGF) mice. We characterized and transferred fecal microbiota from healthy patients and patients with defined Crohn's ileocolitis (CD_L3) to germ-free mice and analyzed the resulting microbial and mucosal homeostasis by 16S profiling, shotgun metagenomics, histology, immunofluorescence (IF) and RNAseq analysis. We observed a markedly reduced engraftment of CD_L3 microbiome compared to healthy control microbiota. FMT from CD_L3 patients did not lead to ileitis but resulted in colitis with features consistent with CD: a discontinued pattern of colitis, more proximal colonic localization, enlarged isolated lymphoid follicles and/or tertiary lymphoid organ neogenesis, and a transcriptomic pattern consistent with epithelial reprograming and promotion of the Paneth cell-like signature in the proximal colon and immune dysregulation characteristic of CD. The observed inflammatory response was associated with persistently increased abundance of Ruminococcus gnavus, Erysipelatoclostridium ramosum, Faecalimonas umbilicate, Blautia hominis, Clostridium butyricum, and C. paraputrificum and unexpected growth of toxigenic C. difficile, which was below the detection level in the community used for inoculation. Our study provides the first evidence that the transfer of a dysbiotic community from CD patients can lead to spontaneous inflammatory changes in the colon of xGF mice and identifies a signature microbial community capable of promoting colonization of pathogenic and conditionally pathogenic bacteria.
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Affiliation(s)
- Irshad Ali Sheikh
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | | | - Daniel Laubitz
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | - Gabriele Schiro
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | - Monica T. Midura-Kiela
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | - David G. Besselsen
- Pediatrics, University Animal Care, University of Arizona, Tucson, AZ, USA
| | - Gayatri Vedantam
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA
| | - Sara Jarmakiewicz
- Institute of Health Sciences, Medical College of Rzeszow, Rzeszow University, Rzeszow, Poland
| | - Rafał Filip
- Institute of Medicine, Medical College of Rzeszow University, Rzeszow, Poland
- Department of Gastroenterology with IBD Unit, Clinical Hospital, Rzeszow, Poland
| | - Fayez K. Ghishan
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Pawel R. Kiela
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, USA
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA
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13
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Hamed SA, Mohan A, Navaneetha Krishnan S, Wang A, Drikic M, Prince NL, Lewis IA, Shearer J, Keita ÅV, Söderholm JD, Shutt TE, McKay DM. Butyrate reduces adherent-invasive E. coli-evoked disruption of epithelial mitochondrial morphology and barrier function: involvement of free fatty acid receptor 3. Gut Microbes 2023; 15:2281011. [PMID: 38078655 PMCID: PMC10730202 DOI: 10.1080/19490976.2023.2281011] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/05/2023] [Indexed: 12/18/2023] Open
Abstract
Gut bacteria provide benefits to the host and have been implicated in inflammatory bowel disease (IBD), where adherent-invasive E. coli (AIEC) pathobionts (e.g., strain LF82) are associated with Crohn's disease. E. coli-LF82 causes fragmentation of the epithelial mitochondrial network, leading to increased epithelial permeability. We hypothesized that butyrate would limit the epithelial mitochondrial disruption caused by E. coli-LF82. Human colonic organoids and the T84 epithelial cell line infected with E. coli-LF82 (MOI = 100, 4 h) showed a significant increase in mitochondrial network fission that was reduced by butyrate (10 mM) co-treatment. Butyrate reduced the loss of mitochondrial membrane potential caused by E. coli-LF82 and increased expression of PGC-1α mRNA, the master regulator of mitochondrial biogenesis. Metabolomics revealed that butyrate significantly altered E. coli-LF82 central carbon metabolism leading to diminished glucose uptake and increased succinate secretion. Correlating with preservation of mitochondrial network form/function, butyrate reduced E. coli-LF82 transcytosis across T84-cell monolayers. The use of the G-protein inhibitor, pertussis toxin, implicated GPCR signaling as critical to the effect of butyrate, and the free fatty acid receptor three (FFAR3, GPR41) agonist, AR420626, reproduced butyrate's effect in terms of ameliorating the loss of barrier function and reducing the mitochondrial fragmentation observed in E. coli-LF82 infected T84-cells and organoids. These data indicate that butyrate helps maintain epithelial mitochondrial form/function when challenged by E. coli-LF82 and that this occurs, at least in part, via FFAR3. Thus, loss of butyrate-producing bacteria in IBD in the context of pathobionts would contribute to loss of epithelial mitochondrial and barrier functions that could evoke disease and/or exaggerate a low-grade inflammation.
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Affiliation(s)
- Samira A. Hamed
- Gastrointestinal Research Group, Inflammation Research Network, Host-Parasite Interactions Program, Department of Physiology & Pharmacology, Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Armaan Mohan
- Departments of Medical Genetics and Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, Hotchkiss Brain Institute, Snyder Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Saranya Navaneetha Krishnan
- Gastrointestinal Research Group, Inflammation Research Network, Host-Parasite Interactions Program, Department of Physiology & Pharmacology, Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Arthur Wang
- Gastrointestinal Research Group, Inflammation Research Network, Host-Parasite Interactions Program, Department of Physiology & Pharmacology, Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Marija Drikic
- Calgary Metabolomics Research Facility, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Canada
| | - Nicole L. Prince
- Gastrointestinal Research Group, Inflammation Research Network, Host-Parasite Interactions Program, Department of Physiology & Pharmacology, Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Ian A. Lewis
- Calgary Metabolomics Research Facility, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Canada
| | - Jane Shearer
- Department of Biochemistry and Molecular Biology, Faculty of Kinesiology, University of Calgary, Calgary, Canada
| | - Åsa V. Keita
- Department of Biomedical and Clinical Sciences, Division of Surgery, Orthopedics and Oncology, Linköping University, Linköping, Sweden
| | - Johan D. Söderholm
- Department of Biomedical and Clinical Sciences, Division of Surgery, Orthopedics and Oncology, Linköping University, Linköping, Sweden
| | - Timothy E. Shutt
- Departments of Medical Genetics and Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, Hotchkiss Brain Institute, Snyder Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Derek M. McKay
- Gastrointestinal Research Group, Inflammation Research Network, Host-Parasite Interactions Program, Department of Physiology & Pharmacology, Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
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14
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Kang DY, Park JL, Yeo MK, Kang SB, Kim JM, Kim JS, Kim SY. Diagnosis of Crohn's disease and ulcerative colitis using the microbiome. BMC Microbiol 2023; 23:336. [PMID: 37951857 PMCID: PMC10640746 DOI: 10.1186/s12866-023-03084-5] [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] [Received: 03/20/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a multifactorial chronic inflammatory disease resulting from dysregulation of the mucosal immune response and gut microbiota. Crohn's disease (CD) and ulcerative colitis (UC) are difficult to distinguish, and differential diagnosis is essential for establishing a long-term treatment plan for patients. Furthermore, the abundance of mucosal bacteria is associated with the severity of the disease. This study aimed to differentiate and diagnose these two diseases using the microbiome and identify specific biomarkers associated with disease activity. RESULTS Differences in the abundance and composition of the microbiome between IBD patients and healthy controls (HC) were observed. Compared to HC, the diversity of the gut microbiome in patients with IBD decreased; the diversity of the gut microbiome in patients with CD was significantly lower. Sixty-eight microbiota members (28 for CD and 40 for UC) associated with these diseases were identified. Additionally, as the disease progressed through different stages, the diversity of the bacteria decreased. The abundances of Alistipes shahii and Pseudodesulfovibrio aespoeensis were negatively correlated with the severity of CD, whereas the abundance of Polynucleobacter wianus was positively correlated. The severity of UC was negatively correlated with the abundance of A. shahii, Porphyromonas asaccharolytica and Akkermansia muciniphilla, while it was positively correlated with the abundance of Pantoea candidatus pantoea carbekii. A regularized logistic regression model was used for the differential diagnosis of the two diseases. The area under the curve (AUC) was used to examine the performance of the model. The model discriminated UC and CD at an AUC of 0.873 (train set), 0.778 (test set), and 0.633 (validation set) and an area under the precision-recall curve (PRAUC) of 0.888 (train set), 0.806 (test set), and 0.474 (validation set). CONCLUSIONS Based on fecal whole-metagenome shotgun (WMS) sequencing, CD and UC were diagnosed using a machine-learning predictive model. Microbiome biomarkers associated with disease activity (UC and CD) are also proposed.
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Affiliation(s)
- Da-Yeon Kang
- Department of New Drug Development, Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, Korea
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Jong-Lyul Park
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Min-Kyung Yeo
- Department of Pathology, Chungnam National University School of Medicine, Munwha-Ro 266, Daejeon, 35015, Korea
| | - Sang-Bum Kang
- Department of Internal Medicine, Division of Gastroenterology, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Daejeon, Korea
| | - Jin-Man Kim
- Department of Pathology, Chungnam National University School of Medicine, Munwha-Ro 266, Daejeon, 35015, Korea
| | - Ju Seok Kim
- Departments of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Korea.
| | - Seon-Young Kim
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.
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15
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Hu M, Caldarelli G, Gili T. Inflammatory bowel disease biomarkers revealed by the human gut microbiome network. Sci Rep 2023; 13:19428. [PMID: 37940667 PMCID: PMC10632483 DOI: 10.1038/s41598-023-46184-y] [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: 08/16/2022] [Accepted: 10/29/2023] [Indexed: 11/10/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) are complex medical conditions in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when exposed to yet unclear environmental factors. The complexity of this class of diseases makes them suitable to be represented and studied with network science. In this paper, the metagenomic data of control, Crohn's disease, and ulcerative colitis subjects' gut microbiota were investigated by representing this data as correlation networks and co-expression networks. We obtained correlation networks by calculating Pearson's correlation between gene expression across subjects. A percolation-based procedure was used to threshold and binarize the adjacency matrices. In contrast, co-expression networks involved the construction of the bipartite subjects-genes networks and the monopartite genes-genes projection after binarization of the biadjacency matrix. Centrality measures and community detection were used on the so-built networks to mine data complexity and highlight possible biomarkers of the diseases. The main results were about the modules of Bacteroides, which were connected in the control subjects' correlation network, Faecalibacterium prausnitzii, where co-enzyme A became central in IBD correlation networks and Escherichia coli, whose module has different patterns of integration within the whole network in the different diagnoses.
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Affiliation(s)
- Mirko Hu
- Department of Medicine and Surgery, University of Parma, 43121, Parma, Italy
| | - Guido Caldarelli
- Department of Molecular Science and Nanosystems, Ca' Foscari University of Venice, 30123, Venice, Italy.
- Institute of Complex Systems, National Research Council (ISC-CNR), 00185, Rome, Italy.
- Fondazione per il Futuro delle Città, FFC, 50133, Firenze, Italy.
- European Centre for Living Technology, (ECLT), 30123, Venice, Italy.
| | - Tommaso Gili
- Networks Unit, IMT School for Advanced Studies Lucca, 55100, Lucca, Italy
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16
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Lawal SA, Voisin A, Olof H, Bording-Jorgensen M, Armstrong H. Diversity of the microbiota communities found in the various regions of the intestinal tract in healthy individuals and inflammatory bowel diseases. Front Immunol 2023; 14:1242242. [PMID: 38022505 PMCID: PMC10654633 DOI: 10.3389/fimmu.2023.1242242] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
The severe and chronic inflammatory bowel diseases (IBD), Crohn disease and ulcerative colitis, are characterized by persistent inflammation and gut damage. There is an increasing recognition that the gut microbiota plays a pivotal role in IBD development and progression. However, studies of the complete microbiota composition (bacteria, fungi, viruses) from precise locations within the gut remain limited. In particular, studies have focused primarily on the bacteriome, with available methods limiting evaluation of the mycobiome (fungi) and virome (virus). Furthermore, while the different segments of the small and large intestine display different functions (e.g., digestion, absorption, fermentation) and varying microenvironment features (e.g., pH, metabolites), little is known about the biogeography of the microbiota in different segments of the intestinal tract or how this differs in IBD. Here, we highlight evidence of the differing microbiota communities of the intestinal sub-organs in healthy and IBD, along with method summaries to improve future studies.
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Affiliation(s)
- Samuel Adefisoye Lawal
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Athalia Voisin
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Hana Olof
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | | | - Heather Armstrong
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
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17
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Martini GR, Tikhonova E, Rosati E, DeCelie MB, Sievers LK, Tran F, Lessing M, Bergfeld A, Hinz S, Nikolaus S, Kümpers J, Matysiak A, Hofmann P, Saggau C, Schneiders S, Kamps AK, Jacobs G, Lieb W, Maul J, Siegmund B, Seegers B, Hinrichsen H, Oberg HH, Wesch D, Bereswill S, Heimesaat MM, Rupp J, Kniemeyer O, Brakhage AA, Brunke S, Hube B, Aden K, Franke A, Iliev ID, Scheffold A, Schreiber S, Bacher P. Selection of cross-reactive T cells by commensal and food-derived yeasts drives cytotoxic T H1 cell responses in Crohn's disease. Nat Med 2023; 29:2602-2614. [PMID: 37749331 PMCID: PMC10579100 DOI: 10.1038/s41591-023-02556-5] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/22/2023] [Indexed: 09/27/2023]
Abstract
Aberrant CD4+ T cell reactivity against intestinal microorganisms is considered to drive mucosal inflammation in inflammatory bowel diseases. The disease-relevant microbial species and the corresponding microorganism-specific, pathogenic T cell phenotypes remain largely unknown. In the present study, we identified common gut commensal and food-derived yeasts, as direct activators of altered CD4+ T cell reactions in patients with Crohn's disease (CD). Yeast-responsive CD4+ T cells in CD display a cytotoxic T helper cell (TH1 cell) phenotype and show selective expansion of T cell clones that are highly cross-reactive to several commensal, as well as food-derived, fungal species. This indicates cross-reactive T cell selection by repeated encounter with conserved fungal antigens in the context of chronic intestinal disease. Our results highlighted a role of yeasts as drivers of aberrant CD4+ T cell reactivity in patients with CD and suggest that both gut-resident fungal commensals and daily dietary intake of yeasts might contribute to chronic activation of inflammatory CD4+ T cell responses in patients with CD.
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Affiliation(s)
- Gabriela Rios Martini
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Ekaterina Tikhonova
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Elisa Rosati
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Meghan Bialt DeCelie
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Laura Katharina Sievers
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Matthias Lessing
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Arne Bergfeld
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Sophia Hinz
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Susanna Nikolaus
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Julia Kümpers
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Anna Matysiak
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Philipp Hofmann
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Carina Saggau
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Stephan Schneiders
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Ann-Kristin Kamps
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Gunnar Jacobs
- Institute of Epidemiology, Christian-Albrechts-University of Kiel and popgen Biobank, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel and popgen Biobank, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jochen Maul
- Gastroenterologie am Bayerischen Platz, Berlin, Germany
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Britta Siegmund
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | | | | | - Hans-Heinrich Oberg
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Daniela Wesch
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Stefan Bereswill
- Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Markus M Heimesaat
- Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
- Friedrich Schiller Universität, Jena, Germany
| | - Sascha Brunke
- Institute of Microbiology, Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Bernhard Hube
- Friedrich Schiller Universität, Jena, Germany
- Institute of Microbiology, Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Iliyan D Iliev
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Petra Bacher
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany.
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany.
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18
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Jingjie W, Jun S. Gut vascular barrier in the pathogenesis and resolution of Crohn's disease: A novel link from origination to therapy. Clin Immunol 2023; 253:109683. [PMID: 37406981 DOI: 10.1016/j.clim.2023.109683] [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: 04/29/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023]
Abstract
The gut vascular barrier (GVB) is the deepest layer of the gut barrier. It mainly comprised gut vascular endothelial cells, enteric glial cells, and pericytes. The GVB facilitates nutrient absorption and blocks bacterial translocation through its size-restricted permeability. Accumulating evidence suggests that dysfunction of this barrier correlates with several clinical pathologies including Crohn's disease (CD). Significant progress has been made to elucidate the mechanism of GVB dysfunction and to confirm the participation of disrupted GVB in the course of CD. However, further analyses are required to pinpoint the specific roles of GVB in CD pathogenesis. Many preclinical models and clinical trials have demonstrated that various agents are effective in protecting the GVB integrity and thus providing a potential CD treatment strategy. Through this review, we established a systemic understanding of the role of GVB in CD pathogenesis and provided novel insights for GVB-targeting strategies in CD treatment.
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Affiliation(s)
- Wang Jingjie
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center; Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease; 160# Pu Jian Ave, Shanghai 200127, China
| | - Shen Jun
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center; Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease; 160# Pu Jian Ave, Shanghai 200127, China.
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19
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Espeschit IF, Bastos DSS, Fonseca Junior A, Cardoso SA, Ferrari MLA, Moreira MAS. Mycobacterium avium subsp. paratuberculosis and Crohn's disease: characterization of the interaction with different aspects of the disease. Braz J Microbiol 2023; 54:1239-1249. [PMID: 36877446 PMCID: PMC10235376 DOI: 10.1007/s42770-023-00932-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 10/26/2022] [Accepted: 02/13/2023] [Indexed: 03/07/2023] Open
Abstract
Crohn's disease (CD) is a chronic granulomatous inflammatory bowel disease with no fully understood etiology and cure. Mycobacterium avium subspecies paratuberculosis (MAP), the etiologic agent of paratuberculosis, is also isolated from samples from human patients with CD. Paratuberculosis is characterized by persistent diarrhea and progressive weight loss and primarily affects ruminants, which eliminate the agent via feces and milk. The involvement of MAP in the pathogenesis of CD and other intestinal diseases is unclear. Thus, the present study aimed to analyze immunological, socioepidemiological, biochemical, and therapeutic variables that may be related to the occurrence of MAP in blood samples and CD patients. The sampling was random, and the population of origin was the patients from the Bowel Outpatient Clinic of the Alpha Institute of Gastroenterology (IAG), Hospital das Clínicas, Universidade Federal de Minas Gerais (HC-UFMG). Blood samples were collected from 20 patients with CD, eight with ulcerative rectocolitis (UCR), and 10 control patients without inflammatory bowel diseases. Samples were subjected to real-time PCR for detection of MAP DNA, oxidative stress analyses, and socioepidemiological variables. MAP was detected in 10 (26.3%) of the patients, seven (70%) were CD patients, 2 (20%) were URC patients, and one (10%) was a non-IBD patient. MAP was found more frequently among CD patients, but not restricted to CD patients. The presence of MAP in the blood of these patients occurred simultaneously with an inflammatory response with an increase in neutrophils and significant alterations in the production of antioxidant enzymes such as catalase and GST.
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Affiliation(s)
- I F Espeschit
- Laboratory of Bacterial Diseases-Preventive Veterinary Medicine and Public Health Sector, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - D S S Bastos
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - A Fonseca Junior
- Ministério da Agricultura Pecuária E Abastecimento, Laboratório Nacional Agropecuário, Pedro Leopoldo, Minas Gerais, Brazil
| | - S A Cardoso
- Department of Medicine, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M L A Ferrari
- Department of Internal Medicine, School of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - M A S Moreira
- Laboratory of Bacterial Diseases-Preventive Veterinary Medicine and Public Health Sector, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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20
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Metwaly A, Jovic J, Waldschmitt N, Khaloian S, Heimes H, Häcker D, Ahmed M, Hammoudi N, Le Bourhis L, Mayorgas A, Siebert K, Basic M, Schwerd T, Allez M, Panes J, Salas A, Bleich A, Zeissig S, Schnupf P, Cominelli F, Haller D. Diet prevents the expansion of segmented filamentous bacteria and ileo-colonic inflammation in a model of Crohn's disease. Microbiome 2023; 11:66. [PMID: 37004103 PMCID: PMC10064692 DOI: 10.1186/s40168-023-01508-y] [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] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/25/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Crohn's disease (CD) is associated with changes in the microbiota, and murine models of CD-like ileo-colonic inflammation depend on the presence of microbial triggers. Increased abundance of unknown Clostridiales and the microscopic detection of filamentous structures close to the epithelium of Tnf ΔARE mice, a mouse model of CD-like ileitis pointed towards segmented filamentous bacteria (SFB), a commensal mucosal adherent bacterium involved in ileal inflammation. RESULTS We show that the abundance of SFB strongly correlates with the severity of CD-like ileal inflammation in two mouse models of ileal inflammation, including Tnf ΔARE and SAMP/Yit mice. SFB mono-colonization of germ-free Tnf ΔARE mice confirmed the causal link and resulted in severe ileo-colonic inflammation, characterized by elevated tissue levels of Tnf and Il-17A, neutrophil infiltration and loss of Paneth and goblet cell function. Co-colonization of SFB in human-microbiota associated Tnf ΔARE mice confirmed that SFB presence is indispensable for disease development. Screening of 468 ileal and colonic mucosal biopsies from adult and pediatric IBD patients, using previously published and newly designed human SFB-specific primer sets, showed no presence of SFB in human tissue samples, suggesting a species-specific functionality of the pathobiont. Simulating the human relevant therapeutic effect of exclusive enteral nutrition (EEN), EEN-like purified diet antagonized SFB colonization and prevented disease development in Tnf ΔARE mice, providing functional evidence for the protective mechanism of diet in modulating microbiota-dependent inflammation in IBD. CONCLUSIONS We identified a novel pathogenic role of SFB in driving severe CD-like ileo-colonic inflammation characterized by loss of Paneth and goblet cell functions in Tnf ΔARE mice. A purified diet antagonized SFB colonization and prevented disease development in Tnf ΔARE mice in contrast to a fiber-containing chow diet, clearly demonstrating the important role of diet in modulating a novel IBD-relevant pathobiont and supporting a direct link between diet and microbial communities in mediating protective functions. Video Abstract.
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Affiliation(s)
- Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Jelena Jovic
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Nadine Waldschmitt
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Sevana Khaloian
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Helena Heimes
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Deborah Häcker
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Mohamed Ahmed
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Nassim Hammoudi
- APHP, Hôpital Saint Louis, Department of Gastroenterology, INSERM UMRS 1160, Paris Diderot, Sorbonne Paris-Cité University, Paris, France
- Université Paris Cité, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Lionel Le Bourhis
- Université Paris Cité, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Aida Mayorgas
- Department of Experimental Pathology, Instituto de Investigaciones Biomédicas de Barcelona CSIC, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Kolja Siebert
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Marijana Basic
- Hannover Medical School, Institute for Laboratory Animal Science, Hannover, Germany
| | - Tobias Schwerd
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Matthieu Allez
- APHP, Hôpital Saint Louis, Department of Gastroenterology, INSERM UMRS 1160, Paris Diderot, Sorbonne Paris-Cité University, Paris, France
- Université Paris Cité, INSERM U1160, EMiLy, Institut de Recherche Saint-Louis, Paris, France
| | - Julian Panes
- Department of Experimental Pathology, Instituto de Investigaciones Biomédicas de Barcelona CSIC, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Azucena Salas
- Department of Experimental Pathology, Instituto de Investigaciones Biomédicas de Barcelona CSIC, IDIBAPS, CIBERehd, Barcelona, Spain
| | - André Bleich
- Hannover Medical School, Institute for Laboratory Animal Science, Hannover, Germany
| | - Sebastian Zeissig
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Pamela Schnupf
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Fabio Cominelli
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany.
- ZIEL-Institute for Food and Health, Technical University of Munich, Freising, Germany.
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21
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Abstract
Increasing attention is being paid to the unique roles gut microbes play in both physiological and pathological processes. Crohn’s disease (CD) is a chronic, relapsing, inflammatory disease of the gastrointestinal tract with unknown etiology. Currently, gastrointestinal infection has been proposed as one initiating factor of CD. Yersinia enterocolitica, a zoonotic pathogen that exists widely in nature, is one of the most common bacteria causing acute infectious gastroenteritis, which displays clinical manifestations similar to CD. However, the specific role of Y. enterocolitica in CD is controversial. In this Review, we discuss the current knowledge on how Y. enterocolitica and derived microbial compounds may link to the pathogenesis of CD. We highlight examples of Y. enterocolitica-targeted interventions in the diagnosis and treatment of CD, and provide perspectives for future basic and translational investigations on this topic.
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Affiliation(s)
| | | | | | | | - Yu Bai
- *Correspondence: Zhao-Shen Li, ; Yu Bai,
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22
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Rodríguez-Díaz C, Martín-Reyes F, Taminiau B, Ho-Plágaro A, Camargo R, Fernandez-Garcia F, Pinazo-Bandera J, Toro-Ortiz JP, Gonzalo M, López-Gómez C, Rodríguez-Pacheco F, Rodríguez de los Ríos D, Daube G, Alcain-Martinez G, García-Fuentes E. The Metagenomic Composition and Effects of Fecal-Microbe-Derived Extracellular Vesicles on Intestinal Permeability Depend on the Patient's Disease. Int J Mol Sci 2023; 24:ijms24054971. [PMID: 36902401 PMCID: PMC10002483 DOI: 10.3390/ijms24054971] [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: 01/10/2023] [Revised: 02/14/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
The composition and impact of fecal-microbe-derived extracellular vesicles (EVs) present in different diseases has not been analyzed. We determined the metagenomic profiling of feces and fecal-microbe-derived EVs from healthy subjects and patients with different diseases (diarrhea, morbid obesity and Crohn's disease (CD)) and the effect of these fecal EVs on the cellular permeability of Caco-2 cells. The control group presented higher proportions of Pseudomonas and Rikenellaceae_RC9_gut_group and lower proportions of Phascolarctobacterium, Veillonella and Veillonellaceae_ge in EVs when compared with the feces from which these EVs were isolated. In contrast, there were significant differences in 20 genera between the feces and EV compositions in the disease groups. Bacteroidales and Pseudomonas were increased, and Faecalibacterium, Ruminococcus, Clostridium and Subdoligranum were decreased in EVs from control patients compared with the other three groups of patients. Tyzzerella, Verrucomicrobiaceae, Candidatus_Paracaedibacter and Akkermansia were increased in EVs from the CD group compared with the morbid obesity and diarrhea groups. Fecal EVs from the morbid obesity, CD and, mainly, diarrhea induced a significant increase in the permeability of Caco-2 cells. In conclusion, the metagenomic composition of fecal-microbe-derived EVs changes depending on the disease of the patients. The modification of the permeability of Caco-2 cells produced by fecal EVs depends on the disease of the patients.
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Affiliation(s)
- Cristina Rodríguez-Díaz
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Flores Martín-Reyes
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
- Facultad de Medicina, Universidad de Málaga, 29010 Malaga, Spain
| | - Bernard Taminiau
- Fundamental and Applied Research for Animals & Health (FARAH), Department of Food Microbiology, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Ailec Ho-Plágaro
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Raquel Camargo
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Felix Fernandez-Garcia
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - José Pinazo-Bandera
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Juan Pedro Toro-Ortiz
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Montserrat Gonzalo
- UCG de Endocrinología y Nutrición, Hospital Regional Universitario, 29009 Malaga, Spain
| | - Carlos López-Gómez
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Francisca Rodríguez-Pacheco
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Dámaris Rodríguez de los Ríos
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Georges Daube
- Fundamental and Applied Research for Animals & Health (FARAH), Department of Food Microbiology, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Guillermo Alcain-Martinez
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
- Correspondence: (G.A.-M.); (E.G.-F.)
| | - Eduardo García-Fuentes
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 29010 Malaga, Spain
- Correspondence: (G.A.-M.); (E.G.-F.)
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23
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O'Connor G, Quintero MA, Deo SK, Abreu MT, Daunert S. Bacterial Quorum-Sensing Molecules in Serum: A Potential Tool for Crohn's Disease Management. Clin Transl Gastroenterol 2022; 13:e00547. [PMID: 36413804 PMCID: PMC9780115 DOI: 10.14309/ctg.0000000000000547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022] Open
Abstract
Crohn's disease (CD) is an idiopathic inflammatory condition of the gastrointestinal tract with the primary method of diagnosis and follow-up being colonoscopy. A disturbed host-microbiome interaction, including the presence of pathobionts, is implicated in initiation and perpetuation of inflammation. As such, we hypothesized that bacterial quorum-sensing (QS) molecules (QSMs), small molecules bacteria generate to regulate gene expression, would be elevated in patients with CD. We collected serum at the time of colonoscopy from patients with CD and healthy controls, determining through biosensors for QSMs that patients with CD had significantly elevated levels of QSMs in serum. Expansion of these studies may allow for QSM levels in serum to serve as a biomarker for intestinal inflammation in patients with CD.
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Affiliation(s)
- Gregory O'Connor
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
- Dr. JT Macdonald Biomedical Nanotechnology Institute, University of Miami, Miami, Florida, USA
| | - Maria A. Quintero
- Division of Gastroenterology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Sapna K. Deo
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
- Dr. JT Macdonald Biomedical Nanotechnology Institute, University of Miami, Miami, Florida, USA
| | - Maria T. Abreu
- Division of Gastroenterology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
- Dr. JT Macdonald Biomedical Nanotechnology Institute, University of Miami, Miami, Florida, USA
- University of Miami Clinical and Translational Science Institute, Miami, Florida, USA
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24
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Ishii PE, Suchodolski JS, Duarte R, Pereira ARC, Lidbury JA, Steiner JM, Giaretta PR. Detection of invasive Escherichia coli in dogs with granulomatous colitis using immunohistochemistry. J Vet Diagn Invest 2022; 34:990-994. [PMID: 35993285 PMCID: PMC9597337 DOI: 10.1177/10406387221119712] [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: 11/17/2022] Open
Abstract
Granulomatous colitis in dogs can be associated with infection of the colonic mucosa by invasive strains of Escherichia coli. To date, fluorescence in situ hybridization (FISH) is the gold-standard method to assess intramucosal and intracellular bacterial invasion. However, FISH requires expensive fluorescence microscopy equipment and is therefore not widely available. We investigated the use of immunohistochemistry (IHC) as an alternative method to detect invasive E. coli in dogs with granulomatous colitis. Archived paraffin-embedded blocks were selected from 26 dogs with colitis, in which FISH had been performed by an outside laboratory. Using a polyclonal antibody, IHC for E. coli was performed on sections cut from the same blocks, and the presence of invasive E. coli was recorded. All 11 specimens in which FISH had detected E. coli were also positive on IHC, with strong immunolabeling in the cytoplasm of macrophages and extracellularly in the lamina propria; all 15 specimens that were negative for invasive bacteria on FISH were also negative on IHC. We found that IHC is a sensitive technique for the detection of invasive E. coli in dogs with granulomatous colitis.
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Affiliation(s)
- Patricia Eri Ishii
- Gastrointestinal Laboratory, Department of Small Animal
Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M
University, College Station, TX, USA
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal
Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M
University, College Station, TX, USA
| | | | - Ana R. C. Pereira
- School of Veterinary Medicine and Animal Science of
University of Sao Paulo, Sao Paulo, Brazil
| | - Jonathan A. Lidbury
- Gastrointestinal Laboratory, Department of Small Animal
Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M
University, College Station, TX, USA
| | - Joerg M. Steiner
- Gastrointestinal Laboratory, Department of Small Animal
Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M
University, College Station, TX, USA
| | - Paula R. Giaretta
- Gastrointestinal Laboratory, Department of Small Animal
Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M
University, College Station, TX, USA
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Gerner RR, Hossain S, Sargun A, Siada K, Norton GJ, Zheng T, Neumann W, Nuccio SP, Nolan EM, Raffatellu M. Siderophore Immunization Restricted Colonization of Adherent-Invasive Escherichia coli and Ameliorated Experimental Colitis. mBio 2022; 13:e0218422. [PMID: 36094114 PMCID: PMC9600343 DOI: 10.1128/mbio.02184-22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are characterized by chronic inflammation of the gastrointestinal tract and profound alterations to the gut microbiome. Adherent-invasive Escherichia coli (AIEC) is a mucosa-associated pathobiont that colonizes the gut of patients with Crohn's disease, a form of IBD. Because AIEC exacerbates gut inflammation, strategies to reduce the AIEC bloom during colitis are highly desirable. To thrive in the inflamed gut, Enterobacteriaceae acquire the essential metal nutrient iron by producing and releasing siderophores. Here, we implemented an immunization-based strategy to target the siderophores enterobactin and its glucosylated derivative salmochelin to reduce the AIEC bloom in the inflamed gut. Using chemical (dextran sulfate sodium) and genetic (Il10-/- mice) IBD mouse models, we showed that immunization with enterobactin conjugated to the mucosal adjuvant cholera toxin subunit B potently elicited mucosal and serum antibodies against these siderophores. Siderophore-immunized mice exhibited lower AIEC gut colonization, diminished AIEC association with the gut mucosa, and reduced colitis severity. Moreover, Peyer's patches and the colonic lamina propria harbored enterobactin-specific B cells that could be identified by flow cytometry. The beneficial effect of siderophore immunization was primarily B cell-dependent because immunized muMT-/- mice, which lack mature B lymphocytes, were not protected during AIEC infection. Collectively, our study identified siderophores as a potential therapeutic target to reduce AIEC colonization and its association with the gut mucosa, which ultimately may reduce colitis exacerbation. Moreover, this work provides the foundation for developing monoclonal antibodies against siderophores, which could provide a narrow-spectrum strategy to target the AIEC bloom in Crohn's disease patients. IMPORTANCE Adherent-invasive Escherichia coli (AIEC) is abnormally prevalent in patients with ileal Crohn's disease and exacerbates intestinal inflammation, but treatment strategies that selectively target AIEC are unavailable. Iron is an essential micronutrient for most living organisms, and bacterial pathogens have evolved sophisticated strategies to capture iron from the host environment. AIEC produces siderophores, small, secreted molecules with a high affinity for iron. Here, we showed that immunization to elicit antibodies against siderophores promoted a reduction of the AIEC bloom, interfered with AIEC association with the mucosa, and mitigated colitis in experimental mouse models. We also established a flow cytometry-based approach to visualize and isolate siderophore-specific B cells, a prerequisite for engineering monoclonal antibodies against these molecules. Together, this work could lead to a more selective and antibiotic-sparing strategy to target AIEC in Crohn's disease patients.
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Affiliation(s)
- Romana R. Gerner
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Suzana Hossain
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Artur Sargun
- Department of Chemistry, Massachusetts Institute of Technologygrid.116068.8, Cambridge, Massachusetts, USA
| | - Kareem Siada
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Grant J. Norton
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Tengfei Zheng
- Department of Chemistry, Massachusetts Institute of Technologygrid.116068.8, Cambridge, Massachusetts, USA
| | - Wilma Neumann
- Department of Chemistry, Massachusetts Institute of Technologygrid.116068.8, Cambridge, Massachusetts, USA
| | - Sean-Paul Nuccio
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technologygrid.116068.8, Cambridge, Massachusetts, USA
| | - Manuela Raffatellu
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Chiba University-University of California-San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, California, USA
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Khorsand B, Asadzadeh Aghdaei H, Nazemalhosseini-Mojarad E, Nadalian B, Nadalian B, Houri H. Overrepresentation of Enterobacteriaceae and Escherichia coli is the major gut microbiome signature in Crohn’s disease and ulcerative colitis; a comprehensive metagenomic analysis of IBDMDB datasets. Front Cell Infect Microbiol 2022; 12:1015890. [PMID: 36268225 PMCID: PMC9577114 DOI: 10.3389/fcimb.2022.1015890] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
Objectives A number of converging strands of research suggest that the intestinal Enterobacteriaceae plays a crucial role in the development and progression of inflammatory bowel disease (IBD), however, the changes in the abundance of Enterobacteriaceae species and their related metabolic pathways in Crohn’s disease (CD) and ulcerative colitis (UC) compared to healthy people are not fully explained by comprehensive comparative metagenomics analysis. In the current study, we investigated the alternations of the Enterobacterales population in the gut microbiome of patients with CD and UC compared to healthy subjects. Methods Metagenomic datasets were selected from the Integrative Human Microbiome Project (HMP2) through the Inflammatory Bowel Disease Multi’omics Database (IBDMDB). We performed metagenome-wide association studies on fecal samples from 191 CD patients, 132 UC patients, and 125 healthy controls (HCs). We used the metagenomics dataset to study bacterial community structure, relative abundance, differentially abundant bacteria, functional analysis, and Enterobacteriaceae-related biosynthetic pathways. Results Compared to the gut microbiome of HCs, six Enterobacteriaceae species were significantly elevated in both CD and UC patients, including Escherichia coli, Klebsiella variicola, Klebsiella quasipneumoniae, Klebsiella pneumoniae, Proteus mirabilis, Citrobacter freundii, and Citrobacter youngae, while Klebsiella oxytoca, Morganella morganii, and Citrobacter amalonaticus were uniquely differentially abundant and enriched in the CD cohort. Four species were uniquely differentially abundant and enriched in the UC cohort, including Citrobacter portucalensis, Citrobacter pasteurii, Citrobacter werkmanii, and Proteus hauseri. Our analysis also showed a dramatically increased abundance of E. coli in their intestinal bacterial community. Biosynthetic pathways of aerobactin siderophore, LPS, enterobacterial common antigen, nitrogen metabolism, and sulfur relay systems encoded by E. coli were significantly elevated in the CD samples compared to the HCs. Menaquinol biosynthetic pathways were associated with UC that belonged to K. pneumoniae strains. Conclusions In conclusion, compared with healthy people, the taxonomic and functional composition of intestinal bacteria in CD and UC patients was significantly shifted to Enterobacteriaceae species, mainly E. coli and Klebsiella species.
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Affiliation(s)
- Babak Khorsand
- Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahareh Nadalian
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Banafsheh Nadalian
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Houri
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Hamidreza Houri,
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Gonzalez CG, Mills RH, Zhu Q, Sauceda C, Knight R, Dulai PS, Gonzalez DJ. Location-specific signatures of Crohn's disease at a multi-omics scale. Microbiome 2022; 10:133. [PMID: 35999575 PMCID: PMC9400277 DOI: 10.1186/s40168-022-01331-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 04/01/2022] [Accepted: 07/15/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Crohn's disease (CD), an inflammatory bowel disease (IBD) subtype, results from pathologic interactions between host cells and its resident gut microbes. CD manifests in both isolated disease locations (ileum or colon) or a combination of locations (ileocolonic). To date, a comprehensive understanding of how isolated CD subtypes influence molecular profiles remains outstanding. To address this, we sought to define CD location signatures by leveraging a large cross-sectional feature set captured from the stool of over 200 IBD patients and healthy controls using metaproteomics, shotgun metagenomics, 16S rRNA sequencing, metabolomic profiling, and host genetics paired with clinical endoscopic assessments. RESULTS Neither metagenomic nor host genetics alone distinguished CD location subtypes. In contrast, ileal and colonic CD were distinguished using mass spectrometry-based methods (metabolomics or metaproteomics) or a combined multi-omic feature set. This multi-omic feature set revealed colonic CD was strongly associated with neutrophil-related proteins. Additionally, colonic CD displayed a disease-severity-related association with Bacteroides vulgatus. Colonic CD and ulcerative colitis profiles harbored strikingly similar feature enrichments compared to ileal CD, including neutrophil-related protein enrichments. Compared to colonic CD, ileal CD profiles displayed increased primary and secondary bile acid levels and concomitant shifts in taxa with noted sensitivities such as Faecalibacterium prausnitzii or affinities for bile acid-rich environments, including Gammaproteobacteria and Blautia sp. Having shown robust molecular and microbial distinctions tied to CD locations, we leveraged these profiles to generate location-specific disease severity biomarkers that surpass the performance of Calprotectin. CONCLUSIONS When compared using multi-omics features, colonic- and ileal-isolated CD subtypes display striking differences that suggest separate location-specific pathologies. Colonic CD's strong similarity to ulcerative colitis, including neutrophil and Bacteroides vulgatus involvement, is also evidence of a shared pathology for colonic-isolated IBD subtypes, while ileal CD maintains a unique, bile acid-driven profile. More broadly, this study demonstrates the power of multi-omics approaches for IBD biomarker discovery and elucidating the underlying biology. Video Abstract.
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Affiliation(s)
- Carlos G Gonzalez
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, 92093, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, 92093, USA
- Department of Computer Science & Engineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Robert H Mills
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, 92093, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, 92093, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Consuelo Sauceda
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, 92093, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, San Diego, CA, 92093, USA
- Department of Computer Science & Engineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Parambir S Dulai
- Department of Medicine, Division of Gastroenterology and Hepatology, Feinberg School of Medicine Northwestern University, Chicago, IL, 60061, USA.
| | - David J Gonzalez
- Department of Pharmacology, University of California San Diego, San Diego, CA, 92093, USA.
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, 92093, USA.
- Center for Microbiome Innovation, University of California San Diego, San Diego, CA, 92093, USA.
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Liu B, Ye D, Yang H, Song J, Sun X, Mao Y, He Z. Two-Sample Mendelian Randomization Analysis Investigates Causal Associations Between Gut Microbial Genera and Inflammatory Bowel Disease, and Specificity Causal Associations in Ulcerative Colitis or Crohn’s Disease. Front Immunol 2022; 13:921546. [PMID: 35860271 PMCID: PMC9289607 DOI: 10.3389/fimmu.2022.921546] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/02/2022] [Indexed: 12/05/2022] Open
Abstract
Background Intestinal dysbiosis is associated with inflammatory bowel disease (IBD). Ulcerative colitis (UC) and Crohn’s disease (CD), two subtypes of IBD, are characterized by unique microbial signatures, respectively. However, it is unclear whether UC or CD has a specific causal relationship with gut microbiota. Objective To investigate the potential causal associations between gut microbial genera and IBD, UC, or CD, two-sample Mendelian randomization (MR) analyses were conducted. Materials and Methods We obtained genome-wide association study (GWAS) summary statistics of gut microbiota and IBD, UC, or CD from published GWASs. Two-sample MR analyses were performed to identify potential causal gut microbial genera for IBD, UC, and CD using the inverse-variance weighted (IVW) method. Sensitivity analyses were also conducted to validate the robustness of the primary results of the MR analyses. Finally, a reverse MR analysis was performed to evaluate the possibility of reverse causation. Results Combining the results from the primary and sensitivity analyses, six bacterial genera were associated with the risk of IBD, UC, or CD in the IVW method. Briefly, Eubacterium ventriosum group was associated with a lower risk of IBD (P=0.011) and UC (P=1.00×10-4), whereas Coprococcus 2 was associated with a higher risk of IBD (P=0.022) and UC (P=0.007). In addition, we found a positive association between Oxalobacter with IBD (P=0.001) and CD (P=0.002), and Ruminococcaceae UCG014 with IBD (P=0.005) and CD (P=0.007). We also noticed a negative association between Enterorhabdus (P=0.044) and IBD, and between Lachnospiraceae UCG001 (P=0.023) and CD. We did not find causal effects of IBD, UC, or CD on these bacterial genera in the reverse MR analysis. Conclusion This study expanded gut microbial genera that were causally associated with the risk of IBD, and also revealed specificity-gut microbial genera for UC or CD.
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Affiliation(s)
- Bin Liu
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ding Ye
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China
| | - Hong Yang
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jie Song
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaohui Sun
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yingying Mao
- Department of Epidemiology, School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhixing He
- Institute of Basic Research in Clinical Medicine, School of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
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Wedenoja S, Saarikivi A, Mälkönen J, Leskinen S, Lehto M, Adeshara K, Tuokkola J, Nikkonen A, Merras-Salmio L, Höyhtyä M, Hörkkö S, Haaramo A, Salonen A, de Vos WM, Korpela K, Kolho KL. Fecal microbiota in congenital chloride diarrhea and inflammatory bowel disease. PLoS One 2022; 17:e0269561. [PMID: 35679312 PMCID: PMC9182261 DOI: 10.1371/journal.pone.0269561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/24/2022] [Indexed: 11/21/2022] Open
Abstract
Background and aims Subjects with congenital chloride diarrhea (CLD; a defect in solute carrier family 26 member 3 (SLC26A3)) are prone to inflammatory bowel disease (IBD). We investigated fecal microbiota in CLD and CLD-associated IBD. We also tested whether microbiota is modulated by supplementation with the short-chain fatty acid butyrate. Subjects and methods We recruited 30 patients with CLD for an observational 3-week follow-up study. Thereafter, 16 consented to oral butyrate substitution for a 3-week observational period. Fecal samples, collected once a week, were assayed for calprotectin and potential markers of inflammation, and studied by 16S ribosomal ribonucleic acid (rRNA) gene amplicon sequencing and compared to that of 19 healthy controls and 43 controls with Crohn’s disease. Data on intestinal symptoms, diet and quality of life were collected. Results Patients with CLD had increased abundances of Proteobacteria, Veillonella, and Prevotella, and lower abundances of normally dominant taxa Ruminococcaceae and Lachnospiraceae when compared with healthy controls and Crohn´s disease. No major differences in fecal microbiota were found between CLD and CLD-associated IBD (including two with yet untreated IBD). Butyrate was poorly tolerated and showed no major effects on fecal microbiota or biomarkers in CLD. Conclusions Fecal microbiota in CLD is different from that of healthy subjects or Crohn´s disease. Unexpectedly, no changes in the microbiota or fecal markers characterized CLD-associated IBD, an entity with high frequency among patients with CLD.
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Affiliation(s)
- Satu Wedenoja
- Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland
| | - Aki Saarikivi
- Children’s Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jani Mälkönen
- Children’s Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Saara Leskinen
- Department of Pediatrics, University of Kuopio and Kuopio University Hospital, Kuopio, Finland
| | - Markku Lehto
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Clinical and Molecular Metabolism, Faculty of Medicine Research Programs, University of Helsinki, Helsinki, Finland
| | - Krishna Adeshara
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Clinical and Molecular Metabolism, Faculty of Medicine Research Programs, University of Helsinki, Helsinki, Finland
| | - Jetta Tuokkola
- Children’s Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anne Nikkonen
- Children’s Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Laura Merras-Salmio
- Children’s Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Miikka Höyhtyä
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sohvi Hörkkö
- Medical Microbiology and Immunology, Research Unit of Biomedicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Anu Haaramo
- Department of Otorhinolaryngology, Helsinki University Hospital, Helsinki, Finland
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Willem M. de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | - Katri Korpela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaija-Leena Kolho
- Children’s Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- * E-mail:
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Abstract
A singular pathogen has been killing animals, contaminating food and causing an array of human diseases. Mycobacterium avium subspecies paratuberculosis (MAP) is the cause of a fatal enteric infectious disease called Johne's (Yo'-nees), a disorder mostly studied in ruminant animals. MAP is globally impacting animal health and imparting significant economic burden to animal agriculture. Confounding the management of Johne's disease is that animals are typically infected as calves and while commonly not manifesting clinical disease for years, they shed MAP in their milk and feces in the interval. This has resulted in a "don't test, don't tell" scenario for the industry resulting in greater prevalence of Johne's disease; furthermore, because MAP survives pasteurization, the contaminated food supply provides a source of exposure to humans. Indeed, greater than 90% of dairy herds in the US have MAP-infected animals within the herd. The same bacterium, MAP, is the putative cause of Crohn's disease in humans. Countries historically isolated from importing/exporting ruminant animals and free of Johne's disease subsequently acquired the disease as a consequence of opening trade with what proved to be infected animals. Crohn's disease in those populations became a lagging indicator of MAP infection. Moreover, MAP is associated with an increasingly long list of human diseases. Despite MAP scientists entreating regulatory agencies to designate MAP a "zoonotic agent," it has not been forthcoming. One Health is a global endeavor applying an integrative health initiative that includes the environment, animals and humans; One Health asserts that stressors affecting one affects all three. Recognizing the impact MAP has on animal and human health as well as on the environment, it is time for One Health, as well as other global regulatory agencies, to recognize that MAP is causing an insidious slow-motion tsunami of zoonosis and implement public health mitigation.
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Affiliation(s)
- Coad Thomas Dow
- Department of Ophthalmology and Visual Sciences, 9431 Wisconsin Institutes for Medical Research (WIMR), McPherson Eye Research Institute, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA.
| | - Briana Lizet Alvarez
- Biology and Global Health, University of Wisconsin-Madison, 120 N Orchard St #1, Madison, WI, 53705, USA
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Xia K, Gao R, Wu X, Sun J, Wan J, Wu T, Fichna J, Yin L, Chen C. Characterization of Specific Signatures of the Oral Cavity, Sputum, and Ileum Microbiota in Patients With Crohn’s Disease. Front Cell Infect Microbiol 2022; 12:864944. [PMID: 35493739 PMCID: PMC9045729 DOI: 10.3389/fcimb.2022.864944] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background Crohn’s disease (CD) is a chronic nonspecific inflammatory bowel disease (IBD) with an increasing incidence worldwide. The etiology of CD is still obscure, but microbial dysbiosis has been recognized as an essential factor contributing to CD. However, few studies have revealed the microbiome’s signatures and reciprocal correlations between multiple sites in patients with CD over different disease stages. This study investigated the specific microbial architectures of the oral cavity, sputum, and ileum in patients with CD in the active and remission stages. Methods Microbial samples from the oral cavity, sputum, and ileum were collected from patients with CD in the active and remission stages and healthy controls. The microbial composition was assessed by 16S ribosomal RNA (rRNA) gene sequencing. In addition, bioinformatics methods were used to demonstrate the microbial signatures, functional changes, and correlations between microbiota and clinical data in CD. Results Compared with healthy controls, a distinct microbiota dysbiosis in the oral cavity, sputum, and ileum of patients with CD was identified, characterized by alterations in microbiota biodiversity and composition. The oral cavity and sputum microbiota showed significantly lower microbial diversity in patients with CD than in healthy controls. In terms of microbiota composition, the microbiota changes in the oral cavity of patients with CD were similar to those in the sputum, while they were different from those in the ileum. In the oral cavity and sputum of patients with CD, a lower relative abundance of Firmicutes and Actinobacteria was observed compared to healthy controls, which was most prominent in the active stage. In contrast, an increased relative abundance of Fusobacteria, Porphyromonas, and Haemophilus was observed in patients with CD. The predicted metabolic pathways involved in the oral cavity, sputum, and ileum were similar, predominantly involving metabolism, environmental information processing, and genetic information processing. Conclusion The results revealed the alterations of microbiota architecture in the oral cavity, sputum, and ileum of patients with CD, which varied across disease stages. Studying microbiota dysbiosis may bring new insights into the etiology of CD and lead to novel treatments.
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Affiliation(s)
- Kai Xia
- Diagnostic and Treatment Center for Refractory Diseases of Abdomen Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Kai Xia, ; Lu Yin, ; Chunqiu Chen,
| | - Renyuan Gao
- Diagnostic and Treatment Center for Refractory Diseases of Abdomen Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaocai Wu
- Diagnostic and Treatment Center for Refractory Diseases of Abdomen Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jing Sun
- Diagnostic and Treatment Center for Refractory Diseases of Abdomen Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jian Wan
- Diagnostic and Treatment Center for Refractory Diseases of Abdomen Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tianqi Wu
- Diagnostic and Treatment Center for Refractory Diseases of Abdomen Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jakub Fichna
- Department of Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Lu Yin
- Diagnostic and Treatment Center for Refractory Diseases of Abdomen Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Kai Xia, ; Lu Yin, ; Chunqiu Chen,
| | - Chunqiu Chen
- Diagnostic and Treatment Center for Refractory Diseases of Abdomen Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Kai Xia, ; Lu Yin, ; Chunqiu Chen,
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Chiang HY, Lu HH, Sudhakar JN, Chen YW, Shih NS, Weng YT, Shui JW. IL-22 initiates an IL-18-dependent epithelial response circuit to enforce intestinal host defence. Nat Commun 2022; 13:874. [PMID: 35169117 PMCID: PMC8847568 DOI: 10.1038/s41467-022-28478-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [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: 10/25/2020] [Accepted: 01/26/2022] [Indexed: 12/19/2022] Open
Abstract
IL-18 is emerging as an IL-22-induced and epithelium-derived cytokine which contributes to host defence against intestinal infection and inflammation. In contrast to its known role in Goblet cells, regulation of barrier function at the molecular level by IL-18 is much less explored. Here we show that IL-18 is a bona fide IL-22-regulated gate keeper for intestinal epithelial barrier. IL-22 promotes crypt immunity both via induction of phospho-Stat3 binding to the Il-18 gene promoter and via Il-18 independent mechanisms. In organoid culture, while IL-22 primarily increases organoid size and inhibits expression of stem cell genes, IL-18 preferentially promotes organoid budding and induces signature genes of Lgr5+ stem cells via Akt-Tcf4 signalling. During adherent-invasive E. coli (AIEC) infection, systemic administration of IL-18 corrects compromised T-cell IFNγ production and restores Lysozyme+ Paneth cells in Il-22-/- mice, but IL-22 administration fails to restore these parameters in Il-18-/- mice, thereby placing IL-22-Stat3 signalling upstream of the IL-18-mediated barrier defence function. IL-18 in return regulates Stat3-mediated anti-microbial response in Paneth cells, Akt-Tcf4-triggered expansion of Lgr5+ stem cells to facilitate tissue repair, and AIEC clearance by promoting IFNγ+ T cells.
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Affiliation(s)
- Hung-Yu Chiang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsueh-Han Lu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | | | - Yu-Wen Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Nien-Shin Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Ting Weng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jr-Wen Shui
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
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He Z, Wu J, Gong J, Ke J, Ding T, Zhao W, Cheng WM, Luo Z, He Q, Zeng W, Yu J, Jiao N, Liu Y, Zheng B, Dai L, Zhi M, Wu X, Jobin C, Lan P. Microbiota in mesenteric adipose tissue from Crohn's disease promote colitis in mice. Microbiome 2021; 9:228. [PMID: 34814945 PMCID: PMC8609859 DOI: 10.1186/s40168-021-01178-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 09/17/2021] [Accepted: 10/14/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Mesenteric adipose tissue (mAT) hyperplasia, known as creeping fat is a pathologic characteristic of Crohn's disease (CD). The reserve of creeping fat in surgery is associated with poor prognosis of CD patients, but the mechanism remains unknown. METHODS Mesenteric microbiome, metabolome, and host transcriptome were characterized using a cohort of 48 patients with CD and 16 non-CD controls. Multidimensional data including 16S ribosomal RNA gene sequencing (16S rRNA), host RNA sequencing, and metabolome were integrated to reveal network interaction. Mesenteric resident bacteria were isolated from mAT and functionally investigated both in the dextran sulfate sodium (DSS) model and in the Il10 gene-deficient (Il10-/-) mouse colitis model to validate their pro-inflammatory roles. RESULTS Mesenteric microbiota contributed to aberrant metabolites production and transcripts in mATs from patients with CD. The presence of mAT resident microbiota was associated with the development of CD. Achromobacter pulmonis (A. pulmonis) isolated from CD mAT could translocate to mAT and exacerbate both DSS-induced and Il10 gene-deficient (Il10-/-) spontaneous colitis in mice. The levels of A. pulmonis in both mAT and mucous layer from CD patients were higher compared to those from the non-CD group. CONCLUSIONS This study suggests that the mesenteric microbiota from patients with CD sculpt a detrimental microenvironment and promote intestinal inflammation. Video abstract.
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Affiliation(s)
- Zhen He
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong, China
| | - Jinjie Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong, China
| | - Junli Gong
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong, China
| | - Jia Ke
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong, China
| | - Tao Ding
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, Guangdong, China
| | - Wenjing Zhao
- School of Medicine, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Wai Ming Cheng
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong, China
| | - Zhanhao Luo
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong, China
| | - Qilang He
- School of Medicine, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Wanyi Zeng
- School of Medicine, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Jing Yu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong, China
| | - Na Jiao
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong, China
| | - Yanmin Liu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, Guangdong, China
| | - Bin Zheng
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China
| | - Min Zhi
- Department of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, Guangdong, China
| | - Xiaojian Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong, China
| | - Christian Jobin
- Department of Medicine, Division of Gastroenterology, University of Florida, CGRC, 2033 Mowry Rd, Gainesville, Florida, 32610, USA.
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, 32610, USA.
| | - Ping Lan
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, Guangdong, China.
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655, Guangdong, China.
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Shaler CR, Parco AA, Elhenawy W, Dourka J, Jury J, Verdu EF, Coombes BK. Psychological stress impairs IL22-driven protective gut mucosal immunity against colonising pathobionts. Nat Commun 2021; 12:6664. [PMID: 34795263 PMCID: PMC8602651 DOI: 10.1038/s41467-021-26992-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 11/06/2020] [Accepted: 10/28/2021] [Indexed: 12/27/2022] Open
Abstract
Crohn's disease is an inflammatory disease of the gastrointestinal tract characterized by an aberrant response to microbial and environmental triggers. This includes an altered microbiome dominated by Enterobacteriaceae and in particular adherent-invasive E. coli (AIEC). Clinical evidence implicates periods of psychological stress in Crohn's disease exacerbation, and disturbances in the gut microbiome might contribute to the pathogenic mechanism. Here we show that stress-exposed mice develop ileal dysbiosis, dominated by the expansion of Enterobacteriaceae. In an AIEC colonisation model, stress-induced glucocorticoids promote apoptosis of CD45+CD90+ cells that normally produce IL-22, a cytokine that is essential for the maintenance of ileal mucosal barrier integrity. Blockade of glucocorticoid signaling or administration of recombinant IL-22 restores mucosal immunity, prevents ileal dysbiosis, and blocks AIEC expansion. We conclude that psychological stress impairs IL-22-driven protective immunity in the gut, which creates a favorable niche for the expansion of pathobionts that have been implicated in Crohn's disease. Importantly, this work also shows that immunomodulation can counteract the negative effects of psychological stress on gut immunity and hence disease-associated dysbiosis.
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Affiliation(s)
- Christopher R Shaler
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Alexandra A Parco
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Wael Elhenawy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Jasmeen Dourka
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Jennifer Jury
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | - Elena F Verdu
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada.
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada.
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Cao Y, Wang Z, Yan Y, Ji L, He J, Xuan B, Shen C, Ma Y, Jiang S, Ma D, Tong T, Zhang X, Gao Z, Zhu X, Fang JY, Chen H, Hong J. Enterotoxigenic Bacteroidesfragilis Promotes Intestinal Inflammation and Malignancy by Inhibiting Exosome-Packaged miR-149-3p. Gastroenterology 2021; 161:1552-1566.e12. [PMID: 34371001 DOI: 10.1053/j.gastro.2021.08.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND & AIMS Enterotoxigenic Bacteroides fragilis (ETBF) is strongly associated with the occurrence of inflammatory bowel disease (IBD), colitis-associated colorectal cancer, and colorectal cancer (CRC). However, the mechanism of ETBF-induced intestinal inflammation and tumorigenesis remains unclear. METHODS microRNA sequencing was used to detect the differentially expressed microRNAs in both ETBF-treated cells and exosomes derived from ETBF-inoculated cells. Cell Counting Kit 8 assays were used to evaluate the effect of ETBF and exosomes on CRC cell proliferation. The biological role and mechanism of ETBF-mediated miR-149-3p in colitis and colon carcinogenesis were determined both in vitro and in vivo. RESULTS ETBF promoted CRC cell proliferation by down-regulating miR-149-3p both in vitro and in vivo. ETBF-down-regulated miR-149-3p depended on METTL14-mediated N6-methyladenosine methylation. As the target gene of miR-149-3p, PHF5A transactivated SOD2 through regulating KAT2A messenger RNA alternative splicing after ETBF treatment in CRC cells. miR-149-3p could be released in exosomes and mediated intercellular communication by modulating T-helper type 17 cell differentiation. The level of plasma exosomal miR-149-3p was gradually decreased from healthy control individuals to patients with IBD and CRC. miR-149-3p, existing in plasma exosomes, negatively correlated with the abundance of ETBF in patients with IBD and CRC. CONCLUSIONS Exosomal miR-149-3p derived from ETBF-treated cells facilitated T-helper type 17 cell differentiation. ETBF-induced colorectal carcinogenesis depended on down-regulating miR-149-3p and further promoting PHF5A-mediated RNA alternative splicing of KAT2A in CRC cells. Targeting the ETBF/miR-149-3p pathway presents a promising approach to treat patients with intestinal inflammation and CRC with a high amount of ETBF.
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MESH Headings
- Animals
- Bacteroides fragilis/pathogenicity
- Cell Differentiation
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Colitis, Ulcerative/genetics
- Colitis, Ulcerative/metabolism
- Colitis, Ulcerative/microbiology
- Colitis, Ulcerative/pathology
- Colon/metabolism
- Colon/microbiology
- Colon/pathology
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/metabolism
- Colorectal Neoplasms/microbiology
- Colorectal Neoplasms/pathology
- Crohn Disease/genetics
- Crohn Disease/metabolism
- Crohn Disease/microbiology
- Crohn Disease/pathology
- Disease Models, Animal
- Exosomes/genetics
- Exosomes/metabolism
- Exosomes/microbiology
- HCT116 Cells
- Histone Acetyltransferases/genetics
- Histone Acetyltransferases/metabolism
- Host-Pathogen Interactions
- Humans
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Nude
- MicroRNAs/genetics
- MicroRNAs/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Th17 Cells/immunology
- Th17 Cells/metabolism
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Mice
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Affiliation(s)
- Yingying Cao
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenhua Wang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqing Yan
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Linhua Ji
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie He
- Department of Gastroenterology and Guangzhou Key Laboratory of Digestive Disease, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Baoqin Xuan
- State Key Laboratory for Oncogenes and Related Genes; Shanghai Cancer Institute; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chaoqin Shen
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanru Ma
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shanshan Jiang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Ma
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tianying Tong
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyu Zhang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ziyun Gao
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoqiang Zhu
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing-Yuan Fang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haoyan Chen
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jie Hong
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology and Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Buisson A, Vazeille E, Fumery M, Pariente B, Nancey S, Seksik P, Peyrin‐Biroulet L, Allez M, Ballet N, Filippi J, Yzet C, Nachury M, Boschetti G, Billard E, Dubois A, Rodriguez S, Chevarin C, Goutte M, Bommelaer G, Pereira B, Hebuterne X, Barnich N. Faster and less invasive tools to identify patients with ileal colonization by adherent-invasive E. coli in Crohn's disease. United European Gastroenterol J 2021; 9:1007-1018. [PMID: 34791806 PMCID: PMC8598958 DOI: 10.1002/ueg2.12161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 03/25/2021] [Accepted: 07/27/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND AND AIMS The identification of Crohn's disease (CD)-associated adherent and invasive Escherichia coli (AIEC) is time-consuming and requires ileal biopsies. We aimed to identify a faster and less invasive methods to detect ileal colonization by AIEC in CD patients. METHODS CD patients requiring ileo-colonoscopy were consecutively enrolled in this prospective multicenter study. Samples from saliva, serum, stools, and ileal biopsies of CD patients were collected. RESULTS Among 102 CD patients, the prevalence of AIEC on ileal biopsies was 24.5%. The abundance and global invasive ability of ileal-associated total E. coli were respectively ten-fold (p = 0.0065) and two-fold (p = 0.0007) higher in AIEC-positive (vs. AIEC-negative), while abundance of total E. coli in the feces was not correlated with AIEC status in the ileum. The best threshold of ileal total E. coli was 60 cfu/biopsy to detect AIEC-positive patients, with high negative predictive value (NPV) (94.1%[80.3-99.3]), while the global invasive ability (>9000 internalized bacteria) was able to detect the presence of AIEC with high positive predictive value (80.0% [55.2-100.0]). Overall, 78.1% of the AIEC + patients were colonized by two or less different AIEC strains. The level of serum anti-total E. coli antibodies (AEcAb) was higher in AIEC-positive patients (p = 0.038) with a very high negative predictive value (96.6% [89.9-100.0]) (p = 0.038) for a cut-off value > 1.9 × 10-3 . CONCLUSIONS More than two thirds of AIEC-positive CD patients were colonized by two or less AIEC strains. While stools samples are not accurate to screen AIEC status, the AEcAb level appears to be an attractive, rapid and easier biomarker to identify patients with Crohn's disease harboring AIEC.
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Affiliation(s)
- Anthony Buisson
- Université Clermont Auvergne/Inserm U1071USC‐INRAe 2018Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH)Clermont‐FerrandFrance
- Université Clermont AuvergneInserm3iHPCHU Clermont‐FerrandService d'Hépato‐Gastro EntérologieClermont‐FerrandFrance
| | - Emilie Vazeille
- Université Clermont Auvergne/Inserm U1071USC‐INRAe 2018Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH)Clermont‐FerrandFrance
- Université Clermont AuvergneInserm3iHPCHU Clermont‐FerrandService d'Hépato‐Gastro EntérologieClermont‐FerrandFrance
| | - Mathurin Fumery
- Department of HepatogastroenterologyAmiens University Hospital, and PeriTox UMR‐I 01AmiensFrance
| | - Benjamin Pariente
- Department of GastroenterologyClaude Huriez HospitalUniversity of LilleLilleFrance
| | - Stéphane Nancey
- Department of GastroenterologyLyon Sud HospitalHospices Civils de Lyonand INSERM U‐1111CIRILyonFrance
| | - Philippe Seksik
- GastroenterologySorbonne UniversitésAP‐HPHospital Saint‐AntoineParisFrance
| | - Laurent Peyrin‐Biroulet
- Department of GastroenterologyNancy University HospitalNancyFrance
- Inserm U1256 NGERELorraine UniversityNancyFrance
| | - Matthieu Allez
- Inserm UMR 1160AP‐HP Gastroenterology Hôpital Saint LouisUniversité ParisDiderotFrance
| | | | - Jérôme Filippi
- Gastroenterology and Clinical NutritionCHU of Nice and University Côte d'Azur NiceFrance
| | - Clara Yzet
- Department of HepatogastroenterologyAmiens University Hospital, and PeriTox UMR‐I 01AmiensFrance
| | - Maria Nachury
- Department of GastroenterologyClaude Huriez HospitalUniversity of LilleLilleFrance
| | - Gilles Boschetti
- Department of GastroenterologyLyon Sud HospitalHospices Civils de Lyonand INSERM U‐1111CIRILyonFrance
| | - Elisabeth Billard
- Université Clermont Auvergne/Inserm U1071USC‐INRAe 2018Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH)Clermont‐FerrandFrance
| | - Anaëlle Dubois
- Université Clermont Auvergne/Inserm U1071USC‐INRAe 2018Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH)Clermont‐FerrandFrance
| | - Stéphanie Rodriguez
- Université Clermont Auvergne/Inserm U1071USC‐INRAe 2018Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH)Clermont‐FerrandFrance
| | - Caroline Chevarin
- Université Clermont Auvergne/Inserm U1071USC‐INRAe 2018Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH)Clermont‐FerrandFrance
| | - Marion Goutte
- Université Clermont Auvergne/Inserm U1071USC‐INRAe 2018Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH)Clermont‐FerrandFrance
- Université Clermont AuvergneInserm3iHPCHU Clermont‐FerrandService d'Hépato‐Gastro EntérologieClermont‐FerrandFrance
| | - Gilles Bommelaer
- Université Clermont Auvergne/Inserm U1071USC‐INRAe 2018Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH)Clermont‐FerrandFrance
- Université Clermont AuvergneInserm3iHPCHU Clermont‐FerrandService d'Hépato‐Gastro EntérologieClermont‐FerrandFrance
| | - Bruno Pereira
- Université Clermont AuvergneCHU Clermont‐FerrandDRCIUnité de BiostatistiquesClermont‐FerrandFrance
- Université Clermont AuvergneCHU Clermont‐FerrandCNRSSIGMA ClermontInstitut PascalClermont‐FerrandFrance
| | - Xavier Hebuterne
- Gastroenterology and Clinical NutritionCHU of Nice and University Côte d'Azur NiceFrance
| | - Nicolas Barnich
- Université Clermont Auvergne/Inserm U1071USC‐INRAe 2018Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH)Clermont‐FerrandFrance
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Kameli N, Becker HEF, Welbers T, Jonkers DMAE, Penders J, Savelkoul P, Stassen FR. Metagenomic Profiling of Fecal-Derived Bacterial Membrane Vesicles in Crohn's Disease Patients. Cells 2021; 10:cells10102795. [PMID: 34685776 PMCID: PMC8535131 DOI: 10.3390/cells10102795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In the past, many studies suggested a crucial role for dysbiosis of the gut microbiota in the etiology of Crohn's disease (CD). However, despite being important players in host-bacteria interaction, the role of bacterial membrane vesicles (MV) has been largely overlooked in the pathogenesis of CD. In this study, we addressed the composition of the bacterial and MV composition in fecal samples of CD patients and compared this to the composition in healthy individuals. METHODS Fecal samples from six healthy subjects (HC) in addition to twelve CD patients (six active, six remission) were analyzed in this study. Fecal bacterial membrane vesicles (fMVs) were isolated by a combination of ultrafiltration and size exclusion chromatography. DNA was obtained from the fMV fraction, the pellet of dissolved feces as bacterial DNA (bDNA), or directly from feces as fecal DNA (fDNA). The fMVs were characterized by nanoparticle tracking analysis and cryo-electron microscopy. Amplicon sequencing of 16s rRNA V4 hypervariable gene regions was conducted to assess microbial composition of all fractions. RESULTS Beta-diversity analysis showed that the microbial community structure of the fMVs was significantly different from the microbial profiles of the fDNA and bDNA. However, no differences were observed in microbial composition between fDNA and bDNA. The microbial richness of fMVs was significantly decreased in CD patients compared to HC, and even lower in active patients. Profiling of fDNA and bDNA demonstrated that Firmicutes was the most dominant phylum in these fractions, while in fMVs Bacteroidetes was dominant. In fMV, several families and genera belonging to Firmicutes and Proteobacteria were significantly altered in CD patients when compared to HC. CONCLUSION The microbial alterations of MVs in CD patients particularly in Firmicutes and Proteobacteria suggest a possible role of MVs in host-microbe symbiosis and induction or progression of inflammation in CD pathogenesis. Yet, the exact role for these fMV in the pathogenesis of the disease needs to be elucidated in future studies.
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Affiliation(s)
- Nader Kameli
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands; (H.E.F.B.); (T.W.); (J.P.); (P.S.)
- Department of Medical Microbiology, Faculty of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Correspondence: (N.K.); (F.R.S.)
| | - Heike E. F. Becker
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands; (H.E.F.B.); (T.W.); (J.P.); (P.S.)
- Department of Internal Medicine, Division of Gastroenterology/Hepatology, NUTRIM school of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, 6200 MD Maastricht, The Netherlands;
| | - Tessa Welbers
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands; (H.E.F.B.); (T.W.); (J.P.); (P.S.)
| | - Daisy M. A. E. Jonkers
- Department of Internal Medicine, Division of Gastroenterology/Hepatology, NUTRIM school of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, 6200 MD Maastricht, The Netherlands;
| | - John Penders
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands; (H.E.F.B.); (T.W.); (J.P.); (P.S.)
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Centre+, 6229 ER Maastricht, The Netherlands
| | - Paul Savelkoul
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands; (H.E.F.B.); (T.W.); (J.P.); (P.S.)
- Department of Medical Microbiology and Infection Control, VU University Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Frank R. Stassen
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, 6229 ER Maastricht, The Netherlands; (H.E.F.B.); (T.W.); (J.P.); (P.S.)
- Correspondence: (N.K.); (F.R.S.)
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Jones E, Stentz R, Telatin A, Savva GM, Booth C, Baker D, Rudder S, Knight SC, Noble A, Carding SR. The Origin of Plasma-Derived Bacterial Extracellular Vesicles in Healthy Individuals and Patients with Inflammatory Bowel Disease: A Pilot Study. Genes (Basel) 2021; 12:1636. [PMID: 34681030 PMCID: PMC8535827 DOI: 10.3390/genes12101636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/09/2021] [Revised: 09/10/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal tract harbors the gut microbiota, structural alterations of which (dysbiosis) are linked with an increase in gut permeability ("leaky gut"), enabling luminal antigens and bacterial products such as nanosized bacterial extracellular vesicles (BEVs) to access the circulatory system. Blood-derived BEVs contain various cargoes and may be useful biomarkers for diagnosis and monitoring of disease status and relapse in conditions such as inflammatory bowel disease (IBD). To progress this concept, we developed a rapid, cost-effective protocol to isolate BEV-associated DNA and used 16S rRNA gene sequencing to identify bacterial origins of the blood microbiome of healthy individuals and patients with Crohn's disease and ulcerative colitis. The 16S rRNA gene sequencing successfully identified the origin of plasma-derived BEV DNA. The analysis showed that the blood microbiota richness, diversity, or composition in IBD, healthy control, and protocol control groups were not significantly distinct, highlighting the issue of 'kit-ome' contamination in low-biomass studies. Our pilot study provides the basis for undertaking larger studies to determine the potential use of blood microbiota profiling as a diagnostic aid in IBD.
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Affiliation(s)
- Emily Jones
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
| | - Régis Stentz
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
| | - Andrea Telatin
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
| | - George M. Savva
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
| | - Catherine Booth
- Core Science Resources, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK;
| | - David Baker
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
| | - Steven Rudder
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
| | - Stella C. Knight
- Antigen Presentation Research Group, Northwick Park & St. Mark’s Hospital Campus, Imperial College London, Harrow HA1 3UJ, UK; (S.C.K.); (A.N.)
| | - Alistair Noble
- Antigen Presentation Research Group, Northwick Park & St. Mark’s Hospital Campus, Imperial College London, Harrow HA1 3UJ, UK; (S.C.K.); (A.N.)
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
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Lau TC, Fiebig-Comyn AA, Shaler CR, McPhee JB, Coombes BK, Schertzer JD. Low dietary fiber promotes enteric expansion of a Crohn's disease-associated pathobiont independent of obesity. Am J Physiol Endocrinol Metab 2021; 321:E338-E350. [PMID: 34280051 DOI: 10.1152/ajpendo.00134.2021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Obesity is associated with metabolic, immunological, and infectious disease comorbidities, including an increased risk of enteric infection and inflammatory bowel disease such as Crohn's disease (CD). Expansion of intestinal pathobionts such as adherent-invasive Escherichia coli (AIEC) is a common dysbiotic feature of CD, which is amplified by prior use of oral antibiotics. Although high-fat, high-sugar diets are associated with dysbiotic expansion of E. coli, it is unknown if the content of fat or another dietary component in obesogenic diets is sufficient to promote AIEC expansion. Here, we found that administration of an antibiotic combined with feeding mice an obesogenic low-fiber, high-sucrose, high-fat diet (HFD) that is typically used in rodent-obesity studies promoted AIEC intestinal expansion. Even a short-term (i.e., 1 day) pulse of HFD feeding before infection was sufficient to promote AIEC expansion, indicating that the magnitude of obesity was not the main driver of AIEC expansion. Controlled-diet experiments demonstrated that neither dietary fat nor sugar were the key determinants of AIEC colonization, but that lowering dietary fiber from approximately 13% to 5%-6% was sufficient to promote the intestinal expansion of AIEC when combined with antibiotics in mice. When combined with antibiotics, lowering fiber promoted AIEC intestinal expansion to a similar extent as widely used HFDs in mice. However, lowering dietary fiber was sufficient to promote AIEC intestinal expansion without affecting body mass. Our results show that low dietary fiber combined with oral antibiotics are environmental factors that promote the expansion of Crohn's disease-associated pathobionts in the gut.NEW & NOTEWORTHY It is commonly thought that obesity or a high-fat diet alters pathogenic bacteria and promotes inflammatory gut diseases. We found that lower dietary fiber is a key factor that expands a gut pathobiont linked to Crohn's disease, independent of obesity status in mice.
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Affiliation(s)
- Trevor C Lau
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Aline A Fiebig-Comyn
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Christopher R Shaler
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Joseph B McPhee
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Jonathan D Schertzer
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Centre for Metabolism, Obesity, and Diabetes Research, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
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Khan IA, Nayak B, Markandey M, Bajaj A, Verma M, Kumar S, Singh MK, Kedia S, Ahuja V. Differential prevalence of pathobionts and host gene polymorphisms in chronic inflammatory intestinal diseases: Crohn's disease and intestinal tuberculosis. PLoS One 2021; 16:e0256098. [PMID: 34407136 PMCID: PMC8372915 DOI: 10.1371/journal.pone.0256098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/31/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Crohn's disease (CD) and Intestinal tuberculosis (ITB) are chronic inflammatory ulcero-constrictive intestinal diseases with similar phenotype. Although both are disease models of chronic inflammation and their clinical presentations, imaging, histological and endoscopic findings are very similar, yet their etiologies are diverse. Hence, we aimed to look at differences in the prevalence of pathobionts like adherent-invasive Escherichia coli (AIEC), Listeria monocytogenes, Campylobacter jejuni and Yersinia enterocolitica in CD and ITB as well as their associations with host-associated genetic polymorphisms in genes majorly involved in pathways of microbial handling and immune responses. METHODS The study cohort included 142 subjects (69 patients with CD, 32 with ITB and 41 controls). RT- PCR amplification was used to detect the presence of AIEC, L. monocytogenes, C. jejuni, and Y. enterocolitica DNA in colonic mucosal biopsies. Additionally, we tested three SNPs in IRGM (rs13361189, rs10065172, and rs4958847), one SNP in ATG16L1 (rs2241880) and one SNP in TNFRSF1A (rs4149570) by real-time PCR with SYBR green from peripheral blood samples in this cohort. RESULTS In patients with CD, AIEC was most frequently present (16/ 69, 23.19%) followed by L. monocytogenes (14/69, 20.29%), C. jejuni (9/69, 13.04%), and Y. enterocolitica (7/69, 10.14%). Among them, L. monocytogenes and Y. enterocolitica were significantly associated with CD (p = 0.02). In addition, we identified all the three SNPs in IRGM (rs13361189, rs10065172, and rs4958847), one SNP in ATG16L1 (rs2241880) and TNFRSF1A (rs4149570) with a significant difference in frequency in patients with CD compared with ITB and controls (p<0.05). CONCLUSION Higher prevalence of host gene polymorphisms, as well as the presence of pathobionts, was seen in the colonic mucosa of patients with CD as compared to ITB, although both are disease models of chronic inflammation.
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Affiliation(s)
- Imteyaz Ahmad Khan
- Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences, New Delhi, India
| | - Baibaswata Nayak
- Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences, New Delhi, India
| | - Manasvini Markandey
- Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences, New Delhi, India
| | - Aditya Bajaj
- Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences, New Delhi, India
| | - Mahak Verma
- Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences, New Delhi, India
| | - Sambudhha Kumar
- Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences, New Delhi, India
| | - Mukesh Kumar Singh
- Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences, New Delhi, India
| | - Saurabh Kedia
- Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences, New Delhi, India
- * E-mail:
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Herp S, Durai Raj AC, Salvado Silva M, Woelfel S, Stecher B. The human symbiont Mucispirillum schaedleri: causality in health and disease. Med Microbiol Immunol 2021; 210:173-179. [PMID: 34021796 PMCID: PMC7615636 DOI: 10.1007/s00430-021-00702-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [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] [Received: 02/26/2021] [Accepted: 03/16/2021] [Indexed: 12/26/2022]
Abstract
Trillions of bacteria inhabit the mammalian gastrointestinal tract. In the majority of hosts, these symbionts contribute largely to beneficial functions promoting microbe-host homeostasis. However, an increasing number of human diseases is associated with altered microbiota composition and enrichment of certain bacterial species. A well-known example of this is Mucispirillum schaedleri, which has been associated with inflammatory conditions in the intestine. Mucispirillum spp. belong to the phylum Deferribacteres and are prevalent but low abundant members of the rodent, pig and human microbiota. Recently, M. schaedleri was causally linked to the development of Crohn's disease-like colitis in immunodeficient mice. While this study certifies a considerable pathogenic potential, the same organism can also promote health in the immunocompetent host: M. schaedleri protects from Salmonella enterica serovar Typhimurium (S. Tm)-induced colitis by interfering with the expression of the pathogen´s invasion machinery. In this review, we summarize the current knowledge on the mammalian gut symbiont M. schaedleri and its role in intestinal homeostasis and discuss open questions and perspectives for future research.
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Affiliation(s)
- Simone Herp
- Max-Von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, Munich, Germany.
| | | | - Marta Salvado Silva
- Max-Von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, Munich, Germany
| | - Simon Woelfel
- Max-Von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, Munich, Germany
| | - Bärbel Stecher
- Max-Von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, Munich, Germany
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Park HT, Park WB, Kim S, Lim JS, Nah G, Yoo HS. Revealing immune responses in the Mycobacterium avium subsp. paratuberculosis-infected THP-1 cells using single cell RNA-sequencing. PLoS One 2021; 16:e0254194. [PMID: 34214113 PMCID: PMC8253428 DOI: 10.1371/journal.pone.0254194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/21/2021] [Indexed: 01/13/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic and debilitating disease in ruminants. MAP is also considered to be a possible cause of Crohn’s disease in humans. However, few studies have focused on the interactions between MAP and human macrophages to elucidate the pathogenesis of Crohn’s disease. We sought to determine the initial responses of human THP-1 cells against MAP infection using single-cell RNA-seq analysis. Clustering analysis showed that THP-1 cells were divided into seven different clusters in response to phorbol-12-myristate-13-acetate (PMA) treatment. The characteristics of each cluster were investigated by identifying cluster-specific marker genes. From the results, we found that classically differentiated cells express CD14, CD36, and TLR2, and that this cell type showed the most active responses against MAP infection. The responses included the expression of proinflammatory cytokines and chemokines such as CCL4, CCL3, IL1B, IL8, and CCL20. In addition, the Mreg cell type, a novel cell type differentiated from THP-1 cells, was discovered. Thus, it is suggested that different cell types arise even when the same cell line is treated under the same conditions. Overall, analyzing gene expression patterns via scRNA-seq classification allows a more detailed observation of the response to infection by each cell type.
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Affiliation(s)
- Hong-Tae Park
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Woo Bin Park
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Suji Kim
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Jong-Sung Lim
- Genome Analysis Center, National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea
| | - Gyoungju Nah
- Genome Analysis Center, National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea
| | - Han Sang Yoo
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- * E-mail:
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Bolte LA, Vich Vila A, Imhann F, Collij V, Gacesa R, Peters V, Wijmenga C, Kurilshikov A, Campmans-Kuijpers MJE, Fu J, Dijkstra G, Zhernakova A, Weersma RK. Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome. Gut 2021; 70:1287-1298. [PMID: 33811041 PMCID: PMC8223641 DOI: 10.1136/gutjnl-2020-322670] [Citation(s) in RCA: 214] [Impact Index Per Article: 71.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The microbiome directly affects the balance of pro-inflammatory and anti-inflammatory responses in the gut. As microbes thrive on dietary substrates, the question arises whether we can nourish an anti-inflammatory gut ecosystem. We aim to unravel interactions between diet, gut microbiota and their functional ability to induce intestinal inflammation. DESIGN We investigated the relation between 173 dietary factors and the microbiome of 1425 individuals spanning four cohorts: Crohn's disease, ulcerative colitis, irritable bowel syndrome and the general population. Shotgun metagenomic sequencing was performed to profile gut microbial composition and function. Dietary intake was assessed through food frequency questionnaires. We performed unsupervised clustering to identify dietary patterns and microbial clusters. Associations between diet and microbial features were explored per cohort, followed by a meta-analysis and heterogeneity estimation. RESULTS We identified 38 associations between dietary patterns and microbial clusters. Moreover, 61 individual foods and nutrients were associated with 61 species and 249 metabolic pathways in the meta-analysis across healthy individuals and patients with IBS, Crohn's disease and UC (false discovery rate<0.05). Processed foods and animal-derived foods were consistently associated with higher abundances of Firmicutes, Ruminococcus species of the Blautia genus and endotoxin synthesis pathways. The opposite was found for plant foods and fish, which were positively associated with short-chain fatty acid-producing commensals and pathways of nutrient metabolism. CONCLUSION We identified dietary patterns that consistently correlate with groups of bacteria with shared functional roles in both, health and disease. Moreover, specific foods and nutrients were associated with species known to infer mucosal protection and anti-inflammatory effects. We propose microbial mechanisms through which the diet affects inflammatory responses in the gut as a rationale for future intervention studies.
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Affiliation(s)
- Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Vera Peters
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Marjo J E Campmans-Kuijpers
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
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Prudent V, Demarre G, Vazeille E, Wery M, Quenech'Du N, Ravet A, Dauverd-Girault J, van Dijk E, Bringer MA, Descrimes M, Barnich N, Rimsky S, Morillon A, Espéli O. The Crohn's disease-related bacterial strain LF82 assembles biofilm-like communities to protect itself from phagolysosomal attack. Commun Biol 2021; 4:627. [PMID: 34035436 PMCID: PMC8149705 DOI: 10.1038/s42003-021-02161-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 09/15/2020] [Accepted: 04/28/2021] [Indexed: 11/09/2022] Open
Abstract
Patients with Crohn's disease exhibit abnormal colonization of the intestine by adherent invasive E. coli (AIEC). They adhere to epithelial cells, colonize them and survive inside macrophages. It appeared recently that AIEC LF82 adaptation to phagolysosomal stress involves a long lag phase in which many LF82 cells become antibiotic tolerant. Later during infection, they proliferate in vacuoles and form colonies harboring dozens of LF82 bacteria. In the present work, we investigated the mechanism sustaining this phase of growth. We found that intracellular LF82 produced an extrabacterial matrix that acts as a biofilm and controls the formation of LF82 intracellular bacterial communities (IBCs) for several days post infection. We revealed the crucial role played by the pathogenicity island encoding the yersiniabactin iron capture system to form IBCs and for optimal LF82 survival. These results illustrate that AIECs use original strategies to establish their replicative niche within macrophages.
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Affiliation(s)
- Victoria Prudent
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Gaëlle Demarre
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Emilie Vazeille
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte. UMR Inserm/ Université de Clermont -Auvergne U1071, USC INRA 2018, Clermont, Ferrand, France
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne University, CNRS UMR 3244, Paris, France
| | - Nicole Quenech'Du
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Antinéa Ravet
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Julie Dauverd-Girault
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Erwin van Dijk
- Next-Generation Sequencing Service - I2BC, I2BC-CNRS, Gif-sur-Yvette, France
| | - Marie-Agnès Bringer
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte. UMR Inserm/ Université de Clermont -Auvergne U1071, USC INRA 2018, Clermont, Ferrand, France
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Marc Descrimes
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne University, CNRS UMR 3244, Paris, France
| | - Nicolas Barnich
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte. UMR Inserm/ Université de Clermont -Auvergne U1071, USC INRA 2018, Clermont, Ferrand, France
| | - Sylvie Rimsky
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne University, CNRS UMR 3244, Paris, France
| | - Olivier Espéli
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France.
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Elhenawy W, Hordienko S, Gould S, Oberc AM, Tsai CN, Hubbard TP, Waldor MK, Coombes BK. High-throughput fitness screening and transcriptomics identify a role for a type IV secretion system in the pathogenesis of Crohn's disease-associated Escherichia coli. Nat Commun 2021; 12:2032. [PMID: 33795670 PMCID: PMC8016931 DOI: 10.1038/s41467-021-22306-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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] [Received: 08/24/2020] [Accepted: 03/05/2021] [Indexed: 02/06/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) are pathogenic bacteria frequently isolated from patients who have Crohn's disease (CD). Despite the phenotypic differences between AIEC and commensal E. coli, comparative genomic approaches have been unable to differentiate these two groups, making the identification of key virulence factors a challenge. Here, we conduct a high-resolution, in vivo genetic screen to map AIEC genes required for intestinal colonization of mice. In addition, we use in vivo RNA-sequencing to define the host-associated AIEC transcriptome. We identify diverse metabolic pathways required for efficient gut colonization by AIEC and show that a type IV secretion system (T4SS) is required to form biofilms on the surface of epithelial cells, thereby promoting AIEC persistence in the gut. E. coli isolated from CD patients are enriched for a T4SS, suggesting a possible connection to disease activity. Our findings establish the T4SS as a principal AIEC colonization factor and highlight the use of genome-wide screens in decoding the infection biology of CD-associated bacteria that otherwise lack a defined genetic signature.
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Affiliation(s)
- Wael Elhenawy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Sarah Hordienko
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Steven Gould
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Alexander M Oberc
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Caressa N Tsai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Troy P Hubbard
- Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada.
- Farncombe Family Digestive Health Research Institute, Hamilton, ON, Canada.
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Ding ZH, Xu XP, Wang TR, Liang X, Ran ZH, Lu H. The prevalence of Helicobacter pylori infection in inflammatory bowel disease in China: A case-control study. PLoS One 2021; 16:e0248427. [PMID: 33711050 PMCID: PMC7954320 DOI: 10.1371/journal.pone.0248427] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/25/2021] [Indexed: 12/30/2022] Open
Abstract
Background & aims Helicobacter pylori (H. pylori) infection remains high in China though the incidence of inflammatory bowel disease (IBD) has increased. Our aim was to investigate the relationship between the prevalence of H. pylori and inflammatory bowel disease. Methods Hospitalized IBD patients including Crohn’s disease (CD) and ulcerative colitis (UC) who had tested H. pylori antibody were enrolled. Controls were chose from age- and sex- matched healthy physical examination people who had H. pylori antibody test in a 1:2 fashion (IBD patients:controls). IBD medical history was recorded. All patients were typed by the Montreal classification. Mayo Clinic score and the Harvey-Bradshaw Severity Index were used to evaluate their disease activity. Patients and controls that had H. pylori eradication therapy before were excluded. Results Two hundred and sixty IBD patients including 213 CD patients and 47 UC patients, and 520 controls were involved in this study. The prevalence of H. pylori infection in IBD patients (9.6%, 25/260) and IBD newly diagnosed patients (12.1%, 8/66), as well as CD patients (8.9%, 19/213) including CD newly diagnosed patients (10.6%, 5/47) and UC patients (12.8%, 6/47) was significantly lower than controls (29.8%, 155/520) (p = 2.796*10−10, 0.007, 5.723*10−9, 0.016, 0.014), while there was no statistically difference between UC newly diagnosed patients and the controls, and IBD patients with different disease type, disease activity and treatment history. Conclusions H. pylori infection had a negative association with IBD, especially CD.
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Affiliation(s)
- Zhao-Hui Ding
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Ping Xu
- Clinical Biochemistry Laboratory, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tian-Rong Wang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Liang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Hua Ran
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Lu
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- * E-mail:
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47
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Rana T, Korolkova OY, Rachakonda G, Williams AD, Hawkins AT, James SD, Sakwe AM, Hui N, Wang L, Yu C, Goodwin JS, Izban MG, Offodile RS, Washington MK, Ballard BR, Smoot DT, Shi XZ, Forbes DS, Shanker A, M’Koma AE. Linking bacterial enterotoxins and alpha defensin 5 expansion in the Crohn's colitis: A new insight into the etiopathogenetic and differentiation triggers driving colonic inflammatory bowel disease. PLoS One 2021; 16:e0246393. [PMID: 33690604 PMCID: PMC7942995 DOI: 10.1371/journal.pone.0246393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/17/2021] [Indexed: 02/05/2023] Open
Abstract
Evidence link bacterial enterotoxins to apparent crypt-cell like cells (CCLCs), and Alpha Defensin 5 (DEFA5) expansion in the colonic mucosa of Crohn's colitis disease (CC) patients. These areas of ectopic ileal metaplasia, positive for Paneth cell (PC) markers are consistent with diagnosis of CC. Retrospectively, we: 1. Identified 21 patients with indeterminate colitis (IC) between 2000-2007 and were reevaluation their final clinical diagnosis in 2014 after a followed-up for mean 8.7±3.7 (range, 4-14) years. Their initial biopsies were analyzed by DEFA5 bioassay. 2. Differentiated ulcer-associated cell lineage (UACL) analysis by immunohistochemistry (IHC) of the CC patients, stained for Mucin 6 (MUC6) and DEFA5. 3. Treated human immortalized colonic epithelial cells (NCM460) and colonoids with pure DEFA5 on the secretion of signatures after 24hr. The control colonoids were not treated. 4. Treated colonoids with/without enterotoxins for 14 days and the spent medium were collected and determined by quantitative expression of DEFA5, CCLCs and other biologic signatures. The experiments were repeated twice. Three statistical methods were used: (i) Univariate analysis; (ii) LASSO; and (iii) Elastic net. DEFA5 bioassay discriminated CC and ulcerative colitis (UC) in a cohort of IC patients with accuracy. A fit logistic model with group CC and UC as the outcome and the DEFA5 as independent variable differentiator with a positive predictive value of 96 percent. IHC staining of CC for MUC6 and DEFA5 stained in different locations indicating that DEFA5 is not co-expressed in UACL and is therefore NOT the genesis of CC, rather a secretagogue for specific signature(s) that underlie the distinct crypt pathobiology of CC. Notably, we observed expansion of signatures after DEFA5 treatment on NCM460 and colonoids cells expressed at different times, intervals, and intensity. These factors are key stem cell niche regulators leading to DEFA5 secreting CCLCs differentiation 'the colonic ectopy ileal metaplasia formation' conspicuously of pathogenic importance in CC.
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Affiliation(s)
- Tanu Rana
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Olga Y. Korolkova
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Girish Rachakonda
- Department of Microbiology and Immunology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Amanda D. Williams
- Department of Biology, Lipscomb University, Nashville, Tennessee, United States of America
| | - Alexander T. Hawkins
- Division of General Surgery, Section of Colon and Rectal Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Samuel D. James
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Tennessee Valley Health Systems VA Medical Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Amos M. Sakwe
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Graduate Studies and Research, Nashville, Tennessee, United States of America
| | - Nian Hui
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Li Wang
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Chang Yu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jeffrey S. Goodwin
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Michael G. Izban
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
| | - Regina S. Offodile
- Department of Professional and Medical Education, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
| | - Mary K. Washington
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Billy R. Ballard
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
| | - Duane T. Smoot
- Department of Medicine, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
| | - Xuan-Zheng Shi
- Department of Medicine, University of Texas Medical Branch (UTMB) in Galveston, Galveston, Texas, United States of America
| | - Digna S. Forbes
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
| | - Anil Shanker
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Amosy E. M’Koma
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
- Division of General Surgery, Section of Colon and Rectal Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
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48
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Agrawal G, Aitken J, Hamblin H, Collins M, Borody TJ. Putting Crohn's on the MAP: Five Common Questions on the Contribution of Mycobacterium avium subspecies paratuberculosis to the Pathophysiology of Crohn's Disease. Dig Dis Sci 2021; 66:348-358. [PMID: 33089484 PMCID: PMC7577843 DOI: 10.1007/s10620-020-06653-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/02/2020] [Indexed: 02/06/2023]
Abstract
For decades, Mycobacterium avium subspecies paratuberculosis (MAP) has been linked to the pathogenesis of Crohn's disease. Despite many investigations and research efforts, there remains no clear unifying explanation of its pathogenicity to humans. Proponents argue Crohn's disease shares many identical features with a granulomatous infection in ruminants termed Johne's disease and similarities with ileo-cecal tuberculosis. Both are caused by species within the Mycobacterium genus. Sceptics assert that since MAP is found in individuals diagnosed with Crohn's disease as well as in healthy population controls, any association with CD is coincidental. This view is supported by the uncertain response of patients to antimicrobial therapy. This report aims to address the controversial aspects of this proposition with information and knowledge gathered from several disciplines, including microbiology and veterinary medicine. The authors hope that this discussion will stimulate further research aimed at confirming or refuting the contribution of MAP to the pathogenesis of Crohn's disease and ultimately lead to advanced targeted clinical therapies.
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Affiliation(s)
- Gaurav Agrawal
- Gastroenterology and Infectious Diseases, Centre for Digestive Diseases, Sydney, Australia.
- Guy's and St. Thomas' NHS Foundation Trust & King's College, London, UK.
| | - John Aitken
- Microbiology, Otakaro Pathways, Christchurch, New Zealand
| | - Harrison Hamblin
- Gastroenterology and Infectious Diseases, Centre for Digestive Diseases, Sydney, Australia
| | - Michael Collins
- Veterinary Microbiology, Department of Pathobiological Sciences, University of Wisconsin, Madison, USA
| | - Thomas J Borody
- Gastroenterology and Infectious Diseases, Centre for Digestive Diseases, Sydney, Australia
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49
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Patankar JV, Chiriac MT, Lehmann M, Kühl AA, Atreya R, Becker C, Gonzalez-Acera M, Schmitt H, Gamez-Belmonte R, Mahapatro M, Diemand L, Hartmann L, Mascia F, Hracsko Z, Thonn V, Schödel L, Zielinska M, Yu Y, Erkert L, Li W, Zeitler M, Ruder B, Ganzleben I, Günther C, Voehringer D, Zundler S, Neurath MF, Siegmund B. Severe Acute Respiratory Syndrome Coronavirus 2 Attachment Receptor Angiotensin-Converting Enzyme 2 Is Decreased in Crohn's Disease and Regulated By Microbial and Inflammatory Signaling. Gastroenterology 2021; 160:925-928.e4. [PMID: 33075345 PMCID: PMC7567698 DOI: 10.1053/j.gastro.2020.10.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/23/2020] [Accepted: 10/12/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Jay Vasant Patankar
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | | | - Malte Lehmann
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Berlin, Germany; The Transregio 241 IBDome Consortium, Berlin, Germany
| | - Anja A Kühl
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Berlin, Germany; The Transregio 241 IBDome Consortium, Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, iPATH.Berlin, Berlin, Germany
| | - Raja Atreya
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany; The Transregio 241 IBDome Consortium, Berlin, Germany; Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Christoph Becker
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany; The Transregio 241 IBDome Consortium, Berlin, Germany.
| | | | - Heike Schmitt
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | | | - Mousumi Mahapatro
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Leonard Diemand
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Leonie Hartmann
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Fabrizio Mascia
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Zsuzsanna Hracsko
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Veronika Thonn
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Lena Schödel
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Marta Zielinska
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany; Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Yuqiang Yu
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Lena Erkert
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Wei Li
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany; College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China
| | - Melanie Zeitler
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Barbara Ruder
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Ingo Ganzleben
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Claudia Günther
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
| | - David Voehringer
- Department of Infection Biology, University Hospital Erlangen, Erlangen, Germany
| | - Sebastian Zundler
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany; Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany; The Transregio 241 IBDome Consortium, Berlin, Germany; Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Britta Siegmund
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Berlin, Germany; The Transregio 241 IBDome Consortium, Berlin, Germany
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50
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Shapiro JM, de Zoete MR, Palm NW, Laenen Y, Bright R, Mallette M, Bu K, Bielecka AA, Xu F, Hurtado-Lorenzo A, Shah SA, Cho JH, LeLeiko NS, Sands BE, Flavell RA, Clemente JC. Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease. Cell Host Microbe 2021; 29:83-93.e3. [PMID: 33385335 PMCID: PMC10477929 DOI: 10.1016/j.chom.2020.12.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [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] [Received: 04/20/2020] [Revised: 09/18/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022]
Abstract
The immunopathogenesis of inflammatory bowel disease (IBD) has been attributed to a combination of host genetics and intestinal dysbiosis. Previous work in a small cohort of IBD patients suggested that pro-inflammatory bacterial taxa are highly coated with secretory immunoglobulin IgA. Using bacterial fluorescence-activated cell sorting coupled with 16S rRNA gene sequencing (IgA-SEQ), we profiled IgA coating of intestinal microbiota in a large cohort of IBD patients and identified bacteria associated with disease and treatment. Forty-three bacterial taxa displayed significantly higher IgA coating in IBD compared with controls, including 8 taxa exhibiting differential IgA coating but similar relative abundance. Patients treated with anti-TNF-α therapies exhibited dramatically altered microbiota-specific IgA responses compared with controls. Furthermore, increased IgA coating of Oscillospira was associated with a delay in time to surgery. These results demonstrate that investigating IgA responses to microbiota can uncover potential disease-modifying taxa and reveal improved biomarkers of clinical course in IBD.
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Affiliation(s)
- Jason M Shapiro
- Division of Pediatric Gastroenterology, Nutrition and Liver Diseases, Hasbro Children's Hospital, Providence, RI 02903, USA; Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Marcel R de Zoete
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Noah W Palm
- Human and Translational Immunobiology Program, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Yaro Laenen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rene Bright
- Division of Gastroenterology, Rhode Island Hospital, Providence, RI 02903, USA
| | - Meaghan Mallette
- Division of Gastroenterology, Rhode Island Hospital, Providence, RI 02903, USA
| | - Kevin Bu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Agata A Bielecka
- Human and Translational Immunobiology Program, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Fang Xu
- Division of Population Health, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
| | | | - Samir A Shah
- Alpert Medical School of Brown University, Providence, RI 02903, USA; Division of Gastroenterology, Rhode Island Hospital, Providence, RI 02903, USA
| | - Judy H Cho
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Neal S LeLeiko
- Division of Pediatric Gastroenterology, Nutrition and Liver Diseases, Hasbro Children's Hospital, Providence, RI 02903, USA; Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Bruce E Sands
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard A Flavell
- Human and Translational Immunobiology Program, Yale University School of Medicine, New Haven, CT 06519, USA
| | - J C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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