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Yao J, Sun T, Zheng S, Ma J, Zeng Q, Liu K, Zhang W, Yu Y. The protective effect of teprenone in TNBS-induced ulcerative colitis rats by modulating the gut microbiota and reducing inflammatory response. Immunopharmacol Immunotoxicol 2024; 46:255-263. [PMID: 38252282 DOI: 10.1080/08923973.2024.2308252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
OBJECTIVE Ulcerative colitis (UC), a chronic and refractory nonspecific inflammatory bowel disease, affects millions of patients worldwide and increases the risk of colorectal cancer. Teprenone is an acylic polyisoprenoid that exerts anti-inflammatory properties in rat models of peptic ulcer disease. This in vitro and in vivo study was designed to investigate the effects of teprenone on UC and to explore the underlying mechanisms. METHODS Human intestinal epithelial cells (Caco-2 cells) serve as the in vitro experimental model. Lipopolysaccharide (LPS, 1 μg/mL) was employed to stimulate the production of pro-inflammatory cytokines (interleukin [IL]-6, IL-1β, and tumor necrosis factor [TNF]-α), Toll-like receptor-4 (TLR4), MyD88 expression, and NF-κB activation. A trinitrobenzene sulfonic acid (TNBS)-induced chronic UC rat model was employed for the in vivo assay. RESULTS Pro-inflammatory cytokine stimulation by LPS in Caco-2 cells was inhibited by teprenone at 40 μg/mL through the TLR4/NF-κB signaling pathway. Teprenone attenuated TNBS-induced UC, decreased myeloperoxidase and malondialdehyde, induced TLR4 expression and NF-κB activation, and increased glutathione and zonula occludens-1 level in the rat colonic tissue. Moreover, Fusobacterium, Escherichia coli, Porphyromonas gingivalis elevation, and Mogibacterium timidum decline in UC rats were inhibited by teprenone. CONCLUSION Based on our results, the protective effects of teprenone for UC may be related to its ability to modulate the gut microbiota and reduce the inflammatory response.
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Affiliation(s)
- Jianfeng Yao
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Tao Sun
- Department of Endoscopy, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Songbai Zheng
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Jianxia Ma
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Qinglian Zeng
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Kangwei Liu
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Wei Zhang
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Yang Yu
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
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2
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Lima SF, Pires S, Rupert A, Oguntunmibi S, Jin WB, Marderstein A, Funez-dePagnier G, Maldarelli G, Viladomiu M, Putzel G, Yang W, Tran N, Xiang G, Grier A, Guo CJ, Lukin D, Mandl LA, Scherl EJ, Longman RS. The gut microbiome regulates the clinical efficacy of sulfasalazine therapy for IBD-associated spondyloarthritis. Cell Rep Med 2024; 5:101431. [PMID: 38378002 PMCID: PMC10982976 DOI: 10.1016/j.xcrm.2024.101431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/28/2023] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Sulfasalazine is a prodrug known to be effective for the treatment of inflammatory bowel disease (IBD)-associated peripheral spondyloarthritis (pSpA), but the mechanistic role for the gut microbiome in regulating its clinical efficacy is not well understood. Here, treatment of 22 IBD-pSpA subjects with sulfasalazine identifies clinical responders with a gut microbiome enriched in Faecalibacterium prausnitzii and the capacity for butyrate production. Sulfapyridine promotes butyrate production and transcription of the butyrate synthesis gene but in F. prausnitzii in vitro, which is suppressed by excess folate. Sulfasalazine therapy enhances fecal butyrate production and limits colitis in wild-type and gnotobiotic mice colonized with responder, but not non-responder, microbiomes. F. prausnitzii is sufficient to restore sulfasalazine protection from colitis in gnotobiotic mice colonized with non-responder microbiomes. These findings reveal a mechanistic link between the efficacy of sulfasalazine therapy and the gut microbiome with the potential to guide diagnostic and therapeutic approaches for IBD-pSpA.
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Affiliation(s)
- Svetlana F Lima
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Silvia Pires
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Amanda Rupert
- Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Seun Oguntunmibi
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Wen-Bing Jin
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew Marderstein
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA
| | - Gabriela Funez-dePagnier
- Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Grace Maldarelli
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Monica Viladomiu
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Gregory Putzel
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA
| | - Wei Yang
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Nancy Tran
- Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Grace Xiang
- Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Alex Grier
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chun-Jun Guo
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dana Lukin
- Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Lisa A Mandl
- Division of Rheumatology, Hospital for Special Surgery and Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Ellen J Scherl
- Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Randy S Longman
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, NY 10065, USA; Division of Gastroenterology and Hepatology, Department of Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA; Jill Roberts Center for IBD, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY 10065, USA.
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Sugihara K, Kamada N. Metabolic network of the gut microbiota in inflammatory bowel disease. Inflamm Regen 2024; 44:11. [PMID: 38443988 PMCID: PMC10913301 DOI: 10.1186/s41232-024-00321-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024] Open
Abstract
Gut dysbiosis is closely linked to the pathogenesis of inflammatory bowel disease (IBD). Emerging studies highlight the relationship between host metabolism and the modulation of gut microbiota composition through regulating the luminal microenvironment. In IBD, various disease-associated factors contribute to the significant perturbation of host metabolism. Such disturbance catalyzes the selective proliferation of specific microbial populations, particularly pathobionts such as adherent invasive Escherichia coli and oral-derived bacteria. Pathobionts employ various strategies to adapt better to the disease-associated luminal environments. In addition to the host-microbe interaction, recent studies demonstrate that the metabolic network between commensal symbionts and pathobionts facilitates the expansion of pathobionts in the inflamed gut. Understanding the metabolic network among the host, commensal symbionts, and pathobionts provides new insights into the pathogenesis of IBD and novel avenues for treating IBD.
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Affiliation(s)
- Kohei Sugihara
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Nobuhiko Kamada
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA.
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
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Cisek AA, Szymańska E, Aleksandrzak-Piekarczyk T, Cukrowska B. The Role of Methanogenic Archaea in Inflammatory Bowel Disease-A Review. J Pers Med 2024; 14:196. [PMID: 38392629 PMCID: PMC10890621 DOI: 10.3390/jpm14020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/28/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Methanogenic archaea are a part of the commensal gut microbiota responsible for hydrogen sink and the efficient production of short-chain fatty acids. Dysbiosis of methanogens is suspected to play a role in pathogenesis of variety of diseases, including inflammatory bowel disease (IBD). Unlike bacteria, the diversity of archaea seems to be higher in IBD patients compared to healthy subjects, whereas the prevalence and abundance of gut methanogens declines in IBD, especially in ulcerative colitis. To date, studies focusing on methanogens in pediatric IBD are very limited; nevertheless, the preliminary results provide some evidence that methanogens may be influenced by the chronic inflammatory process in IBD. In this review, we demonstrated the development and diversity of the methanogenic community in IBD, both in adults and children.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathomorphology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Edyta Szymańska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | | | - Bożena Cukrowska
- Department of Pathomorphology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
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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] [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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6
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Zhangni L, Mofan X, Yuling C, Yingchao L. Clinical features and fecal microbiota characteristics of patients with both ulcerative colitis and axial spondyloarthritis. BMC Gastroenterol 2024; 24:56. [PMID: 38297219 PMCID: PMC10832282 DOI: 10.1186/s12876-024-03150-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/26/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND The role of the intestinal microbiota in the pathogenesis of inflammatory bowel disease combined with axial spondyloarthritis (axSpA) is gaining widespread interest. AIMS This study was conducted to investigate the clinical and fecal microbiota characteristics of patients with both ulcerative colitis (UC) and axSpA. METHODS Clinical data were collected from patients with UC. Patients were divided into the axSpA and non-axSpA groups according to human leukocyte antigen-B27 serology and sacroiliac joint imaging results. We obtained fecal specimens from 14 axSpA and 26 non-axSpA patients. All samples underwent 16S ribosomal DNA sequencing. RESULTS Seventy-three patients with UC were included in this study, and the axSpA incidence was 19.2%. This incidence was significantly higher in patients with C-reactive protein > 10 mg/L. Firmicutes and Faecalibacterium abundances were decreased, and Proteobacteria and Escherichia_Shigella abundances were increased in the axSpA group compared with those of the non-axSpA group. Indicator analysis showed that Escherichia_Shigella was more likely to be an indicator species of axSpA. Additionally, many biosynthetic and metabolic pathways, including glutathione metabolism, fatty acid degradation, geraniol degradation, and biosynthesis of siderophore group nonribosomal peptides, were upregulated in the axSpA group. CONCLUSION Patients with UC have a high axSpA incidence, which may be related to the relative abundances of Escherichia_Shigella in these patients. The abundances of various biosynthetic and metabolic pathways of the fecal flora were upregulated in patients with axSpA.
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Affiliation(s)
- Lei Zhangni
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, 710061, China
| | - Xiao Mofan
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, 710061, China
| | - Chen Yuling
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, 710061, China
| | - Li Yingchao
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, 710061, China.
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7
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Paris T, Kiss A, Signor L, Lutfalla G, Blaise M, Boeri Erba E, Chaloin L, Yatime L. The IbeA protein from adherent invasive Escherichia coli is a flavoprotein sharing structural homology with FAD-dependent oxidoreductases. FEBS J 2024; 291:177-203. [PMID: 37786987 DOI: 10.1111/febs.16969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/22/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Invasion of brain endothelium protein A (IbeA) is a virulence factor specific to pathogenic Escherichia coli. Originally identified in the K1 strain causing neonatal meningitis, it was more recently found in avian pathogenic Escherichia coli (APEC) and adherent invasive Escherichia coli (AIEC). In these bacteria, IbeA facilitates host cell invasion and intracellular survival, in particular, under harsh conditions like oxidative stress. Furthermore, IbeA from AIEC contributes to intramacrophage survival and replication, thus enhancing the inflammatory response within the intestine. Therefore, this factor is a promising drug target for anti-AIEC strategies in the context of Crohn's disease. Despite such an important role, the biological function of IbeA remains largely unknown. In particular, its exact nature and cellular localization, i.e., membrane-bound invasin versus cytosolic factor, are still of debate. Here, we developed an efficient protocol for recombinant expression of IbeA under native conditions and demonstrated that IbeA from AIEC is a soluble, homodimeric flavoprotein. Using mass spectrometry and tryptophan fluorescence measurements, we further showed that IbeA preferentially binds flavin adenine dinucleotide (FAD), with an affinity in the one-hundred nanomolar range and optimal binding under reducing conditions. 3D-modeling with AlphaFold revealed that IbeA shares strong structural homology with FAD-dependent oxidoreductases. Finally, we used ligand docking, mutational analyses, and molecular dynamics simulations to identify the FAD binding pocket within IbeA and characterize possible conformational changes occurring upon ligand binding. Overall, we suggest that the role of IbeA in the survival of AIEC within host cells, notably macrophages, is linked to modulation of redox processes.
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Affiliation(s)
- Théo Paris
- LPHI, Univ. Montpellier, CNRS, INSERM, France
| | - Agneta Kiss
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Luca Signor
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
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Bleich RM, Li C, Sun S, Ahn JH, Dogan B, Barlogio CJ, Broberg CA, Franks AR, Bulik-Sullivan E, Carroll IM, Simpson KW, Fodor AA, Arthur JC. A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice. MICROBIOME 2023; 11:277. [PMID: 38124090 PMCID: PMC10731797 DOI: 10.1186/s40168-023-01710-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/26/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in vitro definition fully predicts mucosal colonization in vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis. RESULTS Germ-free inflammation-susceptible interleukin-10-deficient (Il10-/-) and inflammation-resistant WT mice were colonized with a consortium of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10-/- mice. These E. coli expand in Il10-/- mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization. CONCLUSIONS Our findings establish the in vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in vivo colonization dynamics of patient-derived bacteria in murine models. Video Abstract.
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Affiliation(s)
- Rachel M Bleich
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biology, Appalachian State University, Boone, NC, USA
| | - Chuang Li
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shan Sun
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Ju-Hyun Ahn
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Belgin Dogan
- Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Cassandra J Barlogio
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher A Broberg
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adrienne R Franks
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily Bulik-Sullivan
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ian M Carroll
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth W Simpson
- Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Anthony A Fodor
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Janelle C Arthur
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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9
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Flores E, Dutta S, Bosserman R, van Hoof A, Krachler AM. Colonization of larval zebrafish ( Danio rerio) with adherent-invasive Escherichia coli prevents recovery of the intestinal mucosa from drug-induced enterocolitis. mSphere 2023; 8:e0051223. [PMID: 37971273 PMCID: PMC10732064 DOI: 10.1128/msphere.00512-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/07/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Although inflammatory bowel diseases are on the rise, what factors influence IBD risk and severity, and the underlying mechanisms remain to be fully understood. Although host genetics, microbiome, and environmental factors have all been shown to correlate with the development of IBD, cause and effect are difficult to disentangle in this context. For example, AIEC is a known pathobiont found in IBD patients, but it remains unclear if gut inflammation during IBD facilitates colonization with AIEC, or if AIEC colonization makes the host more susceptible to pro-inflammatory stimuli. It is critical to understand the mechanisms that contribute to AIEC infections in a susceptible host in order to develop successful therapeutics. Here, we show that the larval zebrafish model recapitulates key features of AIEC infections in other animal models and can be utilized to address these gaps in knowledge.
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Affiliation(s)
- Erika Flores
- Microbiology and Infectious Diseases Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Soumita Dutta
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Rachel Bosserman
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ambro van Hoof
- Microbiology and Infectious Diseases Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Anne-Marie Krachler
- Microbiology and Infectious Diseases Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
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Zangara MT, Darwish L, Coombes BK. Characterizing the Pathogenic Potential of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. EcoSal Plus 2023; 11:eesp00182022. [PMID: 37220071 DOI: 10.1128/ecosalplus.esp-0018-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/04/2023] [Indexed: 01/28/2024]
Abstract
The microbiome of Crohn's disease (CD) patients is composed of a microbial community that is considered dysbiotic and proinflammatory in nature. The overrepresentation of Enterobacteriaceae species is a common feature of the CD microbiome, and much attention has been given to understanding the pathogenic role this feature plays in disease activity. Over 2 decades ago, a new Escherichia coli subtype called adherent-invasive E. coli (AIEC) was isolated and linked to ileal Crohn's disease. Since the isolation of the first AIEC strain, additional AIEC strains have been isolated from both inflammatory bowel disease (IBD) patients and non-IBD individuals using the original in vitro phenotypic characterization methods. Identification of a definitive molecular marker of the AIEC pathotype has been elusive; however, significant advancements have been made in understanding the genetic, metabolic, and virulence determinants of AIEC infection biology. Here, we review the current knowledge of AIEC pathogenesis to provide additional, objective measures that could be considered in defining AIEC and their pathogenic potential.
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Affiliation(s)
- Megan T Zangara
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Lena Darwish
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Brian K Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, Hamilton, Ontario, Canada
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Fujiki J, Schnabl B. Phage therapy: Targeting intestinal bacterial microbiota for the treatment of liver diseases. JHEP Rep 2023; 5:100909. [PMID: 37965159 PMCID: PMC10641246 DOI: 10.1016/j.jhepr.2023.100909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/16/2023] Open
Abstract
Phage therapy has been overshadowed by antibiotics for decades. However, it is being revisited as a powerful approach against antimicrobial-resistant bacteria. As bacterial microbiota have been mechanistically linked to gastrointestinal and liver diseases, precise editing of the gut microbiota via the selective bactericidal action of phages has prompted renewed interest in phage therapy. In this review, we summarise the basic virological properties of phages and the latest findings on the composition of the intestinal phageome and the changes associated with liver diseases. We also review preclinical and clinical studies assessing phage therapy for the treatment of gastrointestinal and liver diseases, as well as future prospects and challenges.
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Affiliation(s)
- Jumpei Fujiki
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
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12
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Wang K, Zhou M, Si H, Ma J. Gut microbiota-mediated IL-22 alleviates metabolic inflammation. Life Sci 2023; 334:122229. [PMID: 37922980 DOI: 10.1016/j.lfs.2023.122229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/25/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023]
Abstract
Low-grade chronic inflammation, also known as metabolic inflammation, promotes the development of metabolic diseases. Increasing evidence suggests that changes in gut microbes and metabolites disrupt the integrity of the gut barrier and exert significant effects on the metabolism of various tissues, including the liver and adipose tissue, thereby contributing to metabolic inflammation. We observed that IL-22 is a key signaling molecule that serves as a bridge between intestinal microbes and the host, effectively alleviating metabolic inflammation by modulating the host immunomodulatory network. Here, we focused on elucidating the underlying mechanisms by which the gut microbiota and their metabolites reduce inflammation via IL-22, highlighting the favorable impact of IL-22 on metabolic inflammation. Furthermore, we discuss the potential of IL-22 as a therapeutic target for the management of metabolic inflammation and related diseases.
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Affiliation(s)
- Kaijun Wang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China; Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Miao Zhou
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Hongbin Si
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Jie Ma
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China.
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13
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Li J, Ji Y, Chen N, Dai L, Deng H. Colitis-associated carcinogenesis: crosstalk between tumors, immune cells and gut microbiota. Cell Biosci 2023; 13:194. [PMID: 37875976 PMCID: PMC10594787 DOI: 10.1186/s13578-023-01139-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. One of the main causes of colorectal cancer is inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD). Intestinal epithelial cells (IECs), intestinal mesenchymal cells (IMCs), immune cells, and gut microbiota construct the main body of the colon and maintain colon homeostasis. In the development of colitis and colitis-associated carcinogenesis, the damage, disorder or excessive recruitment of different cells such as IECs, IMCs, immune cells and intestinal microbiota play different roles during these processes. This review aims to discuss the various roles of different cells and the crosstalk of these cells in transforming intestinal inflammation to cancer, which provides new therapeutic methods for chemotherapy, targeted therapy, immunotherapy and microbial therapy.
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Affiliation(s)
- Junshu Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Yanhong Ji
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Na Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Lei Dai
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China.
| | - Hongxin Deng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China.
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14
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Liu Z, Wang Q, Ma A, Feng S, Chung D, Zhao J, Ma Q, Liu B. Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data. Comput Biol Med 2023; 165:107458. [PMID: 37703713 DOI: 10.1016/j.compbiomed.2023.107458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/22/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
The identification of microbial characteristics associated with diseases is crucial for disease diagnosis and therapy. However, the presence of heterogeneity, high dimensionality, and large amounts of microbial data presents tremendous challenges in discovering key microbial features. In this paper, we present IDAM, a novel computational method for inferring disease-associated gene modules from metagenomic and metatranscriptomic data. This method integrates gene context conservation (uber-operons) and regulatory mechanisms (gene co-expression patterns) within a mathematical graph model to explore gene modules associated with specific diseases. It alleviates reliance on prior meta-data. We applied IDAM to publicly available datasets from inflammatory bowel disease, melanoma, type 1 diabetes mellitus, and irritable bowel syndrome. The results demonstrated the superior performance of IDAM in inferring disease-associated characteristics compared to existing popular tools. Furthermore, we showcased the high reproducibility of the gene modules inferred by IDAM using independent cohorts with inflammatory bowel disease. We believe that IDAM can be a highly advantageous method for exploring disease-associated microbial characteristics. The source code of IDAM is freely available at https://github.com/OSU-BMBL/IDAM, and the web server can be accessed at https://bmblx.bmi.osumc.edu/idam/.
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Affiliation(s)
- Zhaoqian Liu
- School of Mathematics, Shandong University, Jinan, Shandong, 250100, China
| | - Qi Wang
- School of Mathematics, Shandong University, Jinan, Shandong, 250100, China
| | - Anjun Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Shaohong Feng
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Dongjun Chung
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, 43210, USA
| | - Jing Zhao
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Bingqiang Liu
- School of Mathematics, Shandong University, Jinan, Shandong, 250100, China; Shandong National Center for Applied Mathematics, Jinan, Shandong, 250100, China.
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15
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Cai X, Zhou N, Zou Q, Peng Y, Xu L, Feng L, Liu X. Integration of taxa abundance and occurrence frequency to identify key gut bacteria correlated to clinics in Crohn's disease. BMC Microbiol 2023; 23:247. [PMID: 37661264 PMCID: PMC10476393 DOI: 10.1186/s12866-023-02999-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 08/29/2023] [Indexed: 09/05/2023] Open
Abstract
Bacteria abundance alternation in the feces or mucosa of Crohn's disease (CD) patients has long been applied to identify potential biomarkers for this disease, while the taxa occurrence frequency and their correlations with clinical traits were understudied. A total of 97 samples from the feces and gut mucosa were collected from CD patients and healthy controls (HCs), 16S rRNA-based analyses were performed to determine the changes in taxa abundance and occurrence frequency along CD and to correlate them with clinical traits. The results showed that bacteria communities were divergent between feces and mucosa, while the taxa abundance and occurrence frequency in both partitions showed similar exponential correlations. The decrease of specific fecal bacteria was much more effective in classifying the CD and HCs than that of the mucosal bacteria. Among them, Christensenellaceae_R-7_group and Ruminococcus were predicted as biomarkers by using random forest algorithm, which were persistently presented (> 71.40% in frequency) in the feces of the HCs with high abundance, whereas transiently presented in the feces (< 5.5% in frequency) and mucosa (< 18.18% in frequency) of CD patients with low abundance. Co-occurrence network analysis then identified them as hub taxa that drive the alternations of other bacteria and were positively correlated to the circuiting monocytes. The loss of specific bacteria in the healthy gut may cause great disturbance of gut microbiota, causing gut bacteria dysbiosis and correlated to immune disorders along CD, which might not only be developed as effective noninvasive biomarkers but also as therapy targets.
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Affiliation(s)
- Xunchao Cai
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Nan Zhou
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qian Zou
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Yao Peng
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Long Xu
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Lijuan Feng
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China.
| | - Xiaowei Liu
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, 410008, China.
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Cheng T, Xu C, Shao J. Updated immunomodulatory roles of gut flora and microRNAs in inflammatory bowel diseases. Clin Exp Med 2023; 23:1015-1031. [PMID: 36385416 PMCID: PMC9668223 DOI: 10.1007/s10238-022-00935-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 10/27/2022] [Indexed: 11/17/2022]
Abstract
Inflammatory bowel disease is a heterogeneous intestinal inflammatory disorder, including ulcerative colitis (UC) and Crohn's disease (CD). Existing studies have shown that the pathogenesis of IBD is closely related to the host's genetic susceptibility, intestinal flora disturbance and mucosal immune abnormalities, etc. It is generally believed that there are complicated interactions between host immunity and intestinal microflora/microRNAs during the occurrence and progression of IBD. Intestinal flora is mainly composed of bacteria, fungi, viruses and helminths. These commensals are highly implicated in the maintenance of intestinal microenvironment homeostasis alone or in combination. MiRNA is an endogenous non-coding small RNA with a length of 20 to 22 nucleotides, which can perform a variety of biological functions by silencing or activating target genes through complementary pairing bonds. A large quantity of miRNAs are involved in intestinal inflammation, mucosal barrier integrity, autophagy, vesicle transportation and other small RNA alterations in IBD circumstance. In this review, the immunomodulatory roles of gut flora and microRNAs are updated in the occurrence and progression of IBD. Meanwhile, the gut flora and microRNA targeted therapeutic strategies as well as other immunomodulatory approaches including TNF-α monoclonal antibodies are also emphasized in the treatment of IBD.
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Affiliation(s)
- Ting Cheng
- Laboratory of Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 433 Room, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, People's Republic of China
| | - Chen Xu
- Laboratory of Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 433 Room, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, People's Republic of China
| | - Jing Shao
- Laboratory of Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 433 Room, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, People's Republic of China.
- Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, People's Republic of China.
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17
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Lopez LR, Miller CM, Jeyachandran JN, Li C, Simpson KW, Arthur JC. Heterogeneity among Clinical Intestinal Escherichia coli Isolates upon Acquired Streptomycin Resistance. Microbiol Spectr 2023; 11:e0350022. [PMID: 37184392 PMCID: PMC10269711 DOI: 10.1128/spectrum.03500-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/25/2023] [Indexed: 05/16/2023] Open
Abstract
Escherichia coli isolates from inflammatory bowel disease (IBD) patients are often multidrug resistant, including to streptomycin. Streptomycin resistance (StrR) mutations can alter bacterial behavior, which may influence intestinal disease. We generated a spontaneous StrR strain of the intestinal adherent-invasive E. coli (AIEC) strain NC101. Whole-genome sequencing revealed a single missense mutation in rpsL that commonly confers StrR, rpsL-K43N. StrR NC101 exhibited a striking loss of aggregation and significantly increased motility, behaviors that can impact host-microbe interactions. Behavioral changes were associated with reduced transcription of csgA, encoding the biofilm component curli, and increased transcription of fliC, encoding flagellin. Scanning electron microscopy (SEM) detailed morphologic changes consistent with the observed alterations in multicellular behavior. Because intestinal E. coli isolates exhibit remarkable strain-specific differences, we generated spontaneous StrR mutants of 10 clinical E. coli phylotype B2 strains from patients with IBD, colorectal cancer, and urinary tract infection. Out of these 10 StrR clinical strains, two had altered colony morphology on Congo red agar (suggesting changes in extracellular products), and three had significant changes in motility. These changes were not associated with a particular rpsL mutation nor with the presence of virulence genes encoding the inflammation-associated E. coli metabolites yersiniabactin or colibactin. We conclude that common mutations in rpsL, which confer StrR, can differentially alter disease-associated phenotypes across intestinal E. coli strains. These findings highlight the heterogeneity among seemingly similar intestinal E. coli strains and reveal the need to carefully study the strain-specific effects of antibiotic resistance mutations, particularly when using these mutations during strain selection studies. IMPORTANCE We demonstrate that StrR, commonly acquired through a single point mutation in rpsL (a gene encoding part of the 30S bacterial ribosome), strikingly alters the morphology and behavior of a key intestinal AIEC strain, NC101. These changes include remarkably diminished aggregation and significantly increased motility, traits that are linked to AIEC-defining features and disease development. Phenotypic changes were heterogeneous among other StrR clinical E. coli strains, underscoring the need to evaluate the strain-specific effects of commonly acquired antibiotic resistance mutations. This is important, as the results of studies using mutant StrR Enterobacteriaceae strains (e.g., for cloning or in vivo selection) may be confounded beyond our demonstrated effects. Long term, these findings can help researchers better distinguish the contribution of specific E. coli traits to functional changes in the microbiota. Evaluating these strain-level differences could provide insight into the diversity of IBD symptoms and lead to improved therapies for microbiota-driven intestinal disorders.
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Affiliation(s)
- Lacey R. Lopez
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Claire M. Miller
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joanna N. Jeyachandran
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Chuang Li
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kenneth W. Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Janelle C. Arthur
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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18
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Bleich RM, Li C, Sun S, Barlogio CJ, Broberg CA, Franks AR, Bulik-Sullivan E, Dogan B, Simpson KW, Carroll IM, Fodor AA, Arthur JC. A consortia of clinical E. coli strains with distinct in-vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice. RESEARCH SQUARE 2023:rs.3.rs-2899665. [PMID: 37214858 PMCID: PMC10197778 DOI: 10.21203/rs.3.rs-2899665/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in-vitro definition fully predicts mucosal colonization in-vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis. Results Germ-free inflammation-susceptible interleukin-10-deficient (Il10-/-) and inflammation-resistant WT mice were colonized with a consortia of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10-/- mice. These E. coli expand in Il10-/- mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization. Conclusions Our findings establish the in-vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in-vivo colonization dynamics of patient-derived bacteria in murine models.
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Affiliation(s)
| | - Chuang Li
- University of North Carolina at Chapel Hill
| | - Shan Sun
- University of North Carolina at Charlotte
| | | | | | | | | | - Belgin Dogan
- Cornell University College of Veterinary Medicine
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19
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Li L, Peng P, Ding N, Jia W, Huang C, Tang Y. Oxidative Stress, Inflammation, Gut Dysbiosis: What Can Polyphenols Do in Inflammatory Bowel Disease? Antioxidants (Basel) 2023; 12:antiox12040967. [PMID: 37107341 PMCID: PMC10135842 DOI: 10.3390/antiox12040967] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a long-term, progressive, and recurrent intestinal inflammatory disorder. The pathogenic mechanisms of IBD are multifaceted and associated with oxidative stress, unbalanced gut microbiota, and aberrant immune response. Indeed, oxidative stress can affect the progression and development of IBD by regulating the homeostasis of the gut microbiota and immune response. Therefore, redox-targeted therapy is a promising treatment option for IBD. Recent evidence has verified that Chinese herbal medicine (CHM)-derived polyphenols, natural antioxidants, are able to maintain redox equilibrium in the intestinal tract to prevent abnormal gut microbiota and radical inflammatory responses. Here, we provide a comprehensive perspective for implementing natural antioxidants as potential IBD candidate medications. In addition, we demonstrate novel technologies and stratagems for promoting the antioxidative properties of CHM-derived polyphenols, including novel delivery systems, chemical modifications, and combination strategies.
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Affiliation(s)
- Lei Li
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Peilan Peng
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Ning Ding
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Wenhui Jia
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Canhua Huang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yong Tang
- School of Health and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
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20
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Zhang N, Mou D, Li T, Chen Z, Ma C, Liang L, He Q. Integrated analysis reveals important differences in the gut and oropharyngeal microbiota between children with mild and severe hand, foot and mouth disease. Emerg Microbes Infect 2023; 12:2192819. [PMID: 36927539 PMCID: PMC10071984 DOI: 10.1080/22221751.2023.2192819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Little is known about alternation and difference in gut microbiota between patients with mild and severe hand, foot and mouth disease (HFMD). We investigated the differences in gut and oropharynx microbiotas between mild and severe HFMD in young children and changes in bacterial profiles as the disease progresses from acute to convalescent phase. Forty-two patients with confirmed HFMD were studied, among which thirty-two had severe HFMD and ten had mild HFMD. First rectal swabs were collected from all patients at an average of 2 days (acute phase) after the onset of symptoms, and second rectal swabs were collected from 8 severe patients at day 9 (convalescent phase) after the onset. Oropharyngeal swabs were obtained from 10 patients in the acute phase and 6 in the convalescent phase. 16S rRNA sequencing was performed for all 70 samples. Compared with mild HFMD, severe HFMD exhibited significantly decreased diversity and richness of gut microbiota. Gut microbiota bacterial profiles observed in the acute and convalescent phases resembled each other, but differed from those in mild cases. Additionally, 50% of patients with severe HFMD in the acute phase harbored a dominant pathobiontic bacterial genus. However, none of patients with mild HFMD had such bacteria. Similar bacterial compositions in oropharynx microbiota were detected between mild and severe cases. Our findings indicate that severe HFMD exhibits significantly impaired diversity of gut microbiota and frequent gut and oropharyngeal inflammation-inducing bacteria. However, the results should be interpreted with caution as the number of the subjects was limited.
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Affiliation(s)
- Nan Zhang
- Department of Medical Microbiology, Capital Medical University. No. 10 Xi Tou Tiao, You'an Meng Wai, Feng Tai District, Beijing 100069, China (N.Z.: ; Z.C.: )
| | - Danlei Mou
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, No. 8 Xi TouTiao, You'an Men Wai, Feng Tai District, Beijing 100069, China (D.M.: ; T.L.: ; C.M.: ; L.L.: )
| | - Tongzeng Li
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, No. 8 Xi TouTiao, You'an Men Wai, Feng Tai District, Beijing 100069, China (D.M.: ; T.L.: ; C.M.: ; L.L.: )
| | - Zhiyun Chen
- Department of Medical Microbiology, Capital Medical University. No. 10 Xi Tou Tiao, You'an Meng Wai, Feng Tai District, Beijing 100069, China (N.Z.: ; Z.C.: )
| | - Chunhua Ma
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, No. 8 Xi TouTiao, You'an Men Wai, Feng Tai District, Beijing 100069, China (D.M.: ; T.L.: ; C.M.: ; L.L.: )
| | - Lianchun Liang
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, No. 8 Xi TouTiao, You'an Men Wai, Feng Tai District, Beijing 100069, China (D.M.: ; T.L.: ; C.M.: ; L.L.: )
| | - Qiushui He
- Department of Medical Microbiology, Capital Medical University. No. 10 Xi Tou Tiao, You'an Meng Wai, Feng Tai District, Beijing 100069, China (N.Z.: ; Z.C.: ).,Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, Turku 20520, Finland (Q.H.: )
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21
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Jochum SB, Engen PA, Shaikh M, Naqib A, Wilber S, Raeisi S, Zhang L, Song S, Sanzo G, Chouhan V, Ko F, Post Z, Tran L, Ramirez V, Green SJ, Khazaie K, Hayden DM, Brown MJ, Voigt RM, Forsyth CB, Keshavarzian A, Swanson GR. Colonic Epithelial Circadian Disruption Worsens Dextran Sulfate Sodium-Induced Colitis. Inflamm Bowel Dis 2023; 29:444-457. [PMID: 36287037 PMCID: PMC9977234 DOI: 10.1093/ibd/izac219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Indexed: 12/09/2022]
Abstract
BACKGROUND Disruption of central circadian rhythms likely mediated by changes in microbiota and a decrease in gut-derived metabolites like short chain fatty acids (SCFAs) negatively impacts colonic barrier homeostasis. We aimed to explore the effects of isolated peripheral colonic circadian disruption on the colonic barrier in a mouse model of colitis and explore the mechanisms, including intestinal microbiota community structure and function. METHODS Colon epithelial cell circadian rhythms were conditionally genetically disrupted in mice: TS4Cre-BMAL1lox (cBMAL1KO) with TS4Cre as control animals. Colitis was induced through 5 days of 2% dextran sulfate sodium (DSS). Disease activity index and intestinal barrier were assessed, as were fecal microbiota and metabolites. RESULTS Colitis symptoms were worse in mice with peripheral circadian disruption (cBMAL1KO). Specifically, the disease activity index and intestinal permeability were significantly higher in circadian-disrupted mice compared with control animals (TS4Cre) (P < .05). The worsening of colitis appears to be mediated, in part, through JAK (Janus kinase)-mediated STAT3 (signal transducer and activator of transcription 3), which was significantly elevated in circadian-disrupted (cBMAL1KO) mice treated with DSS (P < .05). Circadian-disrupted (cBMAL1KO) mice also had decreased SCFA metabolite concentrations and decreased relative abundances of SCFA-producing bacteria in their stool when compared with control animals (TS4Cre). CONCLUSIONS Disruption of intestinal circadian rhythms in colonic epithelial cells promoted more severe colitis, increased inflammatory mediators (STAT3 [signal transducer and activator of transcription 3]), and decreased gut microbiota-derived SCFAs compared with DSS alone. Further investigation elucidating the molecular mechanisms behind these findings could provide novel circadian directed targets and strategies in the treatment of inflammatory bowel disease.
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Affiliation(s)
- Sarah B Jochum
- Department of Surgery, Rush University Medical Center, Chicago, IL, USA
| | - Phillip A Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
| | - Maliha Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
| | - Ankur Naqib
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
| | - Sherry Wilber
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
| | - Shohreh Raeisi
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
| | - Lijuan Zhang
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
| | - Shiwen Song
- Department of Pathology, GoPath Global Pathology Service, Buffalo Grove, IL, USA
| | - Gabriella Sanzo
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
| | - Vijit Chouhan
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
| | - Frank Ko
- Department of Cell and Molecular Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Zoe Post
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
- Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Laura Tran
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
| | - Vivian Ramirez
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
| | - Stefan J Green
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, IL, USA
| | | | - Dana M Hayden
- Division of Colon and Rectal Surgery, Department of Surgery, Rush University Medical Center, Chicago, IL, USA
| | - Mark J Brown
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Robin M Voigt
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
- Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Christopher B Forsyth
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
- Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
- Department of Medicine, Rush University Medical Center, Chicago, IL, USA
- Department of Physiology, Rush University Medical Center, Chicago, IL, USA
| | - Garth R Swanson
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, IL, USA
- Department of Medicine, Rush University Medical Center, Chicago, IL, USA
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22
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Wang Z, Tan C, Duan C, Wu J, Zhou D, Hou L, Qian W, Han C, Hou X. FUT2-dependent fucosylation of HYOU1 protects intestinal stem cells against inflammatory injury by regulating unfolded protein response. Redox Biol 2023; 60:102618. [PMID: 36724577 PMCID: PMC9923227 DOI: 10.1016/j.redox.2023.102618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 01/30/2023] Open
Abstract
The intestinal epithelial repair after injury is coordinated by intestinal stem cells (ISCs). Fucosylation catalyzed by fucosyltransferase 2 (FUT2) of the intestinal epithelium is beneficial to mucosal healing but poorly defined is the influence on ISCs. The dextran sulfate sodium (DSS) and lipopolysaccharide (LPS) model were used to assess the role of FUT2 on ISCs after injury. The apoptosis, function, and stemness of ISCs were analyzed using intestinal organoids from WT and Fut2ΔISC (ISC-specific Fut2 knockout) mice incubated with LPS and fucose. N-glycoproteomics, UEA-1 chromatography, and site-directed mutagenesis were monitored to dissect the regulatory mechanism, identify the target fucosylated protein and the corresponding modification site. Fucose could alleviate intestinal epithelial damage via upregulating FUT2 and α-1,2-fucosylation of ISCs. Oxidative stress, mitochondrial dysfunction, and cell apoptosis were impeded by fucose. Meanwhile, fucose sustained the growth and proliferation capacity of intestinal organoids treated with LPS. Contrarily, FUT2 depletion in ISCs aggravated the epithelial damage and disrupted the growth and proliferation capacity of ISCs via escalating LPS-induced endoplasmic reticulum (ER) stress and initiating the IRE1/TRAF2/ASK1/JNK branch of unfolded protein response (UPR). Fucosylation of the chaperone protein HYOU1 at the N-glycosylation site of asparagine (Asn) 862 mediated by FUT2 was identified to facilitate ISCs survival and self-renewal, and improve ISCs resistance to ER stress and inflammatory injury. Our study highlights a fucosylation-dependent protective mechanism of ISCs against inflammation, which may provide a fascinating strategy for treating intestinal injury disorders.
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Affiliation(s)
| | | | | | | | | | | | | | - Chaoqun Han
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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23
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Elson CO. Adherent invasive Escherichia coli in Crohn's disease: guilt by association? Gut 2023; 72:2-3. [PMID: 35676086 DOI: 10.1136/gutjnl-2022-327342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/22/2022] [Indexed: 02/04/2023]
Affiliation(s)
- Charles O Elson
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
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24
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Larabi AB, Masson HLP, Bäumler AJ. Bile acids as modulators of gut microbiota composition and function. Gut Microbes 2023; 15:2172671. [PMID: 36740850 PMCID: PMC9904317 DOI: 10.1080/19490976.2023.2172671] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
Changes in the composition of gut-associated microbial communities are associated with many human illnesses, but the factors driving dysbiosis remain incompletely understood. One factor governing the microbiota composition in the gut is bile. Bile acids shape the microbiota composition through their antimicrobial activity and by activating host signaling pathways that maintain gut homeostasis. Although bile acids are host-derived, their functions are integrally linked to bacterial metabolism, which shapes the composition of the intestinal bile acid pool. Conditions that change the size or composition of the bile acid pool can trigger alterations in the microbiota composition that exacerbate inflammation or favor infection with opportunistic pathogens. Therefore, manipulating the composition or size of the bile acid pool might be a promising strategy to remediate dysbiosis.
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Affiliation(s)
- Anaïs B. Larabi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Hugo L. P. Masson
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
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25
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Xu Y, Qian W, Huang L, Wen W, Li Y, Guo F, Zhu Z, Li Z, Gong J, Yu Z, Zhou Y, Lu N, Zhu W, Guo Z. Crohn's disease-associated AIEC inhibiting intestinal epithelial cell-derived exosomal let-7b expression regulates macrophage polarization to exacerbate intestinal fibrosis. Gut Microbes 2023; 15:2193115. [PMID: 36945126 PMCID: PMC10038049 DOI: 10.1080/19490976.2023.2193115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
The interaction between adherent-invasive Escherichia coli (AIEC) and intestinal macrophages is implicated in the pathogenesis of Crohn's disease (CD). However, its role in intestinal fibrogenesis and the underlying molecular mechanisms are poorly understood. In addition, miRNAs such as let-7b may participate in AIEC-macrophage interactions. In this study, we identified that the colonization of AIEC in the ileum was associated with enhanced intestinal fibrosis and reduced let-7b expression by enrolling a prospective cohort of CD patients undergoing ileocolectomy. Besides, AIEC-infected IL-10-/- mice presented more severe intestinal fibrosis and could be improved by exogenous let-7b. Mechanistically, intestinal macrophages were found to be the main target of let-7b. Transferring let-7b-overexpressing macrophages to AIEC-infected IL-10-/- mice significantly alleviated intestinal fibrosis. In vitro, AIEC suppressed exosomal let-7b derived from intestinal epithelial cells (IECs), instead of the direct inhibition of let-7b in macrophages, to promote macrophages to a fibrotic phenotype. Finally, TGFβR1 was identified as one target of let-7b that regulates macrophage polarization. Overall, the results of our work indicate that AIEC is associated with enhanced intestinal fibrosis in CD. AIEC could inhibit exosomal let-7b from IECs to promote intestinal macrophages to a fibrotic phenotype and then contributed to fibrogenesis. Thus, anti-AIEC or let-7b therapy may serve as novel therapeutic approaches to ameliorate intestinal fibrosis.
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Affiliation(s)
- Yihan Xu
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wenwei Qian
- Department of General Surgery, Jinling Hospital, Medical School of Southeast University, Nanjing, China
| | - Liangyu Huang
- Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Weiwei Wen
- Department of General Surgery, Jinling Hospital, Medical School of Southeast University, Nanjing, China
| | - Yi Li
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Feilong Guo
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zhenxing Zhu
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zhun Li
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jianfeng Gong
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zeqian Yu
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yan Zhou
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Nan Lu
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Weiming Zhu
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zhen Guo
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
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26
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Feofanova NA, Bets VD, Borisova MA, Litvinova EA. L-fucose reduces gut inflammation due to T-regulatory response in Muc2 null mice. PLoS One 2022; 17:e0278714. [PMID: 36584066 PMCID: PMC9803192 DOI: 10.1371/journal.pone.0278714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/21/2022] [Indexed: 12/31/2022] Open
Abstract
Fucose, the terminal glycan of the intestinal glycoprotein Mucin2, was shown to have an anti-inflammatory effect in mouse colitis models and modulate immune response due to macrophage polarization changes. In this study we evaluated the effect of 0.05% L-fucose supplementation of drinking water on immune parameters in the intestine of homozygous mutant Muc2-/-, compared to Muc2+/+ mice. To get into innate and adaptive immunity mechanisms of gut inflammation, we tested PrkdcSCIDMuc2-/- strain, Muc2 knockout on SCID background, that is characterized by lack of lymphocytes, in comparison with PrkdcSCID mice. We evaluated intestinal cytokine profiling, macrophage and eosinophil infiltration, and expression of Nos2 and Arg1 markers of macrophage activation in all strains. Markers of Th1, Treg and Th17 cells (Tbx21, Foxp3, and Rorc expression) were evaluated in Muc2-/- and Muc2+/+ mice. Both Muc2-/- and PrkdcSCIDMuc2-/- mice demonstrated increased numbers of macrophages, eosinophils, elevated levels of TNFa, GM-CSF, and IL-10 cytokines. In Muc2-/- mice we observed a wide range of pro-inflammatory cytokines elevated, such as IFN-gamma, IL-1b, IL-12p70, IL-6, M-CSF, G-CSF, IL-17, MCP-1, RANTES, MIP1b, MIP2. Muc2-/- mice demonstrated increase of Nos2, Tbx21 and Foxp3 genes mRNA, while in PrkdcSCIDMuc2-/- mice Arg1 expression was increased. We found that in Muc2-/- mice L-fucose reduced macrophage infiltration and IL-1a, TNFa, IFNgamma, IL-6, MCP-1, RANTES, MIP1b levels, decreased Nos2 expression, and induced the expression of Treg marker Foxp3 gene. On the contrary, in PrkdcSCIDMuc2-/- mice L-fucose had no effect on macrophage and eosinophil numbers, but increased TNFa, GM-CSF, IL-12p70, IL-6, IL-15, IL-10, MCP1, G-CSF, IL-3 levels and Nos2 gene expression, and decreased Arg1 gene expression. We demonstrated that anti-inflammatory effect of L-fucose observed in Muc2-/- mice is not reproduced in PrkdcSCIDMuc2-/-, which lack lymphocytes. We conclude that activation of Treg cells is a key event that leads to resolution of inflammation upon L-fucose supplementation in Muc2-/- mice.
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Affiliation(s)
- Natalia A. Feofanova
- Research Institute of Fundamental and Clinical Immunology, Novosibirsk, Russia
- Research Institute of Neurosciences and Medicine, Novosibirsk, Russia
- * E-mail:
| | - Victoria D. Bets
- Faculty of Physical Engineering, Novosibirsk State Technical University, Novosibirsk, Russia
| | - Mariya A. Borisova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Ekaterina A. Litvinova
- Research Institute of Neurosciences and Medicine, Novosibirsk, Russia
- Faculty of Physical Engineering, Novosibirsk State Technical University, Novosibirsk, Russia
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27
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Liang B, Wu C, Wang C, Sun W, Chen W, Hu X, Liu N, Xing D. New insights into bacterial mechanisms and potential intestinal epithelial cell therapeutic targets of inflammatory bowel disease. Front Microbiol 2022; 13:1065608. [PMID: 36590401 PMCID: PMC9802581 DOI: 10.3389/fmicb.2022.1065608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
The global incidence of inflammatory bowel disease (IBD) has increased rapidly in recent years, but its exact etiology remains unclear. In the past decade, IBD has been reported to be associated with dysbiosis of gut microbiota. Although not yet proven to be a cause or consequence of IBD, the common hypothesis is that at least some alterations in the microbiome are protective or pathogenic. Furthermore, intestinal epithelial cells (IECs) serve as a protective physical barrier for gut microbiota, essential for maintaining intestinal homeostasis and actively contributes to the mucosal immune system. Thus, dysregulation within the intestinal epithelium increases intestinal permeability, promotes the entry of bacteria, toxins, and macromolecules, and disrupts intestinal immune homeostasis, all of which are associated with the clinical course of IBD. This article presents a selective overview of recent studies on bacterial mechanisms that may be protective or promotive of IBD in biological models. Moreover, we summarize and discuss the recent discovery of key modulators and signaling pathways in the IECs that could serve as potential IBD therapeutic targets. Understanding the role of the IECs in the pathogenesis of IBD may help improve the understanding of the inflammatory process and the identification of potential therapeutic targets to help ameliorate this increasingly common disease.
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Affiliation(s)
- Bing Liang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Changhao Wu
- Department of Biochemistry and Physiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Chao Wang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenshe Sun
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wujun Chen
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaokun Hu
- Intervention Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ning Liu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China,*Correspondence: Ning Liu, ; Dongming Xing,
| | - Dongming Xing
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao, China,School of Life Sciences, Tsinghua University, Beijing, China,*Correspondence: Ning Liu, ; Dongming Xing,
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28
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Zhao C, Hu X, Bao L, Wu K, Zhao Y, Xiang K, Li S, Wang Y, Qiu M, Feng L, Meng X, Zhang N, Fu Y. Gut dysbiosis induces the development of mastitis through a reduction in host anti-inflammatory enzyme activity by endotoxemia. MICROBIOME 2022; 10:205. [PMID: 36451232 PMCID: PMC9714159 DOI: 10.1186/s40168-022-01402-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/24/2022] [Indexed: 05/26/2023]
Abstract
BACKGROUND Mounting experimental evidence has shown that the gut microbiota plays a significant role in the pathogenesis of mastitis, and clinical investigations have found that the occurrence of mastitis is correlated with ruminal dysbiosis. However, the underlying mechanism by which the ruminal microbiota participates in the development of mastitis remains unknown. RESULTS In the present study, we found that cows with clinical mastitis had marked systemic inflammation, which was associated with significant ruminal dysbiosis, especially enriched Proteobacteria in the rumen. Ruminal microbiota transplantation from mastitis cows (M-RMT) to mice induced mastitis symptoms in recipient mice along with increased mammary proinflammatory signature activation of the TLR4-cGAS-STING-NF-κB/NLRP3 pathways. M-RMT also induced mucosal inflammation and impaired intestinal barrier integrity, leading to increased endotoxemia and systemic inflammation. Moreover, we showed that M-RMT mirrored ruminal microbiota disruption in the gut of recipient mice, as evidenced by enriched Proteobacteria and similar bacterial functions, which were correlated with most proinflammatory parameters and serum lipopolysaccharide (LPS) levels in mice. Recurrent low-grade LPS treatment mirrored gut dysbiosis-induced endotoxemia and caused severe mastitis in mice. Furthermore, we found that gut dysbiosis-derived LPS reduced host alkaline phosphatase activity by activating neuraminidase (Neu), which facilitates low-grade LPS exposure and E. coli-induced mastitis in mice. Conversely, treatment with calf intestinal alkaline phosphatase or the Neu inhibitor zanamivir alleviated low-grade LPS exposure and E. coli-induced mastitis in mice. CONCLUSIONS Our results suggest that ruminal dysbiosis-derived low-grade endotoxemia can cause mastitis and aggravate pathogen-induced mastitis by impairing host anti-inflammatory enzymes, which implies that regulating the ruminal or gut microbiota to prevent low-grade systemic inflammation is a potential strategy for mastitis intervention. Video Abstract.
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Affiliation(s)
- Caijun Zhao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Xiaoyu Hu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Lijuan Bao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Keyi Wu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Yihong Zhao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Kaihe Xiang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Shuang Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Ying Wang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Min Qiu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Lianjun Feng
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Xiangyue Meng
- Department of Breast Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Naisheng Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China
| | - Yunhe Fu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin Province, China.
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29
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Cummins EA, Hall RJ, Connor C, McInerney JO, McNally A. Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types. Microb Genom 2022; 8:mgen000903. [PMID: 36748558 PMCID: PMC9836092 DOI: 10.1099/mgen.0.000903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E. coli sequence type pangenomes using comparative pangenomics to identify variance in both pangenome structure and content. We present functional breakdowns of sequence type core genomes and identify sequence types that are enriched in metabolism, transcription and cell membrane biogenesis genes. We also uncover metabolism genes that have variable core classification, depending on which allele is present. Our comparative pangenomics approach allows for detailed exploration of sequence type pangenomes within the context of the species. We show that ongoing gene gain and loss in the E. coli pangenome is sequence type-specific, which may be a consequence of distinct sequence type-specific evolutionary drivers.
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Affiliation(s)
- Elizabeth A. Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J. Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Chris Connor
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK,Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia
| | - James O. McInerney
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK,*Correspondence: Alan McNally,
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30
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Zheng L, Duan SL, Dai YC, Wu SC. Role of adherent invasive Escherichia coli in pathogenesis of inflammatory bowel disease. World J Clin Cases 2022; 10:11671-11689. [PMID: 36405271 PMCID: PMC9669839 DOI: 10.12998/wjcc.v10.i32.11671] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/04/2022] [Accepted: 10/11/2022] [Indexed: 02/05/2023] Open
Abstract
Gut microbiota imbalances play an important role in inflammatory bowel disease (IBD), but no single pathogenic microorganism critical to IBD that is specific to the IBD terminal ileum mucosa or can invade intestinal epithelial cells has been found. Invasive Escherichia coli (E. coli) adhesion to macrophages is considered to be closely related to the pathogenesis of inflammatory bowel disease. Further study of the specific biological characteristics of adherent invasive E. coli (AIEC) may contribute to a further understanding of IBD pathogenesis. This review explores the relationship between AIEC and the intestinal immune system, discusses the prevalence and relevance of AIEC in Crohn's disease and ulcerative colitis patients, and describes the relationship between AIEC and the disease site, activity, and postoperative recurrence. Finally, we highlight potential therapeutic strategies to attenuate AIEC colonization in the intestinal mucosa, including the use of phage therapy, antibiotics, and anti-adhesion molecules. These strategies may open up new avenues for the prevention and treatment of IBD in the future.
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Affiliation(s)
- Lie Zheng
- Department of Gastroenterology, Shaanxi Provincial Hospital of Traditional Chinese Medicine, Xi’an 322000, Shaanxi Province, China
| | - Sheng-Lei Duan
- Department of Gastroenterology, Shaanxi Provincial Hospital of Traditional Chinese Medicine, Xi’an 322000, Shaanxi Province, China
| | - Yan-Cheng Dai
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Shi-Cheng Wu
- Department of Proctology, Gansu Academy of Traditional Chinese Medicine, Gansu Hospital of Traditional Chinese Medicine, Lanzhou 730050, Gansu Province, China
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31
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Viladomiu M, Khounlotham M, Dogan B, Lima SF, Elsaadi A, Cardakli E, Castellanos JG, Ng C, Herzog J, Schoenborn AA, Ellermann M, Liu B, Zhang S, Gulati AS, Sartor RB, Simpson KW, Lipkin SM, Longman RS. Agr2-associated ER stress promotes adherent-invasive E. coli dysbiosis and triggers CD103 + dendritic cell IL-23-dependent ileocolitis. Cell Rep 2022; 41:111637. [PMID: 36384110 PMCID: PMC9805753 DOI: 10.1016/j.celrep.2022.111637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/06/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Endoplasmic reticulum (ER) stress is associated with Crohn's disease (CD), but its impact on host-microbe interaction in disease pathogenesis is not well defined. Functional deficiency in the protein disulfide isomerase anterior gradient 2 (AGR2) has been linked with CD and leads to epithelial cell ER stress and ileocolitis in mice and humans. Here, we show that ileal expression of AGR2 correlates with mucosal Enterobactericeae abundance in human inflammatory bowel disease (IBD) and that Agr2 deletion leads to ER-stress-dependent expansion of mucosal-associated adherent-invasive Escherichia coli (AIEC), which drives Th17 cell ileocolitis in mice. Mechanistically, our data reveal that AIEC-induced epithelial cell ER stress triggers CD103+ dendritic cell production of interleukin-23 (IL-23) and that IL-23R is required for ileocolitis in Agr2-/- mice. Overall, these data reveal a specific and reciprocal interaction of the expansion of the CD pathobiont AIEC with ER-stress-associated ileocolitis and highlight a distinct cellular mechanism for IL-23-dependent ileocolitis.
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Affiliation(s)
- Monica Viladomiu
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Manirath Khounlotham
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Belgin Dogan
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Svetlana F. Lima
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ahmed Elsaadi
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Emre Cardakli
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jim G. Castellanos
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Charles Ng
- Department of Pathology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jeremy Herzog
- Departments of Medicine and Microbiology and Immunology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexi A. Schoenborn
- Department of Pediatrics, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Melissa Ellermann
- Departments of Medicine and Microbiology and Immunology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Present address: Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Bo Liu
- Departments of Medicine and Microbiology and Immunology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shiying Zhang
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ajay S. Gulati
- Department of Pediatrics, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - R. Balfour Sartor
- Departments of Medicine and Microbiology and Immunology, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenneth W. Simpson
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA,College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Steven M. Lipkin
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA,Correspondence: (S.M.L.), (R.S.L.)
| | - Randy S. Longman
- Department of Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA,Jill Roberts Center for IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA,Lead contact,Correspondence: (S.M.L.), (R.S.L.)
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Geurtsen J, de Been M, Weerdenburg E, Zomer A, McNally A, Poolman J. Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiol Rev 2022; 46:6617594. [PMID: 35749579 PMCID: PMC9629502 DOI: 10.1093/femsre/fuac031] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
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Affiliation(s)
- Jeroen Geurtsen
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | - Mark de Been
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | | | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, the Netherlands
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Jan Poolman
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
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Dubinsky V, Reshef L, Rabinowitz K, Wasserberg N, Dotan I, Gophna U. Escherichia coli Strains from Patients with Inflammatory Bowel Diseases have Disease-specific Genomic Adaptations. J Crohns Colitis 2022; 16:1584-1597. [PMID: 35560165 DOI: 10.1093/ecco-jcc/jjac071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIMS Escherichia coli is over-abundant in the gut microbiome of patients with inflammatory bowel disease [IBD]. Here, we aimed to identify IBD-specific genomic functions of diverse E. coli lineages. METHODS We investigated E. coli genomes from patients with ulcerative colitis [UC], Crohn's disease [CD] or a pouch, and healthy subjects. The majority of genomes were reconstructed from metagenomic samples, including newly sequenced faecal metagenomes. Clinical metadata were collected. Functional analysis at the gene and mutation level were performed and integrated with IBD phenotypes and biomarkers. RESULTS Overall, 530 E. coli genomes were analysed. The E. coli B2 lineage was more prevalent in UC compared with other IBD phenotypes. Genomic metabolic capacities varied across E. coli lineages and IBD phenotypes. Host mucin utilisation enzymes were present in a single lineage and depleted in patients with a pouch, whereas those involved in inulin hydrolysis were enriched in patients with a pouch. E. coli strains from patients with UC were twice as likely to encode the genotoxic molecule colibactin than strains from patients with CD or a pouch. Strikingly, patients with a pouch showed the highest inferred E. coli growth rates, even in the presence of antibiotics. Faecal calprotectin did not correlate with the relative abundance of E. coli. Finally, we identified multiple IBD-specific non-synonymous mutations in E. coli genes encoding for bacterial cell envelope components. CONCLUSIONS Comparative genomics indicates that E. coli is a commensal species adapted to the overactive mucosal immune milieu in IBD, rather than causing it. Our results reveal mutations that may lead to attenuated antigenicity in some E. coli strains.
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Affiliation(s)
- Vadim Dubinsky
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Leah Reshef
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Keren Rabinowitz
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Nir Wasserberg
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel.,Colorectal Unit, Division of Surgery, Rabin Medical Center, Petah-Tikva, Israel
| | - Iris Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Uri Gophna
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
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34
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Characterization and comparative transcriptome analyses of Salmonella enterica Enteritidis strains possessing different chlorine tolerance profiles. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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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] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/03/2022] [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 Technology, 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 Technology, Cambridge, Massachusetts, USA
| | - Wilma Neumann
- Department of Chemistry, Massachusetts Institute of Technology, 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 Technology, 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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36
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Gao J, Zhao X, Hu S, Huang Z, Hu M, Jin S, Lu B, Sun K, Wang Z, Fu J, Weersma RK, He X, Zhou H. Gut microbial DL-endopeptidase alleviates Crohn's disease via the NOD2 pathway. Cell Host Microbe 2022; 30:1435-1449.e9. [PMID: 36049483 DOI: 10.1016/j.chom.2022.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/10/2022] [Accepted: 08/03/2022] [Indexed: 12/13/2022]
Abstract
The pattern-recognition receptor NOD2 senses bacterial muropeptides to regulate host immunity and maintain homeostasis. Loss-of-function mutations in NOD2 are associated with Crohn's disease (CD), but how the variations in microbial factors influence NOD2 signaling and host pathology is elusive. We demonstrate that the Firmicutes peptidoglycan remodeling enzyme, DL-endopeptidase, increased the NOD2 ligand level in the gut and impacted colitis outcomes. Metagenomic analyses of global cohorts (n = 857) revealed that DL-endopeptidase gene abundance decreased globally in CD patients and negatively correlated with colitis. Fecal microbiota from CD patients with low DL-endopeptidase activity predisposed mice to colitis. Administering DL-endopeptidase, but not an active site mutant, alleviated colitis via the NOD2 pathway. Therapeutically restoring NOD2 ligands with a DL-endopeptidase-producing Lactobacillus salivarius strain or mifamurtide, a clinical analog of muramyl dipeptide, exerted potent anti-colitis effects. Our study suggests that the depletion of DL-endopeptidase contributes to CD pathogenesis through NOD2 signaling, providing a therapeutically modifiable target.
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Affiliation(s)
- Jie Gao
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510655, China
| | - Xinmei Zhao
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, the Netherlands
| | - Zhenhe Huang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510655, China
| | - Mengyao Hu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510655, China
| | - Shaoqin Jin
- Department of Gastroenterology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Bingyun Lu
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518101, China
| | - Kai Sun
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong 510515, China
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, the Netherlands.
| | - Xiaolong He
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510655, China; Department of Microbiology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China.
| | - Hongwei Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510655, China; State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, Guangdong 510515, China.
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Gill T, Stauffer P, Asquith M, Laderas T, Martin TM, Davin S, Schleisman M, Ramirez C, Ogle K, Lindquist I, Nguyen J, Planck SR, Shaut C, Diamond S, Rosenbaum JT, Karstens L. Axial spondyloarthritis patients have altered mucosal IgA response to oral and fecal microbiota. Front Immunol 2022; 13:965634. [PMID: 36248884 PMCID: PMC9556278 DOI: 10.3389/fimmu.2022.965634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
Axial spondyloarthritis (axSpA) is an inflammatory arthritis involving the spine and the sacroiliac joint with extra-articular manifestations in the eye, gut, and skin. The intestinal microbiota has been implicated as a central environmental component in the pathogenesis of various types of spondyloarthritis including axSpA. Additionally, alterations in the oral microbiota have been shown in various rheumatological conditions, such as rheumatoid arthritis (RA). Therefore, the aim of this study was to investigate whether axSpA patients have an altered immunoglobulin A (IgA) response in the gut and oral microbial communities. We performed 16S rRNA gene (16S) sequencing on IgA positive (IgA+) and IgA negative (IgA-) fractions (IgA-SEQ) from feces (n=17 axSpA; n=14 healthy) and saliva (n=14 axSpA; n=12 healthy), as well as on IgA-unsorted fecal and salivary samples. PICRUSt2 was used to predict microbial metabolic potential in axSpA patients and healthy controls (HCs). IgA-SEQ analyses revealed enrichment of several microbes in the fecal (Akkermansia, Ruminococcaceae, Lachnospira) and salivary (Prevotellaceae, Actinobacillus) microbiome in axSpA patients as compared with HCs. Fecal microbiome from axSpA patients showed a tendency towards increased alpha diversity in IgA+ fraction and decreased diversity in IgA- fraction in comparison with HCs, while the salivary microbiome exhibits a significant decrease in alpha diversity in both IgA+ and IgA- fractions. Increased IgA coating of Clostridiales Family XIII in feces correlated with disease severity. Inferred metagenomic analysis suggests perturbation of metabolites and metabolic pathways for inflammation (oxidative stress, amino acid degradation) and metabolism (propanoate and butanoate) in axSpA patients. Analyses of fecal and salivary microbes from axSpA patients reveal distinct populations of immunoreactive microbes compared to HCs using the IgA-SEQ approach. These bacteria were not identified by comparing their relative abundance alone. Predictive metagenomic analysis revealed perturbation of metabolites/metabolic pathways in axSpA patients. Future studies on these immunoreactive microbes may lead to better understanding of the functional role of IgA in maintaining microbial structure and human health.
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Affiliation(s)
- Tejpal Gill
- Division of Arthritis and Rheumatic Diseases, Department of Medicine, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Tejpal Gill,
| | - Patrick Stauffer
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Mark Asquith
- Division of Arthritis and Rheumatic Diseases, Department of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Ted Laderas
- Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
| | - Tammy M. Martin
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, United States
| | - Sean Davin
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Matthew Schleisman
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Claire Ramirez
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Kimberly Ogle
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Ingrid Lindquist
- Division of Arthritis and Rheumatic Diseases, Department of Medicine, Oregon Health & Science University, Portland, OR, United States
- Department of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Justine Nguyen
- Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
| | - Stephen R. Planck
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Carley Shaut
- Laboratory of Immunogenetics, Oregon Health & Science University, Portland, OR, United States
| | - Sarah Diamond
- Department of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - James T. Rosenbaum
- Division of Arthritis and Rheumatic Diseases, Department of Medicine, Oregon Health & Science University, Portland, OR, United States
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
- Department of Cell Biology, Oregon Health & Science University, Portland, OR, United States
- Legacy Devers Eye Institute, Portland, OR, United States
| | - Lisa Karstens
- Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
- Division of Urogynecology, Department of Obstetrics and Gynecology Oregon Health & Science University, Portland, OR, United States
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Traditional Chinese Medicine Regulates Th17/Treg Balance in Treating Inflammatory Bowel Disease. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:6275136. [PMID: 36159571 PMCID: PMC9499767 DOI: 10.1155/2022/6275136] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/20/2022] [Indexed: 01/30/2023]
Abstract
Inflammatory bowel disease (IBD), also known as chronic nonspecific inflammatory disease of the colon and rectum, is primarily characterized by mucopurulent bloody stools, diarrhea, abdominal pain, and tenesmus. Its cause is uncertain. IBD patients frequently experience a high rate of recurrence, a protracted treatment course, and a high risk of carcinogenesis. Additionally, the difficulty of treatment is significantly increased by these illness characteristics. Currently, the normal treatment for this illness can lessen symptoms to some amount and even meet clinical treatment requirements, but due to serious side effects, unfavorable reactions, and high costs, we need to develop better complementary and alternative medicines. A number of studies have found that the imbalance of T helper cell 17 (Th17)/regulatory T cells (Treg) contributes significantly to the occurrence and progression of IBD and that Th17/Treg balance restoration is frequently useful in the management of IBD. As a result, regulating the Th17/Treg balance has also emerged as a novel approach to treating IBD. Traditional Chinese medicine (TCM) has gained popularity in recent years due to its advantages of low side effects, a variety of targets, and multiple regulatory mechanisms. A number of studies have shown that TCM can successfully intervene in the Th17/Treg imbalance and restore it, and research on the prevention and treatment of IBD by TCM by restoring Th17/Treg has also shown promising results. The characteristics of the Th17/Treg balance and its role in the pathogenesis of IBD, as well as the role of TCM in regulating the Th17/Treg imbalance, are analyzed. The research results are expected to provide a theoretical basis for the clinical treatment and pathology mechanism research of IBD.
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Crohn’s Disease, Host–Microbiota Interactions, and Immunonutrition: Dietary Strategies Targeting Gut Microbiome as Novel Therapeutic Approaches. Int J Mol Sci 2022; 23:ijms23158361. [PMID: 35955491 PMCID: PMC9369148 DOI: 10.3390/ijms23158361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Crohn’s disease (CD) is a complex, disabling, idiopathic, progressive, and destructive disorder with an unknown etiology. The pathogenesis of CD is multifactorial and involves the interplay between host genetics, and environmental factors, resulting in an aberrant immune response leading to intestinal inflammation. Due to the high morbidity and long-term management of CD, the development of non-pharmacological approaches to mitigate the severity of CD has recently attracted great attention. The gut microbiota has been recognized as an important player in the development of CD, and general alterations in the gut microbiome have been established in these patients. Thus, the gut microbiome has emerged as a pre-eminent target for potential new treatments in CD. Epidemiological and interventional studies have demonstrated that diet could impact the gut microbiome in terms of composition and functionality. However, how specific dietary strategies could modulate the gut microbiota composition and how this would impact host–microbe interactions in CD are still unclear. In this review, we discuss the most recent knowledge on host–microbe interactions and their involvement in CD pathogenesis and severity, and we highlight the most up-to-date information on gut microbiota modulation through nutritional strategies, focusing on the role of the microbiota in gut inflammation and immunity.
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40
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Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H, Hoostal M, McCarthy C, Rosevelt A, Muraleedharan CK, Gillilland MG, Imai J, Omi M, Bishu S, Kao JY, Alteri CJ, Barnich N, Schmidt TM, Nusrat A, Inohara N, Golob JL, Kamada N. Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction. Cell Rep 2022; 40:111093. [PMID: 35858565 PMCID: PMC10903618 DOI: 10.1016/j.celrep.2022.111093] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/26/2022] [Accepted: 06/21/2022] [Indexed: 12/26/2022] Open
Abstract
Pathobionts employ unique metabolic adaptation mechanisms to maximize their growth in disease conditions. Adherent-invasive Escherichia coli (AIEC), a pathobiont enriched in the gut mucosa of patients with inflammatory bowel disease (IBD), utilizes diet-derived L-serine to adapt to the inflamed gut. Therefore, the restriction of dietary L-serine starves AIEC and limits its fitness advantage. Here, we find that AIEC can overcome this nutrient limitation by switching the nutrient source from the diet to the host cells in the presence of mucolytic bacteria. During diet-derived L-serine restriction, the mucolytic symbiont Akkermansia muciniphila promotes the encroachment of AIEC to the epithelial niche by degrading the mucus layer. In the epithelial niche, AIEC acquires L-serine from the colonic epithelium and thus proliferates. Our work suggests that the indirect metabolic network between pathobionts and commensal symbionts enables pathobionts to overcome nutritional restriction and thrive in the gut.
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Affiliation(s)
- Kohei Sugihara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sho Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Prakaimuk Saraithong
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Hiroko Nagao-Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Matthew Hoostal
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Caroline McCarthy
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra Rosevelt
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Merritt G Gillilland
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jin Imai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Maiko Omi
- Department of Biologic and Materials Sciences and Prosthodontics, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Shrinivas Bishu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John Y Kao
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Nicolas Barnich
- M2iSH, UMR1071 Inserm/University Clermont Auvergne, Clermont-Ferrand, France
| | - Thomas M Schmidt
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Asma Nusrat
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Naohiro Inohara
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan L Golob
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
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41
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Lopez LR, Ahn JH, Alves T, Arthur JC. Microenvironmental Factors that Shape Bacterial Metabolites in Inflammatory Bowel Disease. Front Cell Infect Microbiol 2022; 12:934619. [PMID: 35959366 PMCID: PMC9362432 DOI: 10.3389/fcimb.2022.934619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a significant global health problem that involves chronic intestinal inflammation and can involve severe comorbidities, including intestinal fibrosis and inflammation-associated colorectal cancer (CRC). Disease-associated alterations to the intestinal microbiota often include fecal enrichment of Enterobacteriaceae, which are strongly implicated in IBD development. This dysbiosis of intestinal flora accompanies changes in microbial metabolites, shaping host:microbe interactions and disease risk. While there have been numerous studies linking specific bacterial taxa with IBD development, our understanding of microbial function in the context of IBD is limited. Several classes of microbial metabolites have been directly implicated in IBD disease progression, including bacterial siderophores and genotoxins. Yet, our microbiota still harbors thousands of uncharacterized microbial products. In-depth discovery and characterization of disease-associated microbial metabolites is necessary to target these products in IBD treatment strategies. Towards improving our understanding of microbiota metabolites in IBD, it is important to recognize how host relevant factors influence microbiota function. For example, changes in host inflammation status, metal availability, interbacterial community structure, and xenobiotics all play an important role in shaping gut microbial ecology. In this minireview, we outline how each of these factors influences gut microbial function, with a specific focus on IBD-associated Enterobacteriaceae metabolites. Importantly, we discuss how altering the intestinal microenvironment could improve the treatment of intestinal inflammation and associated disorders, like intestinal fibrosis and CRC.
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Affiliation(s)
- Lacey R. Lopez
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ju-Hyun Ahn
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Tomaz Alves
- Division of Comprehensive Oral Health, Adams School of Dentistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Janelle C. Arthur
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Gastrointestinal Biology and Disease, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: Janelle C. Arthur,
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42
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Abstract
Changes in the composition of the gut microbiota are associated with many human diseases. So far, however, we have failed to define homeostasis or dysbiosis by the presence or absence of specific microbial species. The composition and function of the adult gut microbiota is governed by diet and host factors that regulate and direct microbial growth. The host delivers oxygen and nitrate to the lumen of the small intestine, which selects for bacteria that use respiration for energy production. In the colon, by contrast, the host limits the availability of oxygen and nitrate, which results in a bacterial community that specializes in fermentation for growth. Although diet influences microbiota composition, a poor diet weakens host control mechanisms that regulate the microbiota. Hence, quantifying host parameters that control microbial growth could help define homeostasis or dysbiosis and could offer alternative strategies to remediate dysbiosis.
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Affiliation(s)
- Jee-Yon Lee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Renée M Tsolis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA 95616, USA
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43
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Zhang S, Morgan XC, Dogan B, Martin FP, Strickler SR, Oka A, Herzog J, Liu B, Dowd SE, Huttenhower C, Pichaud M, Dogan EI, Satsangi J, Longman R, Yantiss R, Mueller LA, Scherl E, Sartor RB, Simpson KW. Mucosal metabolites fuel the growth and virulence of E. coli linked to Crohn's disease. JCI Insight 2022; 7:157013. [PMID: 35413017 PMCID: PMC9220930 DOI: 10.1172/jci.insight.157013] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
Elucidating how resident enteric bacteria interact with their hosts to promote health or inflammation is of central importance to diarrheal and inflammatory bowel diseases across species. Here, we integrated the microbial and chemical microenvironment of a patient’s ileal mucosa with their clinical phenotype and genotype to identify factors favoring the growth and virulence of adherent and invasive E. coli (AIEC) linked to Crohn’s disease. We determined that the ileal niche of AIEC was characterized by inflammation, dysbiosis, coculture of Enterococcus, and oxidative stress. We discovered that mucosal metabolites supported general growth of ileal E. coli, with a selective effect of ethanolamine on AIEC that was augmented by cometabolism of ileitis-associated amino acids and glutathione and by symbiosis-associated fucose. This metabolic plasticity was facilitated by the eut and pdu microcompartments, amino acid metabolism, γ-glutamyl-cycle, and pleiotropic stress responses. We linked metabolism to virulence and found that ethanolamine and glutamine enhanced AIEC motility, infectivity, and proinflammatory responses in vitro. We connected use of ethanolamine to intestinal inflammation and L-fuculose phosphate aldolase (fucA) to symbiosis in AIEC monoassociated IL10–/– mice. Collectively, we established that AIEC were pathoadapted to utilize mucosal metabolites associated with health and inflammation for growth and virulence, enabling the transition from symbiont to pathogen in a susceptible host.
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Affiliation(s)
- Shiying Zhang
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Belgin Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
| | - Francois-Pierre Martin
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Susan R Strickler
- Plant Research, Boyce Thompson Institute, Ithaca, United States of America
| | - Akihiko Oka
- Department of Internal Medicine II, Shimane University Faculty of Medicine, Izumo, Japan
| | - Jeremy Herzog
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Bo Liu
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Scot E Dowd
- MR DNA: Molecular Research LP, Shallowater, United States of America
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | | | - Esra I Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Randy Longman
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, Cornell University, New York, United States of America
| | - Rhonda Yantiss
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, Cornell University, New York, United States of America
| | - Lukas A Mueller
- Plant Research, Boyce Thompson Institute, Ithaca, United States of America
| | - Ellen Scherl
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, Cornell University, New York, United States of America
| | - R Balfour Sartor
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Kenneth W Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
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44
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Keshavarz M, Faraj Tabrizi S, Ruppert AL, Pfeil U, Schreiber Y, Klein J, Brandenburger I, Lochnit G, Bhushan S, Perniss A, Deckmann K, Hartmann P, Meiners M, Mermer P, Rafiq A, Winterberg S, Papadakis T, Thomas D, Angioni C, Oberwinkler J, Chubanov V, Gudermann T, Gärtner U, Offermanns S, Schütz B, Kummer W. Cysteinyl leukotrienes and acetylcholine are biliary tuft cell cotransmitters. Sci Immunol 2022; 7:eabf6734. [PMID: 35245090 DOI: 10.1126/sciimmunol.abf6734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The gallbladder stores bile between meals and empties into the duodenum upon demand and is thereby exposed to the intestinal microbiome. This exposure raises the need for antimicrobial factors, among them, mucins produced by cholangiocytes, the dominant epithelial cell type in the gallbladder. The role of the much less frequent biliary tuft cells is still unknown. We here show that propionate, a major metabolite of intestinal bacteria, activates tuft cells via the short-chain free fatty acid receptor 2 and downstream signaling involving the cation channel transient receptor potential cation channel subfamily M member 5. This results in corelease of acetylcholine and cysteinyl leukotrienes from tuft cells and evokes synergistic paracrine effects upon the epithelium and the gallbladder smooth muscle, respectively. Acetylcholine triggers mucin release from cholangiocytes, an epithelial defense mechanism, through the muscarinic acetylcholine receptor M3. Cysteinyl leukotrienes cause gallbladder contraction through their cognate receptor CysLTR1, prompting emptying and closing. Our results establish gallbladder tuft cells as sensors of the microbial metabolite propionate, initiating dichotomous innate defense mechanisms through simultaneous release of acetylcholine and cysteinyl leukotrienes.
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Affiliation(s)
- Maryam Keshavarz
- Institute of Anatomy and Cell Biology, German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany.,Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany
| | - Schayan Faraj Tabrizi
- Institute of Anatomy and Cell Biology, German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany.,Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany
| | - Anna-Lena Ruppert
- Institute of Anatomy and Cell Biology, Philipps University, Marburg, Germany
| | - Uwe Pfeil
- Institute of Anatomy and Cell Biology, German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany.,Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany
| | - Yannick Schreiber
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group TMP, Frankfurt, Germany
| | - Jochen Klein
- Department of Pharmacology and Clinical Pharmacy, College of Pharmacy, Goethe University Frankfurt, Frankfurt, Germany
| | - Isabell Brandenburger
- Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany.,Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Günter Lochnit
- Institute of Biochemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Sudhanshu Bhushan
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Alexander Perniss
- Institute of Anatomy and Cell Biology, German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany.,Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany
| | - Klaus Deckmann
- Institute of Anatomy and Cell Biology, German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany.,Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany
| | - Petra Hartmann
- Institute of Anatomy and Cell Biology, German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany.,Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany
| | - Mirjam Meiners
- Institute of Anatomy and Cell Biology, German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany.,Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany
| | - Petra Mermer
- Institute of Anatomy and Cell Biology, German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany.,Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany
| | - Amir Rafiq
- Institute of Anatomy and Cell Biology, German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany.,Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany
| | - Sarah Winterberg
- Institute of Anatomy and Cell Biology, Philipps University, Marburg, Germany
| | - Tamara Papadakis
- Institute of Anatomy and Cell Biology, German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany.,Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany
| | - Dominique Thomas
- Pharmazentrum Frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University Frankfurt, Frankfurt, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt, Germany
| | - Carlo Angioni
- Pharmazentrum Frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University Frankfurt, Frankfurt, Germany
| | - Johannes Oberwinkler
- Philipps-Universität Marburg, Institut für Physiologie und Pathophysiologie, Marburg, Germany
| | - Vladimir Chubanov
- Walther Straub Institute of Pharmacology and Toxicology, German Center for Lung Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Gudermann
- Walther Straub Institute of Pharmacology and Toxicology, German Center for Lung Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ulrich Gärtner
- Institute of Anatomy and Cell Biology, German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany
| | - Stefan Offermanns
- Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany.,Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Burkhard Schütz
- Institute of Anatomy and Cell Biology, Philipps University, Marburg, Germany
| | - Wolfgang Kummer
- Institute of Anatomy and Cell Biology, German Center for Lung Research, Justus Liebig University Giessen, Giessen, Germany.,Excellence Cluster Cardio-Pulmonary Institute, Justus Liebig University Giessen, Giessen, Germany
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45
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Wu WJH, Kim M, Chang LC, Assie A, Saldana-Morales FB, Zegarra-Ruiz DF, Norwood K, Samuel BS, Diehl GE. Interleukin-1β secretion induced by mucosa-associated gut commensal bacteria promotes intestinal barrier repair. Gut Microbes 2022; 14:2014772. [PMID: 34989321 PMCID: PMC8741296 DOI: 10.1080/19490976.2021.2014772] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/23/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiota is essential for maintenance and repair of the intestinal epithelial barrier. As shifts in both intestinal epithelial barrier function and microbiota composition are found in inflammatory bowel disease patients, it is critical to understand the role of distinct bacteria in regulating barrier repair. We identified a mouse commensal E. coli isolate, GDAR2-2, that protects mice from Citrobacter rodentium infection and dextran sulfate sodium-induced colitis. Colonization with GDAR2-2 in mice resulted in expansion of CX3CR1+ mononuclear phagocytes, including CX3CR1+ macrophages/dendritic cells and monocytes, along with IL-22-secreting type 3 innate lymphoid cells and improved epithelial barrier function. In vitro co-culture of macrophages with GDAR2-2 resulted in IL-1β production. In vivo, protection after GDAR2-2 colonization was lost after depletion of CX3CR1+ MNPs, or blockade of IL-1β or IL-22. We further identified human commensal E. coli isolates that similarly protect mice from C. rodentium infection through CX3CR1+ MNP and IL-1β production. Together, these findings demonstrate an unexpected role for commensal bacteria in promoting IL-1β secretion to support intestinal barrier repair.
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Affiliation(s)
- Wan-Jung H. Wu
- Immunology Graduate Program, Baylor College of Medicine, Houston, TX, USA
- Memorial Sloan Kettering Cancer Center, Immunology Program of the Sloan Kettering Institute, New York, NY, USA
| | - Myunghoo Kim
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Present Address: Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang, Korea
| | - Lin-Chun Chang
- Memorial Sloan Kettering Cancer Center, Immunology Program of the Sloan Kettering Institute, New York, NY, USA
| | - Adrien Assie
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Fatima B. Saldana-Morales
- Memorial Sloan Kettering Cancer Center, Immunology Program of the Sloan Kettering Institute, New York, NY, USA
- Neuroscience Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Daniel F. Zegarra-Ruiz
- Memorial Sloan Kettering Cancer Center, Immunology Program of the Sloan Kettering Institute, New York, NY, USA
| | - Kendra Norwood
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Buck S. Samuel
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Gretchen E. Diehl
- Memorial Sloan Kettering Cancer Center, Immunology Program of the Sloan Kettering Institute, New York, NY, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
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46
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Lima SF, Gogokhia L, Viladomiu M, Chou L, Putzel G, Jin WB, Pires S, Guo CJ, Gerardin Y, Crawford CV, Jacob V, Scherl E, Brown SE, Hambor J, Longman RS. Transferable Immunoglobulin A-Coated Odoribacter splanchnicus in Responders to Fecal Microbiota Transplantation for Ulcerative Colitis Limits Colonic Inflammation. Gastroenterology 2022; 162:166-178. [PMID: 34606847 PMCID: PMC8678328 DOI: 10.1053/j.gastro.2021.09.061] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/01/2021] [Accepted: 09/28/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS Fecal microbiota transplantation (FMT) is an emerging treatment modality for ulcerative colitis (UC). Several randomized controlled trials have shown efficacy for FMT in the treatment of UC, but a better understanding of the transferable microbiota and their immune impact is needed to develop more efficient microbiome-based therapies for UC. METHODS Metagenomic analysis and strain tracking was performed on 60 donor and recipient samples receiving FMT for active UC. Sorting and sequencing of immunoglobulin (Ig) A-coated microbiota (called IgA-seq) was used to define immune-reactive microbiota. Colonization of germ-free or genetically engineered mice with patient-derived strains was performed to determine the mechanism of microbial impact on intestinal immunity. RESULTS Metagenomic analysis defined a core set of donor-derived transferable bacterial strains in UC subjects achieving clinical response, which predicted response in an independent trial of FMT for UC. IgA-seq of FMT recipient samples and gnotobiotic mice colonized with donor microbiota identified Odoribacter splanchnicus as a transferable strain shaping mucosal immunity, which correlated with clinical response and the induction of mucosal regulatory T cells. Colonization of mice with O splanchnicus led to an increase in Foxp3+/RORγt+ regulatory T cells, induction of interleukin (IL) 10, and production of short chain fatty acids, all of which were required for O splanchnicus to limit colitis in mouse models. CONCLUSIONS This work provides the first evidence of transferable, donor-derived strains that correlate with clinical response to FMT in UC and reveals O splanchnicus as a key component promoting both metabolic and immune cell protection from colitis. These mechanistic features will help enable strategies to enhance the efficacy of microbial therapy for UC. Clinicaltrials.gov ID NCT02516384.
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MESH Headings
- Animals
- Bacteroidetes/genetics
- Bacteroidetes/immunology
- Bacteroidetes/metabolism
- Clinical Trials as Topic
- Colitis/immunology
- Colitis/metabolism
- Colitis/microbiology
- Colitis/therapy
- Colitis, Ulcerative/diagnosis
- Colitis, Ulcerative/immunology
- Colitis, Ulcerative/metabolism
- Colitis, Ulcerative/microbiology
- Colon/immunology
- Colon/metabolism
- Colon/microbiology
- Disease Models, Animal
- Fecal Microbiota Transplantation
- Forkhead Transcription Factors/metabolism
- Gastrointestinal Microbiome/genetics
- Gastrointestinal Microbiome/immunology
- Germ-Free Life
- Humans
- Immunity, Mucosal
- Immunoglobulin A/genetics
- Immunoglobulin A/immunology
- Immunoglobulin A/metabolism
- Intestinal Mucosa/immunology
- Intestinal Mucosa/metabolism
- Intestinal Mucosa/microbiology
- Intraepithelial Lymphocytes/immunology
- Intraepithelial Lymphocytes/metabolism
- Intraepithelial Lymphocytes/microbiology
- Metagenome
- Metagenomics
- Mice, Inbred C57BL
- Mice, Knockout
- Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- T-Lymphocytes, Regulatory/microbiology
- Treatment Outcome
- Mice
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Affiliation(s)
- Svetlana F Lima
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Lasha Gogokhia
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York; St. Mary's Hospital, Department of Medicine, Waterbury, Connecticut
| | - Monica Viladomiu
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Lance Chou
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Gregory Putzel
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Wen-Bing Jin
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Silvia Pires
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Chun-Jun Guo
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | | | - Carl V Crawford
- Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Vinita Jacob
- Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York; Jill Roberts Center for IBD, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Ellen Scherl
- Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York; Jill Roberts Center for IBD, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Su-Ellen Brown
- Boehringer Ingelheim SHINE Program, Ridgefield, Connecticut
| | - John Hambor
- Boehringer Ingelheim SHINE Program, Ridgefield, Connecticut
| | - Randy S Longman
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York; Jill Roberts Center for IBD, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York.
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47
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Rubin BE, Diamond S, Cress BF, Crits-Christoph A, Lou YC, Borges AL, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Rovinsky R, Smock DCJ, Tang K, Owens TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM, Banfield JF, Doudna JA. Species- and site-specific genome editing in complex bacterial communities. Nat Microbiol 2022; 7:34-47. [PMID: 34873292 PMCID: PMC9261505 DOI: 10.1038/s41564-021-01014-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/29/2021] [Indexed: 12/13/2022]
Abstract
Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of ET-seq and DART in soil and infant gut microbiota, we conduct species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species. These tools enable editing of microbial communities for understanding and control.
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Affiliation(s)
- Benjamin E Rubin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Spencer Diamond
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Brady F Cress
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Yue Clare Lou
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Haridha Shivram
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Christine He
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Michael Xu
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Zeyi Zhou
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sara J Smith
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rachel Rovinsky
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dylan C J Smock
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Kimberly Tang
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Trenton K Owens
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- School of Earth Sciences, University of Melbourne, Melbourne, Victoria, Australia.
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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48
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Feng L, Zhou N, Li Z, Fu D, Guo Y, Gao X, Liu X. Co-occurrence of gut microbiota dysbiosis and bile acid metabolism alteration is associated with psychological disorders in Crohn's disease. FASEB J 2021; 36:e22100. [PMID: 34939244 DOI: 10.1096/fj.202101088rrr] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022]
Abstract
This study aims to elucidate the relationships between gut microbiota, bile acid metabolism, and psychological comorbidity in Crohn's disease (CD). We profiled the fecal microbiota composition and quantified the bile acid pool of 39 CD patients and 14 healthy controls using 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry, respectively. Significant reductions in the secondary bile acids, LCA and DCA, were found in both the feces and serum samples of CD patients, while the concentration of 7-DHCA was particularly higher in the serum of CD patients with psychological disorders. The fecal levels of HDCA and 12-DHCA of the CD patients were inversely correlated with their Self-Rated Depression Scale (SDS) scores, whereas the serum level of 7-DHCA was positively correlated with the SDS scores. In addition, the fecal levels of TDCA, TLCA, and TβMCA showed a positive correlation with the Self-Rated Anxiety Scale (SAS) scores. The fecal microbiota biodiversity was particularly declined in CD patients with psychological disorders. An enrichment of Ruminococcus gnavus in CD patients may cause psychological disorders by affecting the microbiota-gut-brain axis via its ability to degrade the gut barrier, regulate the tryptophan-kynurenine metabolism, and modulate bile acid metabolism. In addition, the overabundant Enterobacteriaceae and Lachnospiraceae in CD patients may contribute to psychological comorbidity via dysregulating their bile acids metabolism. Taken together, changes in the gut microbiota composition may cooperate with alterations in the bile acid metabolism that are involved in the development of psychological disorders in CD.
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Affiliation(s)
- Lijuan Feng
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China.,Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, China
| | - Nan Zhou
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
| | - Zichun Li
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
| | - Dongni Fu
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
| | - Ying Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Xuefeng Gao
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, China.,Central Laboratory, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Xiaowei Liu
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
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49
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Kamali Dolatabadi R, Feizi A, Halaji M, Fazeli H, Adibi P. The Prevalence of Adherent-Invasive Escherichia coli and Its Association With Inflammatory Bowel Diseases: A Systematic Review and Meta-Analysis. Front Med (Lausanne) 2021; 8:730243. [PMID: 34926490 PMCID: PMC8678049 DOI: 10.3389/fmed.2021.730243] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are known as chronic gastrointestinal inflammatory disorders. The present systematic review and meta analysis was conducted to estimate the prevalence of adherent-invasive Escherichia coli (AIEC) isolates and their phylogenetic grouping among IBD patients compared with the controls. A systematic literature search was conducted among published papers by international authors until April 30, 2020 in Web of Science, Scopus, EMBASE, and PubMed databases. The pooled prevalence of AIEC isolates and their phylogenetic grouping among IBD patients as well as in controls was estimated using fixed or random effects models. Furthermore, for estimating the association of colonization by AIEC with IBD, odds ratio along with 95% confidence interval was reported. A total of 205 articles retrieved by the initial search of databases, 13 case–control studies met the eligibility criteria for inclusion in the meta analysis. There were 465 IBD cases (348 CD and 117 UC) and 307 controls. The pooled prevalence of AIEC isolates were 28% (95% CI: 18–39%), 29% (95% CI: 20–40%), 13% (95% CI: 1–30%), and 9% (95% CI: 3–19%), respectively among IBD, CD, UC, and control group, respectively. Our results revealed that the most frequent AIEC phylogroup in the IBD, CD, and control groups was B2. Fixed-effects meta analysis showed that colonization of AIEC is significantly associated with IBD (OR: 2.93; 95% CI: 1.90–4.52; P < 0.001) and CD (OR: 3.07; 95% CI: 1.99–4.74; P < 0.001), but not with UC (OR: 2.29; 95% CI: 0.81–6.51; P = 0.11). In summary, this meta analysis revealed that colonization by AIEC is more frequent in IBD and is associated with IBD (CD and UC). Our results suggested that the affects of IBD in patients colonized with the AIEC pathovar is not random, it is in fact a specific disease-related pathovar.
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Affiliation(s)
- Razie Kamali Dolatabadi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Awat Feizi
- Department of Biostatistics and Epidemiology, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehrdad Halaji
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran.,Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Hossein Fazeli
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Peyman Adibi
- Gastroenterology and Hepatology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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50
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The Short-Chain Fatty Acids Propionate and Butyrate Augment Adherent-Invasive Escherichia coli Virulence but Repress Inflammation in a Human Intestinal Enteroid Model of Infection. Microbiol Spectr 2021; 9:e0136921. [PMID: 34612688 PMCID: PMC8510176 DOI: 10.1128/spectrum.01369-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Short-chain fatty acids (SCFAs), which consist of six or fewer carbons, are fermentation products of the bacterial community that inhabits the intestine. Due to an immunosuppressive effect on intestinal tissue, they have been touted as a therapeutic for inflammatory conditions of the bowel. Here, we study the impact of acetate, propionate, and butyrate, the three most abundant SCFAs in the intestine, on gene expression in the intestinal pathobiont adherent-invasive Escherichia coli. We pair this with adherence, invasion, and inflammation in Caco-2 and human intestinal enteroid (HIE)-derived monolayer models of the intestinal epithelium. We report that propionate and butyrate upregulate transcription of adherent-invasive Escherichia coli (AIEC) flagellar synthesis genes and decrease expression of capsule assembly and transport genes. These changes are predicted to augment AIEC invasiveness. In fact, SCFA supplementation increases AIEC adherence to and invasion of the Caco-2 monolayer but has no effect on these parameters in the HIE model. We attribute this to the anti-inflammatory effect of propionate and butyrate on HIEs but not on Caco-2 cells. We conclude that the potential of SCFAs to increase the virulence of intestinal pathogens should be considered in their use as anti-inflammatory agents. IMPORTANCE The human terminal ileum and colon are colonized by a community of microbes known as the microbiota. Short-chain fatty acids (SCFAs) excreted by bacterial members of the microbiota define the intestinal environment. These constitute an important line of communication within the microbiota and between the microbiota and the host epithelium. In inflammatory conditions of the bowel, SCFAs are often low and there is a preponderance of a conditionally virulent bacterium termed adherent-invasive Escherichia coli (AIEC). A connection between SCFA abundance and AIEC has been suggested. Here, we study AIEC in monoculture and in coculture with human intestinal enteroid-derived monolayers and show that the SCFAs propionate and butyrate increase expression of AIEC virulence genes while concurrently bolstering the intestinal epithelial barrier and reducing intestinal inflammation. While these SCFAs have been promoted as a therapy for inflammatory bowel conditions, our findings demonstrate that their effect on bacterial virulence must be considered.
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