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Tanaka R, Imai J, Sugiyama E, Tsubaki S, Hozumi K, Tsugawa H. Cyclic-di-AMP confers an invasive phenotype on Escherichia coli through elongation of flagellin filaments. Gut Pathog 2024; 16:6. [PMID: 38267967 PMCID: PMC10809763 DOI: 10.1186/s13099-024-00600-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/15/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Adherent-invasive Escherichia coli (AIEC) is isolated from patients with Crohn's disease (CD). AIEC can invade the intestinal epithelium, suggesting that it is involved in the development and pathogenesis of CD. However, the mechanism by which AIEC acquired the invasive phenotype remains unknown. RESULTS This study was designed to examine the mechanisms of AIEC invasiveness. We found that the flagellin (fliC) expression in AIEC was two-fold higher than that in non-AIEC strains, and this overexpression induced the formation of long-filament flagellin. Deletion of fliC in the AIEC LF82 strain resulted in the disappearance of flagellar filaments and attenuated the motility and invasive ability of the bacterium, suggesting that the formation of long filament flagellin induced by increased fliC expression is required by AIEC to invade the intestinal epithelium. In AIEC and non-AIEC K12 strains cultured in the presence of cyclic-di-AMP (c-di-AMP), the expression of fliC was enhanced, and flagellar filaments were elongated. Stimulation with c-di-AMP enhanced the bacterial motility and ability to invade epithelial cells, even in the non-AIEC K12 strain. CONCLUSIONS Our findings show that c-di-AMP confers an AIEC-like phenotype on non-AIEC strains by enhancing the expression of fliC. The results should be useful for understanding the pathogenesis of CD.
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Affiliation(s)
- Rika Tanaka
- Department of Immunology, Division of Host Defense Mechanism, Tokai University School of Medicine, Isehara, Japan
| | - Jin Imai
- Department of Clinical Health Science, Tokai University School of Medicine, Isehara, Japan
| | - Eiji Sugiyama
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Shogo Tsubaki
- Transkingdom Signaling Research Unit, Division of Host Defense Mechanism, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Katsuto Hozumi
- Department of Immunology, Division of Host Defense Mechanism, Tokai University School of Medicine, Isehara, Japan
| | - Hitoshi Tsugawa
- Transkingdom Signaling Research Unit, Division of Host Defense Mechanism, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan.
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2
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Gilliland A, Chan JJ, De Wolfe TJ, Yang H, Vallance BA. Pathobionts in Inflammatory Bowel Disease: Origins, Underlying Mechanisms, and Implications for Clinical Care. Gastroenterology 2024; 166:44-58. [PMID: 37734419 DOI: 10.1053/j.gastro.2023.09.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 08/28/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
The gut microbiota plays a significant role in the pathogenesis of both forms of inflammatory bowel disease (IBD), namely, Crohn's disease (CD) and ulcerative colitis (UC). Although evidence suggests dysbiosis and loss of beneficial microbial species can exacerbate IBD, many new studies have identified microbes with pathogenic qualities, termed "pathobionts," within the intestines of patients with IBD. The concept of pathobionts initiating or driving the chronicity of IBD has largely focused on the putative aggravating role that adherent invasive Escherichia coli may play in CD. However, recent studies have identified additional bacterial and fungal pathobionts in patients with CD and UC. This review will highlight the characteristics of these pathobionts and their implications for IBD treatment. Beyond exploring the origins of pathobionts, we discuss those associated with specific clinical features and the potential mechanisms involved, such as creeping fat (Clostridium innocuum) and impaired wound healing (Debaryomyces hansenii) in patients with CD as well as the increased fecal proteolytic activity (Bacteroides vulgatus) seen as a biomarker for UC severity. Finally, we examine the potential impact of pathobionts on current IBD therapies, and several new approaches to target pathobionts currently in the early stages of development. Despite recognizing that pathobionts likely contribute to the pathogenesis of IBD, more work is needed to define their modes of action. Determining whether causal relationships exist between pathobionts and specific disease characteristics could pave the way for improved care for patients, particularly for those not responding to current IBD therapies.
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Affiliation(s)
- Ashley Gilliland
- Division of Gastroenterology, Department of Pediatrics, BC Children's Hospital and the University of British Columbia, Vancouver, British Columbia, Canada
| | - Jocelyn J Chan
- Division of Gastroenterology, Department of Pediatrics, BC Children's Hospital and the University of British Columbia, Vancouver, British Columbia, Canada
| | - Travis J De Wolfe
- Division of Gastroenterology, Department of Pediatrics, BC Children's Hospital and the University of British Columbia, Vancouver, British Columbia, Canada
| | - Hyungjun Yang
- Division of Gastroenterology, Department of Pediatrics, BC Children's Hospital and the University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce A Vallance
- Division of Gastroenterology, Department of Pediatrics, BC Children's Hospital and the University of British Columbia, Vancouver, British Columbia, Canada.
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3
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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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4
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Li N, Ma P, Li Y, Shang X, Nan X, Shi L, Han X, Liu J, Hong Y, Li Q, Cui J, Li J, Peng G. Gut microbiota-derived 12-ketolithocholic acid suppresses the IL-17A secretion from colonic group 3 innate lymphoid cells to prevent the acute exacerbation of ulcerative colitis. Gut Microbes 2023; 15:2290315. [PMID: 38062857 PMCID: PMC10730201 DOI: 10.1080/19490976.2023.2290315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Intestinal microbiota dysbiosis and metabolic disruption are well-known as the primary triggers of ulcerative colitis (UC). However, their role in regulating the group 3 innate lymphoid cells (ILC3s), which are essential for intestinal health, remains unexplored during the development of disease severity. Here, our results showed that the microbiota structure of patients with severe UC (SUCs) differed from those with mild UC (MiUCs), moderate UC (MoUCs), and healthy controls (HCs). Microbes producing secondary bile acids (SBAs) and SBAs decreased with the aggravation of UC, and a strong positive correlation existed between them. Next, fecal microbiota transfer was used to reproduce the human-derived microbiota in mice and decipher the microbiota-mediated inflammatory modulation during an increase in disease severity. Mice receiving SUC-derived microbiota exhibited enhancive inflammation, a lowered percentage of ILC3s, and the down-regulated expressions of bile acid receptors, including vitamin D receptor (VDR) and pregnane X receptor (PXR), in the colon. Similar to clinical results, SBA-producing microbes, deoxycholic acids (DCA), and 12-ketolithocholic acids (12-KLCA) were diminished in the intestine of these recipients. Finally, we compared the therapeutic potential of DCA and 12-KLCA in preventing colitis and the regulatory mechanisms mediated by ILC3s. 12-KLCA but not DCA represented a strong anti-inflammatory effect associated with the higher expression of VDR and the lower secretion of IL-17A from colonic ILC3s. Collectively, these findings provide new signatures for monitoring the acute deterioration of UC by targeting gut microbiota and bile acid metabolism and demonstrate the therapeutic and preventive potential of a novel microbiota-derived metabolite, 12-KLCA.
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Affiliation(s)
- Na Li
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Peiguang Ma
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Yalan Li
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Xuekai Shang
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Xinmei Nan
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Lei Shi
- Department of Gastroenterology, Dong Fang Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Xiao Han
- Department of Gastroenterology, Dong Fang Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Jiajing Liu
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Yanfei Hong
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Qiuyi Li
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Jiaqi Cui
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Junxiang Li
- Department of Gastroenterology, Dong Fang Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Guiying Peng
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
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5
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Ma X, Zhao C, Xu Y, Zhang H. Roles of host SUMOylation in bacterial pathogenesis. Infect Immun 2023; 91:e0028323. [PMID: 37725062 PMCID: PMC10580907 DOI: 10.1128/iai.00283-23] [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] [Indexed: 09/21/2023] Open
Abstract
Bacteria frequently interfere with the post-translational modifications of host cells to facilitate their survival and growth after invasion. SUMOylation, a reversible post-translational modification process, plays an important role in biological life activities. In addition to being critical to host cell metabolism and survival, SUMOylation also regulates gene expression and cell signal transmission. Moreover, SUMOylation in eukaryotic cells can be used by a variety of bacterial pathogens to advance bacterial invasion. In this minireview, we focused on the role and mechanism of host SUMOylation in the pathogenesis of six important clinical bacterial pathogens (Listeria monocytogenes, Shigella flexneri, Salmonella Typhimurium, Klebsiella pneumoniae, Staphylococcus aureus, and Escherichia coli). Taken together, this review provided new insights for understanding the unique pathogen-host interaction based on host SUMOylation and provided a novel perspective on the development of new strategies to combat bacterial infections in the future.
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Affiliation(s)
- Xin Ma
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chenhao Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yuyao Xu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Clinical Laboratory, Zhangjiagang Traditional Chinese Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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6
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Fang X, Kang L, Qiu YF, Li ZS, Bai Y. Yersinia enterocolitica in Crohn’s disease. Front Cell Infect Microbiol 2023; 13:1129996. [PMID: 36968108 PMCID: PMC10031030 DOI: 10.3389/fcimb.2023.1129996] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
Increasing attention is being paid to the unique roles gut microbes play in both physiological and pathological processes. Crohn’s disease (CD) is a chronic, relapsing, inflammatory disease of the gastrointestinal tract with unknown etiology. Currently, gastrointestinal infection has been proposed as one initiating factor of CD. Yersinia enterocolitica, a zoonotic pathogen that exists widely in nature, is one of the most common bacteria causing acute infectious gastroenteritis, which displays clinical manifestations similar to CD. However, the specific role of Y. enterocolitica in CD is controversial. In this Review, we discuss the current knowledge on how Y. enterocolitica and derived microbial compounds may link to the pathogenesis of CD. We highlight examples of Y. enterocolitica-targeted interventions in the diagnosis and treatment of CD, and provide perspectives for future basic and translational investigations on this topic.
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Affiliation(s)
| | | | | | | | - Yu Bai
- *Correspondence: Zhao-Shen Li, ; Yu Bai,
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7
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Wang H, Tian Q, Xu Z, Du M, Zhu MJ. Metabolomic profiling for the preventive effects of dietary grape pomace against colorectal cancer. J Nutr Biochem 2023; 116:109308. [PMID: 36868505 DOI: 10.1016/j.jnutbio.2023.109308] [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: 03/01/2022] [Revised: 12/22/2022] [Accepted: 02/24/2023] [Indexed: 03/05/2023]
Abstract
Colorectal cancer (CRC) is one of the most common and deadly cancers worldwide. Grape pomace (GP) is a rich source of bioactive compounds with anti-inflammatory, and anticancer effects. We recently found that dietary GP had protective effects against CRC development in the azoxymethane (AOM)/dextran sulfate sodium (DSS) CRC mouse model through suppression of cell proliferation and modulation of DNA methylation. However, the underlying molecular mechanisms associated with changes in metabolites remain unexamined. This study profiled fecal metabolomic changes in a mouse CRC model in response to GP supplementation using gas chromatography-mass spectrometry (GC-MS) based metabolomic analysis. A total of 29 compounds showed significant changes due to GP supplementation, including bile acids, amino acids, fatty acids, phenols/flavonoids, glycerolipids, carbohydrates, organic acids, and others. The major changes in metabolites of feces include increased deoxycholic acid (DCA) and decreased amino acid content. Dietary GP upregulated the expression of farnesoid X receptor (FXR) downstream genes while decreasing fecal urease activity. DNA repair enzyme MutS Homolog 2 (MSH2) was upregulated by GP supplementation. Consistently, γ-H2AX, as a DNA damage marker, decreased in GP supplemented mice. Moreover, MDM2, a protein in the ataxia telangiectasia mutated (ATM) signaling, was decreased by GP supplementation. These data provided valuable metabolic clues for unraveling the protective effects of GP supplementation against CRC development.
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Affiliation(s)
- Hongbin Wang
- School of Food Science, Washington State University, Pullman, WA 99164, USA,; Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Qiyu Tian
- School of Food Science, Washington State University, Pullman, WA 99164, USA,; Department of Animal Science, Washington State University, Pullman, WA 99164, USA
| | - Zhixin Xu
- School of Food Science, Washington State University, Pullman, WA 99164, USA
| | - Min Du
- Department of Animal Science, Washington State University, Pullman, WA 99164, USA
| | - Mei-Jun Zhu
- School of Food Science, Washington State University, Pullman, WA 99164, USA,.
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8
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Differentiation of Escherichia fergusonii and Escherichia coli Isolated from Patients with Inflammatory Bowel Disease/Ischemic Colitis and Their Antimicrobial Susceptibility Patterns. Antibiotics (Basel) 2023; 12:antibiotics12010154. [PMID: 36671355 PMCID: PMC9854958 DOI: 10.3390/antibiotics12010154] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Genotypically, 16S rRNA gene sequence analysis clearly differentiates between species. However, species delineation between Escherichia fergusonii and Escherichia coli is much more difficult and cannot be distinguished by 16S rRNA gene sequences alone. Hence, in this study, we attempted to differentiate E. fergusonii and E. coli isolated from faecal samples of disease-associated Korean individuals with inflammatory bowel disease (IBD)/ischemic colitis (IC) and test the antimicrobial susceptibility patterns of isolated strains. Phylogenetic analysis was performed using the adenylate kinase (adk) housekeeping gene from the E. coli multi locus sequence typing (MLST) scheme. Antimicrobial susceptibility and minimum inhibitory concentration (MIC) of all disease-associated strains in addition to healthy control isolates to 14 antibiotics were determined by broth microdilution-based technique. Next, 83 isolates from 11 disease-associated faecal samples were identified as E. fergusonii using 16S rRNA gene sequence analysis. Phylogenetic analysis using the adk gene from E. coli MLST scheme revealed that most of the strains (94%) were E. coli. A total of 58 resistance patterns were obtained from 83 strains of disease-associated (IBD/IC) isolates. All isolates were resistant to at least one tested antimicrobial agent, with the highest resistance against erythromycin (88.0%), ampicillin (86.7%), ciprofloxacin (73.5%), cephalothin (72.3%), gentamicin (59%), trimethoprim-sulfamethoxazole (53%), cefotaxime (49.4%), and ceftriaxone (48.2%). A total of 90.7% of isolates were extended-spectrum beta-lactamase (ESBL)-producers among the resistant strains to third-generation cephalosporins (cefotaxime or ceftriaxone). ESBL-producing E. coli isolates from patients with Crohn's disease (CD), ulcerative colitis (UC), and ischemic colitis (IC) were 92.3%, 82.4%, and 100%, respectively. In conclusion, adk-based phylogenetic analysis may be the most accurate method for distinguishing E. coli and E. fergusonii from Escherichia genus. We identified four loci in adk gene sequences which makes it easier to discriminate between E. coli and E. fergusonii. Additionally, we believe that gut colonization by multidrug-resistant ESBL-producing E. coli may play a significant role in IBD/IC pathogenesis.
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9
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López-Cauce B, Puerto M, García JJ, Ponce-Alonso M, Becerra-Aparicio F, del Campo R, Peligros I, Fernández-Aceñero MJ, Gómez-Navarro Y, Lara JM, Miranda-Bautista J, Marín-Jiménez I, Bañares R, Menchén L. Akkermansia deficiency and mucin depletion are implicated in intestinal barrier dysfunction as earlier event in the development of inflammation in interleukin-10-deficient mice. Front Microbiol 2023; 13:1083884. [PMID: 36699599 PMCID: PMC9869054 DOI: 10.3389/fmicb.2022.1083884] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
Background Dysbiosis and mucin depletion are related with intestinal barrier dysfunction and seems to be an early pathophysiological event in inflammatory bowel disease (IBD). The objective of this work is to study these parameters in the natural history of colitis in IL-10 deficient mice (IL-10-/-). Methods Wild type (WT) and IL-10-/-. mice were followed until sacrifice at 3, 5, 10, 20, 57, and 70 weeks. Body weight, colonic weight/length ratio and in vivo intestinal permeability were registered. Expression of inflammatory and adhesion molecules in the colon was explored by qPCR as Mucin-2 (MUC-2) and molecules involved in goblet cell maturation Interleukin-18 (IL-18) and WAP Four-Disulfide Core Domain 2 (WFDC2), the endoplasmic reticulum stress markers X-box-binding protein (Xbp-1) and Reticulon-4B (RTN-4B). Bacterial composition in feces and colonic mucosa was determined by massive sequencing of the V3-V4 regions of 16S rDNA gene. Results IL-10-/- mice showed histological inflammation at weeks 20 and 57, but most notably the intestinal permeability was significantly higher from week 10. Concordantly, the number of goblet cells and expression of MUC-2, IL-18, WFDC2 and Xbp-1 were significantly lower in KO from week 10. Nevertheless, no significant differences were found in the mRNA expression of MUC-2 or Xbp-1 between both groups-derived colon organoids. Significant bacterial differences began at week 5, being the Akkermansia deficiency in KO the most relevant result. Conclusion Gut microbiota alterations and mucin depletion are associated with early intestinal barrier dysfunction and precede overt gut inflammation in this animal model of IBD.
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Affiliation(s)
- Beatriz López-Cauce
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain,Departamento de Microbiología y Parasitología Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - Marta Puerto
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Juan José García
- Departamento de Microbiología y Parasitología Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - Manuel Ponce-Alonso
- Servicio de Microbiología, Hospital Ramón y Cajal, CIBERINFEC, IRYCIS, Madrid, Spain
| | | | - Rosa del Campo
- Servicio de Microbiología, Hospital Ramón y Cajal, CIBERINFEC, IRYCIS, Madrid, Spain
| | - Isabel Peligros
- Servicio de Anatomía Patológica, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | | | - Yésica Gómez-Navarro
- Servicio de Anatomía Patológica, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - José M. Lara
- Servicio de Anatomía Patológica, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - José Miranda-Bautista
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Ignacio Marín-Jiménez
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Rafael Bañares
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain,Departamento de Medicina, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Luis Menchén
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain,Departamento de Medicina, Facultad de Medicina, Universidad Complutense, Madrid, Spain,*Correspondence: Luis Menchén,
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10
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Wang EJ, Wu MY, Ren ZY, Zheng Y, Ye RD, TAN CSH, Wang Y, Lu JH. Targeting macrophage autophagy for inflammation resolution and tissue repair in inflammatory bowel disease. BURNS & TRAUMA 2023; 11:tkad004. [PMID: 37152076 PMCID: PMC10157272 DOI: 10.1093/burnst/tkad004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/22/2022] [Accepted: 01/16/2023] [Indexed: 05/09/2023]
Abstract
Inflammatory bowel disease (IBD) is a chronic, non-specific, recurrent inflammatory disease, majorly affecting the gastrointestinal tract. Due to its unclear pathogenesis, the current therapeutic strategy for IBD is focused on symptoms alleviation. Autophagy is a lysosome-mediated catabolic process for maintaining cellular homeostasis. Genome-wide association studies and subsequent functional studies have highlighted the critical role of autophagy in IBD via a number of mechanisms, including modulating macrophage function. Macrophages are the gatekeepers of intestinal immune homeostasis, especially involved in regulating inflammation remission and tissue repair. Interestingly, many autophagic proteins and IBD-related genes have been revealed to regulate macrophage function, suggesting that macrophage autophagy is a potentially important process implicated in IBD regulation. Here, we have summarized current understanding of macrophage autophagy function in pathogen and apoptotic cell clearance, inflammation remission and tissue repair regulation in IBD, and discuss how this knowledge can be used as a strategy for IBD treatment.
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Affiliation(s)
- Er-jin Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Ming-Yue Wu
- Center for Metabolic Liver Diseases and Center for Cholestatic Liver Diseases, Department of Gastroenterology, The First Affiliated Hospital (Southwest Hospital), Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Zheng-yu Ren
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Ying Zheng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Richard D Ye
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 518172, China
| | - Chris Soon Heng TAN
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
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11
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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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12
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Lourenço TGB, de Oliveira AM, Tsute Chen G, Colombo APV. Oral-gut bacterial profiles discriminate between periodontal health and diseases. J Periodontal Res 2022; 57:1227-1237. [PMID: 36261869 DOI: 10.1111/jre.13059] [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: 03/18/2022] [Revised: 07/19/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVE This investigation explored oral-gut microbial signatures with potential to distinguish among periodontal conditions. BACKGROUND DATA The interplay between the oral and gut microbiomes may be a critical pathway linking periodontal diseases and systemic inflammatory disorders. The mechanisms by which oral microorganisms translocate to the gut and cause microbial dysbiosis, favoring an inflammatory state, are still unknown. As a first approach, characterization of oral-gut microbial profiles associated with periodontal health and diseases can provide insights on such mechanisms of etiology and pathogenesis. METHODS Fecal and saliva samples from individuals with periodontal health (PH, 8), gingivitis (GG, 17), and periodontitis (PD, 24) were analyzed for their microbial composition by 16S rRNA gene sequencing. Microbial taxa were compared and correlated to periodontal parameters. Multivariate discriminant analysis (MDA) was carried out to identify profiles related to health and disease. RESULTS Few significant differences in oral-gut taxa were detected among clinical groups, although increase in fecal Fusobacterium nucleatum ss vincentii and salivary Aggregatibacter actinomycetemcomitans, Parvimonas micra, and Fretibacterium sp. HMT358 were strongly correlated with deep pockets and inflammation (p < .01). Over 50% of the fecal microbiota comprised microorganisms shared between oral and gut sites, whereas oral taxa were detected in approximately 9%, particularly enriched in GG fecal samples (p = .04). Trends for lower fecal richness and higher salivary diversity in PD compared to PH were observed. MDA was able to classify correctly 82% of the patients into the clinical groups. Main classifiers of periodontitis were high BMI, older age, and enrichment of oral-fecal Leptotrichia sp. HMT4, Peptostreptococcus stomatis, Dialister invisus, and a novel Lautropia sp. HMTC89-like organism. CONCLUSION Within the limitations of an exploratory investigation, specific profiles of oral-gut taxa, including known and potential novel organisms, combined with social-demographic features were able to discriminate individuals with periodontal diseases in this study population.
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Affiliation(s)
- Talita Gomes Baêta Lourenço
- Laboratory of Oral Microbiology, Department of Medical Microbiology, Institute of Microbiology, Rio de Janeiro, Brazil
| | - Adriana Miranda de Oliveira
- Laboratory of Oral Microbiology, Department of Medical Microbiology, Institute of Microbiology, Rio de Janeiro, Brazil.,School of Dentistry, Postgraduate program in Periodontics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Ana Paula Vieira Colombo
- Laboratory of Oral Microbiology, Department of Medical Microbiology, Institute of Microbiology, Rio de Janeiro, Brazil.,School of Dentistry, Postgraduate program in Periodontics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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13
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Rudiansyah M, Abdalkareem Jasim S, S Azizov B, Samusenkov V, Kamal Abdelbasset W, Yasin G, Mohammad HJ, Jawad MA, Mahmudiono T, Hosseini-Fard SR, Mirzaei R, Karampoor S. The emerging microbiome-based approaches to IBD therapy: From SCFAs to urolithin A. J Dig Dis 2022; 23:412-434. [PMID: 36178158 DOI: 10.1111/1751-2980.13131] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/19/2022] [Accepted: 09/27/2022] [Indexed: 12/11/2022]
Abstract
Inflammatory bowel disease (IBD) is a group of chronic gastrointestinal inflammatory conditions which can be life-threatening, affecting both children and adults. Crohn's disease and ulcerative colitis are the two main forms of IBD. The pathogenesis of IBD is complex and involves genetic background, environmental factors, alteration in gut microbiota, aberrant immune responses (innate and adaptive), and their interactions, all of which provide clues to the identification of innovative diagnostic or prognostic biomarkers and the development of novel treatments. Gut microbiota provide significant benefits to its host, most notably via maintaining immunological homeostasis. Furthermore, changes in gut microbial populations may promote immunological dysregulation, resulting in autoimmune diseases, including IBD. Investigating the interaction between gut microbiota and immune system of the host may lead to a better understanding of the pathophysiology of IBD as well as the development of innovative immune- or microbe-based therapeutics. In this review we summarized the most recent findings on innovative therapeutics for IBD, including microbiome-based therapies such as fecal microbiota transplantation, probiotics, live biotherapeutic products, short-chain fatty acids, bile acids, and urolithin A.
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Affiliation(s)
- Mohammad Rudiansyah
- Division of Nephrology & Hypertension, Department of Internal Medicine, Faculty of Medicine, Universitas Lambung Mangkurat, Ulin Hospital, Banjarmasin, Indonesia
| | - Saade Abdalkareem Jasim
- Al-Maarif University College Medical Laboratory Techniques Department Al-Anbar-Ramadi, Ramadi, Iraq
| | - Bakhadir S Azizov
- Department of Therapeutic Disciplines No.1, Tashkent State Dental Institute, Tashkent, Uzbekistan
| | | | - Walid Kamal Abdelbasset
- Department of Health and Rehabilitation Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al Kharj, Saudi Arabia
| | - Ghulam Yasin
- Department of Botany University of Bahauddin Zakariya University, Multan, Pakistan
| | | | | | - Trias Mahmudiono
- Department of Nutrition Faculty of Public Health Universitas, Airlangga, Indonesia
| | - Seyed Reza Hosseini-Fard
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
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14
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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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15
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Exploring Different Effects of Exclusive Enteral Nutrition (EEN) and Corticosteroids on the Gut Microbiome in Crohn’s Disease Based on a Three-Stage Strategy. Gastroenterol Res Pract 2022; 2022:6147124. [PMID: 35935714 PMCID: PMC9348958 DOI: 10.1155/2022/6147124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
The objective of this study was to compare the efficacy of exclusive enteral nutrition (EEN) and corticosteroids on the gut microbiome in Crohn's disease. Methods. Data were collected for 16 patients newly diagnosed with CD as the test group and 10 healthy volunteers as the control group. The 16 patients were randomly divided into the EEN group and the corticosteroids group. For subsequent analysis, 6 patients in the EEN group with follow-up were enrolled to compare the 0-month, 1-month, and 3-month outcomes. We analyzed and compared gut microbiota between different groups in 3 stages. To evaluate the clinical outcome of treatment, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), hemoglobin (HB), albumin (ALB), and Crohn's disease activity (CDAI) were recorded. Results. There are significant differences in microbiota between patients with CD and healthy people, and there are intuitive differences in the main components of the microbiota. 16 patients were included in stage 2, in which both corticosteroids and EEN can induce CD remission well. However, corticosteroids have a greater impact on inflammatory indicators, while EEN has a more obvious effect on nutritional indicators. Principal component analysis suggests that there are different compositional changes in the gut microbiome after corticosteroids and EEN treatment. After 3 months of dynamic observation, we found that EEN can effectively maintain CD remission, reduce inflammatory indicators, and improve nutritional indicators. Conclusions. Both EEN and corticosteroids can increase the diversity of the microbiome in inducing CD remission, while they have different effects on the proportion of microbiome species. This trial is registered with NCT02056418.
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16
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French T, Steffen J, Glas A, Osbelt L, Strowig T, Schott BH, Schüler T, Dunay IR. Persisting Microbiota and Neuronal Imbalance Following T. gondii Infection Reliant on the Infection Route. Front Immunol 2022; 13:920658. [PMID: 35898505 PMCID: PMC9311312 DOI: 10.3389/fimmu.2022.920658] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/25/2022] [Indexed: 12/18/2022] Open
Abstract
Toxoplasma gondii is a highly successful parasite capable of infecting all warm-blooded animals. The natural way of infection in intermediate hosts is the oral ingestion of parasite-contaminated water or food. In murine experimental models, oral infection (p.o.) of mice with T. gondii is applied to investigate mucosal and peripheral immune cell dynamics, whereas intraperitoneal infection (i.p.) is frequently used to study peripheral inflammation as well as immune cell – neuronal interaction in the central nervous system (CNS). However, the two infection routes have not yet been systematically compared along the course of infection. Here, C57BL/6 mice were infected p.o. or i.p. with a low dose of T. gondii cysts, and the acute and chronic stages of infection were compared. A more severe course of infection was detected following i.p. challenge, characterized by an increased weight loss and marked expression of proinflammatory cytokines particularly in the CNS during the chronic stage. The elevated proinflammatory cytokine expression in the ileum was more prominent after p.o. challenge that continued following the acute phase in both i.p. or p.o. infected mice. This resulted in sustained microbial dysbiosis, especially after p.o. challenge, highlighted by increased abundance of pathobionts from the phyla proteobacteria and a reduction of beneficial commensal species. Further, we revealed that in the CNS of i.p. infected mice CD4 and CD8 T cells displayed higher IFNγ production in the chronic stage. This corresponded with an increased expression of C1q and CD68 in the CNS and reduced expression of genes involved in neuronal signal transmission. Neuroinflammation-associated synaptic alterations, especially PSD-95, VGLUT, and EAAT2 expression, were more pronounced in the cortex upon i.p. infection highlighting the profound interplay between peripheral inflammation and CNS homeostasis.
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Affiliation(s)
- Timothy French
- Institute of Inflammation and Neurodegeneration, Health Campus Immunology, Infectiology and Inflammation (GC-I), Otto-von-Guericke University, Magdeburg, Germany
| | - Johannes Steffen
- Institute of Inflammation and Neurodegeneration, Health Campus Immunology, Infectiology and Inflammation (GC-I), Otto-von-Guericke University, Magdeburg, Germany
| | - Albert Glas
- Institute of Inflammation and Neurodegeneration, Health Campus Immunology, Infectiology and Inflammation (GC-I), Otto-von-Guericke University, Magdeburg, Germany
| | - Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Björn H. Schott
- Institute of Inflammation and Neurodegeneration, Health Campus Immunology, Infectiology and Inflammation (GC-I), Otto-von-Guericke University, Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
- Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Thomas Schüler
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Ildiko Rita Dunay
- Institute of Inflammation and Neurodegeneration, Health Campus Immunology, Infectiology and Inflammation (GC-I), Otto-von-Guericke University, Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
- *Correspondence: Ildiko Rita Dunay,
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Bile Acids and the Microbiome: Making Sense of This Dynamic Relationship in Their Role and Management in Crohn's Disease. Can J Gastroenterol Hepatol 2022; 2022:8416578. [PMID: 35360442 PMCID: PMC8964223 DOI: 10.1155/2022/8416578] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/05/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Bile acids help maintain the physiological balance of the gut microbiome and the integrity of the intestinal epithelial barrier. Similarly, intestinal bacteria play a major role in bile acid metabolism as they are involved in crucial biotransformation steps in the enterohepatic circulation pathway. Understanding the relationship between bile acid signalling and the gut microbiome in Crohn's disease can help target new and innovative treatment strategies. AIMS This review summarises the relationship between bile acids and the microbiome in Crohn's disease and discusses potential novel therapeutic options. METHODS We performed a literature review on bile acid signalling, its effect on the gut microbiome, and therapeutic applications in Crohn's disease. RESULTS Current research suggests that there is a strong interplay between the dysregulated microbiota, bile acid metabolism, and the mucosal immune system that can result in a changed immunological function, triggering the inflammatory response in Crohn's disease. Recent studies have demonstrated an association with altering the enterohepatic circulation and activating the farnesoid X receptor signalling pathway with the use of probiotics and faecal microbial transplantation, respectively. Bile acid sequestrants have been shown to have anti-inflammatory, cytoprotective, and anti-apoptotic properties with the potential to alter the intestinal microbial composition, suggesting a possible role in inducing and maintaining Crohn's disease. CONCLUSIONS Active Crohn's disease has been correlated with changes in bacterial concentrations, which may be associated with changes in bile acid modification. Further research should focus on targeting these areas for future therapeutic options.
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Inactivation of the Pyrimidine Biosynthesis pyrD Gene Negatively Affects Biofilm Formation and Virulence Determinants in the Crohn’s Disease-Associated Adherent Invasive Escherichia coli LF82 Strain. Microorganisms 2022; 10:microorganisms10030537. [PMID: 35336113 PMCID: PMC8956108 DOI: 10.3390/microorganisms10030537] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/17/2022] [Accepted: 02/26/2022] [Indexed: 01/07/2023] Open
Abstract
In Crohn’s disease (CD) patients, the adherent-invasive Escherichia coli (AIEC) pathovar contributes to the chronic inflammation typical of the disease via its ability to invade gut epithelial cells and to survive in macrophages. We show that, in the AIEC strain LF82, inactivation of the pyrD gene, encoding dihydroorotate dehydrogenase (DHOD), an enzyme of the de novo pyrimidine biosynthetic pathway, completely abolished its ability of to grow in a macrophage environment-mimicking culture medium. In addition, pyrD inactivation reduced flagellar motility and strongly affected biofilm formation by downregulating transcription of both type 1 fimbriae and curli subunit genes. Thus, the pyrD gene appears to be essential for several cellular processes involved in AIEC virulence. Interestingly, vidofludimus (VF), a DHOD inhibitor, has been proposed as an effective drug in CD treatment. Despite displaying a potentially similar binding mode for both human and E. coli DHOD in computational molecular docking experiments, VF showed no activity on either growth or virulence-related processes in LF82. Altogether, our results suggest that the crucial role played by the pyrD gene in AIEC virulence, and the presence of structural differences between E. coli and human DHOD allowing for the design of specific inhibitors, make E. coli DHOD a promising target for therapeutical strategies aiming at counteracting chronic inflammation in CD by acting selectively on its bacterial triggers.
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19
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Bacteriophages and their potential for treatment of gastrointestinal diseases. Nat Rev Gastroenterol Hepatol 2022; 19:135-144. [PMID: 34782783 PMCID: PMC8966578 DOI: 10.1038/s41575-021-00536-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 02/08/2023]
Abstract
Although bacteriophages have been overshadowed as therapeutic agents by antibiotics for decades, the emergence of multidrug-resistant bacteria and a better understanding of the role of the gut microbiota in human health and disease have brought them back into focus. In this Perspective, we briefly introduce basic phage biology and summarize recent discoveries about phages in relation to their role in the gut microbiota and gastrointestinal diseases, such as inflammatory bowel disease and chronic liver disease. In addition, we review preclinical studies and clinical trials of phage therapy for enteric disease and explore current challenges and potential future directions.
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20
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Zheng Y, Yu Y, Chen XF, Yang SL, Tang XL, Xiang ZG. Intestinal Macrophage Autophagy and its Pharmacological Application in Inflammatory Bowel Disease. Front Pharmacol 2021; 12:803686. [PMID: 34899362 PMCID: PMC8652230 DOI: 10.3389/fphar.2021.803686] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/09/2021] [Indexed: 11/28/2022] Open
Abstract
Inflammatory bowel disease (IBD), comprised of Crohn’s disease (CD) and ulcerative colitis (UC), is a group of chronic inflammatory disorders. IBD is regarded as a severe healthcare problem worldwide, with high morbidity and lethality. So far, despite of numerous studies on this issue, the specific mechanisms of IBD still remain unclarified and ideal treatments are not available for IBD. The intestinal mucosal barrier is vital for maintaining the function of the intestinal self-defensive system. Among all of the components, macrophage is an important one in the intestinal self-defensive system, normally protecting the gut against exotic invasion. However, the over-activation of macrophages in pathological conditions leads to the overwhelming induction of intestinal inflammatory and immune reaction, thus damaging the intestinal functions. Autophagy is an important catabolic mechanism. It has been proven to participate the regulation of various kinds of inflammation- and immune-related disorders via the regulation of inflammation in related cells. Here in this paper, we will review the role and mechanism of intestinal macrophage autophagy in IBD. In addition, several well-studied kinds of agents taking advantage of intestinal macrophage autophagy for the treatment of IBD will also be discussed. We aim to bring novel insights in the development of therapeutic strategies against IBD.
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Affiliation(s)
- Yang Zheng
- Department of Gastroenterology, 904 Hospital of PLA Joint Logistic Support Force, Wuxi, China
| | - Yang Yu
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xu-Feng Chen
- Department of Gastroenterology, 904 Hospital of PLA Joint Logistic Support Force, Wuxi, China
| | - Sheng-Lan Yang
- Department of Gastroenterology, 904 Hospital of PLA Joint Logistic Support Force, Wuxi, China
| | - Xiao-Long Tang
- Department of Gastroenterology, 904 Hospital of PLA Joint Logistic Support Force, Wuxi, China
| | - Zheng-Guo Xiang
- Department of Gastroenterology, 904 Hospital of PLA Joint Logistic Support Force, Wuxi, China
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21
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Hsu CL, Duan Y, Fouts DE, Schnabl B. Intestinal virome and therapeutic potential of bacteriophages in liver disease. J Hepatol 2021; 75:1465-1475. [PMID: 34437908 PMCID: PMC8929164 DOI: 10.1016/j.jhep.2021.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 12/19/2022]
Abstract
Humans harbour a large quantity of microbes in the intestinal tract and have evolved symbiotic relationships with many of them. However, several specific bacterial pathobionts are associated with liver disease pathogenesis. Although bacteriophages (phages) and eukaryotic viruses (collectively known as "the virome") outnumber bacteria and fungi in the intestine, little is known about the intestinal virome in patients with liver disease. As natural predators of bacteria, phages can precisely edit the bacterial microbiota. Hence, there is interest in using them to target bacterial pathobionts in several diseases, including those of the liver. Herein, we will summarise changes in the faecal virome associated with fatty liver diseases and cirrhosis, and describe the therapeutic potential of phages and potential challenges to their clinical application.
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Affiliation(s)
- Cynthia L Hsu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yi Duan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - 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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22
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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: 25] [Impact Index Per Article: 8.3] [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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Iriflophenone-3-C-β-d Glucopyranoside from Dryopteris ramosa (Hope) C. Chr. with Promising Future as Natural Antibiotic for Gastrointestinal Tract Infections. Antibiotics (Basel) 2021; 10:antibiotics10091128. [PMID: 34572710 PMCID: PMC8466121 DOI: 10.3390/antibiotics10091128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022] Open
Abstract
Ethnopharmacological approaches provide clues for the search of bioactive compounds. Dryopteris ramosa (Hope) C. Chr. (plant family: Dryopteridaceae) is an ethnomedicinal plant of the Galliyat region of Pakistan. The aqueous fraction (AqF) of D. ramosa is being used by inhabitants of the Galliyat region of Pakistan to treat their gastrointestinal tract ailments, especially those caused by bacteria. The aims of the present study were as follows: (i) to justify the ethnomedicinal uses of the AqF of D. ramosa; (ii) to isolate a bioactive compound from the AqF of D. ramosa; and (iii) to evaluate the antibacterial and cytotoxic potential of the isolated compound. Column chromatography (CC) techniques were used for the isolation studies. Spectroscopic techniques (UV–Vis, MS, 1&2D NMR) were used for structural elucidation. The agar-well diffusion method was used to evaluate the antibacterial potential of “i3CβDGP” against five bacterial strains, and compare it with the known antibiotic “Cefixime”. The brine shrimp lethality test (BSLT) was used for cytotoxic studies. The AqF of D. ramosa afforded “iriflophenone-3-C-β-D glucopyranoside (i3CβDGP)” when subjected to LH20 Sephadex, followed by MPLC silica gel60, and purified by preparative TLC. The “i3CβDGP” showed a strong potential (MIC = 31.1 ± 7.2, 62.5 ± 7.2, and 62.5 ± 7.2 µg/mL) against Klebsiella pneumoniae, Staphylococcus aureus, and Escherichia coli, respectively. On the other hand, the least antibacterial potential was shown by “i3CβDGP” (MIC = 125 ± 7.2 µg/mL), against Bacillus subtilis, in comparison to Cefixime (MIC = 62.5 ± 7.2 µg/mL). The cytotoxicity of “i3CβDGP” was significantly low (LD50 = 10.037 ± 2.8 µg/mL) against Artemia salina nauplii. This study not only justified the ethnomedicinal use of D. ramosa, but also highlighted the importance of ethnomedicinal knowledge. Further studies on AqF and other fractions of D. ramosa are in progress.
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Meza-Torres J, Auria E, Dupuy B, Tremblay YDN. Wolf in Sheep's Clothing: Clostridioides difficile Biofilm as a Reservoir for Recurrent Infections. Microorganisms 2021; 9:1922. [PMID: 34576818 PMCID: PMC8470499 DOI: 10.3390/microorganisms9091922] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 12/21/2022] Open
Abstract
The microbiota inhabiting the intestinal tract provide several critical functions to its host. Microorganisms found at the mucosal layer form organized three-dimensional structures which are considered to be biofilms. Their development and functions are influenced by host factors, host-microbe interactions, and microbe-microbe interactions. These structures can dictate the health of their host by strengthening the natural defenses of the gut epithelium or cause disease by exacerbating underlying conditions. Biofilm communities can also block the establishment of pathogens and prevent infectious diseases. Although these biofilms are important for colonization resistance, new data provide evidence that gut biofilms can act as a reservoir for pathogens such as Clostridioides difficile. In this review, we will look at the biofilms of the intestinal tract, their contribution to health and disease, and the factors influencing their formation. We will then focus on the factors contributing to biofilm formation in C. difficile, how these biofilms are formed, and their properties. In the last section, we will look at how the gut microbiota and the gut biofilm influence C. difficile biofilm formation, persistence, and transmission.
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Affiliation(s)
- Jazmin Meza-Torres
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Emile Auria
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Yannick D. N. Tremblay
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
- Health Sciences Building, Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK S7N 5E5, Canada
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Jergens AE, Parvinroo S, Kopper J, Wannemuehler MJ. Rules of Engagement: Epithelial-Microbe Interactions and Inflammatory Bowel Disease. Front Med (Lausanne) 2021; 8:669913. [PMID: 34513862 PMCID: PMC8432614 DOI: 10.3389/fmed.2021.669913] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are complex, multifactorial disorders that lead to chronic and relapsing intestinal inflammation. The exact etiology remains unknown, however multiple factors including the environment, genetic, dietary, mucosal immunity, and altered microbiome structure and function play important roles in disease onset and progression. Supporting this notion that the gut microbiota plays a pivotal role in IBD pathogenesis, studies in gnotobiotic mice have shown that mouse models of intestinal inflammation require a microbial community to develop colitis. Additionally, antimicrobial therapy in some IBD patients will temporarily induce remission further demonstrating an association between gut microbes and intestinal inflammation. Finally, a dysfunctional intestinal epithelial barrier is also recognized as a key pathogenic factor in IBD. The intestinal epithelium serves as a barrier between the luminal environment and the mucosal immune system and guards against harmful molecules and microorganisms while being permeable to essential nutrients and solutes. Beneficial (i.e., mutualists) bacteria promote mucosal health by strengthening barrier integrity, increasing local defenses (mucin and IgA production) and inhibiting pro-inflammatory immune responses and apoptosis to promote mucosal homeostasis. In contrast, pathogenic bacteria and pathobionts suppress expression and localization of tight junction proteins, cause dysregulation of apoptosis/proliferation and increase pro-inflammatory signaling that directly damages the intestinal mucosa. This review article will focus on the role of intestinal epithelial cells (IECs) and the luminal environment acting as mediators of barrier function in IBD. We will also share some of our translational observations of interactions between IECs, immune cells, and environmental factors contributing to maintenance of mucosal homeostasis, as it relates to GI inflammation and IBD in different animal models.
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Affiliation(s)
- Albert E. Jergens
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Shadi Parvinroo
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Jamie Kopper
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Michael J. Wannemuehler
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
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Bhattacharjee A, Burr AHP, Overacre-Delgoffe AE, Tometich JT, Yang D, Huckestein BR, Linehan JL, Spencer SP, Hall JA, Harrison OJ, Morais da Fonseca D, Norton EB, Belkaid Y, Hand TW. Environmental enteric dysfunction induces regulatory T cells that inhibit local CD4+ T cell responses and impair oral vaccine efficacy. Immunity 2021; 54:1745-1757.e7. [PMID: 34348118 DOI: 10.1016/j.immuni.2021.07.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 04/21/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022]
Abstract
Environmental enteric dysfunction (EED) is a gastrointestinal inflammatory disease caused by malnutrition and chronic infection. EED is associated with stunting in children and reduced efficacy of oral vaccines. To study the mechanisms of oral vaccine failure during EED, we developed a microbiota- and diet-dependent mouse EED model. Analysis of E. coli-labile toxin vaccine-specific CD4+ T cells in these mice revealed impaired CD4+ T cell responses in the small intestine and but not the lymph nodes. EED mice exhibited increased frequencies of small intestine-resident RORγT+FOXP3+ regulatory T (Treg) cells. Targeted deletion of RORγT from Treg cells restored small intestinal vaccine-specific CD4 T cell responses and vaccine-mediated protection upon challenge. However, ablation of RORγT+FOXP3+ Treg cells made mice more susceptible to EED-induced stunting. Our findings provide insight into the poor efficacy of oral vaccines in EED and highlight how RORγT+FOXP3+ Treg cells can regulate intestinal immunity while leaving systemic responses intact.
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Affiliation(s)
- Amrita Bhattacharjee
- R.K. Mellon Institute for Pediatric Research, Pediatrics Department, Infectious Disease Section, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224 USA
| | - Ansen H P Burr
- R.K. Mellon Institute for Pediatric Research, Pediatrics Department, Infectious Disease Section, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224 USA; Program in Microbiology and Immunology, Department of Immunology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15261, USA
| | - Abigail E Overacre-Delgoffe
- R.K. Mellon Institute for Pediatric Research, Pediatrics Department, Infectious Disease Section, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224 USA
| | - Justin T Tometich
- R.K. Mellon Institute for Pediatric Research, Pediatrics Department, Infectious Disease Section, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224 USA
| | - Deyi Yang
- R.K. Mellon Institute for Pediatric Research, Pediatrics Department, Infectious Disease Section, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224 USA; Central South University, Xiangya School of Medicine, Changsha, PRC
| | - Brydie R Huckestein
- Program in Microbiology and Immunology, Department of Immunology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15261, USA
| | - Jonathan L Linehan
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Sean P Spencer
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Jason A Hall
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Oliver J Harrison
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Denise Morais da Fonseca
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth B Norton
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Timothy W Hand
- R.K. Mellon Institute for Pediatric Research, Pediatrics Department, Infectious Disease Section, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224 USA; Program in Microbiology and Immunology, Department of Immunology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15261, USA.
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27
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Atreya R, Siegmund B. Location is important: differentiation between ileal and colonic Crohn's disease. Nat Rev Gastroenterol Hepatol 2021; 18:544-558. [PMID: 33712743 DOI: 10.1038/s41575-021-00424-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/29/2021] [Indexed: 01/31/2023]
Abstract
Crohn's disease can affect any part of the gastrointestinal tract; however, current European and national guidelines worldwide do not differentiate between small-intestinal and colonic Crohn's disease for medical treatment. Data from the past decade provide evidence that ileal Crohn's disease is distinct from colonic Crohn's disease in several intestinal layers. Remarkably, colonic Crohn's disease shows an overlap with regard to disease behaviour with ulcerative colitis, underlining the fact that there is more to inflammatory bowel disease than just Crohn's disease and ulcerative colitis, and that subtypes, possibly defined by location and shared pathophysiology, are also important. This Review provides a structured overview of the differentiation between ileal and colonic Crohn's disease using data in the context of epidemiology, genetics, macroscopic differences such as creeping fat and histological findings, as well as differences in regard to the intestinal barrier including gut microbiota, mucus layer, epithelial cells and infiltrating immune cell populations. We also discuss the translation of these basic findings to the clinic, emphasizing the important role of treatment decisions. Thus, this Review provides a conceptual outlook on a new mechanism-driven classification of Crohn's disease.
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Affiliation(s)
- Raja Atreya
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Britta Siegmund
- Department of Gastroenterology, Infectious Diseases and Rheumatology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
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Zhang Y, Thompson KN, Huttenhower C, Franzosa EA. Statistical approaches for differential expression analysis in metatranscriptomics. Bioinformatics 2021; 37:i34-i41. [PMID: 34252963 PMCID: PMC8275336 DOI: 10.1093/bioinformatics/btab327] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Motivation Metatranscriptomics (MTX) has become an increasingly practical way to profile the functional activity of microbial communities in situ. However, MTX remains underutilized due to experimental and computational limitations. The latter are complicated by non-independent changes in both RNA transcript levels and their underlying genomic DNA copies (as microbes simultaneously change their overall abundance in the population and regulate individual transcripts), genetic plasticity (as whole loci are frequently gained and lost in microbial lineages) and measurement compositionality and zero-inflation. Here, we present a systematic evaluation of and recommendations for differential expression (DE) analysis in MTX. Results We designed and assessed six statistical models for DE discovery in MTX that incorporate different combinations of DNA and RNA normalization and assumptions about the underlying changes of gene copies or species abundance within communities. We evaluated these models on multiple simulated and real multi-omic datasets. Models adjusting transcripts relative to their encoding gene copies as a covariate were significantly more accurate in identifying DE from MTX in both simulated and real datasets. Moreover, we show that when paired DNA measurements (metagenomic data) are not available, models normalizing MTX measurements within-species while also adjusting for total-species RNA balance sensitivity, specificity and interpretability of DE detection, as does filtering likely technical zeros. The efficiency and accuracy of these models pave the way for more effective MTX-based DE discovery in microbial communities. Availability and implementation The analysis code and synthetic datasets used in this evaluation are available online at http://huttenhower.sph.harvard.edu/mtx2021. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yancong Zhang
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Eric A Franzosa
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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29
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Nadalian B, Yadegar A, Houri H, Olfatifar M, Shahrokh S, Asadzadeh Aghdaei H, Suzuki H, Zali MR. Prevalence of the pathobiont adherent-invasive Escherichia coli and inflammatory bowel disease: a systematic review and meta-analysis. J Gastroenterol Hepatol 2021; 36:852-863. [PMID: 32929762 DOI: 10.1111/jgh.15260] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/08/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIM Escherichia coli pathobionts and particularly the adherent-invasive E. coli (AIEC) may play a putative role in initiating and maintaining the inflammatory process in the intestinal tissues of inflammatory bowel disease (IBD) patients, by providing stimulatory factors that trigger gut immune system activation. The aim of this study is to conduct a systematic review and meta-analysis to determine the prevalence of AIEC among patients with Crohn's disease (CD) and ulcerative colitis (UC). METHODS Electronic databases were searched up to February 2020 for relevant publications reporting the prevalence of AIEC in IBD patients. The prevalence rate of AIEC among CD and UC patients, the odds ratio (OR) and 95% confidence interval (CI) were calculated compared to non-IBD controls. RESULTS The final dataset included 12 studies, all investigating AIEC isolates from ileal/colonic specimens. The OR for prevalence of AIEC in CD patients was 3.27 (95% CI 1.79-5.9) compared with non-IBD controls. The overall pooled prevalence of AIEC among CD patients was 29% (95% CI 0.17-0.45), whereas this prevalence was calculated to be 9% (95% CI 0.03-0.19) in controls. Moreover, the prevalence of AIEC in UC subjects was calculated 12% (95% CI 0.01-0.34), while AIEC showed a prevalence of 5% (95% CI 0.0-0.17) among the controls. The OR for prevalence of AIEC in UC patients was 2.82 (95% CI 1.11-7.14) compared with controls. CONCLUSIONS There is a substantial increase in the prevalence of AIEC in IBD patients compared with controls. This review supports the growing evidence that AIEC could be involved in both CD and UC pathogenesis.
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Affiliation(s)
- Banafsheh Nadalian
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Houri
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Meysam Olfatifar
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hidekazu Suzuki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, School of Medicine, Tokai University, Isehara, Japan
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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The Role of Enterobacteriaceae in Gut Microbiota Dysbiosis in Inflammatory Bowel Diseases. Microorganisms 2021; 9:microorganisms9040697. [PMID: 33801755 PMCID: PMC8066304 DOI: 10.3390/microorganisms9040697] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are a group of chronic gastrointestinal inflammatory diseases with unknown etiology. There is a combination of well documented factors in their pathogenesis, including intestinal microbiota dysbiosis. The symbiotic microbiota plays important functions in the host, and the loss of beneficial microbes could favor the expansion of microbial pathobionts. In particular, the bloom of potentially harmful Proteobacteria, especially Enterobacteriaceae, has been described as enhancing the inflammatory response, as observed in IBDs. Herein, we seek to investigate the contribution of Enterobacteriaceae to IBD pathogenesis whilst considering the continuous expansion of the literature and data. Despite the mechanism of their expansion still remaining unclear, their expansion could be correlated with the increase in nitrate and oxygen levels in the inflamed gut and with the bile acid dysmetabolism described in IBD patients. Furthermore, in several Enterobacteriaceae studies conducted at a species level, it has been suggested that some adherent-invasive Escherichia coli (AIEC) play an important role in IBD pathogenesis. Overall, this review highlights the pivotal role played by Enterobacteriaceae in gut dysbiosis associated with IBD pathogenesis and progression.
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Gasaly N, Hermoso MA, Gotteland M. Butyrate and the Fine-Tuning of Colonic Homeostasis: Implication for Inflammatory Bowel Diseases. Int J Mol Sci 2021; 22:ijms22063061. [PMID: 33802759 PMCID: PMC8002420 DOI: 10.3390/ijms22063061] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
This review describes current evidence supporting butyrate impact in the homeostatic regulation of the digestive ecosystem in health and inflammatory bowel diseases (IBDs). Butyrate is mainly produced by bacteria from the Firmicutes phylum. It stimulates mature colonocytes and inhibits undifferentiated malignant and stem cells. Butyrate oxidation in mature colonocytes (1) produces 70–80% of their energetic requirements, (2) prevents stem cell inhibition by limiting butyrate access to crypts, and (3) consumes oxygen, generating hypoxia and maintaining luminal anaerobiosis favorable to the microbiota. Butyrate stimulates the aryl hydrocarbon receptor (AhR), the GPR41 and GPR109A receptors, and inhibits HDAC in different cell types, thus stabilizing the gut barrier function and decreasing inflammatory processes. However, some studies indicate contrary effects according to butyrate concentrations. IBD patients exhibit a lower abundance of butyrate-producing bacteria and butyrate content. Additionally, colonocyte butyrate oxidation is depressed in these subjects, lowering luminal anaerobiosis and facilitating the expansion of Enterobacteriaceae that contribute to inflammation. Accordingly, gut dysbiosis and decreased barrier function in IBD seems to be secondary to the impaired mitochondrial disturbance in colonic epithelial cells.
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Affiliation(s)
- Naschla Gasaly
- Department of Nutrition, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile;
- Laboratory of Innate Immunity, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile;
| | - Marcela A. Hermoso
- Laboratory of Innate Immunity, Program of Immunology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile;
| | - Martín Gotteland
- Department of Nutrition, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile;
- Department of Human Nutrition, Institute of Nutrition and Food Technology (INTA), Universidad de Chile, Santiago 7830490, Chile
- Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago 8380453, Chile
- Correspondence: ; Tel.: +56-989-059-222
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Yoshimatsu Y, Mikami Y, Kanai T. Bacteriotherapy for inflammatory bowel disease. Inflamm Regen 2021; 41:3. [PMID: 33441186 PMCID: PMC7807454 DOI: 10.1186/s41232-020-00153-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
The number of patients with inflammatory bowel disease is rapidly increasing in developed countries. The main cause of this increase is thought not to be genetic, but secondary to rapidly modernized environmental change. Changes in the environment have been detrimental to enteric probiotics useful for fermentation, inducing an increase in pathobionts that survive by means other than fermentation. This dysregulated microbiota composition, the so-called dysbiosis, is believed to have increased the incidence of inflammatory bowel disease. Bacteriotherapy, a treatment that prophylactically and therapeutically corrects the composition of disturbed intestinal microbiota, is a promising recent development. In fact, fecal microbiome transplantation for recurrent Clostridioides difficile infection in 2013 was a significant contribution for bacteriotherapy. In this paper, we comprehensively review bacteriotherapy in an easy-to-understand format.
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Affiliation(s)
- Yusuke Yoshimatsu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
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De Musis C, Granata L, Dallio M, Miranda A, Gravina AG, Romano M. Inflammatory Bowel Diseases: The Role of Gut Microbiota. Curr Pharm Des 2021; 26:2951-2961. [PMID: 32310042 DOI: 10.2174/1381612826666200420144128] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/13/2020] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel diseases (IBD) are chronic multifactorial diseases characterized by partially unclear pathogenic mechanisms including changes in intestinal microbiota. Despite the microbiota, alteration is well established in IBD patients, as reported by 16RNA sequencing analysis, an important goal is to define if it is just a consequence of the disease progression or a trigger factor of the disease itself. To date, gut microbiota composition and gut microbiota-related metabolites seem to affect the host healthy state both by modulating metabolic pathways or acting on the expression of different genes through epigenetic effects. Because of this, it has been suggested that intestinal microbiota might represent a promising therapeutic target for IBD patients. The aim of this review is to summarize both the most recent acquisitions in the field of gut microbiota and its involvement in intestinal inflammation together with the available strategies for the modulation of microbiota, such as prebiotics and/or probiotics administration or fecal microbiota transplantation.
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Affiliation(s)
- Cristiana De Musis
- Departments of Precision Medicine and Polyspecialistic Internal Medicine, University of Campania ''Luigi Vanvitelli'' and University Hospital, Naples, Italy
| | - Lucia Granata
- Departments of Precision Medicine and Polyspecialistic Internal Medicine, University of Campania ''Luigi Vanvitelli'' and University Hospital, Naples, Italy
| | - Marcello Dallio
- Departments of Precision Medicine and Polyspecialistic Internal Medicine, University of Campania ''Luigi Vanvitelli'' and University Hospital, Naples, Italy
| | - Agnese Miranda
- Departments of Precision Medicine and Polyspecialistic Internal Medicine, University of Campania ''Luigi Vanvitelli'' and University Hospital, Naples, Italy
| | - Antonietta G Gravina
- Departments of Precision Medicine and Polyspecialistic Internal Medicine, University of Campania ''Luigi Vanvitelli'' and University Hospital, Naples, Italy
| | - Marco Romano
- Departments of Precision Medicine and Polyspecialistic Internal Medicine, University of Campania ''Luigi Vanvitelli'' and University Hospital, Naples, Italy
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Nejadghaderi SA, Nazemalhosseini-Mojarad E, Asadzadeh Aghdaei H. Fecal microbiota transplantation for COVID-19; a potential emerging treatment strategy. Med Hypotheses 2020; 147:110476. [PMID: 33482620 PMCID: PMC7774521 DOI: 10.1016/j.mehy.2020.110476] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/05/2020] [Accepted: 12/26/2020] [Indexed: 02/06/2023]
Abstract
At the end of 2019, an emerging outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that first reported from Wuhan, China. The first manifestations of patients infected with SARS-CoV-2 was flu-like symptoms, while other type of manifestations, especially gastrointestinal manifestations were discovered recently. As of June 2020, there is no specific drug or treatment strategy for COVID-19, a disease caused by SARS-CoV-2, so different combination of antiviral drugs is currently being used. Gut microbiota mostly consists of four phyla, including Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. The interaction between gut microbiota and immune system through releasing some cytokines such as IL-1β, IL-2, IL-10, TNF-α, and IFN-γ that play roles in the severity of COVID-19. In this article, a new potential treatment for COVID-19 by fecal microbiota transplantation (FMT) is described. FMT revealed promising results in different diseases, especially recurrent clostridium difficile infection, and it might reduce length of hospital admission and severity of the disease by modification of gut microbiota composition.
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Affiliation(s)
- Seyed Aria Nejadghaderi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology & Liver Diseases Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Govindarajan DK, Viswalingam N, Meganathan Y, Kandaswamy K. Adherence patterns of Escherichia coli in the intestine and its role in pathogenesis. MEDICINE IN MICROECOLOGY 2020. [DOI: 10.1016/j.medmic.2020.100025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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36
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Metwaly A, Dunkel A, Waldschmitt N, Raj ACD, Lagkouvardos I, Corraliza AM, Mayorgas A, Martinez-Medina M, Reiter S, Schloter M, Hofmann T, Allez M, Panes J, Salas A, Haller D. Integrated microbiota and metabolite profiles link Crohn's disease to sulfur metabolism. Nat Commun 2020; 11:4322. [PMID: 32859898 PMCID: PMC7456324 DOI: 10.1038/s41467-020-17956-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Gut microbial and metabolite alterations have been linked to the pathogenesis of inflammatory bowel diseases. Here we perform a multi-omics microbiome and metabolite analysis of a longitudinal cohort of Crohn's disease patients undergoing autologous hematopoietic stem cell transplantation, and investigational therapy that induces drug free remission in a subset of patients. Via comparison of patients who responded and maintained remission, responded but experienced disease relapse and patients who did not respond to therapy, we identify shared functional signatures that correlate with disease activity despite the variability of gut microbiota profiles at taxonomic level. These signatures reflect the disease state when transferred to gnotobiotic mice. Taken together, the integration of microbiome and metabolite profiles from human cohort and mice improves the predictive modelling of disease outcome, and allows the identification of a network of bacteria-metabolite interactions involving sulfur metabolism as a key mechanism linked to disease activity in Crohn's disease.
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Affiliation(s)
- Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Andreas Dunkel
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, Freising, Germany
| | - Nadine Waldschmitt
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Abilash Chakravarthy Durai Raj
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Munich, Germany
| | - Ilias Lagkouvardos
- ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - Ana Maria Corraliza
- Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Aida Mayorgas
- Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | | | - Sinah Reiter
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Freising, Germany
| | - Michael Schloter
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Munich, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Freising, Germany
| | - Matthieu Allez
- APHP, Hôpital Saint Louis, Department of Gastroenterology, INSERM UMRS 1160, Paris Diderot, Sorbonne Paris-Cité University, Paris, France
| | - Julian Panes
- Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Azucena Salas
- Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany.
- ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany.
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Bilski J, Wojcik D, Danielak A, Mazur-Bialy A, Magierowski M, Tønnesen K, Brzozowski B, Surmiak M, Magierowska K, Pajdo R, Ptak-Belowska A, Brzozowski T. Alternative Therapy in the Prevention of Experimental and Clinical Inflammatory Bowel Disease. Impact of Regular Physical Activity, Intestinal Alkaline Phosphatase and Herbal Products. Curr Pharm Des 2020; 26:2936-2950. [DOI: 10.2174/1381612826666200427090127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/18/2020] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel diseases (IBD), such as ulcerative colitis and Crohn's disease, are multifactorial, chronic, disabling, and progressive diseases characterised by cyclical nature, alternating between active and quiescent states. While the aetiology of IBD is not fully understood, this complex of diseases involve a combination of factors including the genetic predisposition and changes in microbiome as well as environmental risk factors such as high-fat and low-fibre diets, reduced physical activity, air pollution and exposure to various toxins and drugs such as antibiotics. The prevalence of both IBD and obesity is increasing in parallel, undoubtedly proving the existing interactions between these risk factors common to both disorders to unravel poorly recognized cell signaling and molecular alterations leading to human IBD. Therefore, there is still a significant and unmet need for supportive and adjunctive therapy for IBD patients directed against the negative consequences of visceral obesity and bacterial dysbiosis. Among the alternative therapies, a moderate-intensity exercise can benefit the health and well-being of IBD patients and improve both the healing of human IBD and experimental animal colitis. Intestinal alkaline phosphatase (IAP) plays an essential role in the maintenance of intestinal homeostasis intestinal and the mechanism of mucosal defence. The administration of exogenous IAP could be recommended as a therapeutic strategy for the cure of diseases resulting from the intestinal barrier dysfunction such as IBD. Curcumin, a natural anti-inflammatory agent, which is capable of stimulating the synthesis of endogenous IAP, represents another alternative approach in the treatment of IBD. This review was designed to discuss potential “nonpharmacological” alternative and supplementary therapeutic approaches taking into account epidemiological and pathophysiological links between obesity and IBD, including changes in the functional parameters of the intestinal mucosa and alterations in the intestinal microbiome.
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Affiliation(s)
- Jan Bilski
- Department of Ergonomics and Exercise Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, Cracow, Poland
| | - Dagmara Wojcik
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Aleksandra Danielak
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Agnieszka Mazur-Bialy
- Department of Ergonomics and Exercise Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, Cracow, Poland
| | - Marcin Magierowski
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Katherine Tønnesen
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Bartosz Brzozowski
- Gastroenterology and Hepatology Clinic, Jagiellonian University Medical College, Cracow, Poland
| | - Marcin Surmiak
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Katarzyna Magierowska
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Robert Pajdo
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Agata Ptak-Belowska
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Tomasz Brzozowski
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
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Risk of colorectal cancer in inflammatory bowel diseases. Semin Cancer Biol 2020; 64:51-60. [DOI: 10.1016/j.semcancer.2019.05.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 12/21/2022]
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A Comparative Study of the Adherent-Invasive Escherichia coli Population and Gut Microbiota of Healthy Vegans versus Omnivores. Microorganisms 2020; 8:microorganisms8081165. [PMID: 32751971 PMCID: PMC7465959 DOI: 10.3390/microorganisms8081165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strains carry virulence genes (VGs) which are rarely found in strains other than E. coli. These strains are abundantly found in gut mucosa of patients with inflammatory bowel disease (IBD); however, it is not clear whether their prevalence in the gut is affected by the diet of the individual. Therefore, in this study, we compared the population structure of E. coli and the prevalence of AIEC as well as the composition of gut microbiota in fecal samples of healthy participants (n = 61) on either a vegan (n = 34) or omnivore (n = 27) diet to determine whether diet is associated with the presence of AIEC. From each participant, 28 colonies of E. coli were typed using Random Amplified Polymorphic DNA (RAPD)–PCR. A representative of each common type within an individual was tested for the presence of six AIEC-associated VGs. Whole genomic DNA of the gut microbiota was also analyzed for its diversity profiles, utilizing the V5-V6 region of the16S rRNA gene sequence. There were no significant differences in the abundance and diversity of E. coli between the two diet groups. The occurrence of AIEC-associated VGs was also similar among the two groups. However, the diversity of fecal microbiota in vegans was generally higher than omnivores, with Prevotella and Bacteroides dominant in both groups. Whilst 88 microbial taxa were present in both diet groups, 28 taxa were unique to vegans, compared to seven unique taxa in the omnivores. Our results indicate that a vegan diet may not affect the number and diversity of E. coli populations and AIEC prevalence compared to omnivores. The dominance of Prevotella and Bacteroides among omnivores might be accounted for the effect of diet in these groups.
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Whole brain radiotherapy induces cognitive dysfunction in mice: key role of gut microbiota. Psychopharmacology (Berl) 2020; 237:2089-2101. [PMID: 32494972 DOI: 10.1007/s00213-020-05520-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/10/2020] [Indexed: 12/16/2022]
Abstract
RATIONALE Approximately 20-40% of patients with cancer will experience brain metastasis (BM), which has a great impact on the quality of life and survival rates of patients. Whole brain radiotherapy (WBRT) is an effective method for the treatment of BM. However, it cannot be ignored that WBRT might induce a series of neuropsychiatric side effects, including cognitive dysfunction (CD). Accumulating evidence shows that the gut microbiota and the gut-microbiota-brain axis may play a vital role in the pathogenesis of CD. OBJECTIVE AND METHODS We adopted WBRT to mimic CD after a hierarchical cluster analysis of the Morris water maze test (MWMT) results. In addition, we observed the effects of antibiotics and prebiotics on WBRT-induced CD. Variations were revealed via the 16S rRNA sequencing analysis at different levels. RESULTS The 16S rRNA sequencing analysis revealed an altered composition of gut microbiota between CD and non-CD phenotypes. Furthermore, we observed a decrease in the levels of Phylum-Bacteroidete, Class-Bacteroidia, and Order-Bacteroidales in the CD group and an increase in the Genus-Allobaculum level after WBRT. Pretreatment with antibiotics caused a significant decrease in the level of Phylum-TM7 01, whereas an increase in the levels of Class-Gammaproteobacteria, Order-Enterobacteriales, and Species-Escherichia coli. After pretreatment with probiotics, the levels of Phylum-Cyanobacteria, Class-4C0d-2, and Order-YS2 were decreased, while the levels of Family-Bacteroidaceae, Genus-Bacteroides, and Species-Parabacteroides distasonis were increased. CONCLUSIONS WBRT-induced CD might be highly related to abnormal composition of gut microbiota. Strategies improving the composition of the gut microbiota may provide beneficial effects on CD in individuals exposed to WBRT.
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Park SK, Kim HN, Choi CH, Im JP, Cha JM, Eun CS, Kim TO, Kang SB, Bang KB, Kim HG, Jung Y, Yoon H, Han DS, Lee CW, Ahn K, Kim HL, Park DI. Differentially Abundant Bacterial Taxa Associated with Prognostic Variables of Crohn's Disease: Results from the IMPACT Study. J Clin Med 2020; 9:E1748. [PMID: 32516912 PMCID: PMC7357029 DOI: 10.3390/jcm9061748] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/30/2020] [Accepted: 06/02/2020] [Indexed: 12/18/2022] Open
Abstract
Limited studies have examined the intestinal microbiota composition in relation to Crohn's disease (CD) prognosis. We analyzed the differences in microbial communities and relevant metabolic pathways associated with prognostic variables in patients with CD. We applied 16S rRNA gene sequencing to analyze a cohort of 1110 CD and healthy control (HC) fecal samples. We categorized patients with CD into good (CD-G), intermediate (CD-I) and poor (CD-P) prognosis groups, according to the history of using biologics and intestinal resection. Microbiota α-diversity decreased more in CD-P than CD-G and CD-I. Microbiota ß-diversity in CD-P differed from that in CD-G and CD-I. Thirteen genera and 10 species showed differential abundance between CD-G and CD-P groups. Escherichia coli (p = 0.001) and species Producta (p = 0.01) and genera Lactobacillus (p = 0.003) and Coprococcus (p = 0.01) consistently showed differences between CD-G and CD-P groups after adjusting for confounding variables. Functional profiling suggested that the microbial catabolic pathways and pathways related to enterobacterial common antigen and lipopolysaccharide biosynthesis were better represented in the CD-P group than in the CD-G group, and E. coli were the top contributors to these pathways. CD prognosis is associated with altered microbiota composition and decreased diversity, and E. coli might be causally involved in CD progression, and may have adapted to live in inflammatory environments.
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Affiliation(s)
- Soo-kyung Park
- Division of Gastroenterology, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea;
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea; (H.-N.K.); (C.-W.L.)
- Inflammatory Bowel Disease Study Group of the Korean Association for the Study of Intestinal Diseases, Seoul 06193, Korea; (C.H.C.); (J.P.I.); (T.-O.K.); (H.Y.)
| | - Han-Na Kim
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea; (H.-N.K.); (C.-W.L.)
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul 03063, Korea
| | - Chang Hwan Choi
- Inflammatory Bowel Disease Study Group of the Korean Association for the Study of Intestinal Diseases, Seoul 06193, Korea; (C.H.C.); (J.P.I.); (T.-O.K.); (H.Y.)
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul 06973, Korea
| | - Jong Pil Im
- Inflammatory Bowel Disease Study Group of the Korean Association for the Study of Intestinal Diseases, Seoul 06193, Korea; (C.H.C.); (J.P.I.); (T.-O.K.); (H.Y.)
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jae Myung Cha
- Department of Internal Medicine, Kyung Hee University Hospital at Gang Dong, Kyung Hee University School of Medicine, Seoul 02447, Korea;
| | - Chang Soo Eun
- Department of Internal Medicine, Hanyang University Guri Hospital, Guri 11923, Korea; (C.S.E.); (D.-S.H.)
| | - Tae-Oh Kim
- Inflammatory Bowel Disease Study Group of the Korean Association for the Study of Intestinal Diseases, Seoul 06193, Korea; (C.H.C.); (J.P.I.); (T.-O.K.); (H.Y.)
- Division of Gastroenterology, Department of Internal Medicine, Inje University Haeundae Paik Hospital, Busan 48108, Korea
| | - Sang-Bum Kang
- Division of Gastroenterology, Department of Internal medicine, Daejeon St. Mary’s Hospital, The Catholic University of Korea, Daejeon 34943, Korea;
| | - Ki Bae Bang
- Department of Internal Medicine, Dankook University College of Medicine, Cheonan 31116, Korea;
| | - Hyun Gun Kim
- Division of Gastroenterology, Department of Internal Medicine, Soonchunhyang University College of Medicine, Seoul Hospital, Seoul 04401, Korea;
| | - Yunho Jung
- Division of Gastroenterology, Department of Internal Medicine, Soonchunhyang University College of Medicine, Cheonan Hospital, Cheonan 31151, Korea;
| | - Hyuk Yoon
- Inflammatory Bowel Disease Study Group of the Korean Association for the Study of Intestinal Diseases, Seoul 06193, Korea; (C.H.C.); (J.P.I.); (T.-O.K.); (H.Y.)
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Dong-Soo Han
- Department of Internal Medicine, Hanyang University Guri Hospital, Guri 11923, Korea; (C.S.E.); (D.-S.H.)
| | - Chil-Woo Lee
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea; (H.-N.K.); (C.-W.L.)
| | - Kwangsung Ahn
- Functional Genome Institute, PDXen Biosystems Inc., Daejeon 34129, Korea;
| | - Hyung-Lae Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul 07804, Korea;
| | - Dong Il Park
- Division of Gastroenterology, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea;
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea; (H.-N.K.); (C.-W.L.)
- Inflammatory Bowel Disease Study Group of the Korean Association for the Study of Intestinal Diseases, Seoul 06193, Korea; (C.H.C.); (J.P.I.); (T.-O.K.); (H.Y.)
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Yan Y, Drew DA, Markowitz A, Lloyd-Price J, Abu-Ali G, Nguyen LH, Tran C, Chung DC, Gilpin KK, Meixell D, Parziale M, Schuck M, Patel Z, Richter JM, Kelsey PB, Garrett WS, Chan AT, Stadler ZK, Huttenhower C. Structure of the Mucosal and Stool Microbiome in Lynch Syndrome. Cell Host Microbe 2020; 27:585-600.e4. [PMID: 32240601 PMCID: PMC7453618 DOI: 10.1016/j.chom.2020.03.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/22/2019] [Accepted: 03/10/2020] [Indexed: 12/12/2022]
Abstract
The gut microbiota has been associated with colorectal cancer (CRC), but causal alterations preceding CRC have not been elucidated. To prospectively assess microbiome changes prior to colorectal neoplasia, we investigated samples from 100 Lynch syndrome patients using 16S rRNA gene sequencing of colon biopsies, coupled with metagenomic and metatranscriptomic sequencing of feces. Colectomy and CRC history represented the largest effects on microbiome profiles. A subset of Clostridiaceae were depleted in stool corresponding with baseline adenomas, while Desulfovibrio was enriched both in stool and in mucosal biopsies. A classifier leveraging stool metatranscriptomes resulted in modest power to predict interval development of preneoplastic colonic adenoma. Predictive transcripts corresponded with a shift in flagellin contributors and oxidative metabolic microenvironment, potentially factors in local CRC pathogenesis. This suggests that the effectiveness of prospective microbiome monitoring for adenomas may be limited but supports the potential causality of these consistent, early microbial changes in colonic neoplasia.
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Affiliation(s)
- Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David A Drew
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Arnold Markowitz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason Lloyd-Price
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Galeb Abu-Ali
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Long H Nguyen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Christina Tran
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel C Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Katherine K Gilpin
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dana Meixell
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Melanie Parziale
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Madeline Schuck
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Zalak Patel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James M Richter
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter B Kelsey
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wendy S Garrett
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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Camprubí-Font C, Martinez-Medina M. Why the discovery of adherent-invasive Escherichia coli molecular markers is so challenging? World J Biol Chem 2020; 11:1-13. [PMID: 32405343 PMCID: PMC7205867 DOI: 10.4331/wjbc.v11.i1.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/18/2020] [Accepted: 03/31/2020] [Indexed: 02/05/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strains have been extensively related to Crohn’s disease (CD) etiopathogenesis. Higher AIEC prevalence in CD patients versus controls has been reported, and its mechanisms of pathogenicity have been linked to CD physiopathology. In CD, the therapeutic armamentarium remains limited and non-curative; hence, the necessity to better understand AIEC as a putative instigator or propagator of the disease is certain. Nonetheless, AIEC identification is currently challenging because it relies on phenotypic assays based on infected cell cultures which are highly time-consuming, laborious and non-standardizable. To address this issue, AIEC molecular mechanisms and virulence genes have been studied; however, a specific and widely distributed genetic AIEC marker is still missing. The finding of molecular tools to easily identify AIEC could be useful in the identification of AIEC carriers who could profit from personalized treatment. Also, it would significantly promote AIEC epidemiological studies. Here, we reviewed the existing data regarding AIEC genetics and presented those molecular markers that could assist with AIEC identification. Finally, we highlighted the problems behind the discovery of exclusive AIEC biomarkers and proposed strategies to facilitate the search of AIEC signature sequences.
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Affiliation(s)
- Carla Camprubí-Font
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Girona 17003, Spain
| | - Margarita Martinez-Medina
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Girona 17003, Spain
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Newman KM, Vaughn BP. Efficacy of intestinal microbiota transplantation in ulcerative colitis: a review of current literature and knowledge. MINERVA GASTROENTERO 2020; 65. [DOI: 10.23736/s1121-421x.19.02610-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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45
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The role of major virulence factors and pathogenicity of adherent-invasive Escherichia coli in patients with Crohn's disease. GASTROENTEROLOGY REVIEW 2020; 15:279-288. [PMID: 33777266 PMCID: PMC7988836 DOI: 10.5114/pg.2020.93235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel disease (IBD) is a term that describes Crohn's disease (CD) and ulcerative colitis (UC), and these two conditions are characterised by chronic inflammation of the gastrointestinal tract. Dysbiosis of intestinal microbiota has been consistently linked to patients with IBD. In the last two decades, the progressive implication of adherent-invasive Escherichia coli (AIEC) pathogenesis in patients with CD has been increasing. Here we discuss recent findings that indicate the role and mechanisms of AIEC in IBD. We also highlight AIEC virulence factor genes and mechanisms that suggest an important role in the severity of inflammation in CD patients. Finally, we emphasise data on the prevalence of AIEC in CD patients.
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Li Y, Liu H, Zhang L, Yang Y, Lin Y, Zhuo Y, Fang Z, Che L, Feng B, Xu S, Li J, Wu D. Maternal Dietary Fiber Composition during Gestation Induces Changes in Offspring Antioxidative Capacity, Inflammatory Response, and Gut Microbiota in a Sow Model. Int J Mol Sci 2019; 21:ijms21010031. [PMID: 31861629 PMCID: PMC6981455 DOI: 10.3390/ijms21010031] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/27/2019] [Accepted: 12/10/2019] [Indexed: 12/29/2022] Open
Abstract
To study the effects of maternal dietary fiber composition during gestation on offspring antioxidant capacity, inflammation, and gut microbiota composition, we randomly assigned 64 gilts to four treatments and administered diets with an insoluble/soluble fiber ratio of 3.89 (R1), 5.59 (R2), 9.12 (R3), and 12.81 (R4). Sow samples (blood and feces at gestation 110) and neonatal samples (blood, liver, and colonic contents) were collected. The results showed that sows and piglets in R1 and R2 had higher antioxidant enzyme activity and lower pro-inflammatory factor levels than those in R3 and R4. Moreover, piglets in R1 and R2 had higher liver mRNA expression of Nrf2 and HO-1 and lower NF-κB than piglets in R4. Interestingly, maternal fiber composition not only affected the production of short-chain fatty acids (SCFAs) in sow feces but also influenced the concentrations of SCFAs in the neonatal colon. Results of high-throughput sequencing showed that piglets as well as sows in R1 and R2 had microbial community structures distinct from those in R3 and R4. Therefore, the composition of dietary fiber in pregnancy diet had an important role in improving antioxidant capacity and decreasing inflammatory response of mothers and their offspring through modulating the composition of gut microbiota.
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Aggeletopoulou I, Konstantakis C, Assimakopoulos SF, Triantos C. The role of the gut microbiota in the treatment of inflammatory bowel diseases. Microb Pathog 2019; 137:103774. [PMID: 31586663 DOI: 10.1016/j.micpath.2019.103774] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 02/07/2023]
Abstract
The human intestinal microbiota coevolves with its host through a symbiotic relationship and exerts great influence on substantial functions including aspects of physiology, metabolism, nutrition and regulation of immune responses leading to physiological homeostasis. Over the last years, several studies have been conducted toward the assessment of the host-gut microbiota interaction, aiming to elucidate the mechanisms underlying the pathogenesis of several diseases. A defect on the microbiota-host crosstalk and the concomitant dysregulation of immune responses combined with genetic and environmental factors have been implicated in the pathogenesis of inflammatory bowel diseases (IBD). To this end, novel therapeutic options based on the gut microbiota modulation have been an area of extensive research interest. In this review we present the recent findings on the association of dysbiosis with IBD pathogenesis, we focus on the role of gut microbiota on the treatment of IBD and discuss the novel and currently available therapeutic strategies in manipulating the composition and function of gut microbiota in IBD patients. Applicable and emerging microbiota treatment modalities, such as the use of antibiotics, prebiotics, probiotics, postbiotics, synbiotics and fecal microbiota transplantation (FMT) constitute promising therapeutic options. However, the therapeutic potential of the aforementioned approaches is a topic of investigation and further studies are needed to elucidate their position in the present treatment algorithms of IBD.
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Affiliation(s)
- Ioanna Aggeletopoulou
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, Patras, 26504, Greece.
| | - Christos Konstantakis
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, Patras, 26504, Greece.
| | | | - Christos Triantos
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, Patras, 26504, Greece.
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Lepanto MS, Rosa L, Cutone A, Scotti MJ, Conte AL, Marazzato M, Zagaglia C, Longhi C, Berlutti F, Musci G, Valenti P, Conte MP. Bovine Lactoferrin Pre-Treatment Induces Intracellular Killing of AIEC LF82 and Reduces Bacteria-Induced DNA Damage in Differentiated Human Enterocytes. Int J Mol Sci 2019; 20:ijms20225666. [PMID: 31726759 PMCID: PMC6888356 DOI: 10.3390/ijms20225666] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 11/10/2019] [Indexed: 12/17/2022] Open
Abstract
LF82, a prototype of adherent-invasive E. coli (AIEC), is able to adhere to, invade, survive and replicate into intestinal epithelial cells. LF82 is able to enhance either its adhesion and invasion by up-regulating carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM-6), the main cell surface molecule for bacterial adhesion, and its intracellular survival by inducing host DNA damage, thus blocking the cellular cycle. Lactoferrin (Lf) is a multifunctional cationic glycoprotein of natural immunity, exerting an anti-invasive activity against LF82 when added to Caco-2 cells at the moment of infection. Here, the infection of 12 h Lf pre-treated Caco-2 cells was carried out at a time of 0 or 3 or 10 h after Lf removal from culture medium. The effect of Lf pre-treatment on LF82 invasiveness, survival, cell DNA damage, CEACAM-6 expression, apoptosis induction, as well as on Lf subcellular localization, has been evaluated. Lf, even if removed from culture medium, reduced LF82 invasion and survival as well as bacteria-induced DNA damage in Caco-2 cells independently from induction of apoptosis, modulation of CEACAM-6 expression and Lf sub-cellular localization. At our knowledge, this is the first study showing that the sole Lf pre-treatment can activate protective intracellular pathways, reducing LF82 invasiveness, intracellular survival and cell-DNA damages.
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Affiliation(s)
- Maria Stefania Lepanto
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (M.J.S.); (A.L.C.); (M.M.); (C.Z.); (C.L.); (F.B.); (P.V.)
| | - Luigi Rosa
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (M.J.S.); (A.L.C.); (M.M.); (C.Z.); (C.L.); (F.B.); (P.V.)
| | - Antimo Cutone
- Department of Biosciences and Territory, University of Molise, 86090 Pesche, Italy; (A.C.); (G.M.)
| | - Mellani Jinnett Scotti
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (M.J.S.); (A.L.C.); (M.M.); (C.Z.); (C.L.); (F.B.); (P.V.)
| | - Antonietta Lucia Conte
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (M.J.S.); (A.L.C.); (M.M.); (C.Z.); (C.L.); (F.B.); (P.V.)
| | - Massimiliano Marazzato
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (M.J.S.); (A.L.C.); (M.M.); (C.Z.); (C.L.); (F.B.); (P.V.)
| | - Carlo Zagaglia
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (M.J.S.); (A.L.C.); (M.M.); (C.Z.); (C.L.); (F.B.); (P.V.)
| | - Catia Longhi
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (M.J.S.); (A.L.C.); (M.M.); (C.Z.); (C.L.); (F.B.); (P.V.)
| | - Francesca Berlutti
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (M.J.S.); (A.L.C.); (M.M.); (C.Z.); (C.L.); (F.B.); (P.V.)
| | - Giovanni Musci
- Department of Biosciences and Territory, University of Molise, 86090 Pesche, Italy; (A.C.); (G.M.)
| | - Piera Valenti
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (M.J.S.); (A.L.C.); (M.M.); (C.Z.); (C.L.); (F.B.); (P.V.)
| | - Maria Pia Conte
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (M.J.S.); (A.L.C.); (M.M.); (C.Z.); (C.L.); (F.B.); (P.V.)
- Correspondence:
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Intestinal cytotoxicity induced by Escherichia coli is fully prevented by red wine polyphenol extract: Mechanistic insights in epithelial cells. Chem Biol Interact 2019; 310:108711. [DOI: 10.1016/j.cbi.2019.06.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/08/2019] [Accepted: 06/11/2019] [Indexed: 12/14/2022]
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Deutschmann C, Sowa M, Murugaiyan J, Roesler U, Röber N, Conrad K, Laass MW, Bogdanos D, Sipeki N, Papp M, Rödiger S, Roggenbuck D, Schierack P. Identification of Chitinase-3-Like Protein 1 as a Novel Neutrophil Antigenic Target in Crohn's Disease. J Crohns Colitis 2019; 13:894-904. [PMID: 30753386 PMCID: PMC6657965 DOI: 10.1093/ecco-jcc/jjz012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND AIMS There is an increasing incidence of inflammatory bowel disease [IBD]. Autoimmune responses are involved in the pathophysiology of IBD, but their underlying pathways and target antigens have not yet been fully elucidated. METHODS Autoantigenic targets in IBD were identified after separation of whole cell proteins isolated from neutrophils using two-dimensional electrophoresis and matrix assisted laser desorption ionization - time of flight mass spectrometry-based protein identification of the spots that displayed Western blotting signals with anti-neutrophil cytoplasmic antibody-positive sera. The prevalence of IgG, IgA and secretory IgA [sIgA] to chitinase 3-like protein 1 [CHI3L1] was analysed by enzyme-linked immunosorbent assays using recombinant CHI3L1 in 110 patients with Crohn's disease [CD], 95 with ulcerative colitis [UC], 126 with coeliac disease [CeD] and 86 healthy controls [HCs]. RESULTS The 18-glycosylhydrolase family member CHI3L1 was identified as a neutrophil autoantigenic target. CD patients displayed significantly higher levels of IgG to CHI3L1 than patients with UC and CeD (p < 0.0001, respectively). IgA and sIgA to CHI3L1 was significantly higher in CD than in UC, CeD and HCs [p < 0.0001, respectively]. IgA and sIgA to CHI3L1 demonstrated the highest prevalence in CD [25.5%, 28/110; and 41.8%%, 46/110] compared to HCs [2.3%, 2/86; and 4.7%%, 4/86; p = 0.0015 and p < 0.0001] and are associated with a more complicated progression of CD. CONCLUSION CHI3L1 is a novel neutrophil autoantigenic target in CD. IgA and sIgA to CHI3L1 may serve as novel markers for CD and may facilitate the serological diagnosis of IBD.
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Affiliation(s)
- Claudia Deutschmann
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz, Senftenberg, Germany
| | - Mandy Sowa
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz, Senftenberg, Germany,Medipan/GA Generic Assays GmbH, Ludwig-Erhard-Ring, Dahlewitz, Berlin, Germany
| | - Jayaseelan Murugaiyan
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Centre for Infectious Medicine, Robert-von-Ostertag-Str., Berlin, Germany,Department of Biotechnology, SRM University-AP, Amaravati, India
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Centre for Infectious Medicine, Robert-von-Ostertag-Str., Berlin, Germany
| | - Nadja Röber
- Institute of Immunology, Medical Faculty Carl Gustav Carus, Technical University Dresden, Fetscherstraße, Dresden, Germany
| | - Karsten Conrad
- Institute of Immunology, Medical Faculty Carl Gustav Carus, Technical University Dresden, Fetscherstraße, Dresden, Germany
| | - Martin W Laass
- Children’s Hospital, Medical Faculty Carl Gustav Carus, Technical University Dresden, Fetscherstraße, Dresden, Germany
| | - Dimitrios Bogdanos
- Department of Rheumatology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Nora Sipeki
- Department of Internal Medicine, Division of Gastroenterology, Faculty of Medicine, University of Debrecen, Nagyerdei krt., Debrecen, Hungary
| | - Maria Papp
- Department of Internal Medicine, Division of Gastroenterology, Faculty of Medicine, University of Debrecen, Nagyerdei krt., Debrecen, Hungary
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz, Senftenberg, Germany
| | - Dirk Roggenbuck
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz, Senftenberg, Germany,Medipan/GA Generic Assays GmbH, Ludwig-Erhard-Ring, Dahlewitz, Berlin, Germany
| | - Peter Schierack
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz, Senftenberg, Germany,Corresponding author: Prof. Dr Peter Schierack, Faculty Environment and Natural Sciences, Brandenburg University of Technology, Universitätsplatz 1, 01968 Senftenberg, Germany. Tel: +49 (0) 3573 85 932; Fax: +49 (0) 3573 85 909;
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