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Sugihara K, Kamada N. Metabolic network of the gut microbiota in inflammatory bowel disease. Inflamm Regen 2024; 44:11. [PMID: 38443988 PMCID: PMC10913301 DOI: 10.1186/s41232-024-00321-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024] Open
Abstract
Gut dysbiosis is closely linked to the pathogenesis of inflammatory bowel disease (IBD). Emerging studies highlight the relationship between host metabolism and the modulation of gut microbiota composition through regulating the luminal microenvironment. In IBD, various disease-associated factors contribute to the significant perturbation of host metabolism. Such disturbance catalyzes the selective proliferation of specific microbial populations, particularly pathobionts such as adherent invasive Escherichia coli and oral-derived bacteria. Pathobionts employ various strategies to adapt better to the disease-associated luminal environments. In addition to the host-microbe interaction, recent studies demonstrate that the metabolic network between commensal symbionts and pathobionts facilitates the expansion of pathobionts in the inflamed gut. Understanding the metabolic network among the host, commensal symbionts, and pathobionts provides new insights into the pathogenesis of IBD and novel avenues for treating IBD.
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Affiliation(s)
- Kohei Sugihara
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Nobuhiko Kamada
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA.
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
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2
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Akouris PP, Stuivenberg GA, Chmiel JA, Kiattiburut W, Poon A, Reid G, Burton JP. Ethanolamine enhances adhesion, promotes microcompartment formation, and modulates gene expression in Levilactobacillus brevis ATCC 14869. Gut Microbes 2024; 16:2350778. [PMID: 38717446 PMCID: PMC11086012 DOI: 10.1080/19490976.2024.2350778] [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: 08/08/2023] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Ethanolamine is an abundant compound in the gastrointestinal tract and a valuable source of carbon and nitrogen for pathogenic bacteria harboring ethanolamine utilization (eut) genes. Eut-positive pathogens can consume free ethanolamine to outcompete commensal microbes, which often lack eut genes, and establish infection. Ethanolamine can also act as a host recognition signal for eut-positive pathogens to upregulate virulence genes during colonization. Therefore, reducing free ethanolamine titers may represent a novel approach to preventing infection by eut-positive pathogens. Interestingly, the commensal microorganism Levilactobacillus brevis ATCC 14869 was found to encode over 18 eut genes within its genome. This led us to hypothesize that L. brevis can compete with eut-positive pathogens by clearing free ethanolamine from the environment. Our results demonstrate that despite being unable to metabolize ethanolamine under most conditions, L. brevis ATCC 14869 responds to the compound by increasing the expression of genes encoding proteins involved in microcompartment formation and adhesion to the intestinal epithelial barrier. The improved intestinal adhesion of L. brevis in the presence of ethanolamine also enhanced the exclusion of eut-positive pathogens from adhering to intestinal epithelial cells. These findings support further studies to test whether L. brevis ATCC 14869 can counter enteric pathogens and prevent or reduce the severity of infections. Overall, the metabolic capabilities of L. brevis ATCC 14869 offer a unique opportunity to add to the armamentarium of antimicrobial therapies as well as our understanding of the mechanisms used by beneficial microbes to sense and adapt to host microenvironments.
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Affiliation(s)
- Polycronis P. Akouris
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Canadian Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, ON, Canada
| | - Gerrit A. Stuivenberg
- Canadian Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - John A. Chmiel
- Canadian Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Wongsakorn Kiattiburut
- Canadian Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Annabel Poon
- Canadian Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Gregor Reid
- Canadian Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Jeremy P. Burton
- Canadian Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, Western University, London, ON, Canada
- Department of Surgery, Division of Urology, Western University, London, ON, Canada
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3
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Zangara MT, Darwish L, Coombes BK. Characterizing the Pathogenic Potential of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. EcoSal Plus 2023; 11:eesp00182022. [PMID: 37220071 PMCID: PMC10729932 DOI: 10.1128/ecosalplus.esp-0018-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/04/2023] [Indexed: 01/28/2024]
Abstract
The microbiome of Crohn's disease (CD) patients is composed of a microbial community that is considered dysbiotic and proinflammatory in nature. The overrepresentation of Enterobacteriaceae species is a common feature of the CD microbiome, and much attention has been given to understanding the pathogenic role this feature plays in disease activity. Over 2 decades ago, a new Escherichia coli subtype called adherent-invasive E. coli (AIEC) was isolated and linked to ileal Crohn's disease. Since the isolation of the first AIEC strain, additional AIEC strains have been isolated from both inflammatory bowel disease (IBD) patients and non-IBD individuals using the original in vitro phenotypic characterization methods. Identification of a definitive molecular marker of the AIEC pathotype has been elusive; however, significant advancements have been made in understanding the genetic, metabolic, and virulence determinants of AIEC infection biology. Here, we review the current knowledge of AIEC pathogenesis to provide additional, objective measures that could be considered in defining AIEC and their pathogenic potential.
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Affiliation(s)
- Megan T. Zangara
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Lena Darwish
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Brian K. Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, Hamilton, Ontario, Canada
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4
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Wu R, Xiong R, Li Y, Chen J, Yan R. Gut microbiome, metabolome, host immunity associated with inflammatory bowel disease and intervention of fecal microbiota transplantation. J Autoimmun 2023; 141:103062. [PMID: 37246133 DOI: 10.1016/j.jaut.2023.103062] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/30/2023]
Abstract
Gut dysbiosis has been associated with inflammatory bowel disease (IBD), one of the most common gastrointestinal diseases. The microbial communities play essential roles in host physiology, with profound effects on immune homeostasis, directly or via their metabolites and/or components. There are increasing clinical trials applying fecal microbiota transplantation (FMT) with Crohn's disease (CD) and ulcerative colitis (UC). The restoration of dysbiotic gut microbiome is considered as one of the mechanisms of FMT therapy. In this work, latest advances in the alterations in gut microbiome and metabolome features in IBD patients and experimental mechanistic understanding on their contribution to the immune dysfunction were reviewed. Then, the therapeutic outcomes of FMT on IBD were summarized based on clinical remission, endoscopic remission and histological remission of 27 clinical trials retrieved from PubMed which have been registered on ClinicalTrials.gov with the results been published in the past 10 years. Although FMT is established as an effective therapy for both subtypes of IBD, the promising outcomes are not always achieved. Among the 27 studies, only 11 studies performed gut microbiome profiling, 5 reported immune response alterations and 3 carried out metabolome analysis. Generally, FMT partially restored typical changes in IBD, resulted in increased α-diversity and species richness in responders and similar but less pronounced shifts of patient microbial and metabolomics profiles toward donor profiles. Measurements of immune responses to FMT mainly focused on T cells and revealed divergent effects on pro-/anti-inflammatory functions. The very limited information and the extremely confounding factors in the designs of the FMT trials significantly hindered a reasonable conclusion on the mechanistic involvement of gut microbiota and metabolites in clinical outcomes and an analysis of the inconsistencies.
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Affiliation(s)
- Rongrong Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Rui Xiong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Yan Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Junru Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Ru Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
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5
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Kolli U, Jalodia R, Moidunny S, Singh PK, Ban Y, Tao J, Cantu GN, Valdes E, Ramakrishnan S, Roy S. Multi-omics analysis revealing the interplay between gut microbiome and the host following opioid use. Gut Microbes 2023; 15:2246184. [PMID: 37610102 PMCID: PMC10448978 DOI: 10.1080/19490976.2023.2246184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/18/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
Opioid crisis is an ongoing epidemic since the past several decades in the United States. Opioid use-associated microbial dysbiosis is emerging as a key regulator of intestinal homeostasis and behavioral responses to opioid. However, the mechanistic insight into the role of microbial community in modulating host response is unavailable. To uncover the role of opioid-induced dysbiosis in disrupting intestinal homeostasis we utilized whole genome sequencing, untargeted metabolomics, and mRNA sequencing to identify changes in microbiome, metabolome, and host transcriptome respectively. Morphine treatment resulted in significant expansion of Parasuterella excrementihominis, Burkholderiales bacterium 1_1_47, Enterococcus faecalis, Enterorhabdus caecimuris and depletion of Lactobacillus johnsonii. These changes correlated with alterations in lipid metabolites and flavonoids. Significant alteration in microbial metabolism (metabolism of lipids, amino acids, vitamins and cofactors) and increased expression of virulence factors and biosynthesis of lipopolysaccharides (LPS) and lipoteichoic acid (LTA) were observed in microbiome of morphine-treated animals. In concurrence with changes in microbiome and metabolome extensive changes in innate and adaptive immune response, lipid metabolism, and gut barrier dysfunction were observed in the host transcriptome. Microbiome depleted mice displayed lower levels of inflammation, immune response and tissue destruction compared to mice harboring a dysbiotic microbiome in response to morphine treatment, thus establishing dysbiotic microbiome as mediator of morphine gut pathophysiology. Integrative analysis of multi-omics data highlighted the associations between Parasutterella excrementihominis, Burkholderiales bacterium 1_1_47, Enterococcus faecalis, Enterorhabdus caecimuris and altered levels of riboflavin, flavonoids, and lipid metabolites including phosphocholines, carnitines, bile acids, and ethanolamines with host gene expression changes involved in inflammation and barrier integrity of intestine. Omic analysis also highlighted the role of probiotic bacteria Lactobacillus johnsonii, metabolites flavonoids and riboflavin that were depleted with morphine as important factors for intestinal homeostasis. This study presents for the first time ever an interactive view of morphine-induced changes in microbial metabolism, strain level gut microbiome analysis and comprehensive view of changes in gut transcriptome. We also identified areas of potential therapeutic interventions to limit microbial dysbiosis and present a unique resource to the opioid research community.
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Affiliation(s)
- Udhghatri Kolli
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Richa Jalodia
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shamsudheen Moidunny
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Praveen Kumar Singh
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Yuguang Ban
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, Fl, USA
| | - Junyi Tao
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Eridania Valdes
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sundaram Ramakrishnan
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sabita Roy
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
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Faqerah N, Walker D, Gerasimidis K. Review article: The complex interplay between diet and Escherichia coli in inflammatory bowel disease. Aliment Pharmacol Ther 2023; 58:984-1004. [PMID: 37771255 DOI: 10.1111/apt.17720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/23/2022] [Accepted: 09/05/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND Although no causative microbe has been yet identified or successfully targeted in the treatment of inflammatory bowel disease (IBD), the role of Escherichia coli in the pathogenesis of Crohn's disease has attracted considerable interest. AIM In this review, we present a literature overview of the interactions between diet and E. coli and other Proteobacteria in the aetiology, outcomes and management of IBD and suggest future research directions. METHODS An extensive literature search was performed to identify in vitro studies and research in animal models that explored mechanisms by which dietary components can interact with E. coli or Proteobacteria to initiate or propagate gut inflammation. We also explored the effect diet and dietary therapies have on the levels of E. coli or Proteobacteria in patients with IBD. RESULTS Preclinical data suggest that the Western diet and its components influence the abundance, colonisation and phenotypic behaviour of E. coli in the gut, which may in turn initiate or contribute to gut inflammation. In contrast, the Mediterranean diet and specific dietary fibres may abrogate these effects and protect from inflammation. There are limited data from clinical trials, mostly from patients with Crohn's disease during treatment with exclusive enteral nutrition, with findings often challenging observations from preclinical research. Data from patients with ulcerative colitis are sparse. CONCLUSIONS Preclinical and some clinical trial data suggest that E. coli and other Proteobacteria interact with certain dietary components to promote gut inflammation. Well-designed clinical trials are required before dietary recommendations for disease management can be made.
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Affiliation(s)
- Nojoud Faqerah
- Human Nutrition, School of Medicine, Dentistry and Life Sciences, University of Glasgow, New Lister Building, Glasgow Royal Infirmary, Glasgow, UK
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Microbiology, Rabigh Medical College, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Daniel Walker
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, Dentistry and Life Sciences, University of Glasgow, New Lister Building, Glasgow Royal Infirmary, Glasgow, UK
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7
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Shi H, Hu X, Zhang J, Li W, Xu J, Hu B, Ma L, Lou L. Soil minerals and organic matters affect ARGs transformation by changing the morphology of plasmid and bacterial responses. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131727. [PMID: 37257383 DOI: 10.1016/j.jhazmat.2023.131727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/18/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023]
Abstract
Soil environment is a vital place for the occurrence and spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Extracellular DNA-mediated transformation is an important pathway for ARGs horizontal transfer and widely exists in soil environment. However, little information is available on how common soil components affect ARGs transformation. Here, three minerals (quartz, kaolinite, and montmorillonite) and three organic matters (humic acid, biochar, and soot) were selected as typical soil components. A small amount in suspension (0.2 g/L) of most soil components (except for quartz and montmorillonite) promoted transformant production by 1.1-1.6 folds. For a high amount (8 g/L), biochar significantly promoted transformant production to 1.5 times, kaolinite exerted a 30 % inhibitory effect. From the perspective of plasmid, biochar induced a higher proportion of supercoiled plasmid than kaolinite; more dissolved organic matter and metal ions facilitated plasmid aggregation under the near-neutral pH, thus promoted transformation. As for the influence of materials on recipient, although biochar and kaolinite both increased reactive oxygen species (ROS) level and membrane permeability, biochar up-regulated more ROS related genes, resulting in intracellular ROS production and up-regulating the expression of carbohydrate metabolism and transformation related genes. While kaolinite inhibited transformation mainly by causing nutrient deficiency.
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Affiliation(s)
- Hongyu Shi
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Xinyi Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Jin Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Wenxuan Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Jiang Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Liping Ma
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China.
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China.
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8
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Larabi AB, Masson HLP, Bäumler AJ. Bile acids as modulators of gut microbiota composition and function. Gut Microbes 2023; 15:2172671. [PMID: 36740850 PMCID: PMC9904317 DOI: 10.1080/19490976.2023.2172671] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
Changes in the composition of gut-associated microbial communities are associated with many human illnesses, but the factors driving dysbiosis remain incompletely understood. One factor governing the microbiota composition in the gut is bile. Bile acids shape the microbiota composition through their antimicrobial activity and by activating host signaling pathways that maintain gut homeostasis. Although bile acids are host-derived, their functions are integrally linked to bacterial metabolism, which shapes the composition of the intestinal bile acid pool. Conditions that change the size or composition of the bile acid pool can trigger alterations in the microbiota composition that exacerbate inflammation or favor infection with opportunistic pathogens. Therefore, manipulating the composition or size of the bile acid pool might be a promising strategy to remediate dysbiosis.
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Affiliation(s)
- Anaïs B. Larabi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Hugo L. P. Masson
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
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9
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Moreira de Gouveia MI, Daniel J, Garrivier A, Bernalier-Donadille A, Jubelin G. Diversity of ethanolamine utilization by human commensal Escherichiacoli. Res Microbiol 2023; 174:103989. [PMID: 35988812 DOI: 10.1016/j.resmic.2022.103989] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 01/11/2023]
Abstract
Ethanolamine (EA) is a substrate naturally present in the human gut and its catabolism by bacteria relies on the presence of eut genes encoding specific metabolic enzymes and accessory proteins. To date, EA utilization has been mostly investigated in gut bacterial pathogens. The aim of this study was to evaluate the ability of human gut commensal Escherichia coli isolates to utilize EA as a nitrogen and/or carbon sources. Although the capacity to consume EA is heterogeneous between the 40 strains of our collection, we determined that most of them could degrade EA to generate ammonia, a useful nitrogen resource for growth. Three isolates were also able to exploit EA as a carbon source. We also revealed that the inability of some strains to catabolize EA is explained either by mutations in the eut locus or by a defect in gene transcription. Finally, we demonstrated the importance of EA utilization for an optimal fitness of commensal E. coli in vivo. Our study provides new insights on the diversity of commensal E. coli strains to utilize EA as a nutrient in the gut and opens the way for new research in the field of interactions between host, gut microbiota and pathogens.
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Affiliation(s)
| | - Julien Daniel
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
| | - Annie Garrivier
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
| | | | - Gregory Jubelin
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
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10
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Zheng L, Duan SL, Dai YC, Wu SC. Role of adherent invasive Escherichia coli in pathogenesis of inflammatory bowel disease. World J Clin Cases 2022; 10:11671-11689. [PMID: 36405271 PMCID: PMC9669839 DOI: 10.12998/wjcc.v10.i32.11671] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/04/2022] [Accepted: 10/11/2022] [Indexed: 02/05/2023] Open
Abstract
Gut microbiota imbalances play an important role in inflammatory bowel disease (IBD), but no single pathogenic microorganism critical to IBD that is specific to the IBD terminal ileum mucosa or can invade intestinal epithelial cells has been found. Invasive Escherichia coli (E. coli) adhesion to macrophages is considered to be closely related to the pathogenesis of inflammatory bowel disease. Further study of the specific biological characteristics of adherent invasive E. coli (AIEC) may contribute to a further understanding of IBD pathogenesis. This review explores the relationship between AIEC and the intestinal immune system, discusses the prevalence and relevance of AIEC in Crohn's disease and ulcerative colitis patients, and describes the relationship between AIEC and the disease site, activity, and postoperative recurrence. Finally, we highlight potential therapeutic strategies to attenuate AIEC colonization in the intestinal mucosa, including the use of phage therapy, antibiotics, and anti-adhesion molecules. These strategies may open up new avenues for the prevention and treatment of IBD in the future.
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Affiliation(s)
- Lie Zheng
- Department of Gastroenterology, Shaanxi Provincial Hospital of Traditional Chinese Medicine, Xi’an 322000, Shaanxi Province, China
| | - Sheng-Lei Duan
- Department of Gastroenterology, Shaanxi Provincial Hospital of Traditional Chinese Medicine, Xi’an 322000, Shaanxi Province, China
| | - Yan-Cheng Dai
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Shi-Cheng Wu
- Department of Proctology, Gansu Academy of Traditional Chinese Medicine, Gansu Hospital of Traditional Chinese Medicine, Lanzhou 730050, Gansu Province, China
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11
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Chervy M, Sivignon A, Dambrine F, Buisson A, Sauvanet P, Godfraind C, Allez M, Le Bourhis L, The Remind Group, Barnich N, Denizot J. Epigenetic master regulators HDAC1 and HDAC5 control pathobiont Enterobacteria colonization in ileal mucosa of Crohn's disease patients. Gut Microbes 2022; 14:2127444. [PMID: 36175163 PMCID: PMC9542275 DOI: 10.1080/19490976.2022.2127444] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
AIEC Adherent-Invasive Escherichia coli; BSA Bovine serum albumin; CD Crohn's disease; CEABAC10 Carcinoembryonic antigen bacterial artificial chromosome 10; CEACAM Carcinoembryonic antigen-related cell adhesion molecule; FBS Fetal bovine serum; IBD Inflammatory Bowel Disease; HAT Histone acetyltransferase; HDAC Histone deacetylase; kDa KiloDalton; SAHA Suberoylanilide Hydroxamic Acid; Scr Scramble.
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Affiliation(s)
- Mélissa Chervy
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France
| | - Adeline Sivignon
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France,Institut Universitaire de Technologie, Génie Biologique, Aubière, France
| | - Flavie Dambrine
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France
| | - Anthony Buisson
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France,Gastroenterology Department, CHU Estaing, Clermont-Ferrand, France
| | - Pierre Sauvanet
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France,Surgery and Oncology Digestive Department, CHU Estaing, Clermont-Ferrand, France
| | - Catherine Godfraind
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France,Neuropathology Unit, CHU Gabriel Montpied, Clermont-Ferrand, France
| | - Matthieu Allez
- Gastroenterology Department, Hôpital Saint-Louis - APHP, Paris, France,Université De Paris, Institut de Recherche Saint-Louis, EMily, INSERM U1160, Paris, France,Hôpital Saint-Louis, Paris, France
| | - Lionel Le Bourhis
- Université De Paris, Institut de Recherche Saint-Louis, EMily, INSERM U1160, Paris, France
| | | | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France,Institut Universitaire de Technologie, Génie Biologique, Aubière, France
| | - Jérémy Denizot
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France,Institut Universitaire de Technologie, Génie Biologique, Aubière, France,CONTACT Jérémy Denizot M2iSH, UMR 1071 Inserm/Université Clermont Auvergne, CBRV, 28 place Henri Dunant, Clermont-Ferrand63001, France
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12
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Tang H, Zhan Z, Zhang Y, Huang X. Propionylation of lysine, a new mechanism of short-chain fatty acids affecting bacterial virulence. Am J Transl Res 2022; 14:5773-5784. [PMID: 36105019 PMCID: PMC9452321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Propionic acid (PA) is a major component of short-chain fatty acids produced by Bacteroidetes spp. Lysine propionylation is a novel type of protein regulatory posttranslational modification that is widespread in prokaryotes and eukaryotes, as well as in cellular processes, it affects DNA binding affinity, protein stability, and enzyme activity. In this review of published literature, we provide evidence that the level of propionyl modification is influenced by the concentration of PA and the PA metabolic intermediate (propionyl-CoA) and discuss the possibility of PA affecting enteropathogenic bacterial virulence. The understanding of propionyl modification is helpful to better understand the mechanism of PA-producing Bacteroidetes affecting the virulence of pathogenic intestinal bacteria. It may provide novel choices for the prevention and treatment of pathogenic intestinal bacteria.
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Affiliation(s)
- Hao Tang
- Department of Biochemistry & Molecular Biology, School of Medicine, Jiangsu University 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Ziyang Zhan
- Department of Biochemistry & Molecular Biology, School of Medicine, Jiangsu University 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Ying Zhang
- Department of Biochemistry & Molecular Biology, School of Medicine, Jiangsu University 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
| | - Xinxiang Huang
- Department of Biochemistry & Molecular Biology, School of Medicine, Jiangsu University 301 Xuefu Road, Zhenjiang 212013, Jiangsu, China
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13
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Nag D, Farr D, Raychaudhuri S, Withey JH. An adult zebrafish model for adherent-invasive Escherichia coli indicates protection from AIEC infection by probiotic E. coli Nissle. iScience 2022; 25:104572. [PMID: 35769878 PMCID: PMC9234234 DOI: 10.1016/j.isci.2022.104572] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/02/2022] [Accepted: 06/06/2022] [Indexed: 12/30/2022] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) is an opportunistic pathogen associated with major inflammatory bowel disease, Crohn disease, and ulcerative colitis. Unfavorable conditions push commensal AIEC to induce gut inflammation, sometimes progressing to inflammation-induced colon cancer. Recently, zebrafish have emerged as a useful model to study human intestinal pathogens. Here, a zebrafish model to study AIEC infection was developed. Bath inoculation with AIEC resulted in colonization and tissue disruption in the zebrafish intestine. Gene expression of pro-inflammatory markers including interleukin-1β (IL-1β), tumor necrosis factor alpha (TNFα), interferon-γ (IFNγ), and S100A-10b (akin to human calprotectin) in the zebrafish intestine was significantly induced by AIEC infection. The probiotic E. coli Nissle 1917 (EcN) was tested as a therapeutic and prophylactic against AIEC infection and reduced AIEC colonization, tissue damage, and pro-inflammatory responses in zebrafish. Furthermore, EcN diminished the propionic-acid-augmented hyperinfection of AIEC in zebrafish. Thus, this study shows the efficacy of EcN against AIEC in an AIEC-zebrafish model. AIEC can colonize, invade, and induce inflammation in the zebrafish gut Probiotic E. coli Nissle can protect zebrafish from AIEC infection EcN is effective both prophylactically and therapeutically against AIEC-induced IBD
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Affiliation(s)
- Dhrubajyoti Nag
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Dustin Farr
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Saumya Raychaudhuri
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Jeffrey H. Withey
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
- Corresponding author
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14
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Lopez LR, Ahn JH, Alves T, Arthur JC. Microenvironmental Factors that Shape Bacterial Metabolites in Inflammatory Bowel Disease. Front Cell Infect Microbiol 2022; 12:934619. [PMID: 35959366 PMCID: PMC9362432 DOI: 10.3389/fcimb.2022.934619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a significant global health problem that involves chronic intestinal inflammation and can involve severe comorbidities, including intestinal fibrosis and inflammation-associated colorectal cancer (CRC). Disease-associated alterations to the intestinal microbiota often include fecal enrichment of Enterobacteriaceae, which are strongly implicated in IBD development. This dysbiosis of intestinal flora accompanies changes in microbial metabolites, shaping host:microbe interactions and disease risk. While there have been numerous studies linking specific bacterial taxa with IBD development, our understanding of microbial function in the context of IBD is limited. Several classes of microbial metabolites have been directly implicated in IBD disease progression, including bacterial siderophores and genotoxins. Yet, our microbiota still harbors thousands of uncharacterized microbial products. In-depth discovery and characterization of disease-associated microbial metabolites is necessary to target these products in IBD treatment strategies. Towards improving our understanding of microbiota metabolites in IBD, it is important to recognize how host relevant factors influence microbiota function. For example, changes in host inflammation status, metal availability, interbacterial community structure, and xenobiotics all play an important role in shaping gut microbial ecology. In this minireview, we outline how each of these factors influences gut microbial function, with a specific focus on IBD-associated Enterobacteriaceae metabolites. Importantly, we discuss how altering the intestinal microenvironment could improve the treatment of intestinal inflammation and associated disorders, like intestinal fibrosis and CRC.
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Affiliation(s)
- Lacey R. Lopez
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ju-Hyun Ahn
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Tomaz Alves
- Division of Comprehensive Oral Health, Adams School of Dentistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Janelle C. Arthur
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Gastrointestinal Biology and Disease, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: Janelle C. Arthur,
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15
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Analysis of the Therapeutic Effect of Changyanning on Intestinal Flora in Inflammatory Bowel Disease. CONTRAST MEDIA & MOLECULAR IMAGING 2022; 2022:3757763. [PMID: 35845725 PMCID: PMC9242759 DOI: 10.1155/2022/3757763] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/29/2022]
Abstract
Research Purposes. Inflammatory bowel disease (IBD) is an autoimmune disease coinduced by genes, environment, and immune response, mainly including ulcerative colitis (UC) and Crohn's disease (CD). There are a large number and variety of intestinal bacteria in the human intestinal tract. These bacteria maintain a balance with the human environment and participate in the normal physiological processes of the human body. They play a unique role in defending against pathogen invasion, maintaining the homeostasis of the human immune system and metabolizing substances. Intestinal flora imbalance may be one of the pathogenic factors of IBD, and restoring the disturbed intestinal flora has become a research hotspot in the prevention and treatment of IBD. Changyanning is mainly composed of Dijincao grass, yellow hairy ear grass, camphor tree roots, maple leaves, and so on. Clinical studies have shown that Changyanning alone or in combination has a significant effect on ulcerative colitis, but the treatment mechanism is not yet clear. In this study, we established an IBD animal model to explore the therapeutic mechanism of Changyanning on inflammatory bowel disease and its effect on intestinal flora. Research Methods. Male C57BL/6 SPF mice were given free access to 4% dextran sulfate sodium (DSS) solution for 7 days to establish an ulcerative colitis model. After the model was established, different doses of Changyanning tablets, Changyanning granules, and sulfasalazine were given by gavage for 7 days. The relieving effects of the above drugs on the symptoms of inflammatory bowel disease were evaluated by evaluating the mouse/rat body weight, survival rate, disease activity index, colon length, pathological tissue score, and other indicators. Results. The DSS-induced IBD mouse model showed significant increases in weight loss, DAI score, and pathological score. Both Changyanning tablets and granules can relieve the weight loss of mice, restore the colon length, and protect the colon tissue structure of mice. In reducing DAI and pathological scores in mice, Changyanning granules had a better effect. In conclusion, Changyanning can significantly improve the quality of life of IBD model animals, relieve intestinal inflammatory response, and relieve colonic edema, ulceration, and necrosis. The results show that Changyanning has a certain therapeutic effect on IBD. This study also provides experimental evidence for the application of Changyanning in the treatment of IBD, which is of great significance to its clinical application. The trail is registered in ChiCTR with number (TRN) ChiCTR2000028830.
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16
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Bosch S, Acharjee A, Quraishi MN, Rojas P, Bakkali A, Jansen EEW, Brizzio Brentar M, Kuijvenhoven J, Stokkers P, Struys E, Beggs AD, Gkoutos GV, de Meij TGJ, de Boer NKH. The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma. Gut Microbes 2022; 14:2038863. [PMID: 35188868 PMCID: PMC8865277 DOI: 10.1080/19490976.2022.2038863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The risk of recurrent dysplastic colonic lesions is increased following polypectomy. Yield of endoscopic surveillance after adenoma removal is low, while interval colorectal cancers occur. To longitudinally assess the dynamics of fecal microbiota and amino acids in the presence of adenomatous lesions and after their endoscopic removal. In this longitudinal case-control study, patients collected fecal samples prior to bowel preparation before scheduled colonoscopy and 3 months after this intervention. Based on colonoscopy outcomes, patients with advanced adenomas and nonadvanced adenomas (0.5-1.0 cm) who underwent polypectomy during endoscopy (n = 19) were strictly matched on age, body-mass index, and smoking habits to controls without endoscopic abnormalities (n = 19). Microbial taxa were measured by 16S RNA sequencing, and amino acids (AA) were measured by high-performance liquid chromatography (HPLC). Adenoma patients were discriminated from controls based on AA and microbial composition. Levels of proline (p = .001), ornithine (p = .02) and serine (p = .02) were increased in adenoma patients compared to controls but decreased to resemble those of controls after adenoma removal. These AAs were combined as a potential adenoma-specific panel (AUC 0.79(0.64-0.94)). For bacterial taxa, differences between patients with adenomas and controls were found (Bifidobacterium spp.↓, Anaerostipes spp.↓, Butyricimonas spp.↑, Faecalitalea spp.↑ and Catenibacterium spp.↑), but no alterations in relative abundance were observed after polypectomy. Furthermore, Faecalitalea spp. and Butyricimonas spp. were significantly correlated with adenoma-specific amino acids. We selected an amino acid panel specifically increased in the presence of adenomas and a microbial signature present in adenoma patients, irrespective of polypectomy. Upon validation, these panels may improve the effectiveness of the surveillance program by detection of high-risk individuals and determination of surveillance endoscopy timing, leading to less unnecessary endoscopies and less interval cancer.
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Affiliation(s)
- Sofie Bosch
- Amsterdam Umc, Vu University Medical Center, Department of Gastroenterology and Hepatology, Ag&m Research Institute, Amsterdam, The Netherlands,contact Sofie Bosch Amsterdam UMC, VU University Medical Center, De Boelelaan 11181081HZ, Amsterdam, The Netherlands
| | - Animesh Acharjee
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Center for Computational Biology, University of Birmingham, UK,Institute of Translational Medicine, University Hospitals Birmingham Nhs, Foundation Trust, UK,Nihr Surgical Reconstruction and Microbiology Research Center, University Hospital Birmingham, Birmingham, UK
| | - Mohammed N Quraishi
- Department of Gastroenterology, University Hospitals Birmingham Nhs Foundation Trust, Birmingham, UK,Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK,University of Birmingham Microbiome Treatment Center, University of Birmingham, UK,Center for Liver and Gastroenterology Research, Nihr Birmingham Biomedical Research Center, University of Birmingham, Birmingham, UK
| | - Patricia Rojas
- Institute of Applied Health Research, University of Birmingham, UK
| | - Abdellatif Bakkali
- Department of Clinical Chemistry, Vu University Medical Center, Amsterdam, The Netherlands
| | - Erwin EW Jansen
- Department of Clinical Chemistry, Vu University Medical Center, Amsterdam, The Netherlands
| | - Marina Brizzio Brentar
- Amsterdam Umc, Vu University Medical Center, Department of Gastroenterology and Hepatology, Ag&m Research Institute, Amsterdam, The Netherlands
| | - Johan Kuijvenhoven
- Spaarne Gasthuis, Department of Gastroenterology and Hepatology, Spaarne Gasthuis (primary institute), Hoofddorp and Haarlem, The Netherlands
| | - Pieter Stokkers
- Olvg West, Department of Gastroenterology and Hepatology, Onze Lieve Vrouwe Gasthuis West, Amsterdam, The Netherlands
| | - Eduard Struys
- Department of Clinical Chemistry, Vu University Medical Center, Amsterdam, The Netherlands
| | - Andrew D Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Georgios V Gkoutos
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Center for Computational Biology, University of Birmingham, UK,Institute of Translational Medicine, University Hospitals Birmingham Nhs, Foundation Trust, UK,Nihr Surgical Reconstruction and Microbiology Research Center, University Hospital Birmingham, Birmingham, UK,Medical Research Counsil, MRC Health Data Research, UK,NIHR Experimental Cancer Medicine Center, National Institute for Health Research, Birmingham, UK,NIHR Biomedical Research Center, University Hospital Birmingham, Birmingham, UK
| | - Tim GJ de Meij
- Amsterdam Umc, Vu University Amsterdam, Department of Paediatric Gastroenterology, Ag&m Research Institute, Amsterdam, The Netherlands
| | - Nanne KH de Boer
- Amsterdam Umc, Vu University Medical Center, Department of Gastroenterology and Hepatology, Ag&m Research Institute, Amsterdam, The Netherlands
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17
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Zhang S, Morgan XC, Dogan B, Martin FP, Strickler SR, Oka A, Herzog J, Liu B, Dowd SE, Huttenhower C, Pichaud M, Dogan EI, Satsangi J, Longman R, Yantiss R, Mueller LA, Scherl E, Sartor RB, Simpson KW. Mucosal metabolites fuel the growth and virulence of E. coli linked to Crohn's disease. JCI Insight 2022; 7:157013. [PMID: 35413017 PMCID: PMC9220930 DOI: 10.1172/jci.insight.157013] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
Elucidating how resident enteric bacteria interact with their hosts to promote health or inflammation is of central importance to diarrheal and inflammatory bowel diseases across species. Here, we integrated the microbial and chemical microenvironment of a patient’s ileal mucosa with their clinical phenotype and genotype to identify factors favoring the growth and virulence of adherent and invasive E. coli (AIEC) linked to Crohn’s disease. We determined that the ileal niche of AIEC was characterized by inflammation, dysbiosis, coculture of Enterococcus, and oxidative stress. We discovered that mucosal metabolites supported general growth of ileal E. coli, with a selective effect of ethanolamine on AIEC that was augmented by cometabolism of ileitis-associated amino acids and glutathione and by symbiosis-associated fucose. This metabolic plasticity was facilitated by the eut and pdu microcompartments, amino acid metabolism, γ-glutamyl-cycle, and pleiotropic stress responses. We linked metabolism to virulence and found that ethanolamine and glutamine enhanced AIEC motility, infectivity, and proinflammatory responses in vitro. We connected use of ethanolamine to intestinal inflammation and L-fuculose phosphate aldolase (fucA) to symbiosis in AIEC monoassociated IL10–/– mice. Collectively, we established that AIEC were pathoadapted to utilize mucosal metabolites associated with health and inflammation for growth and virulence, enabling the transition from symbiont to pathogen in a susceptible host.
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Affiliation(s)
- Shiying Zhang
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Belgin Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
| | - Francois-Pierre Martin
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Susan R Strickler
- Plant Research, Boyce Thompson Institute, Ithaca, United States of America
| | - Akihiko Oka
- Department of Internal Medicine II, Shimane University Faculty of Medicine, Izumo, Japan
| | - Jeremy Herzog
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Bo Liu
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Scot E Dowd
- MR DNA: Molecular Research LP, Shallowater, United States of America
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | | | - Esra I Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Randy Longman
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, Cornell University, New York, United States of America
| | - Rhonda Yantiss
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, Cornell University, New York, United States of America
| | - Lukas A Mueller
- Plant Research, Boyce Thompson Institute, Ithaca, United States of America
| | - Ellen Scherl
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, Cornell University, New York, United States of America
| | - R Balfour Sartor
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Kenneth W Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
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18
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Ding Y, Liu X, Huang PJJ, Liu J. Homogeneous assays for aptamer-based ethanolamine sensing: no indication of target binding. Analyst 2022; 147:1348-1356. [PMID: 35244657 DOI: 10.1039/d2an00145d] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ethanolamine is an important analyte for environmental chemistry and biological sciences. A few DNA aptamers were previously reported for binding ethanolamine with a dissociation constant (Kd) as low as 9.6 nM. However, most of the previous binding assays and sensing work used either immobilized ethanolamine or immobilized aptamers. In this work, we studied three previously reported DNA sequences, two of which were supposed to bind ethanolamine while the other could not bind. Isothermal titration calorimetry revealed no binding for any of these sequences. In addition, due to their guanine-rich sequences, thioflavin T was used as a probe. Little fluorescence change was observed with up to 1 μM ethanolamine. Responses within the millimolar range of ethanolamine were attributed to the general fluorescence quenching effect of ethanolamine instead of aptamer binding. Finally, after studying the adsorption of ethanolamine to gold nanoparticles (AuNPs), we confirmed the feasibility of using AuNPs as a probe when the concentration of ethanolamine was below 0.1 mM. However, no indication of specific aptamer binding was observed by comparing the three DNA sequences for their color changing trends. This work articulates the importance of careful homogeneous binding assays using free target molecules.
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Affiliation(s)
- Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
| | - Xun Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
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19
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Agus A, Richard D, Faïs T, Vazeille E, Chervy M, Bonnin V, Dalmasso G, Denizot J, Billard E, Bonnet R, Buisson A, Barnich N, Delmas J. Propionate catabolism by CD-associated adherent-invasive E. coli counteracts its anti-inflammatory effect. Gut Microbes 2022; 13:1-18. [PMID: 33769191 PMCID: PMC8007151 DOI: 10.1080/19490976.2020.1839318] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Crohn's disease (CD) is a chronic and disabling inflammatory disorder of the gut that is profoundly influenced by intestinal microbiota composition, host genetics and environmental factors. Several groups worldwide have described an imbalance of the gut microbiome composition, called dysbiosis, in CD patients, with an increase in Proteobacteria and Bacteroidetes and a decrease in Firmicutes. A high prevalence of adherent-invasive Escherichia coli (AIEC) pathobionts has been identified in the intestinal mucosa of CD patients. A significant loss in the bacteria that produce short-chain fatty acids (SCFAs) with anti-inflammatory properties, such as propionate, is also a consequence of dysbiosis in CD patients. Here, the AIEC reference strain LF82 was able to degrade propionate in the gut, which was sufficient to counteract the anti-inflammatory effect of propionate both in in vitro models and in mice with DSS-induced colitis. The consumption of propionate by AIEC pathobionts leads to an increase in TNF-α production by macrophages upon infection through the bacterial methyl-citrate pathway. To induce the protective effects of SCFAs on the inflamed gut, we used a G-protein-coupled receptor 43 agonist (GPR43 agonist) that is not metabolizable by intestinal bacteria. Interestingly, this agonist showed anti-inflammatory properties and decreased the severity of colitis in AIEC-infected mice, as assessed by an improvement in the disease activity index (DAI) and a decrease in AIEC pathobiont encroachment. Taken together, these results highlight the effectiveness of GPR43 agonist treatment in the control of gut inflammation and improved our understanding of the ability of AIEC to modulate propionate availability to create an infectious niche to its advantage.
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Affiliation(s)
- Allison Agus
- Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2ISH), Centre De Recherche En Nutrition Humaine Auvergne University Clermont Auvergne, Clermont-Ferrand, France,INRAE, AgroParisTech, Micalis Institute, University Paris-Saclay, Jouy-en-Josas, France,Allison Agus Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2iSH), Centre De Recherche En Nutrition Humaine Auvergne, University Clermont Auvergne, Clermont-Ferrand, France
| | - Damien Richard
- Department of Pharmacology, University Hospital of Clermont-Ferrand, France
| | - Tiphanie Faïs
- Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2ISH), Centre De Recherche En Nutrition Humaine Auvergne University Clermont Auvergne, Clermont-Ferrand, France,Department of Bacteriology, University Hospital of Clermont-Ferrand, France
| | - Emilie Vazeille
- Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2ISH), Centre De Recherche En Nutrition Humaine Auvergne University Clermont Auvergne, Clermont-Ferrand, France,Service d’Hépato-Gastro Entérologie, 3iHP, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Mélissa Chervy
- Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2ISH), Centre De Recherche En Nutrition Humaine Auvergne University Clermont Auvergne, Clermont-Ferrand, France
| | - Virginie Bonnin
- Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2ISH), Centre De Recherche En Nutrition Humaine Auvergne University Clermont Auvergne, Clermont-Ferrand, France
| | - Guillaume Dalmasso
- Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2ISH), Centre De Recherche En Nutrition Humaine Auvergne University Clermont Auvergne, Clermont-Ferrand, France
| | - Jérémy Denizot
- Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2ISH), Centre De Recherche En Nutrition Humaine Auvergne University Clermont Auvergne, Clermont-Ferrand, France,Institut Universitaire De Technologie, University Clermont Auvergne, Clermont-Ferrand, France
| | - Elisabeth Billard
- Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2ISH), Centre De Recherche En Nutrition Humaine Auvergne University Clermont Auvergne, Clermont-Ferrand, France,Institut Universitaire De Technologie, University Clermont Auvergne, Clermont-Ferrand, France
| | - Richard Bonnet
- Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2ISH), Centre De Recherche En Nutrition Humaine Auvergne University Clermont Auvergne, Clermont-Ferrand, France,Department of Bacteriology, University Hospital of Clermont-Ferrand, France
| | - Anthony Buisson
- Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2ISH), Centre De Recherche En Nutrition Humaine Auvergne University Clermont Auvergne, Clermont-Ferrand, France,Service d’Hépato-Gastro Entérologie, 3iHP, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Nicolas Barnich
- Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2ISH), Centre De Recherche En Nutrition Humaine Auvergne University Clermont Auvergne, Clermont-Ferrand, France,Institut Universitaire De Technologie, University Clermont Auvergne, Clermont-Ferrand, France
| | - Julien Delmas
- Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation Et Susceptibilité De l’Hôte (M2ISH), Centre De Recherche En Nutrition Humaine Auvergne University Clermont Auvergne, Clermont-Ferrand, France,Department of Bacteriology, University Hospital of Clermont-Ferrand, France,CONTACT Julien Delmas
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20
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Kamali Dolatabadi R, Feizi A, Halaji M, Fazeli H, Adibi P. The Prevalence of Adherent-Invasive Escherichia coli and Its Association With Inflammatory Bowel Diseases: A Systematic Review and Meta-Analysis. Front Med (Lausanne) 2021; 8:730243. [PMID: 34926490 PMCID: PMC8678049 DOI: 10.3389/fmed.2021.730243] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are known as chronic gastrointestinal inflammatory disorders. The present systematic review and meta analysis was conducted to estimate the prevalence of adherent-invasive Escherichia coli (AIEC) isolates and their phylogenetic grouping among IBD patients compared with the controls. A systematic literature search was conducted among published papers by international authors until April 30, 2020 in Web of Science, Scopus, EMBASE, and PubMed databases. The pooled prevalence of AIEC isolates and their phylogenetic grouping among IBD patients as well as in controls was estimated using fixed or random effects models. Furthermore, for estimating the association of colonization by AIEC with IBD, odds ratio along with 95% confidence interval was reported. A total of 205 articles retrieved by the initial search of databases, 13 case–control studies met the eligibility criteria for inclusion in the meta analysis. There were 465 IBD cases (348 CD and 117 UC) and 307 controls. The pooled prevalence of AIEC isolates were 28% (95% CI: 18–39%), 29% (95% CI: 20–40%), 13% (95% CI: 1–30%), and 9% (95% CI: 3–19%), respectively among IBD, CD, UC, and control group, respectively. Our results revealed that the most frequent AIEC phylogroup in the IBD, CD, and control groups was B2. Fixed-effects meta analysis showed that colonization of AIEC is significantly associated with IBD (OR: 2.93; 95% CI: 1.90–4.52; P < 0.001) and CD (OR: 3.07; 95% CI: 1.99–4.74; P < 0.001), but not with UC (OR: 2.29; 95% CI: 0.81–6.51; P = 0.11). In summary, this meta analysis revealed that colonization by AIEC is more frequent in IBD and is associated with IBD (CD and UC). Our results suggested that the affects of IBD in patients colonized with the AIEC pathovar is not random, it is in fact a specific disease-related pathovar.
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Affiliation(s)
- Razie Kamali Dolatabadi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Awat Feizi
- Department of Biostatistics and Epidemiology, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehrdad Halaji
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran.,Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Hossein Fazeli
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Peyman Adibi
- Gastroenterology and Hepatology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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21
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Wurster JI, Peterson RL, Brown CE, Penumutchu S, Guzior DV, Neugebauer K, Sano WH, Sebastian MM, Quinn RA, Belenky P. Streptozotocin-induced hyperglycemia alters the cecal metabolome and exacerbates antibiotic-induced dysbiosis. Cell Rep 2021; 37:110113. [PMID: 34910917 PMCID: PMC8722030 DOI: 10.1016/j.celrep.2021.110113] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 10/08/2021] [Accepted: 11/18/2021] [Indexed: 01/02/2023] Open
Abstract
It is well established in the microbiome field that antibiotic (ATB) use and metabolic disease both impact the structure and function of the gut microbiome. But how host and microbial metabolism interacts with ATB susceptibility to affect the resulting dysbiosis remains poorly understood. In a streptozotocin-induced model of hyperglycemia (HG), we use a combined metagenomic, metatranscriptomic, and metabolomic approach to profile changes in microbiome taxonomic composition, transcriptional activity, and metabolite abundance both pre- and post-ATB challenge. We find that HG impacts both microbiome structure and metabolism, ultimately increasing susceptibility to amoxicillin. HG exacerbates drug-induced dysbiosis and increases both phosphotransferase system activity and energy catabolism compared to controls. Finally, HG and ATB co-treatment increases pathogen susceptibility and reduces survival in a Salmonella enterica infection model. Our data demonstrate that induced HG is sufficient to modify the cecal metabolite pool, worsen the severity of ATB dysbiosis, and decrease colonization resistance.
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Affiliation(s)
- Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Rachel L Peterson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Claire E Brown
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Douglas V Guzior
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Kerri Neugebauer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - William H Sano
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Manu M Sebastian
- Department of Epigenetics and Molecular Carcinogenesis, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA.
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22
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Mirzaei R, Dehkhodaie E, Bouzari B, Rahimi M, Gholestani A, Hosseini-Fard SR, Keyvani H, Teimoori A, Karampoor S. Dual role of microbiota-derived short-chain fatty acids on host and pathogen. Biomed Pharmacother 2021; 145:112352. [PMID: 34840032 DOI: 10.1016/j.biopha.2021.112352] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
A growing body of documents shows microbiota produce metabolites such as short-chain fatty acids (SCFAs) as crucial executors of diet-based microbial influence the host and bacterial pathogens. The production of SCFAs depends on the metabolic activity of intestinal microflora and is also affected by dietary changes. SCFAs play important roles in maintaining colonic health as an energy source, as a regulator of gene expression and cell differentiation, and as an anti-inflammatory agent. Additionally, the regulated expression of virulence genes is critical for successful infection by an intestinal pathogen. Bacteria rely on sensing environmental signals to find preferable niches and reach the infectious state. This review will present data supporting the diverse functional roles of microbiota-derived butyrate, propionate, and acetate on host cellular activities such as immune modulation, energy metabolism, nervous system, inflammation, cellular differentiation, and anti-tumor effects, among others. On the other hand, we will discuss and summarize data about the role of these SCFAs on the virulence factor of bacterial pathogens. In this regard, receptors and signaling routes for SCFAs metabolites in host and pathogens will be introduced.
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Affiliation(s)
- Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Elahe Dehkhodaie
- Department of Biology, Science and Research Branch, Islamic Azad University Tehran, Iran
| | - Behnaz Bouzari
- Department of Pathology, Firouzgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mandana Rahimi
- Department of Pathology, School of Medicine, Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Gholestani
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Hosseini-Fard
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Keyvani
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Ali Teimoori
- Department of Virology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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23
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Kennedy NW, Mills CE, Nichols TM, Abrahamson CH, Tullman-Ercek D. Bacterial microcompartments: tiny organelles with big potential. Curr Opin Microbiol 2021; 63:36-42. [PMID: 34126434 DOI: 10.1016/j.mib.2021.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/13/2021] [Accepted: 05/17/2021] [Indexed: 11/28/2022]
Abstract
Organization of metabolic processes within the space of a cell is critical for the survival of many organisms. In bacteria, spatial organization is achieved via proteinaceous organelles called bacterial microcompartments, which encapsulate pathway enzymes, substrates, and co-factors to drive the safe and efficient metabolism of niche carbon sources. Microcompartments are self-assembled from shell proteins that encapsulate a core comprising various enzymes. This review discusses how recent advances in understanding microcompartment structure and assembly have informed engineering efforts to repurpose compartments and compartment-based structures for non-native functions. These advances, both in understanding of the native structure and function of compartments, as well as in the engineering of new functions, will pave the way for the use of these structures in bacterial cell factories.
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Affiliation(s)
- Nolan W Kennedy
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, 2205 Tech Drive, 2-100 Hogan Hall, Evanston, IL, 60208, USA
| | - Carolyn E Mills
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA
| | - Taylor M Nichols
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA
| | - Charlotte H Abrahamson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA; Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological Institute B486, Evanston, IL, 60208, USA.
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24
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Prentice MB. Bacterial microcompartments and their role in pathogenicity. Curr Opin Microbiol 2021; 63:19-28. [PMID: 34107380 DOI: 10.1016/j.mib.2021.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/26/2021] [Accepted: 05/17/2021] [Indexed: 02/08/2023]
Abstract
Catabolic bacterial microcompartments (BMC), or metabolosomes, are self-assembling structures formed by enzymes enclosed by porous protein shells. They provide a specialised environment inside bacterial cells separating a short catabolic pathway with reactive or toxic intermediates from the cytoplasm. Substrates for microcompartment metabolism like ethanolamine and 1,2-propanediol are constantly produced in the human intestine by bacterial metabolism of food or host cell components. Enteric pathogens gain a competitive advantage in the intestine by metabolising these substrates, an advantage enhanced by the host inflammatory response. They exploit the intestinal specificity of signature metabolosome substrates by adopting substrate sensors and regulators encoded by BMC operons for governance of non-metabolic processes in pathogenesis. In turn, products of microcompartment metabolism regulate the host immune system.
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Affiliation(s)
- Michael B Prentice
- Department of Pathology, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland.
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25
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Whittemore JC, Price JM, Moyers T, Suchodolski JS. Effects of Synbiotics on the Fecal Microbiome and Metabolomic Profiles of Healthy Research Dogs Administered Antibiotics: A Randomized, Controlled Trial. Front Vet Sci 2021; 8:665713. [PMID: 34124225 PMCID: PMC8187564 DOI: 10.3389/fvets.2021.665713] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Antibiotic-associated gastrointestinal signs occurred in 100% of dogs administered enrofloxacin with metronidazole in a previous study, and signs partially were mitigated by synbiotics. The objective of this randomized, double-blinded, placebo-controlled trial was to compare the fecal microbiome and metabolome of dogs administered enrofloxacin and metronidazole, followed by either a placebo or a bacterial/yeast synbiotic combination. Methods: Twenty-two healthy research dogs were randomized to two treatment groups. There were three study periods: baseline, treatment, and washout. Dogs were administered enrofloxacin (10 mg/kg qd) and metronidazole (12.5 mg/kg BID), followed 1 h later by placebo or a commercially-available synbiotic combination (BID), per os for 21 days with reevaluation 56 days thereafter. Fecal samples were collected on days 5–7 (baseline), 26–28, and 82–84. The fecal microbiome was analyzed by qPCR and sequencing of 16S rRNA genes; time-of-flight mass spectrometry was used to determine metabolomic profiles. Split plot repeated measures mixed model ANOVA was used to compare results between treatment groups. P < 0.05 was considered significant, with Benjamini and Hochberg's False Discovery Rate used to adjust for multiple comparisons. Results: Alpha diversity metrics differed significantly over time in both treatment groups, with incomplete recovery by days 82–84. Beta diversity and the dysbiosis index differed significantly over time and between treatment groups, with incomplete recovery at days 82–84 for dogs in the placebo group. Significant group-by-time interactions were noted for 15 genera, including Adlercreutzia, Bifidobacterium, Slackia, Turicibacter, Clostridium (including C. hiranonis) [Ruminococcus], Erysipelotrichaceae_g_, [Eubacterium], and Succinivibrionaceae_g_. Concurrent group and time effects were present for six genera, including Collinsella, Ruminococcaceae_g_, and Prevotella. Metabolite profiles differed significantly by group-by-time, group, and time for 28, 20, and 192 metabolites, respectively. These included short-chain fatty acid, bile acid, tryptophan, sphingolipid, benzoic acid, and cinnaminic acid metabolites, as well as fucose and ethanolamine. Changes in many taxa and metabolites persisted through days 82–84. Conclusion: Antibiotic administration causes sustained dysbiosis and dysmetabolism in dogs. Significant group-by-time interactions were noted for a number of taxa and metabolites, potentially contributing to decreased antibiotic-induced gastrointestinal effects in dogs administered synbiotics.
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Affiliation(s)
- Jacqueline C Whittemore
- Small Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN, United States
| | - Joshua M Price
- Office of Information Technology, University of Tennessee, Knoxville, TN, United States
| | - Tamberlyn Moyers
- Small Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN, United States
| | - Jan S Suchodolski
- The Gastrointestinal Laboratory, Small Animal Clinical Sciences, Texas A&M University, College Station, TX, United States
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26
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Gerasimidis K, Godny L, Sigall-Boneh R, Svolos V, Wall C, Halmos E. Current recommendations on the role of diet in the aetiology and management of IBD. Frontline Gastroenterol 2021; 13:160-167. [PMID: 35300465 PMCID: PMC8862489 DOI: 10.1136/flgastro-2020-101429] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/18/2021] [Indexed: 02/06/2023] Open
Abstract
Diet is a key modifier of risk of inflammatory bowel disease development and potentially a treatment option in patients with established disease. International organisations in gastroenterology and inflammatory bowel disease have published guidelines for the role of diet in disease onset and its management. Here, we discuss the major overarching themes arising from these guidelines and appraise recent literature on the role of diet for inflammatory bowel disease prevention, treatment of active disease and maintenance of remission, considering these themes. Except for exclusive enteral nutrition in active Crohn's disease, we currently possess very little evidence to make any further dietary recommendations for the management of inflammatory bowel disease. There is also currently uncertainty on the extrapolation of epidemiological dietary signals on risk of disease development and preclinical experiments in animal models to management, once disease is established. Until high-quality evidence from clinical research becomes available, the only specific recommendations for inflammatory bowel disease we might safely give are those of healthy eating which apply for the general population for overall health and well-being.
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Affiliation(s)
| | - Lihi Godny
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva and the Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Rotem Sigall-Boneh
- Paediatric Gastroenterology and Nutrition Unit, Wolfson Medical Center, Holon and the Sackler Faculty of Medicine, Tel Aviv University, Israel, Holon, Israel
| | - Vaios Svolos
- Human Nutrition, School of Medicine, University of Glasgow, Glasgow, UK
| | - Catherine Wall
- Department of Medicine and Department of Human Nutrition, University of Otago Dunedin School of Medicine, Christchurch, New Zealand
| | - Emma Halmos
- Department of Gastroenterology, Central Clinical School, Monash University, The Alfred Hospital, Melbourne, Victoria, Australia
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27
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Pokhrel A, Kang SY, Schmidt-Dannert C. Ethanolamine bacterial microcompartments: from structure, function studies to bioengineering applications. Curr Opin Microbiol 2021; 62:28-37. [PMID: 34034083 DOI: 10.1016/j.mib.2021.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022]
Abstract
Two decades of structural and functional studies have revealed functions, structures and diversity of bacterial microcompartments. The protein-based organelles encapsulate diverse metabolic pathways in semipermeable, icosahedral or pseudo-icosahedral shells. One of the first discovered and characterized microcompartments are those involved in ethanolamine degradation. This review will summarize their function and assembly along with shared and unique characteristics with other microcompartment types. The modularity and self-assembling properties of their shell proteins make them valuable targets for bioengineering. Advances and prospects for shell protein engineering in vivo and in vitro for synthetic biology and biotechnology applications will be discussed.
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Affiliation(s)
- Anaya Pokhrel
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Sun-Young Kang
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA.
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28
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Asija K, Sutter M, Kerfeld CA. A Survey of Bacterial Microcompartment Distribution in the Human Microbiome. Front Microbiol 2021; 12:669024. [PMID: 34054778 PMCID: PMC8156839 DOI: 10.3389/fmicb.2021.669024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/13/2021] [Indexed: 01/04/2023] Open
Abstract
Bacterial microcompartments (BMCs) are protein-based organelles that expand the metabolic potential of many bacteria by sequestering segments of enzymatic pathways in a selectively permeable protein shell. Sixty-eight different types/subtypes of BMCs have been bioinformatically identified based on the encapsulated enzymes and shell proteins encoded in genomic loci. BMCs are found across bacterial phyla. The organisms that contain them, rather than strictly correlating with specific lineages, tend to reflect the metabolic landscape of the environmental niches they occupy. From our recent comprehensive bioinformatic survey of BMCs found in genome sequence data, we find many in members of the human microbiome. Here we survey the distribution of BMCs in the different biotopes of the human body. Given their amenability to be horizontally transferred and bioengineered they hold promise as metabolic modules that could be used to probiotically alter microbiomes or treat dysbiosis.
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Affiliation(s)
- Kunica Asija
- Environmental Genomics and Systems Biology Division, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Markus Sutter
- Environmental Genomics and Systems Biology Division, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Michigan State University-U.S. Department of Energy (MSU-DOE) Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Cheryl A. Kerfeld
- Environmental Genomics and Systems Biology Division, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Michigan State University-U.S. Department of Energy (MSU-DOE) Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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29
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Chu W, Han Q, Xu J, Wang J, Sun Y, Li W, Chen ZJ, Du Y. Metagenomic analysis identified microbiome alterations and pathological association between intestinal microbiota and polycystic ovary syndrome. Fertil Steril 2021; 113:1286-1298.e4. [PMID: 32482258 DOI: 10.1016/j.fertnstert.2020.01.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/25/2019] [Accepted: 01/21/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To identify different microbial species in women with polycystic ovary syndrome (PCOS) and reveal a possible relationship between gut dysbiosis and pathological changes. DESIGN Cross-sectional study. SETTING Academic institution. PATIENT(S) Reproductive-aged women with PCOS (n = 14) and controls (n = 14) from the Centre for Reproductive Medicine. INTERVENTION(S) Shotgun metagenomic sequencing on fecal samples from patients, and clinical parameters (including body mass index, endocrine hormone levels, and glycemia level) gathered for correlation analysis. MAIN OUTCOME MEASURE(S) Identification of different gut microbial strains and relativity between microbiota and clinical parameters. RESULT(S) We found several microbial strains were statistically significantly more abundant in the PCOS group, including Parabacteroides merdae, Bacteroides fragilis, and strains of Escherichia and Shigella, whereas Faecalibacterium prausnitzii was enriched in the control group. Metagenomic species (MGS) analysis revealed that the microbes of the PCOS group were negatively correlated with those of the control group. Of note, we observed a positive correlation between MGS relevant to PCOS and endocrine disorders, including body mass index and elevated levels of serum testosterone, luteinizing hormone, and antimüllerian hormone. Functional alterations, reflected by Kyoto Encyclopedia of Genes and Genomes orthologues, could imply potential mechanisms of microbial involvement in the developmental progress of PCOS. CONCLUSION(S) Our findings suggest an intimate association and potential mechanisms linking microbial dysbiosis and the pathophysiologic changes of PCOS. We address the importance of monitoring and modulating microbial composition and functional shifts in future clinical practice.
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Affiliation(s)
- Weiwei Chu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Qixin Han
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Jieying Xu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Juan Wang
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Yun Sun
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Weiping Li
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China; National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory for Reproductive Endocrinology of Ministry of Education, Center for Reproductive Medicine, Shandong University, Jinan, People's Republic of China
| | - Yanzhi Du
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China.
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Abstract
There are 100 trillion diverse bacterial residents in the mammalian gut. Commensal bacterial species/strains cooperate and compete with each other to establish a well-balanced community, crucial for the maintenance of host health. Pathogenic bacteria hijack cooperative mechanisms or use strategies to evade competitive mechanisms to establish infection. Moreover, pathogenic bacteria cause marked environmental changes in the gut, such as the induction of inflammation, which fosters the selective growth of pathogens. In this review, we summarize the latest findings concerning the mechanisms by which commensal bacterial species/strains colonize the gut through cooperative or competitive behaviors. We also review the mechanisms by which pathogenic bacteria adapt to the inflamed gut and thrive at the expense of commensal bacteria. The understanding of bacterial adaptation to the healthy and the inflamed gut may provide new bacteria-targeted therapeutic approaches that selectively promote the expansion of beneficial commensal bacteria or limit the growth of pathogenic bacteria.
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Affiliation(s)
- Yijie Guo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA,Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Sho Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA,CONTACT Nobuhiko Kamada Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
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31
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Hurtado-Lorenzo A, Honig G, Heller C. Precision Nutrition Initiative: Toward Personalized Diet Recommendations for Patients With Inflammatory Bowel Diseases. CROHN'S & COLITIS 360 2020; 2:otaa087. [PMID: 36777761 PMCID: PMC9802167 DOI: 10.1093/crocol/otaa087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 12/14/2022] Open
Affiliation(s)
- Andrés Hurtado-Lorenzo
- Research Department, Crohn’s & Colitis Foundation, New York, New York, USA,Address correspondence to: Andrés Hurtado-Lorenzo, PhD, Research Department, Crohn’s & Colitis Foundation, 733 3rd Avenue Suite 510, New York, NY 10017 ()
| | - Gerard Honig
- Research Department, Crohn’s & Colitis Foundation, New York, New York, USA
| | - Caren Heller
- Research Department, Crohn’s & Colitis Foundation, New York, New York, USA
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Stewart KL, Stewart AM, Bobik TA. Prokaryotic Organelles: Bacterial Microcompartments in E. coli and Salmonella. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0025-2019. [PMID: 33030141 PMCID: PMC7552817 DOI: 10.1128/ecosalplus.esp-0025-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Indexed: 02/07/2023]
Abstract
Bacterial microcompartments (MCPs) are proteinaceous organelles consisting of a metabolic pathway encapsulated within a selectively permeable protein shell. Hundreds of species of bacteria produce MCPs of at least nine different types, and MCP metabolism is associated with enteric pathogenesis, cancer, and heart disease. This review focuses chiefly on the four types of catabolic MCPs (metabolosomes) found in Escherichia coli and Salmonella: the propanediol utilization (pdu), ethanolamine utilization (eut), choline utilization (cut), and glycyl radical propanediol (grp) MCPs. Although the great majority of work done on catabolic MCPs has been carried out with Salmonella and E. coli, research outside the group is mentioned where necessary for a comprehensive understanding. Salient characteristics found across MCPs are discussed, including enzymatic reactions and shell composition, with particular attention paid to key differences between classes of MCPs. We also highlight relevant research on the dynamic processes of MCP assembly, protein targeting, and the mechanisms that underlie selective permeability. Lastly, we discuss emerging biotechnology applications based on MCP principles and point out challenges, unanswered questions, and future directions.
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Affiliation(s)
- Katie L. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Andrew M. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Thomas A. Bobik
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
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The Ethanolamine-Sensing Transcription Factor EutR Promotes Virulence and Transmission during Citrobacter rodentium Intestinal Infection. Infect Immun 2020; 88:IAI.00137-20. [PMID: 32631916 DOI: 10.1128/iai.00137-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/26/2020] [Indexed: 12/18/2022] Open
Abstract
Enteric pathogens exploit chemical and nutrient signaling to gauge their location within a host and control expression of traits important for infection. Ethanolamine-containing molecules are essential in host physiology and play important roles in intestinal processes. The transcription factor EutR is conserved in the Enterobacteriaceae and is required for ethanolamine sensing and metabolism. In enterohemorrhagic Escherichia coli (EHEC) O157:H7, EutR responds to ethanolamine to activate expression of traits required for host colonization and disease; however, the importance of EutR to EHEC intestinal infection has not been examined. Because EHEC does not naturally colonize or cause disease in mice, we employed the natural murine pathogen Citrobacter rodentium as a model of EHEC virulence to investigate the importance of EutR in vivo EHEC and C. rodentium possess the locus of enterocyte effacement (LEE), which is the canonical virulence trait of attaching and effacing pathogens. Our findings demonstrate that ethanolamine sensing and EutR-dependent regulation of the LEE are conserved in C. rodentium Moreover, during infection, EutR is required for maximal LEE expression, colonization, and transmission efficiency. These findings reveal that EutR not only is important for persistence during the primary host infection cycle but also is required for maintenance in a host population.
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Short Chain Fatty Acids Modulate the Growth and Virulence of Pathosymbiont Escherichia coli and Host Response. Antibiotics (Basel) 2020; 9:antibiotics9080462. [PMID: 32751519 PMCID: PMC7460008 DOI: 10.3390/antibiotics9080462] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022] Open
Abstract
Short chain fatty acids (SCFA), principally acetate, propionate, and butyrate, are produced by fermentation of dietary fibers by the gut microbiota. SCFA regulate the growth and virulence of enteric pathogens, such as enterohemorrhagic E. coli (EHEC), Klebsiella and Salmonella. We sought to investigate the impact of SCFA on growth and virulence of pathosymbiont E. coli associated with inflammatory bowel disease (IBD) and colorectal cancer (CRC), and their role in regulating host responses to bacterial infection in vitro. We found that under ileal conditions (pH = 7.4; 12 mM total SCFA), SCFA significantly (p < 0.05) potentiate the growth and motility of pathosymbiont E. coli. However, under colonic conditions (pH = 6.5; 65 to 123 mM total SCFA), SCFA significantly (p < 0.05) inhibit growth in a pH dependent fashion (up to 60%), and down-regulate virulence gene expression (e.g., fliC, fimH, htrA, chuA, pks). Functional analysis reveals that colonic SCFA significantly (p < 0.05) inhibit E. coli motility (up to 95%), infectivity (up to 60%), and type 1 fimbria-mediated agglutination (up to 50%). In addition, SCFA significantly (p < 0.05) inhibit the activation of NF-κB, and IL-8 production by epithelial cells. Our findings provide novel insights on the role of the regional chemical microenvironment in regulating the growth and virulence of pathosymbiont E. coli and opportunities for therapeutic intervention.
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Pobeguts OV, Ladygina VG, Evsyutina DV, Eremeev AV, Zubov AI, Matyushkina DS, Scherbakov PL, Rakitina DV, Fisunov GY. Propionate Induces Virulent Properties of Crohn's Disease-Associated Escherichia coli. Front Microbiol 2020; 11:1460. [PMID: 32733408 PMCID: PMC7360682 DOI: 10.3389/fmicb.2020.01460] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 06/04/2020] [Indexed: 12/16/2022] Open
Abstract
Crohn's disease (CD) is a severe chronic immune-mediated granulomatous inflammatory disease of the gastrointestinal tract. The mechanisms of CD pathogenesis remain obscure. Metagenomic analysis of samples from CD patients revealed that several of them have the elevated level of Escherichia coli with adhesive-invasive phenotype (AIEC). Previously, we isolated an E. coli strain CD isolate ZvL2 from a patient with CD, which features AIEC phenotype. Here, we demonstrate that prolonged growth on propionate containing medium stimulates virulent properties of CD isolate ZvL2, while prolonged growth on glucose reduces these properties to levels indistinguishable from laboratory strain K-12 MG1655. Propionate presence also boosts the ability of CD isolate ZvL2 to penetrate and colonize macrophages. The effect of propionate is reversible, re-passaging of CD isolate on M9 medium supplemented with glucose leads to the loss of its virulent properties. Proteome analysis of CD isolate ZvL2 growth in medium supplemented with propionate or glucose revealed that propionate induces expression porins OmpA and OmpW, transcription factors PhoP and OmpR, and universal stress protein UspE, which were previously found to be important for macrophage colonization by enteropathogenic bacteria.
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Affiliation(s)
- Olga V. Pobeguts
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Valentina G. Ladygina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Daria V. Evsyutina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Artem V. Eremeev
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Aleksandr I. Zubov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Daria S. Matyushkina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | | | - Daria V. Rakitina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Gleb Y. Fisunov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
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Chervy M, Barnich N, Denizot J. Adherent-Invasive E. coli: Update on the Lifestyle of a Troublemaker in Crohn's Disease. Int J Mol Sci 2020; 21:E3734. [PMID: 32466328 PMCID: PMC7279240 DOI: 10.3390/ijms21103734] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 12/12/2022] Open
Abstract
Besides genetic polymorphisms and environmental factors, the intestinal microbiota is an important factor in the etiology of Crohn's disease (CD). Among microbiota alterations, a particular pathotype of Escherichia coli involved in the pathogenesis of CD abnormally colonizes the intestinal mucosa of patients: the adherent-invasive Escherichia coli (AIEC) pathobiont bacteria, which have the abilities to adhere to and to invade intestinal epithelial cells (IECs), as well as to survive and replicate within macrophages. AIEC have been the subject of many studies in recent years to unveil some genes linked to AIEC virulence and to understand the impact of AIEC infection on the gut and consequently their involvement in CD. In this review, we describe the lifestyle of AIEC bacteria within the intestine, from the interaction with intestinal epithelial and immune cells with an emphasis on environmental and genetic factors favoring their implantation, to their lifestyle in the intestinal lumen. Finally, we discuss AIEC-targeting strategies such as the use of FimH antagonists, bacteriophages, or antibiotics, which could constitute therapeutic options to prevent and limit AIEC colonization in CD patients.
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Affiliation(s)
- Mélissa Chervy
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), 63001 Clermont-Ferrand, France; (M.C.); (N.B.)
| | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), 63001 Clermont-Ferrand, France; (M.C.); (N.B.)
- Institut Universitaire de Technologie, Génie Biologique, 63172 Aubière, France
| | - Jérémy Denizot
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), 63001 Clermont-Ferrand, France; (M.C.); (N.B.)
- Institut Universitaire de Technologie, Génie Biologique, 63172 Aubière, France
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Logan M, Gkikas K, Svolos V, Nichols B, Milling S, Gaya DR, Seenan JP, Macdonald J, Hansen R, Ijaz UZ, Russell RK, Gerasimidis K. Analysis of 61 exclusive enteral nutrition formulas used in the management of active Crohn's disease-new insights into dietary disease triggers. Aliment Pharmacol Ther 2020; 51:935-947. [PMID: 32249975 PMCID: PMC8653890 DOI: 10.1111/apt.15695] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/25/2019] [Accepted: 03/01/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Exclusive enteral nutrition (EEN) is an effective treatment for Crohn's disease. AIMS To investigate the hypothesis that ingredients of EEN formulas are unlikely to initiate a disease flare and that their dietary elimination is not essential for disease amelioration. METHODS We performed compositional analysis of EEN formulas with evidence of efficacy in management of active Crohn's disease. Macronutrient content was compared against the dietary reference values (DRV), the UK National Diet and Nutrition Survey (NDNS) and intake of Crohn's disease children. Food additives were cross-referenced against the FAO/WHO database. RESULTS Sixty-one formulas were identified with variable composition (carbohydrates [22.8%-89.3%], protein [7.8%-30.1%], fat [0%-52.5%]). Maltodextrin, milk protein and vegetable/plant oils were the commonest macronutrient sources. Their n-6:n-3 fatty acid ratio varied from 0.25 to 46.5. 56 food additives were identified (median per formula: 11). All formulas were lactose-free, gluten-free, and 82% lacked fibre. The commonest food additives were emulsifiers, stabilisers, antioxidants, acidity regulators and thickeners. Food additives, implicated in Crohn's disease aetiology, were present in formulas (modified starches [100%], carrageenan [22%], carboxymethyl cellulose [13%] and polysorbate 80 [5%]). Remission rates did not differ between EEN formulas with and without those food additives. Analysis including only formulas from randomised controlled trials (RCTs) retained in the latest Cochrane meta-analysis produced similar findings. EEN formulas contained less energy from saturated fat than NDNS intake. CONCLUSION We have identified food ingredients which are present in EEN formulas that are effective in Crohn's disease and challenge perceptions that these ingredients might be harmful.
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Affiliation(s)
- Michael Logan
- Human NutritionSchool of Medicine, Dentistry and NursingUniversity of GlasgowGlasgow Royal InfirmaryGlasgowUK,Civil EngineeringSchool of EngineeringUniversity of GlasgowGlasgowUK
| | - Konstantinos Gkikas
- Human NutritionSchool of Medicine, Dentistry and NursingUniversity of GlasgowGlasgow Royal InfirmaryGlasgowUK
| | - Vaios Svolos
- Human NutritionSchool of Medicine, Dentistry and NursingUniversity of GlasgowGlasgow Royal InfirmaryGlasgowUK
| | - Ben Nichols
- Human NutritionSchool of Medicine, Dentistry and NursingUniversity of GlasgowGlasgow Royal InfirmaryGlasgowUK
| | - Simon Milling
- Institute for Infection, Immunity and InflammationUniversity of GlasgowGlasgowUK
| | - Daniel R. Gaya
- Department of GastroenterologyGlasgow Royal InfirmaryGlasgowUK
| | - John Paul Seenan
- Department of GastroenterologyQueen Elizabeth University HospitalNHS Greater Glasgow & ClydeGlasgowUK
| | - Jonathan Macdonald
- Department of GastroenterologyQueen Elizabeth University HospitalNHS Greater Glasgow & ClydeGlasgowUK
| | - Richard Hansen
- Department of Paediatric GastroenterologyRoyal Hospital for ChildrenGlasgowUK
| | - Umer Z. Ijaz
- Civil EngineeringSchool of EngineeringUniversity of GlasgowGlasgowUK
| | - Richard K. Russell
- Department of Paediatric GastroenterologyRoyal Hospital for ChildrenGlasgowUK
| | - Konstantinos Gerasimidis
- Human NutritionSchool of Medicine, Dentistry and NursingUniversity of GlasgowGlasgow Royal InfirmaryGlasgowUK
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Ormsby MJ, Johnson SA, Carpena N, Meikle LM, Goldstone RJ, McIntosh A, Wessel HM, Hulme HE, McConnachie CC, Connolly JPR, Roe AJ, Hasson C, Boyd J, Fitzgerald E, Gerasimidis K, Morrison D, Hold GL, Hansen R, Walker D, Smith DGE, Wall DM. Propionic Acid Promotes the Virulent Phenotype of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. Cell Rep 2020; 30:2297-2305.e5. [PMID: 32075765 PMCID: PMC7034058 DOI: 10.1016/j.celrep.2020.01.078] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 08/09/2019] [Accepted: 01/22/2020] [Indexed: 02/07/2023] Open
Abstract
Propionic acid (PA) is a bacterium-derived intestinal antimicrobial and immune modulator used widely in food production and agriculture. Passage of Crohn's disease-associated adherent-invasive Escherichia coli (AIEC) through a murine model, in which intestinal PA levels are increased to mimic the human intestine, leads to the recovery of AIEC with significantly increased virulence. Similar phenotypic changes are observed outside the murine model when AIEC is grown in culture with PA as the sole carbon source; such PA exposure also results in AIEC that persists at 20-fold higher levels in vivo. RNA sequencing identifies an upregulation of genes involved in biofilm formation, stress response, metabolism, membrane integrity, and alternative carbon source utilization. PA exposure also increases virulence in a number of E. coli isolates from Crohn's disease patients. Removal of PA is sufficient to reverse these phenotypic changes. Our data indicate that exposure to PA results in AIEC resistance and increased virulence in its presence.
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Affiliation(s)
- Michael J Ormsby
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Síle A Johnson
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Nuria Carpena
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Lynsey M Meikle
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Robert J Goldstone
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Anne McIntosh
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Hannah M Wessel
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Heather E Hulme
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Ceilidh C McConnachie
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - James P R Connolly
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK; Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Andrew J Roe
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Conor Hasson
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Joseph Boyd
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Eamonn Fitzgerald
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
| | - Douglas Morrison
- Scottish Universities Environmental Research Centre, University of Glasgow, Glasgow G75 0QF, UK
| | - Georgina L Hold
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Richard Hansen
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, 1345 Govan Road, Glasgow G51 4TF, UK
| | - Daniel Walker
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK
| | - David G E Smith
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Daniel M Wall
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow G12 8TA, UK.
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Gerasimidis K, Svolos V, Nichols B, Papadopoulou R, Quince C, Ijaz UZ, Milling S, Gaya DR, Russell RK, Hansen R. Reply. Gastroenterology 2019; 157:1161-1162. [PMID: 31408620 DOI: 10.1053/j.gastro.2019.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/08/2019] [Indexed: 12/02/2022]
Affiliation(s)
- Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, UK
| | - Vaios Svolos
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, UK
| | - Ben Nichols
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, UK
| | - Rodanthi Papadopoulou
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, UK
| | | | - Umer Z Ijaz
- School of Engineering, University of Glasgow, Glasgow, UK
| | - Simon Milling
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Daniel R Gaya
- Department of Gastroenterology, Glasgow Royal Infirmary, Glasgow, UK
| | - Richard K Russell
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, Glasgow, UK
| | - Richard Hansen
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, Glasgow, UK
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