1
|
Jandl B, Dighe S, Gasche C, Makristathis A, Muttenthaler M. Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities. Clin Microbiol Rev 2024:e0013323. [PMID: 38995034 DOI: 10.1128/cmr.00133-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
SUMMARYThe human intestinal tract harbors a profound variety of microorganisms that live in symbiosis with the host and each other. It is a complex and highly dynamic environment whose homeostasis directly relates to human health. Dysbiosis of the gut microbiota and polymicrobial biofilms have been associated with gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel diseases, and colorectal cancers. This review covers the molecular composition and organization of intestinal biofilms, mechanistic aspects of biofilm signaling networks for bacterial communication and behavior, and synergistic effects in polymicrobial biofilms. It further describes the clinical relevance and diseases associated with gut biofilms, the role of biofilms in antimicrobial resistance, and the intestinal host defense system and therapeutic strategies counteracting biofilms. Taken together, this review summarizes the latest knowledge and research on intestinal biofilms and their role in gut disorders and provides directions toward the development of biofilm-specific treatments.
Collapse
Affiliation(s)
- Bernhard Jandl
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Satish Dighe
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Christoph Gasche
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Vienna, Vienna, Austria
- Loha for Life, Center for Gastroenterology and Iron Deficiency, Vienna, Austria
| | - Athanasios Makristathis
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Markus Muttenthaler
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
2
|
Zuberi A, Ahmad N, Ahmad H, Saeed M, Ahmad I. Beyond antibiotics: CRISPR/Cas9 triumph over biofilm-associated antibiotic resistance infections. Front Cell Infect Microbiol 2024; 14:1408569. [PMID: 39035353 PMCID: PMC11257871 DOI: 10.3389/fcimb.2024.1408569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/27/2024] [Indexed: 07/23/2024] Open
Abstract
A complex structure known as a biofilm is formed when a variety of bacterial colonies or a single type of cell in a group sticks to a surface. The extracellular polymeric compounds that encase these cells, often consisting of proteins, eDNA, and polysaccharides, exhibit strong antibiotic resistance. Concerns about biofilm in the pharmaceutical industry, public health, and medical fields have sparked a lot of interest, as antibiotic resistance is a unique capacity exhibited by these biofilm-producing bacteria, which increases morbidity and death. Biofilm formation is a complicated process that is controlled by several variables. Insights into the processes to target for the therapy have been gained from multiple attempts to dissect the biofilm formation process. Targeting pathogens within a biofilm is profitable because the bacterial pathogens become considerably more resistant to drugs in the biofilm state. Although biofilm-mediated infections can be lessened using the currently available medications, there has been a lot of focus on the development of new approaches, such as bioinformatics tools, for both treating and preventing the production of biofilms. Technologies such as transcriptomics, metabolomics, nanotherapeutics and proteomics are also used to develop novel anti-biofilm agents. These techniques help to identify small compounds that can be used to inhibit important biofilm regulators. The field of appropriate control strategies to avoid biofilm formation is expanding quickly because of this spurred study. As a result, the current article addresses our current knowledge of how biofilms form, the mechanisms by which bacteria in biofilms resist antibiotics, and cutting-edge treatment approaches for infections caused by biofilms. Furthermore, we have showcased current ongoing research utilizing the CRISPR/Cas9 gene editing system to combat bacterial biofilm infections, particularly those brought on by lethal drug-resistant pathogens, concluded the article with a novel hypothesis and aspirations, and acknowledged certain limitations.
Collapse
Affiliation(s)
- Azna Zuberi
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States
- Department of Obs & Gynae, Northwestern University, Chicago, IL, United States
| | - Nayeem Ahmad
- Department of Biophysics, All India Institute of Medical Science, New Delhi, India
- Department of Microbiology, Immunology, and Infectious Diseases, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Hafiz Ahmad
- Department of Medical Microbiology & Immunology, Ras Al Khaimah (RAK) College of Medical Sciences, Ras Al Khaimah (RAK) Medical and Health Sciences University, Ras Al Khaimah, United Arab Emirates
| | - Mohd Saeed
- Department of Biology, College of Science University of Hail, Hail, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| |
Collapse
|
3
|
El-Sayed A, Kapila D, Taha RSI, El-Sayed S, Mahen MRA, Taha R, Alrubaiy L. The Role of the Gut Microbiome in Inflammatory Bowel Disease: The Middle East Perspective. J Pers Med 2024; 14:652. [PMID: 38929872 PMCID: PMC11204866 DOI: 10.3390/jpm14060652] [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: 05/18/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The gut microbiome is of paramount importance in preserving internal balance in the gastrointestinal tract; therefore, disruptions in its regulation have been linked to the development of inflammatory bowel disease (IBD). This article explores the intricate details of the gastrointestinal microbiome as it pertains to inflammatory bowel disease (IBD), with an emphasis on the Middle East. The study reviews the typical gut microbiome, modifications in inflammatory bowel disease (IBD), determinants impacting the gut microbiome of the Middle East, and prospective therapeutic interventions.
Collapse
Affiliation(s)
- Ahmed El-Sayed
- Hillingdon Hospital NHS Trust, London UB8 3NN, UK; (A.E.-S.); (D.K.)
| | - Diya Kapila
- Hillingdon Hospital NHS Trust, London UB8 3NN, UK; (A.E.-S.); (D.K.)
| | - Rama Sami Issa Taha
- Healthpoint Hospital, Abu Dhabi P.O. Box 112308, United Arab Emirates; (R.S.I.T.); (R.T.)
| | | | - Mohd Rafiw Ahmed Mahen
- Department of Medicine, King’s College Hospital London, Dubai P.O. Box 340901, United Arab Emirates;
| | - Roa’a Taha
- Healthpoint Hospital, Abu Dhabi P.O. Box 112308, United Arab Emirates; (R.S.I.T.); (R.T.)
| | - Laith Alrubaiy
- Healthpoint Hospital, Abu Dhabi P.O. Box 112308, United Arab Emirates; (R.S.I.T.); (R.T.)
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
| |
Collapse
|
4
|
Bulnes R, Utay NS. Therapeutic microbiome modulation: new frontiers in HIV treatment. Curr Opin HIV AIDS 2024:01222929-990000000-00097. [PMID: 38874442 DOI: 10.1097/coh.0000000000000864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
PURPOSE OF REVIEW Dysbiosis may be a key driver of systemic inflammation, which increases the risk of non-AIDS events in people living with HIV (PLWH). Modulation of the microbiome to reverse this dysbiosis may be a novel approach to decrease inflammation and therefore morbidity and mortality in PLWH. RECENT FINDINGS Fecal microbiota transplantation (FMT), probiotics, prebiotics, synbiotics, postbiotics, and dietary modifications have the potential to modulate the microbiome. These interventions have been well tolerated in clinical trials to date. However, these interventions have not resulted in consistent or lasting changes to the microbiome or consistent changes in biomarkers of intestinal permeability, microbial translocation, inflammation, immune activation, or CD4+ T cell counts. Sustained engraftment may require prebiotics and/or dietary modifications added to either probiotics or FMT. SUMMARY Adequately powered randomized controlled trials are needed to elucidate whether microbiome modulation can be achieved and impact systemic inflammation in PLWH.
Collapse
Affiliation(s)
- Rene Bulnes
- Department of Internal Medicine, Division of Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | |
Collapse
|
5
|
Jandl B, Dighe S, Baumgartner M, Makristathis A, Gasche C, Muttenthaler M. Gastrointestinal Biofilms: Endoscopic Detection, Disease Relevance, and Therapeutic Strategies. Gastroenterology 2024:S0016-5085(24)05054-6. [PMID: 38876174 DOI: 10.1053/j.gastro.2024.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 06/16/2024]
Abstract
Gastrointestinal biofilms are highly heterogenic and spatially organized polymicrobial communities that can expand and cover large areas in the gastrointestinal tract. Gut microbiota dysbiosis, mucus disruption, and epithelial invasion are associated with pathogenic biofilms that have been linked to gastrointestinal disorders such as irritable bowel syndrome, inflammatory bowel diseases, gastric cancer, and colon cancer. Intestinal biofilms are highly prevalent in ulcerative colitis and irritable bowel syndrome patients, and most endoscopists will have observed such biofilms during colonoscopy, maybe without appreciating their biological and clinical importance. Gut biofilms have a protective extracellular matrix that renders them challenging to treat, and effective therapies are yet to be developed. This review covers gastrointestinal biofilm formation, growth, appearance and detection, biofilm architecture and signalling, human host defence mechanisms, disease and clinical relevance of biofilms, therapeutic approaches, and future perspectives. Critical knowledge gaps and open research questions regarding the biofilm's exact pathophysiological relevance and key hurdles in translating therapeutic advances into the clinic are discussed. Taken together, this review summarizes the status quo in gut biofilm research and provides perspectives and guidance for future research and therapeutic strategies.
Collapse
Affiliation(s)
- Bernhard Jandl
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria; University of Vienna, Vienna Doctoral School in Chemistry, Vienna, Austria; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia; Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria
| | - Satish Dighe
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Maximillian Baumgartner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Athanasios Makristathis
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Christoph Gasche
- Division of Gastroenterology and Hepatology, Department of Internal Medicine 3, Medical University of Vienna, Vienna, Austria; Loha for Life, Center for Gastroenterology and Iron Deficiency, Vienna, Austria
| | - Markus Muttenthaler
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
| |
Collapse
|
6
|
Stange EF. Dysbiosis in inflammatory bowel diseases: egg, not chicken. Front Med (Lausanne) 2024; 11:1395861. [PMID: 38846142 PMCID: PMC11153678 DOI: 10.3389/fmed.2024.1395861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/06/2024] [Indexed: 06/09/2024] Open
Abstract
There is agreement that inflammatory bowel diseases are, both in terms of species composition and function, associated with an altered intestinal microbiome. This is usually described by the term "dysbiosis," but this is a vague definition lacking quantitative precision. In this brief narrative review, the evidence concerning the primary or secondary role of this dysbiotic state is critically evaluated. Among others, the following facts argue against a primary etiological impact: 1) There is no specific dysbiotic microbiome in IBD, 2) the presence or absence of mucosal inflammation has a profound impact on the composition of the microbiome, 3) dysbiosis is not specific for IBD but linked to many unrelated diseases, 4) antibiotics, probiotics, and microbiome transfer have a very limited therapeutic effect, 5) the microbiome in concordant twins is similar to disease-discordant twins, and 6) the microbiome in relatives of IBD patients later developing IBD is altered, but these individuals already display subclinical inflammation.
Collapse
Affiliation(s)
- Eduard F. Stange
- Klinik für Innere Medizin I, Universitätsklinik Tübingen, Tübingen, Germany
| |
Collapse
|
7
|
Olteanu G, Ciucă-Pană MA, Busnatu ȘS, Lupuliasa D, Neacșu SM, Mititelu M, Musuc AM, Ioniță-Mîndrican CB, Boroghină SC. Unraveling the Microbiome-Human Body Axis: A Comprehensive Examination of Therapeutic Strategies, Interactions and Implications. Int J Mol Sci 2024; 25:5561. [PMID: 38791599 PMCID: PMC11122276 DOI: 10.3390/ijms25105561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
This review scrutinizes the intricate interplay between the microbiome and the human body, exploring its multifaceted dimensions and far-reaching implications. The human microbiome, comprising diverse microbial communities inhabiting various anatomical niches, is increasingly recognized as a critical determinant of human health and disease. Through an extensive examination of current research, this review elucidates the dynamic interactions between the microbiome and host physiology across multiple organ systems. Key topics include the establishment and maintenance of microbiota diversity, the influence of host factors on microbial composition, and the bidirectional communication pathways between microbiota and host cells. Furthermore, we delve into the functional implications of microbiome dysbiosis in disease states, emphasizing its role in shaping immune responses, metabolic processes, and neurological functions. Additionally, this review discusses emerging therapeutic strategies aimed at modulating the microbiome to restore host-microbe homeostasis and promote health. Microbiota fecal transplantation represents a groundbreaking therapeutic approach in the management of dysbiosis-related diseases, offering a promising avenue for restoring microbial balance within the gut ecosystem. This innovative therapy involves the transfer of fecal microbiota from a healthy donor to an individual suffering from dysbiosis, aiming to replenish beneficial microbial populations and mitigate pathological imbalances. By synthesizing findings from diverse fields, this review offers valuable insights into the complex relationship between the microbiome and the human body, highlighting avenues for future research and clinical interventions.
Collapse
Affiliation(s)
- Gabriel Olteanu
- Department of Clinical Laboratory and Food Safety, Faculty of Pharmacy, University of Medicine and Pharmacy Carol Davila, 020956 Bucharest, Romania;
| | - Maria-Alexandra Ciucă-Pană
- Department of Cardiology, Carol Davila University of Medicine and Pharmacy, Bagdasar-Arseni Emergency Hospital, 050474 Bucharest, Romania;
| | - Ștefan Sebastian Busnatu
- Department of Cardio-Thoracic Pathology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Dumitru Lupuliasa
- Department of Pharmaceutical Technology and Bio-Pharmacy, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania; (D.L.); (S.M.N.)
| | - Sorinel Marius Neacșu
- Department of Pharmaceutical Technology and Bio-Pharmacy, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania; (D.L.); (S.M.N.)
| | - Magdalena Mititelu
- Department of Clinical Laboratory and Food Safety, Faculty of Pharmacy, University of Medicine and Pharmacy Carol Davila, 020956 Bucharest, Romania;
| | - Adina Magdalena Musuc
- Institute of Physical Chemistry—Ilie Murgulescu, Romanian Academy, 060021 Bucharest, Romania
| | - Corina-Bianca Ioniță-Mîndrican
- Department of Toxicology, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania;
| | - Steluța Constanța Boroghină
- Department of Complementary Sciences, History of Medicine and Medical Culture, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| |
Collapse
|
8
|
Lin Q, Lin S, Fan Z, Liu J, Ye D, Guo P. A Review of the Mechanisms of Bacterial Colonization of the Mammal Gut. Microorganisms 2024; 12:1026. [PMID: 38792855 PMCID: PMC11124445 DOI: 10.3390/microorganisms12051026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/12/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
A healthy animal intestine hosts a diverse population of bacteria in a symbiotic relationship. These bacteria utilize nutrients in the host's intestinal environment for growth and reproduction. In return, they assist the host in digesting and metabolizing nutrients, fortifying the intestinal barrier, defending against potential pathogens, and maintaining gut health. Bacterial colonization is a crucial aspect of this interaction between bacteria and the intestine and involves the attachment of bacteria to intestinal mucus or epithelial cells through nonspecific or specific interactions. This process primarily relies on adhesins. The binding of bacterial adhesins to host receptors is a prerequisite for the long-term colonization of bacteria and serves as the foundation for the pathogenicity of pathogenic bacteria. Intervening in the adhesion and colonization of bacteria in animal intestines may offer an effective approach to treating gastrointestinal diseases and preventing pathogenic infections. Therefore, this paper reviews the situation and mechanisms of bacterial colonization, the colonization characteristics of various bacteria, and the factors influencing bacterial colonization. The aim of this study was to serve as a reference for further research on bacteria-gut interactions and improving animal gut health.
Collapse
Affiliation(s)
- Qingjie Lin
- College of Animal Science, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou 350002, China; (Q.L.); (S.L.); (Z.F.)
| | - Shiying Lin
- College of Animal Science, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou 350002, China; (Q.L.); (S.L.); (Z.F.)
| | - Zitao Fan
- College of Animal Science, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou 350002, China; (Q.L.); (S.L.); (Z.F.)
| | - Jing Liu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China;
| | - Dingcheng Ye
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China;
| | - Pingting Guo
- College of Animal Science, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou 350002, China; (Q.L.); (S.L.); (Z.F.)
| |
Collapse
|
9
|
Maritan E, Quagliariello A, Frago E, Patarnello T, Martino ME. The role of animal hosts in shaping gut microbiome variation. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230071. [PMID: 38497257 PMCID: PMC10945410 DOI: 10.1098/rstb.2023.0071] [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: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 03/19/2024] Open
Abstract
Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
Collapse
Affiliation(s)
- Elisa Maritan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Enric Frago
- CIRAD, UMR CBGP, INRAE, Institut Agro, IRD, Université Montpellier, 34398 Montpellier, France
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Maria Elena Martino
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| |
Collapse
|
10
|
Lee J, Menon N, Lim CT. Dissecting Gut-Microbial Community Interactions using a Gut Microbiome-on-a-Chip. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2302113. [PMID: 38414327 PMCID: PMC11132043 DOI: 10.1002/advs.202302113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/21/2023] [Indexed: 02/29/2024]
Abstract
While the human gut microbiota has a significant impact on gut health and disease, understanding of the roles of gut microbes, interactions, and collective impact of gut microbes on various aspects of human gut health is limited by the lack of suitable in vitro model system that can accurately replicate gut-like environment and enable the close visualization on causal and mechanistic relationships between microbial constitutents and the gut. , In this study, we present a scalable Gut Microbiome-on-a-Chip (GMoC) with great imaging capability and scalability, providing a physiologically relevant dynamic gut-microbes interfaces. This chip features a reproducible 3D stratified gut epithelium derived from Caco-2 cells (µGut), mimicking key intestinal architecture, functions, and cellular complexity, providing a physiolocially relevant gut environment for microbes residing in the gut. Incorporating tumorigenic bacteria, enterotoxigenic Bacteroides fragilis (ETBF), into the GMoC enable the observation of pathogenic behaviors of ETBF, leading to µGut disruption and pro-tumorigenic signaling activations. Pre-treating the µGut with a beneficial gut microbe Lactobacillus spp., effectively prevent ETBF-mediated gut pathogenesis, preserving the healthy state of the µGut through competition-mediated colonization resistance. The GMoC holds potential as a valuable tool for exploring unknown roles of gut microbes in microbe-induced pathogenesis and microbe-based therapeutic development.
Collapse
Affiliation(s)
- Jeeyeon Lee
- Institute for Health Innovation and Technology (iHealthtech)National University of SingaporeSingapore117599Singapore
| | - Nishanth Menon
- Department of Biomedical EngineeringNational University of SingaporeSingapore117583Singapore
| | - Chwee Teck Lim
- Institute for Health Innovation and Technology (iHealthtech)National University of SingaporeSingapore117599Singapore
- Department of Biomedical EngineeringNational University of SingaporeSingapore117583Singapore
- Mechanobiology InstituteNational University of SingaporeSingapore117411Singapore
| |
Collapse
|
11
|
Holmberg SM, Feeney RH, Prasoodanan P K V, Puértolas-Balint F, Singh DK, Wongkuna S, Zandbergen L, Hauner H, Brandl B, Nieminen AI, Skurk T, Schroeder BO. The gut commensal Blautia maintains colonic mucus function under low-fiber consumption through secretion of short-chain fatty acids. Nat Commun 2024; 15:3502. [PMID: 38664378 PMCID: PMC11045866 DOI: 10.1038/s41467-024-47594-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Beneficial gut bacteria are indispensable for developing colonic mucus and fully establishing its protective function against intestinal microorganisms. Low-fiber diet consumption alters the gut bacterial configuration and disturbs this microbe-mucus interaction, but the specific bacteria and microbial metabolites responsible for maintaining mucus function remain poorly understood. By using human-to-mouse microbiota transplantation and ex vivo analysis of colonic mucus function, we here show as a proof-of-concept that individuals who increase their daily dietary fiber intake can improve the capacity of their gut microbiota to prevent diet-mediated mucus defects. Mucus growth, a critical feature of intact colonic mucus, correlated with the abundance of the gut commensal Blautia, and supplementation of Blautia coccoides to mice confirmed its mucus-stimulating capacity. Mechanistically, B. coccoides stimulated mucus growth through the production of the short-chain fatty acids propionate and acetate via activation of the short-chain fatty acid receptor Ffar2, which could serve as a new target to restore mucus growth during mucus-associated lifestyle diseases.
Collapse
Affiliation(s)
- Sandra M Holmberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Rachel H Feeney
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Vishnu Prasoodanan P K
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Fabiola Puértolas-Balint
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Dhirendra K Singh
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Supapit Wongkuna
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Lotte Zandbergen
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Hans Hauner
- Institute in Nutritional Medicine, TU Munich, Munich, Germany
- TU Munich, School of Medicine, Munich, Germany
| | - Beate Brandl
- ZIEL Institute for Food and Health, TU Munich, Munich, Germany
| | - Anni I Nieminen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Thomas Skurk
- ZIEL Institute for Food and Health, TU Munich, Munich, Germany
| | - Bjoern O Schroeder
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umeå Center for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
| |
Collapse
|
12
|
Yang J, Isaka T, Kikuchi K, Numayama-Tsuruta K, Ishikawa T. Bacterial accumulation in intestinal folds induced by physical and biological factors. BMC Biol 2024; 22:76. [PMID: 38581018 PMCID: PMC10998401 DOI: 10.1186/s12915-024-01874-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The gut microbiota, vital for host health, influences metabolism, immune function, and development. Understanding the dynamic processes of bacterial accumulation within the gut is crucial, as it is closely related to immune responses, antibiotic resistance, and colorectal cancer. We investigated Escherichia coli behavior and distribution in zebrafish larval intestines, focusing on the gut microenvironment. RESULTS We discovered that E. coli spread was considerably suppressed within the intestinal folds, leading to a strong physical accumulation in the folds. Moreover, a higher concentration of E. coli on the dorsal side than on the ventral side was observed. Our in vitro microfluidic experiments and theoretical analysis revealed that the overall distribution of E. coli in the intestines was established by a combination of physical factor and bacterial taxis. CONCLUSIONS Our findings provide valuable insight into how the intestinal microenvironment affects bacterial motility and accumulation, enhancing our understanding of the behavioral and ecological dynamics of the intestinal microbiota.
Collapse
Affiliation(s)
- Jinyou Yang
- School of Intelligent Medicine, China Medical University, Shenyang, 110122, China.
| | - Toma Isaka
- Department of Biomedical Engineering, Graduate School of Biomedical Engineering, Tohoku University, 6-6-01 Aoba, Sendai, 980-8579, Japan
| | - Kenji Kikuchi
- Department of Biomedical Engineering, Graduate School of Biomedical Engineering, Tohoku University, 6-6-01 Aoba, Sendai, 980-8579, Japan
- Department of Finemechanics, Graduate School of Engineering, Tohoku University, 6-6-01 Aoba, Sendai, 980-8579, Japan
| | - Keiko Numayama-Tsuruta
- Department of Biomedical Engineering, Graduate School of Biomedical Engineering, Tohoku University, 6-6-01 Aoba, Sendai, 980-8579, Japan
| | - Takuji Ishikawa
- Department of Biomedical Engineering, Graduate School of Biomedical Engineering, Tohoku University, 6-6-01 Aoba, Sendai, 980-8579, Japan
- Department of Finemechanics, Graduate School of Engineering, Tohoku University, 6-6-01 Aoba, Sendai, 980-8579, Japan
| |
Collapse
|
13
|
Harnett MM, Doonan J, Tarafdar A, Pineda MA, Duncombe-Moore J, Buitrago G, Pan P, Hoskisson PA, Selman C, Harnett W. The parasitic worm product ES-62 protects against collagen-induced arthritis by resetting the gut-bone marrow axis in a microbiome-dependent manner. FRONTIERS IN TROPICAL DISEASES 2024; 4:fitd.2023.1334705. [PMID: 38500783 PMCID: PMC7615750 DOI: 10.3389/fitd.2023.1334705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024] Open
Abstract
The parasitic worm-derived immunomodulator, ES-62 rescues defective levels of IL-10-producing regulatory B cells (Bregs) and suppresses chronic Th1/Th17-driven inflammation to protect against joint destruction in the mouse collagen-induced arthritis (CIA) model of rheumatoid arthritis. Such autoimmune arthritis is also associated with dysbiosis of the gut microbiota and disruption of intestinal barrier integrity. We recently further exploited the CIA model to show that ES-62's prevention of joint destruction is associated with protection of intestinal barrier integrity and normalization of the gut microbiota, thereby suppressing the gut pathology that precedes the onset of autoimmunity and joint damage in CIA-mice. As the status of the gut microbiota impacts on immune responses by influencing haematopoiesis, we have therefore investigated whether ES-62 harnesses the homeostatic mechanisms regulating this gut-bone marrow (BM) axis to resolve the chronic inflammation promoting autoimmunity and joint destruction in CIA. Reflecting this, ES-62 was found to counteract the BM myeloid/lymphoid bias typically associated with chronic inflammation and infection. This was achieved primarily by ES-62 acting to maintain the levels of lymphoid lineages (B220+ and CD3+ cells) observed in naïve, healthy mice but lost from the BM of CIA-mice. Moreover, ES-62's ability to prevent bone-destroying osteoclastogenesis was found to be associated with its suppression of CIA-induced upregulation of osteoclast progenitors (OCPs) in the BM. Critically, and supporting ES-62's targeting of the gut-BM axis, this rewiring of inflammatory haematopoiesis was lost in mice with a depleted microbiome. Underlining the importance of ES-62's actions in restoring steady-state haematopoiesis, the BM levels of B and T lymphoid cells were shown to be inversely correlated, whilst the levels of OCPs positively correlated, with the severity of joint damage in CIA-mice.
Collapse
Affiliation(s)
- Margaret M. Harnett
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - James Doonan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Anuradha Tarafdar
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Miguel A. Pineda
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | | | - Geraldine Buitrago
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Piaopiao Pan
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Colin Selman
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - William Harnett
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| |
Collapse
|
14
|
Doranga S, Krogfelt KA, Cohen PS, Conway T. Nutrition of Escherichia coli within the intestinal microbiome. EcoSal Plus 2024:eesp00062023. [PMID: 38417452 DOI: 10.1128/ecosalplus.esp-0006-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/03/2023] [Indexed: 03/01/2024]
Abstract
In this chapter, we update our 2004 review of "The Life of Commensal Escherichia coli in the Mammalian Intestine" (https://doi.org/10.1128/ecosalplus.8.3.1.2), with a change of title that reflects the current focus on "Nutrition of E. coli within the Intestinal Microbiome." The earlier part of the previous two decades saw incremental improvements in understanding the carbon and energy sources that E. coli and Salmonella use to support intestinal colonization. Along with these investigations of electron donors came a better understanding of the electron acceptors that support the respiration of these facultative anaerobes in the gastrointestinal tract. Hundreds of recent papers add to what was known about the nutrition of commensal and pathogenic enteric bacteria. The fact that each biotype or pathotype grows on a different subset of the available nutrients suggested a mechanism for succession of commensal colonizers and invasion by enteric pathogens. Competition for nutrients in the intestine has also come to be recognized as one basis for colonization resistance, in which colonized strain(s) prevent colonization by a challenger. In the past decade, detailed investigations of fiber- and mucin-degrading anaerobes added greatly to our understanding of how complex polysaccharides support the hundreds of intestinal microbiome species. It is now clear that facultative anaerobes, which usually cannot degrade complex polysaccharides, live in symbiosis with the anaerobic degraders. This concept led to the "restaurant hypothesis," which emphasizes that facultative bacteria, such as E. coli, colonize the intestine as members of mixed biofilms and obtain the sugars they need for growth locally through cross-feeding from polysaccharide-degrading anaerobes. Each restaurant represents an intestinal niche. Competition for those niches determines whether or not invaders are able to overcome colonization resistance and become established. Topics centered on the nutritional basis of intestinal colonization and gastrointestinal health are explored here in detail.
Collapse
Affiliation(s)
- Sudhir Doranga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Karen A Krogfelt
- Department of Science and Environment, Pandemix Center Roskilde University, Roskilde, Denmark
| | - Paul S Cohen
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| |
Collapse
|
15
|
Lizárraga D, Gómez-Gil B, García-Gasca T, Ávalos-Soriano A, Casarini L, Salazar-Oroz A, García-Gasca A. Gestational diabetes mellitus: genetic factors, epigenetic alterations, and microbial composition. Acta Diabetol 2024; 61:1-17. [PMID: 37660305 DOI: 10.1007/s00592-023-02176-y] [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: 06/07/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
Gestational diabetes mellitus (GDM) is a common metabolic disorder, usually diagnosed during the third trimester of pregnancy that usually disappears after delivery. In GDM, the excess of glucose, fatty acids, and amino acids results in foetuses large for gestational age. Hyperglycaemia and insulin resistance accelerate the metabolism, raising the oxygen demand, and creating chronic hypoxia and inflammation. Women who experienced GDM and their offspring are at risk of developing type-2 diabetes, obesity, and other metabolic or cardiovascular conditions later in life. Genetic factors may predispose the development of GDM; however, they do not account for all GDM cases; lifestyle and diet also play important roles in GDM development by modulating epigenetic signatures and the body's microbial composition; therefore, this is a condition with a complex, multifactorial aetiology. In this context, we revised published reports describing GDM-associated single-nucleotide polymorphisms (SNPs), DNA methylation and microRNA expression in different tissues (such as placenta, umbilical cord, adipose tissue, and peripheral blood), and microbial composition in the gut, oral cavity, and vagina from pregnant women with GDM, as well as the bacterial composition of the offspring. Altogether, these reports indicate that a number of SNPs are associated to GDM phenotypes and may predispose the development of the disease. However, extrinsic factors (lifestyle, nutrition) modulate, through epigenetic mechanisms, the risk of developing the disease, and some association exists between the microbial composition with GDM in an organ-specific manner. Genes, epigenetic signatures, and microbiota could be transferred to the offspring, increasing the possibility of developing chronic degenerative conditions through postnatal life.
Collapse
Affiliation(s)
- Dennise Lizárraga
- Laboratory of Molecular and Cell Biology, Centro de Investigación en Alimentación y Desarrollo, Avenida Sábalo Cerritos s/n, 82112, Mazatlán, Sinaloa, Mexico
| | - Bruno Gómez-Gil
- Laboratory of Microbial Genomics, Centro de Investigación en Alimentación y Desarrollo, Avenida Sábalo Cerritos s/n, 82112, Mazatlán, Sinaloa, Mexico
| | - Teresa García-Gasca
- Laboratory of Molecular and Cellular Biology, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de las Ciencias s/n, 76230, Juriquilla, Querétaro, Mexico
| | - Anaguiven Ávalos-Soriano
- Laboratory of Molecular and Cell Biology, Centro de Investigación en Alimentación y Desarrollo, Avenida Sábalo Cerritos s/n, 82112, Mazatlán, Sinaloa, Mexico
| | - Livio Casarini
- Unit of Endocrinology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41125, Modena, Italy
| | - Azucena Salazar-Oroz
- Maternal-Fetal Department, Instituto Vidalia, Hospital Sharp Mazatlán, Avenida Rafael Buelna y Dr. Jesús Kumate s/n, 82126, Mazatlán, Sinaloa, Mexico
| | - Alejandra García-Gasca
- Laboratory of Molecular and Cell Biology, Centro de Investigación en Alimentación y Desarrollo, Avenida Sábalo Cerritos s/n, 82112, Mazatlán, Sinaloa, Mexico.
| |
Collapse
|
16
|
Olovo CV, Wiredu Ocansey DK, Ji Y, Huang X, Xu M. Bacterial membrane vesicles in the pathogenesis and treatment of inflammatory bowel disease. Gut Microbes 2024; 16:2341670. [PMID: 38666762 PMCID: PMC11057571 DOI: 10.1080/19490976.2024.2341670] [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: 01/15/2024] [Accepted: 04/08/2024] [Indexed: 05/01/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic and debilitating condition of relapsing and remitting inflammation in the gastrointestinal tract. Conventional therapeutic approaches for IBD have shown limited efficacy and detrimental side effects, leading to the quest for novel and effective treatment options for the disease. Bacterial membrane vesicles (MVs) are nanosized lipid particles secreted by lysis or blebbing processes from both Gram-negative and Gram-positive bacteria. These vesicles, known to carry bioactive components, are facsimiles of the parent bacterium and have been implicated in the onset and progression, as well as in the amelioration of IBD. This review discusses the overview of MVs and their impact in the pathogenesis, diagnosis, and treatment of IBD. We further discuss the technical challenges facing this research area and possible research questions addressing these challenges. We summarize recent advances in the diverse relationship between IBD and MVs, and the application of this knowledge as a viable and potent therapeutic strategy for IBD.
Collapse
Affiliation(s)
- Chinasa Valerie Olovo
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
- Department of Medical Laboratory Science, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Ying Ji
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xinxiang Huang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Institute of Digestive Diseases, Jiangsu University, Zhenjiang, Jiangsu, China
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Sidner B, Lerma A, Biswas B, Do TVT, Yu Y, Ronish LA, McCullough H, Auchtung JM, Piepenbrink KH. Flagellin is essential for initial attachment to mucosal surfaces by Clostridioides difficile. Microbiol Spectr 2023; 11:e0212023. [PMID: 37823657 PMCID: PMC10714722 DOI: 10.1128/spectrum.02120-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 09/04/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Clostridioides difficile is one of the leading causes of hospital-acquired infections worldwide and presents challenges in treatment due to recurrent gastrointestinal disease after treatment with antimicrobials. The mechanisms by which C. difficile colonizes the gut represent a key gap in knowledge, including its association with host cells and mucosa. Our results show the importance of flagellin for specific adhesion to mucosal hydrogels and can help to explain prior observations of adhesive defects in flagellin and pilin mutants.
Collapse
Affiliation(s)
- Ben Sidner
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Armando Lerma
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Baishakhi Biswas
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Thi Van Thanh Do
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Yafan Yu
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Leslie A. Ronish
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Hugh McCullough
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jennifer M. Auchtung
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Kurt H. Piepenbrink
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| |
Collapse
|
19
|
Su Y, Ding T. Targeting microbial quorum sensing: the next frontier to hinder bacterial driven gastrointestinal infections. Gut Microbes 2023; 15:2252780. [PMID: 37680117 PMCID: PMC10486307 DOI: 10.1080/19490976.2023.2252780] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
Bacteria synchronize social behaviors via a cell-cell communication and interaction mechanism termed as quorum sensing (QS). QS has been extensively studied in monocultures and proved to be intensively involved in bacterial virulence and infection. Despite the role QS plays in pathogens during laboratory engineered infections has been proved, the potential functions of QS related to pathogenesis in context of microbial consortia remain poorly understood. In this review, we summarize the basic molecular mechanisms of QS, primarily focusing on pathogenic microbes driving gastrointestinal (GI) infections. We further discuss how GI pathogens disequilibrate the homeostasis of the indigenous microbial consortia, rebuild a realm dominated by pathogens, and interact with host under worsening infectious conditions via pathogen-biased QS signaling. Additionally, we present recent applications and main challenges of manipulating QS network in microbial consortia with the goal of better understanding GI bacterial sociality and facilitating novel therapies targeting bacterial infections.
Collapse
Affiliation(s)
- Ying Su
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Ministry of Education, Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Guangzhou, China
| | - Tao Ding
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Ministry of Education, Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Guangzhou, China
| |
Collapse
|
20
|
Gao H, He C, Xin S, Hua R, Du Y, Wang B, Gong F, Yu X, Pan L, Liang C, Gao L, Shang H, Xu JD. Rhubarb extract rebuilding the mucus homeostasis and regulating mucin-associated flora to relieve constipation. Exp Biol Med (Maywood) 2023; 248:2449-2463. [PMID: 38073524 PMCID: PMC10903230 DOI: 10.1177/15353702231211859] [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: 04/23/2023] [Accepted: 08/21/2023] [Indexed: 01/23/2024] Open
Abstract
In clinical trials, rhubarb extract (Rb) was demonstrated to efficiently alleviate constipation. We would like to find out the underlying mechanism of rhubarb relieving constipation. However, there are few studies on the effects of rhubarb on colonic mucus secretion and constipation. The aim of this study was to investigate the effects of rhubarb on colonic mucus secretion and its underlying mechanism. The mice were randomly divided into four groups. Group I was the control group and Group II was the rhubarb control group, with Rb (24 g/kg body weight [b.w.]) administered through intragastric administration for three days. Group III mice were given diphenoxylate (20 mg/kg b.w.) for five days via gavage to induce constipation. Group IV received diphenoxylate lasting five days before undergoing Rb administration for three days. The condition of the colon was evaluated using an endoscope. Particularly, the diameter of blood vessels in the colonic mucosa expanded considerably in constipation mice along with diminishing mucus output, which was in line with the observation via scanning electron microscope (SEM) and transmission electron microscope (TEM). We also performed metagenomic analysis to reveal the microbiome related to mucin gene expression level referring to mucin secretion. In conclusion, Rb relieves constipation by rebuilding mucus homeostasis and regulating the microbiome.
Collapse
Affiliation(s)
- Han Gao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Department of Clinical Laboratory, Aerospace Center Hospital, Beijing 100039, China
| | - Chengwei He
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Shuzi Xin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Rongxuan Hua
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Yixuan Du
- Department of Oral Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Boya Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fengrong Gong
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xinyi Yu
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Luming Pan
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Chen Liang
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Lei Gao
- Department of Biomedical Informatics, School of Biomedical Engineering, Capital Medical University, Beijing 100069, China
| | - Hongwei Shang
- Experimental Center for Morphological Research Platform, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jing-dong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| |
Collapse
|
21
|
Bruggeling CE, te Groen M, Garza DR, van Heeckeren tot Overlaer F, Krekels JPM, Sulaiman BC, Karel D, Rulof A, Schaaphok AR, Hornikx DLAH, Nagtegaal ID, Dutilh BE, Hoentjen F, Boleij A. Bacterial Oncotraits Rather than Spatial Organization Are Associated with Dysplasia in Ulcerative Colitis. J Crohns Colitis 2023; 17:1870-1881. [PMID: 37243505 PMCID: PMC10673813 DOI: 10.1093/ecco-jcc/jjad092] [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: 11/07/2022] [Revised: 04/24/2023] [Accepted: 05/25/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Colonic bacterial biofilms are frequently present in ulcerative colitis [UC] and may increase dysplasia risk through pathogens expressing oncotraits. This prospective cohort study aimed to determine [1] the association of oncotraits and longitudinal biofilm presence with dysplasia risk in UC, and [2] the relation of bacterial composition with biofilms and dysplasia risk. METHODS Faeces and left- and right-sided colonic biopsies were collected from 80 UC patients and 35 controls. Oncotraits [FadA of Fusobacterium, BFT of Bacteroides fragilis, colibactin [ClbB] and Intimin [Eae] of Escherichia coli] were assessed in faecal DNA with multiplex quantitative polymerase chain reaction [qPCR]. Biopsies were screened for biofilms [n = 873] with 16S rRNA fluorescent in situ hybridiation. Shotgun metagenomic sequencing [n = 265], and ki67-immunohistochemistry were performed. Associations were determined with a mixed-effects regression model. RESULTS Biofilms were highly prevalent in UC patients [90.8%] with a median persistence of 3 years (interquartile range [IQR] 2-5 years). Biofilm-positive biopsies showed increased epithelial hypertrophy [p = 0.025] and a reduced Shannon diversity independent of disease status [p = 0.015], but were not significantly associated with dysplasia in UC: adjusted odds ratio [aOR] 1.45, 95% confidence interval [CI] 0.63-3.40. In contrast, ClbB independently associated with dysplasia [aOR 7.16, 95% CI 1.75-29.28], and FadA and Fusobacteriales were associated with a decreased dysplasia risk in UC [aOR 0.23, 95% CI 0.06-0.83, p <0.01]. CONCLUSIONS Biofilms are a hallmark of UC; however, because of their high prevalence are a poor biomarker for dysplasia. In contrast, colibactin presence and FadA absence independently associate with dysplasia in UC and might therefore be valuable biomarkers for future risk stratification and intervention strategies.
Collapse
Affiliation(s)
- Carlijn E Bruggeling
- Department of Pathology, Radboud Institute for Molecular Life Sciences [RIMLS], Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maarten te Groen
- Inflammatory Bowel Disease Center, Department of Gastroenterology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daniel R Garza
- Center for Molecular and Biomolecular Informatics [CMBI], Radboud Institute for Molecular Life Sciences [RIMLS], Nijmegen, The Netherlands
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Leuven, Belgium
| | - Famke van Heeckeren tot Overlaer
- Department of Pathology, Radboud Institute for Molecular Life Sciences [RIMLS], Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joyce P M Krekels
- Department of Pathology, Radboud Institute for Molecular Life Sciences [RIMLS], Radboud University Medical Center, Nijmegen, The Netherlands
| | - Basma-Chick Sulaiman
- Department of Pathology, Radboud Institute for Molecular Life Sciences [RIMLS], Radboud University Medical Center, Nijmegen, The Netherlands
| | - Davy Karel
- Department of Pathology, Radboud Institute for Molecular Life Sciences [RIMLS], Radboud University Medical Center, Nijmegen, The Netherlands
| | - Athreyu Rulof
- Department of Pathology, Radboud Institute for Molecular Life Sciences [RIMLS], Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anne R Schaaphok
- Department of Pathology, Radboud Institute for Molecular Life Sciences [RIMLS], Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daniel L A H Hornikx
- Department of Pathology, Radboud Institute for Molecular Life Sciences [RIMLS], Radboud University Medical Center, Nijmegen, The Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud Institute for Molecular Life Sciences [RIMLS], Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bas E Dutilh
- Center for Molecular and Biomolecular Informatics [CMBI], Radboud Institute for Molecular Life Sciences [RIMLS], Nijmegen, The Netherlands
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Frank Hoentjen
- Inflammatory Bowel Disease Center, Department of Gastroenterology, Radboud University Medical Center, Nijmegen, The Netherlands
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Annemarie Boleij
- Department of Pathology, Radboud Institute for Molecular Life Sciences [RIMLS], Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
22
|
Zhang T, Liu Z, Wang H, Zhang H, Li H, Lu W, Zhu J. Multi-omics analysis reveals genes and metabolites involved in Bifidobacterium pseudocatenulatum biofilm formation. Front Microbiol 2023; 14:1287680. [PMID: 38029154 PMCID: PMC10666050 DOI: 10.3389/fmicb.2023.1287680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Bacterial biofilm is an emerging form of life that involves cell populations living embedded in a self-produced matrix of extracellular polymeric substances (EPS). Currently, little is known about the molecular mechanisms of Bifidobacterium biofilm formation. We used the Bifidobacterium biofilm fermentation system to preparation of biofilms on wheat fibers, and multi-omics analysis of both B. pseudocatenulatum biofilms and planktonic cells were performed to identify genes and metabolites involved in biofilm formation. The average diameter of wheat fibers was around 50 μm, while the diameter of particle in wheat fibers culture of B. pseudocatenulatum was over 260 μm at 22 h with 78.96% biofilm formation rate (BR), and the field emission scanning electron microscopy (FESEM) results showed that biofilm cells on the surface of wheat fibers secreted EPS. Transcriptomic analysis indicated that genes associated with stress response (groS, mntH, nth, pdtaR, pstA, pstC, radA, rbpA, whiB, ybjG), quorum sensing (dppC, livM, luxS, sapF), polysaccharide metabolic process (rfbX, galE, zwf, opcA, glgC, glgP, gtfA) may be involved in biofilm formation. In addition, 17 weighted gene co-expression network analysis (WGCNA) modules were identified and two of them positively correlated to BR. Metabolomic analysis indicated that amino acids and amides; organic acids, alcohols and esters; and sugar (trehalose-6-phosphate, uridine diphosphategalactose, uridine diphosphate-N-acetylglucosamine) were main metabolites during biofilm formation. These results indicate that stress response, quorum sensing (QS), and EPS production are essential during B. pseudocatenulatum biofilm formation.
Collapse
Affiliation(s)
- Ting Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Zongmin Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Haitao Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Jinlin Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| |
Collapse
|
23
|
Yang S, Li X, Cang W, Mu D, Ji S, An Y, Wu R, Wu J. Biofilm tolerance, resistance and infections increasing threat of public health. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:233-247. [PMID: 37933277 PMCID: PMC10625689 DOI: 10.15698/mic2023.11.807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/28/2023] [Accepted: 09/14/2023] [Indexed: 11/08/2023]
Abstract
Microbial biofilms can cause chronic infection. In the clinical setting, the biofilm-related infections usually persist and reoccur; the main reason is the increased antibiotic resistance of biofilms. Traditional antibiotic therapy is not effective and might increase the threat of antibiotic resistance to public health. Therefore, it is urgent to study the tolerance and resistance mechanism of biofilms to antibiotics and find effective therapies for biofilm-related infections. The tolerance mechanism and host reaction of biofilm to antibiotics are reviewed, and bacterial biofilm related diseases formed by human pathogens are discussed thoroughly. The review also explored the role of biofilms in the development of bacterial resistance mechanisms and proposed therapeutic intervention strategies for biofilm related diseases.
Collapse
Affiliation(s)
- Shanshan Yang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| | - Xinfei Li
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, P.R. China
| | - Weihe Cang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, P.R. China
| | - Delun Mu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| | - Shuaiqi Ji
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| | - Yuejia An
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| |
Collapse
|
24
|
Mu J, Lin Q, Liang Y. An update on the effects of food-derived active peptides on the intestinal microecology. Crit Rev Food Sci Nutr 2023; 63:11625-11639. [PMID: 35791779 DOI: 10.1080/10408398.2022.2094889] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The intestinal microecology is a research hotspot, and neologisms related to the gut such as gut-brain axis, gut-lung axis, gut-bone axis, gut-skin axis, gut-renal axis, and gut-liver axis have emerged from recent research. Meticulous investigation has discovered that food-derived active peptides (FDAPs) are bioactive substances that optimize the structure of the gut microbiota to improve human health. However, few reviews have summarized and emphasized the nutritional value of FDAPs and their mechanisms of action in regulating the composition of the gut microbiota. We aim to provide an update on the latest research on FDAPs by comparing, summarizing, and discussing the potential food sources of FDAPs, their physiological functions, and regulatory effects on the intestinal microecology. The key findings are that few studies have analyzed the potential mechanisms and molecular pathways through which FDAPs maintain intestinal microecological homeostasis. We found that an imbalance in the ratio of Bacteroidetes and Firmicutes in the gut microbiota and abnormal production of short-chain fatty acids are key to the occurrence and development of various diseases. This review provides theoretical support for future comprehensive research on the digestion, distribution, metabolism, and excretion of FDAPs and the mechanisms underlying the interactions between FDAPs and the intestinal microecology.
Collapse
Affiliation(s)
- Jianfei Mu
- Molecular Nutrition Branch, National Engineering Research Center of Rice and By-Product Deep Processing/College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Qinlu Lin
- Molecular Nutrition Branch, National Engineering Research Center of Rice and By-Product Deep Processing/College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Ying Liang
- Molecular Nutrition Branch, National Engineering Research Center of Rice and By-Product Deep Processing/College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China
| |
Collapse
|
25
|
Martínez-Calvo A, Trenado-Yuste C, Lee H, Gore J, Wingreen NS, Datta SS. Interfacial morphodynamics of proliferating microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563665. [PMID: 37961366 PMCID: PMC10634769 DOI: 10.1101/2023.10.23.563665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In microbial communities, various cell types often coexist by occupying distinct spatial domains. What determines the shape of the interface between such domains-which in turn influences the interactions between cells and overall community function? Here, we address this question by developing a continuum model of a 2D spatially-structured microbial community with two distinct cell types. We find that, depending on the balance of the different cell proliferation rates and substrate friction coefficients, the interface between domains is either stable and smooth, or unstable and develops finger-like protrusions. We establish quantitative principles describing when these different interfacial behaviors arise, and find good agreement both with the results of previous experimental reports as well as new experiments performed here. Our work thus helps to provide a biophysical basis for understanding the interfacial morphodynamics of proliferating microbial communities, as well as a broader range of proliferating active systems.
Collapse
|
26
|
Sahni V, Van Dyke TE. Immunomodulation of periodontitis with SPMs. FRONTIERS IN ORAL HEALTH 2023; 4:1288722. [PMID: 37927821 PMCID: PMC10623003 DOI: 10.3389/froh.2023.1288722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
Inflammation is a critical component in the pathophysiology of numerous disease processes, with most therapeutic modalities focusing on its inhibition in order to achieve treatment outcomes. The resolution of inflammation is a separate, distinct pathway that entails the reversal of the inflammatory process to a state of homoeostasis rather than selective inhibition of specific components of the inflammatory cascade. The discovery of specialized pro-resolving mediators (SPMs) resulted in a paradigm shift in our understanding of disease etiopathology. Periodontal disease, traditionally considered as one of microbial etiology, is now understood to be an inflammation-driven process associated with dysbiosis of the oral microbiome that may be modulated with SPMs to achieve therapeutic benefit.
Collapse
Affiliation(s)
- Vaibhav Sahni
- Immunology and Infectious Disease, The Forsyth Institute, Cambridge, MA, United States
| | - Thomas E. Van Dyke
- Immunology and Infectious Disease, The Forsyth Institute, Cambridge, MA, United States
- Faculty of Medicine, Harvard University, Boston, MA, United States
| |
Collapse
|
27
|
Pai YC, Li YH, Turner JR, Yu LCH. Transepithelial Barrier Dysfunction Drives Microbiota Dysbiosis to Initiate Epithelial Clock-driven Inflammation. J Crohns Colitis 2023; 17:1471-1488. [PMID: 37004200 PMCID: PMC10588795 DOI: 10.1093/ecco-jcc/jjad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Indexed: 04/03/2023]
Abstract
BACKGROUND Factors that contribute to inflammatory bowel disease [IBD] pathogenesis include genetic polymorphisms, barrier loss, and microbial dysbiosis. A major knowledge gap exists in the origins of the colitogenic microbiome and its relationship with barrier impairment. Epithelial myosin light chain kinase [MLCK] is a critical regulator of the paracellular barrier, but the effects of MLCK activation on the intraepithelial bacteria [IEB] and dysbiosis are incompletely understood. We hypothesise that MLCK-dependent bacterial endocytosis promotes pathobiont conversion and shapes a colitogenic microbiome. METHODS To explore this, transgenic [Tg] mice with barrier loss induced by intestinal epithelium-specific expression of a constitutively active MLCK were compared with wild-type [WT] mice. RESULTS When progeny of homozygous MLCK-Tg mice were separated after weaning by genotype [Tg/Tg, Tg/WT, WT/WT], increased IEB numbers associated with dysbiosis and more severe colitis were present in Tg/Tg and Tg/WT mice, relative to WT/WT mice. Cohousing with MLCK-Tg mice induced dysbiosis, increased IEB abundance, and exacerbated colitis in WT mice. Conversely, MLCK-Tg mice colonised with WT microbiota at birth displayed increased Escherichia abundance and greater colitis severity by 6 weeks of age. Microarray analysis revealed circadian rhythm disruption in WT mice co-housed with MLCK-Tg mice relative to WT mice housed only with WT mice. This circadian disruption required Rac1/STAT3-dependent microbial invasion but not MLCK activity, and resulted in increased proinflammatory cytokines and glucocorticoid downregulation. CONCLUSIONS The data demonstrate that barrier dysfunction induces dysbiosis and expansion of invasive microbes that lead to circadian disruption and mucosal inflammation. These results suggest that barrier-protective or bacterium-targeted precision medicine approaches may be of benefit to IBD patients.
Collapse
Affiliation(s)
- Yu-Chen Pai
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan ROC
| | - Yi-Hsuan Li
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan ROC
| | - Jerrold R Turner
- Brigham's Women Hospital, Harvard Medical School, Boston, MA, USA
| | - Linda Chia-Hui Yu
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan ROC
| |
Collapse
|
28
|
Madhu B, Miller BM, Levy M. Single-cell analysis and spatial resolution of the gut microbiome. Front Cell Infect Microbiol 2023; 13:1271092. [PMID: 37860069 PMCID: PMC10582963 DOI: 10.3389/fcimb.2023.1271092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
Over the past decade it has become clear that various aspects of host physiology, metabolism, and immunity are intimately associated with the microbiome and its interactions with the host. Specifically, the gut microbiome composition and function has been shown to play a critical role in the etiology of different intestinal and extra-intestinal diseases. While attempts to identify a common pattern of microbial dysbiosis linked with these diseases have failed, multiple studies show that bacterial communities in the gut are spatially organized and that disrupted spatial organization of the gut microbiome is often a common underlying feature of disease pathogenesis. As a result, focus over the last few years has shifted from analyzing the diversity of gut microbiome by sequencing of the entire microbial community, towards understanding the gut microbiome in spatial context. Defining the composition and spatial heterogeneity of the microbiome is critical to facilitate further understanding of the gut microbiome ecology. Development in single cell genomics approach has advanced our understanding of microbial community structure, however, limitations in approaches exist. Single cell genomics is a very powerful and rapidly growing field, primarily used to identify the genetic composition of microbes. A major challenge is to isolate single cells for genomic analyses. This review summarizes the different approaches to study microbial genomes at single-cell resolution. We will review new techniques for microbial single cell sequencing and summarize how these techniques can be applied broadly to answer many questions related to the microbiome composition and spatial heterogeneity. These methods can be used to fill the gaps in our understanding of microbial communities.
Collapse
Affiliation(s)
| | | | - Maayan Levy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
29
|
Widjaja F, Rietjens IMCM. From-Toilet-to-Freezer: A Review on Requirements for an Automatic Protocol to Collect and Store Human Fecal Samples for Research Purposes. Biomedicines 2023; 11:2658. [PMID: 37893032 PMCID: PMC10603957 DOI: 10.3390/biomedicines11102658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
The composition, viability and metabolic functionality of intestinal microbiota play an important role in human health and disease. Studies on intestinal microbiota are often based on fecal samples, because these can be sampled in a non-invasive way, although procedures for sampling, processing and storage vary. This review presents factors to consider when developing an automated protocol for sampling, processing and storing fecal samples: donor inclusion criteria, urine-feces separation in smart toilets, homogenization, aliquoting, usage or type of buffer to dissolve and store fecal material, temperature and time for processing and storage and quality control. The lack of standardization and low-throughput of state-of-the-art fecal collection procedures promote a more automated protocol. Based on this review, an automated protocol is proposed. Fecal samples should be collected and immediately processed under anaerobic conditions at either room temperature (RT) for a maximum of 4 h or at 4 °C for no more than 24 h. Upon homogenization, preferably in the absence of added solvent to allow addition of a buffer of choice at a later stage, aliquots obtained should be stored at either -20 °C for up to a few months or -80 °C for a longer period-up to 2 years. Protocols for quality control should characterize microbial composition and viability as well as metabolic functionality.
Collapse
Affiliation(s)
- Frances Widjaja
- Division of Toxicology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands;
| | | |
Collapse
|
30
|
Hu M, Zhu J, Peng G, Lu W, Wang H, Xie Z. IMOVNN: incomplete multi-omics data integration variational neural networks for gut microbiome disease prediction and biomarker identification. Brief Bioinform 2023; 24:bbad394. [PMID: 37930027 DOI: 10.1093/bib/bbad394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/03/2023] [Accepted: 10/14/2023] [Indexed: 11/07/2023] Open
Abstract
The gut microbiome has been regarded as one of the fundamental determinants regulating human health, and multi-omics data profiling has been increasingly utilized to bolster the deep understanding of this complex system. However, stemming from cost or other constraints, the integration of multi-omics often suffers from incomplete views, which poses a great challenge for the comprehensive analysis. In this work, a novel deep model named Incomplete Multi-Omics Variational Neural Networks (IMOVNN) is proposed for incomplete data integration, disease prediction application and biomarker identification. Benefiting from the information bottleneck and the marginal-to-joint distribution integration mechanism, the IMOVNN can learn the marginal latent representation of each individual omics and the joint latent representation for better disease prediction. Moreover, owing to the feature-selective layer predicated upon the concrete distribution, the model is interpretable and can identify the most relevant features. Experiments on inflammatory bowel disease multi-omics datasets demonstrate that our method outperforms several state-of-the-art methods for disease prediction. In addition, IMOVNN has identified significant biomarkers from multi-omics data sources.
Collapse
Affiliation(s)
- Mingyi Hu
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China
| | - Jinlin Zhu
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | | | - Wenwei Lu
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hongchao Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Zhenping Xie
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China
| |
Collapse
|
31
|
Poceviciute R, Bogatyrev SR, Romano AE, Dilmore AH, Mondragón-Palomino O, Takko H, Pradhan O, Ismagilov RF. Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa. NPJ Biofilms Microbiomes 2023; 9:64. [PMID: 37679412 PMCID: PMC10485000 DOI: 10.1038/s41522-023-00423-2] [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: 08/25/2022] [Accepted: 07/31/2023] [Indexed: 09/09/2023] Open
Abstract
Because the small intestine (SI) epithelium lacks a thick protective mucus layer, microbes that colonize the thin SI mucosa may exert a substantial effect on the host. For example, bacterial colonization of the human SI may contribute to environmental enteropathy dysfunction (EED) in malnourished children. Thus far, potential bacterial colonization of the mucosal surface of the SI has only been documented in disease states, suggesting mucosal colonization is rare, likely requiring multiple perturbations. Furthermore, conclusive proof of bacterial colonization of the SI mucosal surface is challenging, and the three-dimensional (3D) spatial structure of mucosal colonies remains unknown. Here, we tested whether we could induce dense bacterial association with jejunum mucosa by subjecting mice to a combination of malnutrition and oral co-gavage with a bacterial cocktail (E. coli and Bacteroides spp.) known to induce EED. To visualize these events, we optimized our previously developed whole-tissue 3D imaging tools with third-generation hybridization chain reaction (HCR v3.0) probes. Only in mice that were malnourished and gavaged with the bacterial cocktail did we detect dense bacterial clusters surrounding intestinal villi suggestive of colonization. Furthermore, in these mice we detected villus loss, which may represent one possible consequence that bacterial colonization of the SI mucosa has on the host. Our results suggest that dense bacterial colonization of jejunum mucosa is possible in the presence of multiple perturbations and that whole-tissue 3D imaging tools can enable the study of these rare events.
Collapse
Affiliation(s)
- Roberta Poceviciute
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Said R Bogatyrev
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Medically Associated Science and Technology Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anna E Romano
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Amanda H Dilmore
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Biomedical Sciences Program, University of California San Diego, San Diego, CA, USA
| | - Octavio Mondragón-Palomino
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Heli Takko
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ojas Pradhan
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rustem F Ismagilov
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| |
Collapse
|
32
|
Inaba R, Vujakovic S, Bergstrom K. The gut mucus network: A dynamic liaison between microbes and the immune system. Semin Immunol 2023; 69:101807. [PMID: 37478802 DOI: 10.1016/j.smim.2023.101807] [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: 10/08/2022] [Revised: 06/24/2023] [Accepted: 07/08/2023] [Indexed: 07/23/2023]
Abstract
A complex mucus network made up of large polymers of the mucin-family glycoprotein MUC2 exists between the large intestinal microbial mass and epithelial and immune cells. This has long been understood as an innate immune defense barrier against the microbiota and other luminal threats that reinforces the barrier function of the epithelium and limits microbiota contact with the tissues. However, past and recent studies have provided new evidence of how critical the mucus network is to act as a 'liaison' between host and microbe to mediate anti-inflammatory, mutualistic interactions with the microbiota and protection from pathogens. This review summarizes historical and recent insights into the formation of the gut mucus network, how the microbes and immune system influence mucus, and in turn, how the mucus influences immune responses to the microbiota.
Collapse
Affiliation(s)
- Rain Inaba
- Department of Biology, University of British Columbia, Okanagan Campus, 3187 University Way, Kelowna V1V 1V7, British Columbia, Canada
| | - Sara Vujakovic
- Department of Biology, University of British Columbia, Okanagan Campus, 3187 University Way, Kelowna V1V 1V7, British Columbia, Canada
| | - Kirk Bergstrom
- Department of Biology, University of British Columbia, Okanagan Campus, 3187 University Way, Kelowna V1V 1V7, British Columbia, Canada.
| |
Collapse
|
33
|
Palandurkar GS, Kumar S. Biofilm's Impact on Inflammatory Bowel Diseases. Cureus 2023; 15:e45510. [PMID: 37868553 PMCID: PMC10585119 DOI: 10.7759/cureus.45510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
The colon has a large surface area covered with a thick mucus coating. Colon's biomass consists of about 1,012 colony-forming units per gram of feces and 500-1,000 distinct bacterial species. The term inflammatory bowel disease (IBD) indicates the collection of intestinal illnesses in which the digestive system (esophagus, large intestine, mouth, stomach, and small intestine) experiences persistent inflammation. IBD development is influenced by environmental (infections, stress, and nutrition) and genetic factors. The microbes present in gut microbiota help maintain intestinal homeostasis and support immune and epithelial cell growth, differentiation, as well as proliferation. It has been discovered that a variety of variables and microorganisms are crucial for the development of biofilms and mucosal colonization during IBD. An extracellular matrix formed by bacteria supports biofilm production in our digestive system and harms the host's immunological response. Irritable bowel syndrome (IBS) and IBD considerably affect human socioeconomic well-being and the standard of living. IBD is a serious public health issue, affecting millions of people across the globe. The gut microbiome may significantly influence IBS pathogenesis, even though few diagnostic and treatment options are available. As a result, current research focuses more on disrupting biofilm in IBD patients and stresses primarily on drugs that help improve the quality of life for human well-being. We evaluate studies on IBD and bacterial biofilm to add fresh insights into the existing state of knowledge of biofilm formation in IBD, incidence of IBD patients, molecular level of investigations, bacteria that are involved in the formation of biofilm, and present and down the line regimens and probiotics. Planning advanced ways to control and eradicate bacteria in biofilms should be the primary goal to add fresh insights into generating innovative diagnostic and alternative therapy options for IBD.
Collapse
Affiliation(s)
- Gopal S Palandurkar
- Department of Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Sunil Kumar
- Department of Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| |
Collapse
|
34
|
Wang B, Hu W, Zhang X, Cao Y, Shao L, Xu X, Liu P. Sarcopenia and gut microbiota alterations in patients with hematological diseases before and after hematopoietic stem cell transplantation. Chin J Cancer Res 2023; 35:386-398. [PMID: 37691890 PMCID: PMC10485920 DOI: 10.21147/j.issn.1000-9604.2023.04.05] [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: 04/12/2023] [Accepted: 07/20/2023] [Indexed: 09/12/2023] Open
Abstract
Objective The aim of this study was to investigate the prevalence of sarcopenia (SP) and its relationship with gut microbiota alterations in patients with hematological diseases before and after hematopoietic stem cell transplantation (HSCT). Methods A total of 108 patients with various hematological disorders were selected from Peking University People's Hospital. SP was screened and diagnosed based on the 2019 Asian Sarcopenia Diagnosis Strategy. Physical measurements and fecal samples were collected, and 16S rRNA gene sequencing was conducted. Alpha and beta diversity analyses were performed to evaluate gut microbiota composition and diversity. Results After HSCT, significant decreases in calf circumference and body mass index (BMI) were observed, accompanied by a decline in physical function. Gut microbiota analyses revealed significant differences in the relative abundance of Enterococcus, Bacteroides, Blautia and Dorea species before and after HSCT (P<0.05). Before HSCT, sarcopenic patients had lower Dorea levels and higher Phascolarctobacterium levels than non-sarcopenia patients (P<0.01). After HSCT, no significant differences in species abundance were observed. Alpha diversity analysis showed significant differences in species diversity among the groups, with the highest diversity in the post-HSCT 90-day group and the lowest in the post-HSCT 30-day group. Beta diversity analysis revealed significant differences in species composition between pre- and post-HSCT time points but not between SP groups. Linear discriminant analysis effect size (LEfSe) identified Alistipes, Rikenellaceae, Alistipes putredinis, Prevotellaceae defectiva and Blautia coccoides as biomarkers for the pre-HSCT sarcopenia group. Functional predictions showed significant differences in anaerobic, biofilm-forming and oxidative stress-tolerant functions among the groups (P<0.05). Conclusions This study demonstrated a significant decline in physical function after HSCT and identified potential gut microbiota biomarkers and functional alterations associated with SP in patients with hematological disorders. Further research is needed to explore the underlying mechanisms and potential therapeutic targets.
Collapse
Affiliation(s)
- Boshi Wang
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing 100044, China
| | - Wei Hu
- Peking University People’s Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - Xue Zhang
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing 100044, China
| | - Yanchao Cao
- Peking University People’s Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - Lin Shao
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing 100044, China
| | - Xiaodong Xu
- Peking University People’s Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing 100044, China
| | - Peng Liu
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing 100044, China
| |
Collapse
|
35
|
Perry EK, Tan MW. Bacterial biofilms in the human body: prevalence and impacts on health and disease. Front Cell Infect Microbiol 2023; 13:1237164. [PMID: 37712058 PMCID: PMC10499362 DOI: 10.3389/fcimb.2023.1237164] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023] Open
Abstract
Bacterial biofilms can be found in most environments on our planet, and the human body is no exception. Consisting of microbial cells encased in a matrix of extracellular polymers, biofilms enable bacteria to sequester themselves in favorable niches, while also increasing their ability to resist numerous stresses and survive under hostile circumstances. In recent decades, biofilms have increasingly been recognized as a major contributor to the pathogenesis of chronic infections. However, biofilms also occur in or on certain tissues in healthy individuals, and their constituent species are not restricted to canonical pathogens. In this review, we discuss the evidence for where, when, and what types of biofilms occur in the human body, as well as the diverse ways in which they can impact host health under homeostatic and dysbiotic states.
Collapse
Affiliation(s)
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech, South San Francisco, CA, United States
| |
Collapse
|
36
|
Oliveira M, Cunha E, Tavares L, Serrano I. P. aeruginosa interactions with other microbes in biofilms during co-infection. AIMS Microbiol 2023; 9:612-646. [PMID: 38173971 PMCID: PMC10758579 DOI: 10.3934/microbiol.2023032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/10/2023] [Accepted: 07/26/2023] [Indexed: 01/05/2024] Open
Abstract
This review addresses the topic of biofilms, including their development and the interaction between different counterparts. There is evidence that various diseases, such as cystic fibrosis, otitis media, diabetic foot wound infections, and certain cancers, are promoted and aggravated by the presence of polymicrobial biofilms. Biofilms are composed by heterogeneous communities of microorganisms protected by a matrix of polysaccharides. The different types of interactions between microorganisms gives rise to an increased resistance to antimicrobials and to the host's defense mechanisms, with the consequent worsening of disease symptoms. Therefore, infections caused by polymicrobial biofilms affecting different human organs and systems will be discussed, as well as the role of the interactions between the gram-negative bacteria Pseudomonas aeruginosa, which is at the base of major polymicrobial infections, and other bacteria, fungi, and viruses in the establishment of human infections and diseases. Considering that polymicrobial biofilms are key to bacterial pathogenicity, it is fundamental to evaluate which microbes are involved in a certain disease to convey an appropriate and efficacious antimicrobial therapy.
Collapse
Affiliation(s)
- Manuela Oliveira
- CIISA—Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Eva Cunha
- CIISA—Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Luís Tavares
- CIISA—Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Isa Serrano
- CIISA—Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
| |
Collapse
|
37
|
Stummer N, Feichtinger RG, Weghuber D, Kofler B, Schneider AM. Role of Hydrogen Sulfide in Inflammatory Bowel Disease. Antioxidants (Basel) 2023; 12:1570. [PMID: 37627565 PMCID: PMC10452036 DOI: 10.3390/antiox12081570] [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: 07/10/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Hydrogen sulfide (H2S), originally known as toxic gas, has now attracted attention as one of the gasotransmitters involved in many reactions in the human body. H2S has been assumed to play a role in the pathogenesis of many chronic diseases, of which the exact pathogenesis remains unknown. One of them is inflammatory bowel disease (IBD), a chronic intestinal disease subclassified as Crohn's disease (CD) and ulcerative colitis (UC). Any change in the amount of H2S seems to be linked to inflammation in this illness. These changes can be brought about by alterations in the microbiota, in the endogenous metabolism of H2S and in the diet. As both too little and too much H2S drive inflammation, a balanced level is needed for intestinal health. The aim of this review is to summarize the available literature published until June 2023 in order to provide an overview of the current knowledge of the connection between H2S and IBD.
Collapse
Affiliation(s)
- Nathalie Stummer
- Department of Pediatrics, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (N.S.); (R.G.F.); (D.W.); (B.K.)
| | - René G. Feichtinger
- Department of Pediatrics, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (N.S.); (R.G.F.); (D.W.); (B.K.)
| | - Daniel Weghuber
- Department of Pediatrics, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (N.S.); (R.G.F.); (D.W.); (B.K.)
| | - Barbara Kofler
- Department of Pediatrics, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (N.S.); (R.G.F.); (D.W.); (B.K.)
- Research Program for Receptor Biochemistry and Tumor Metabolism, Paracelsus Medical University (PMU), 5020 Salzburg, Austria
| | - Anna M. Schneider
- Department of Pediatrics, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (N.S.); (R.G.F.); (D.W.); (B.K.)
| |
Collapse
|
38
|
Terrin M, Migliorisi G, Dal Buono A, Gabbiadini R, Mastrorocco E, Quadarella A, Repici A, Santoro A, Armuzzi A. Checkpoint Inhibitor-Induced Colitis: From Pathogenesis to Management. Int J Mol Sci 2023; 24:11504. [PMID: 37511260 PMCID: PMC10380448 DOI: 10.3390/ijms241411504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
The advent of immunotherapy, specifically of immune checkpoint inhibitors (ICIs), for the treatment of solid tumors has deeply transformed therapeutic algorithms in medical oncology. Approximately one-third of patients treated with ICIs may de velop immune-related adverse events, and the gastrointestinal tract is often affected by different grades of mucosal inflammation. Checkpoint inhibitors colitis (CIC) presents with watery or bloody diarrhea and, in the case of severe symptoms, requires ICIs discontinuation. The pathogenesis of CIC is multifactorial and still partially unknown: anti-tumor activity that collaterally effects the colonic tissue and the upregulation of specific systemic inflammatory pathways (i.e., CD8+ cytotoxic and CD4+ T lymphocytes) are mainly involved. Many questions remain regarding treatment timing and options, and biological treatment, especially with anti-TNF alpha, can be offered to these patients with the aim of rapidly resuming oncological therapies. CIC shares similar pathogenesis and aspects with inflammatory bowel disease (IBD) and the use of ICI in IBD patients is under evaluation. This review aims to summarize the pathogenetic mechanism underlying CIC and to discuss the current evidenced-based management options, including the role of biological therapy, emphasizing the relevant clinical impact on CIC and the need for prompt recognition and treatment.
Collapse
Affiliation(s)
- Maria Terrin
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
| | - Giulia Migliorisi
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
| | - Arianna Dal Buono
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
| | - Roberto Gabbiadini
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
| | - Elisabetta Mastrorocco
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
| | - Alessandro Quadarella
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
| | - Alessandro Repici
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
- Division of Gastroenterology and Digestive Endoscopy, Department of Gastroenterology, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Armando Santoro
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
- Medical Oncology and Haematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Alessandro Armuzzi
- IBD Center, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy; (M.T.); (G.M.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy
| |
Collapse
|
39
|
Xu J, Molin G, Davidson S, Roth B, Sjöberg K, Håkansson Å. CRP in Outpatients with Inflammatory Bowel Disease Is Linked to the Blood Microbiota. Int J Mol Sci 2023; 24:10899. [PMID: 37446076 DOI: 10.3390/ijms241310899] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
The circulation is a closed system that has been assumed to be free from bacteria, but evidence for the existence of a low-density blood microbiota is accumulating. The present study aimed to map the blood microbiota of outpatients with Crohn's disease (CD) or with ulcerative colitis (UC) by 16S metagenomics. A diverse microbiota was observed in the blood samples. Regardless of the type of disease, the alpha diversity of the microbiota was positively associated with C-reactive protein (CRP). The blood microbiota had a surprisingly high proportion of Proteobacteria in comparison with human oral and colonic microbiotas. There was no clear difference in the overall pattern of the microbiota between CD and UC. A non-template control (NTC) was included in the whole process to control for the potential contamination from the environment and reagents. Certain bacterial taxa were concomitantly detected in both blood samples and NTC. However, Acinetobacter, Lactobacillus, Thermicanus and Paracoccus were found in blood from both CD and UC patients but not in NTC, indicating the existence of a specific blood-borne microbiota in the patients. Achromobacter dominated in all blood samples, but a minor amount was also found in NTC. Micrococcaceae was significantly enriched in CD, but it was also detected in high abundance in NTC. Whether the composition of the blood microbiota could be a marker of a particular phenotype in inflammatory bowel disease (IBD) or whether the blood microbiota could be used for diagnostic or therapeutic purposes deserves further attention.
Collapse
Affiliation(s)
- Jie Xu
- Department of Food Technology, Engineering and Nutrition, Lund University, 22100 Lund, Sweden
| | - Göran Molin
- Department of Food Technology, Engineering and Nutrition, Lund University, 22100 Lund, Sweden
| | - Sanna Davidson
- Department of Clinical Sciences, Lund University, 21428 Malmö, Sweden
- Department of Gastroenterology and Nutrition, Skåne University Hospital, 20502 Malmö, Sweden
| | - Bodil Roth
- Department of Clinical Sciences, Lund University, 21428 Malmö, Sweden
- Department of Gastroenterology and Nutrition, Skåne University Hospital, 20502 Malmö, Sweden
| | - Klas Sjöberg
- Department of Clinical Sciences, Lund University, 21428 Malmö, Sweden
- Department of Gastroenterology and Nutrition, Skåne University Hospital, 20502 Malmö, Sweden
| | - Åsa Håkansson
- Department of Clinical Sciences, Lund University, 21428 Malmö, Sweden
| |
Collapse
|
40
|
Aromolo IF, Simeoli D, Maronese CA, Altomare A, Noviello D, Caprioli F, Marzano AV. The Bowel-Associated Arthritis-Dermatosis Syndrome (BADAS): A Systematic Review. Metabolites 2023; 13:790. [PMID: 37512497 PMCID: PMC10386568 DOI: 10.3390/metabo13070790] [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: 05/05/2023] [Revised: 06/11/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Bowel-associated arthritis-dermatosis syndrome (BADAS) is a rare neutrophilic dermatosis that was first described in 1971 in patients who underwent bypass surgery for obesity. Over the years, the number of reported cases associated with medical gastroenterological conditions, particularly inflammatory bowel disease (IBD), has progressively increased. To date, there are no systematic reviews in the literature on BADAS. The design of an a priori protocol was based on PRISMA guidelines, and a search of PubMed and Scopus databases was conducted for articles published between 1971 and 2023 related to the topic. Fifty-one articles including 113 patients with BADAS were analyzed in this systematic review. Bariatric surgery and IBD were the most frequently reported causes of BADAS, accounting for 63.7% and 24.7% of all cases, respectively. A total of 85% of cases displayed the typical dermatological presentation, including urticarial maculopapular lesions centered by a vesicopustule, with the majority of lesions located on the upper limbs (73.5%). Polyarthralgia or localized arthritis were always present. Atypical presentations included cellulitis-like, erythema-nodosum-like, Sweet-syndrome-like and pyoderma-gangrenosum-like manifestations. Gastrointestinal symptoms were frequently observed in IBD-related cases (67.9%). The histopathology showed a neutrophilic infiltrate (96.6%). The most commonly used treatment regimens consisted of systemic corticosteroids, metronidazole and tetracyclines, either alone or in combination. A relapsing-remitting course was observed in 52.1% of patients. In conclusion, BADAS is a neutrophilic dermatosis that presents with a wide variety of cutaneous manifestations, both typical and atypical. Gastrointestinal symptoms are frequently observed, particularly in cases related to IBD. The histopathology is clear but not specific compared with other neutrophilic dermatoses. The diagnosis can be challenging, but the relapsing-remitting course and the strong association with polyarthralgia and gastrointestinal disease can aid in the diagnosis.
Collapse
Affiliation(s)
- Italo Francesco Aromolo
- Dermatology Unit, Scientific Institute for Research, Hospitalization and Healthcare Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Domenico Simeoli
- Dermatology Unit, Scientific Institute for Research, Hospitalization and Healthcare Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Carlo Alberto Maronese
- Dermatology Unit, Scientific Institute for Research, Hospitalization and Healthcare Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Andrea Altomare
- Scientific Institute for Research, Hospitalization and Healthcare Istituto Ortopedico Galeazzi, 20122 Milan, Italy
| | - Daniele Noviello
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
- Gastroenterology and Endoscopy Unit, Fondazione Scientific Institute for Research, Hospitalization and Healthcare Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Flavio Caprioli
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
- Gastroenterology and Endoscopy Unit, Fondazione Scientific Institute for Research, Hospitalization and Healthcare Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Angelo Valerio Marzano
- Dermatology Unit, Scientific Institute for Research, Hospitalization and Healthcare Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| |
Collapse
|
41
|
Al-Bayati L, Fasaei BN, Merat S, Bahonar A, Ghoddusi A. Quantitative analysis of the three gut microbiota in UC and non-UC patients using real-time PCR. Microb Pathog 2023:106198. [PMID: 37295481 DOI: 10.1016/j.micpath.2023.106198] [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: 02/11/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND and study aims: Gastrointestinal microbiota are closely related to the pathogenesis of ulcerative colitis (UC). This study aimed at quantification of F. prausnitzii, Provetella, and Peptostreptococcus in UC and non-UC patients using Real-Time PCR and a new set of primers were also validated for this purpose. MATERIALS AND METHODS In this study, the relative abundance of microbial populations between the UC and non-UC subjects were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR). DNA extraction from biopsies and polymerase chain reaction (PCR) amplification of bacterial 16S rRNA gene-targeted species-specific primers was performed to detect the anaerobic bacterial species. The qRT-PCR was used to show the relative change in the bacterial populations of F. prausnitzii, Provetella, and Peptostreptococcus in the UC and non-UC subjects. RESULTS Our data for detection of the anaerobic intestinal flora showed Faecalibacterium prausnitzii, Provetella and Peptostreptococcus were the predominant microflora in the controls and showed significant differences (p = 0.002, 0.025 and 0.039, respectively). The qRT-PCR analyses of F. prausnitzii, Provetella and Peptostreptococcus were 8.69-, 9.38- and 5.77-higher, respectively, in the control group than in the UC group. CONCLUSION The results of this study showed decreased abundance of F. prausnitzii, Provetella and Peptostreptococcus in the intestine of UC patients in comparison to non-UC patients. Quantitative RT-PCR, as a progressive and sensitive method, could be useful for evaluation of bacterial populations in patients with inflammatory bowel diseases to attain appropriate therapeutic strategies.
Collapse
Affiliation(s)
- Luma Al-Bayati
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran; Department of Microbiology, Faculty of Medicine, University of Wassit, Iraq
| | - Bahar Nayeri Fasaei
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Shahin Merat
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Liver and Pancreatobiliary Diseases Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Bahonar
- Department of Food Hygiene, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Arefeh Ghoddusi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| |
Collapse
|
42
|
Barbosa A, Miranda S, Azevedo NF, Cerqueira L, Azevedo AS. Imaging biofilms using fluorescence in situ hybridization: seeing is believing. Front Cell Infect Microbiol 2023; 13:1195803. [PMID: 37284501 PMCID: PMC10239779 DOI: 10.3389/fcimb.2023.1195803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
Biofilms are complex structures with an intricate relationship between the resident microorganisms, the extracellular matrix, and the surrounding environment. Interest in biofilms is growing exponentially given its ubiquity in so diverse fields such as healthcare, environmental and industry. Molecular techniques (e.g., next-generation sequencing, RNA-seq) have been used to study biofilm properties. However, these techniques disrupt the spatial structure of biofilms; therefore, they do not allow to observe the location/position of biofilm components (e.g., cells, genes, metabolites), which is particularly relevant to explore and study the interactions and functions of microorganisms. Fluorescence in situ hybridization (FISH) has been arguably the most widely used method for an in situ analysis of spatial distribution of biofilms. In this review, an overview on different FISH variants already applied on biofilm studies (e.g., CLASI-FISH, BONCAT-FISH, HiPR-FISH, seq-FISH) will be explored. In combination with confocal laser scanning microscopy, these variants emerged as a powerful approach to visualize, quantify and locate microorganisms, genes, and metabolites inside biofilms. Finally, we discuss new possible research directions for the development of robust and accurate FISH-based approaches that will allow to dig deeper into the biofilm structure and function.
Collapse
Affiliation(s)
- Ana Barbosa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Sónia Miranda
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Laura Cerqueira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Andreia S. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| |
Collapse
|
43
|
Sidner B, Lerma A, Biswas B, Ronish LA, McCullough H, Auchtung JM, Piepenbrink KH. Flagellin is essential for initial attachment to mucosal surfaces by Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541533. [PMID: 37292962 PMCID: PMC10245794 DOI: 10.1101/2023.05.19.541533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mucins are glycoproteins which can be found in host cell membranes and as a gelatinous surface formed from secreted mucins. Mucosal surfaces in mammals form a barrier to invasive microbes, particularly bacteria, but are a point of attachment for others. Clostridioides difficile is anaerobic bacterium which colonizes the mammalian GI tract and is a common cause of acute GI inflammation leading to a variety of negative outcomes. Although C. difficile toxicity stems from secreted toxins, colonization is a prerequisite for C. difficile disease. While C. difficile is known to associate with the mucus layer and underlying epithelium, the mechanisms underlying these interactions that facilitate colonization are less well-understood. To understand the molecular mechanisms by which C. difficile interacts with mucins, we used ex vivo mucosal surfaces to test the ability of C. difficile to bind to mucins from different mammalian tissues. We found significant differences in C. difficile adhesion based upon the source of mucins, with highest levels of binding observed to mucins purified from the human colonic adenocarcinoma line LS174T and lowest levels of binding to porcine gastric mucin. We also observed that defects in adhesion by mutants deficient in flagella, but not type IV pili. These results imply that interactions between host mucins and C. difficile flagella facilitate the initial host attachment of C. difficile to host cells and secreted mucus.
Collapse
|
44
|
Markandey M, Bajaj A, Verma M, Virmani S, Singh MK, Gaur P, Das P, Srikanth C, Makharia G, Kedia S, Ahuja V. Fecal microbiota transplantation refurbishes the crypt-associated microbiota in ulcerative colitis. iScience 2023; 26:106738. [PMID: 37216124 PMCID: PMC10192942 DOI: 10.1016/j.isci.2023.106738] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/24/2023] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
A crypt autochthonous microbial population called crypt-associated microbiota (CAM) is localized intimately with gut regenerative and immune machinery. The present report utilizes laser capture microdissection coupled with 16S amplicon sequencing to characterize the CAM in patients with ulcerative colitis (UC) before and after fecal microbiota transplantation with anti-inflammatory diet (FMT-AID). Compositional differences in CAM and its interactions with mucosa-associated microbiota (MAM) were compared between the non-IBD controls and in patients with UC pre- and post-FMT (n = 26). Distinct from the MAM, CAM is dominated by aerobic members of Actinobacteria and Proteobacteria and exhibits resilience of diversity. CAM underwent UC-associated dysbiosis and demonstrated restoration post-FMT-AID. These FMT-restored CAM taxa correlated negatively with disease activity in patients with UC. The positive effects of FMT-AID extended further in refurbishing CAM-MAM interactions, which were obliterated in UC. These results encourage investigation into host-microbiome interactions established by CAM, to understand their role in disease pathophysiology.
Collapse
Affiliation(s)
- Manasvini Markandey
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Aditya Bajaj
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Mahak Verma
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Shubi Virmani
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Mukesh Kumar Singh
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Preksha Gaur
- Regional Centre for Biotechnology, 3rd Milestone Gurugram-Faridabad Expressway, Faridabad 121001, India
| | - Prasenjit Das
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - C.V. Srikanth
- Regional Centre for Biotechnology, 3rd Milestone Gurugram-Faridabad Expressway, Faridabad 121001, India
| | - Govind Makharia
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Saurabh Kedia
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
45
|
Duncan SH, Conti E, Ricci L, Walker AW. Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health. Biomedicines 2023; 11:biomedicines11051338. [PMID: 37239009 DOI: 10.3390/biomedicines11051338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
A dense microbial community resides in the human colon, with considerable inter-individual variability in composition, although some species are relatively dominant and widespread in healthy individuals. In disease conditions, there is often a reduction in microbial diversity and perturbations in the composition of the microbiota. Dietary complex carbohydrates that reach the large intestine are important modulators of the composition of the microbiota and their primary metabolic outputs. Specialist gut bacteria may also transform plant phenolics to form a spectrum of products possessing antioxidant and anti-inflammatory activities. Consumption of diets high in animal protein and fat may lead to the formation of potentially deleterious microbial products, including nitroso compounds, hydrogen sulphide, and trimethylamine. Gut anaerobes also form a range of secondary metabolites, including polyketides that may possess antimicrobial activity and thus contribute to microbe-microbe interactions within the colon. The overall metabolic outputs of colonic microbes are derived from an intricate network of microbial metabolic pathways and interactions; however, much still needs to be learnt about the subtleties of these complex networks. In this review we consider the multi-faceted relationships between inter-individual microbiota variation, diet, and health.
Collapse
Affiliation(s)
- Sylvia H Duncan
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Elena Conti
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Liviana Ricci
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Alan W Walker
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| |
Collapse
|
46
|
Watson AR, Füssel J, Veseli I, DeLongchamp JZ, Silva M, Trigodet F, Lolans K, Shaiber A, Fogarty E, Runde JM, Quince C, Yu MK, Söylev A, Morrison HG, Lee STM, Kao D, Rubin DT, Jabri B, Louie T, Eren AM. Metabolic independence drives gut microbial colonization and resilience in health and disease. Genome Biol 2023; 24:78. [PMID: 37069665 PMCID: PMC10108530 DOI: 10.1186/s13059-023-02924-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 04/07/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. RESULTS Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. CONCLUSIONS These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
Collapse
Affiliation(s)
- Andrea R Watson
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Committee On Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Jessika Füssel
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129, Oldenburg, Germany
| | - Iva Veseli
- Biophysical Sciences Program, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Marisela Silva
- Department of Medicine, The University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Florian Trigodet
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Karen Lolans
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Alon Shaiber
- Biophysical Sciences Program, The University of Chicago, Chicago, IL, 60637, USA
| | - Emily Fogarty
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Committee On Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph M Runde
- Department of Pediatrics, Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, Norwich, NR4 7UZ, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL, 60637, USA
| | - Arda Söylev
- Department of Computer Engineering, Konya Food and Agriculture University, Konya, Turkey
| | - Hilary G Morrison
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Falmouth, MA, 02543, USA
| | - Sonny T M Lee
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Dina Kao
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2G3, Canada
| | - David T Rubin
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Bana Jabri
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Thomas Louie
- Department of Medicine, The University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - A Murat Eren
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
- Committee On Microbiology, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129, Oldenburg, Germany.
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Falmouth, MA, 02543, USA.
- Helmholtz Institute for Functional Marine Biodiversity, 26129, Oldenburg, Germany.
| |
Collapse
|
47
|
Effect of two-week red beetroot juice consumption on modulation of gut microbiota in healthy human volunteers - A pilot study. Food Chem 2023; 406:134989. [PMID: 36527987 DOI: 10.1016/j.foodchem.2022.134989] [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: 06/30/2022] [Revised: 10/18/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
With very little research exploring intestinal effects of red beetroot consumption, the present pilot study investigated gut microbial changes following red beetroot consumption, via a 14-day intervention trial in healthy adults. Compared to baseline, the study demonstrates transient changes in abundance of some taxa e.g., Romboutsia and Christensenella, after different days of intervention (p < 0.05). Enrichment of Akkermansia muciniphila and decrease of Bacteroides fragilis (p < 0.05) were observed after 3 days of juice consumption, followed by restoration in abundance after 14 days. With native betacyanins and catabolites detected in stool after juice consumption, betacyanins were found to correlate positively with Bifidobacterium and Coprococcus, and inversely with Ruminococcus (p < 0.1), potentiating a significant rise in (iso)butyric acid content (172.7 ± 30.9 µmol/g stool). Study findings indicate the potential of red beetroot to influence gut microbial populations and catabolites associated with these changes, emphasizing the potential benefit of red beetroot on intestinal as well as systemic health.
Collapse
|
48
|
Scarsella E, Meineri G, Sandri M, Ganz HH, Stefanon B. Characterization of the Blood Microbiome and Comparison with the Fecal Microbiome in Healthy Dogs and Dogs with Gastrointestinal Disease. Vet Sci 2023; 10:vetsci10040277. [PMID: 37104432 PMCID: PMC10144428 DOI: 10.3390/vetsci10040277] [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: 02/20/2023] [Revised: 03/25/2023] [Accepted: 04/04/2023] [Indexed: 04/28/2023] Open
Abstract
Recent studies have found bacterial DNA in the blood of healthy individuals. To date, most studies on the blood microbiome have focused on human health, but this topic is an expanding research area in animal health as well. This study aims to characterize the blood microbiome of both healthy dogs and those with chronic gastro-enteropathies. For this study, blood and fecal samples were collected from 18 healthy and 19 sick subjects, DNA was extracted through commercial kits, and the V3-V4 regions of the 16S rRNA gene were sequenced on the Illumina platform. The sequences were analyzed for taxonomic annotation and statistical analysis. Alpha and beta diversities of fecal microbiome were significantly different between the two groups of dogs. Principal coordinates analysis revealed that healthy and sick subjects were significantly clustered for both blood and fecal microbiome samples. Moreover, bacterial translocation from the gut to the bloodstream has been suggested because of found shared taxa. Further studies are needed to determine the origin of the blood microbiome and the bacteria viability. The characterization of a blood core microbiome in healthy dogs has potential for use as a diagnostic tool to monitor for the development of gastro-intestinal disease.
Collapse
Affiliation(s)
- Elisa Scarsella
- AnimalBiome, 400 29th Street, Suite 101, Oakland, CA 94609, USA
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Giorgia Meineri
- Department of Veterinary Science, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Misa Sandri
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Holly H Ganz
- AnimalBiome, 400 29th Street, Suite 101, Oakland, CA 94609, USA
| | - Bruno Stefanon
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| |
Collapse
|
49
|
Gowen R, Gamal A, Di Martino L, McCormick TS, Ghannoum MA. Modulating the Microbiome for Crohn's Disease Treatment. Gastroenterology 2023; 164:828-840. [PMID: 36702360 PMCID: PMC10152883 DOI: 10.1053/j.gastro.2023.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/12/2022] [Accepted: 01/06/2023] [Indexed: 01/28/2023]
Abstract
The central role of the gut microbiota in the regulation of health and disease has been convincingly demonstrated. Polymicrobial interkingdom interactions between bacterial (the bacteriome) and fungal (the mycobiome) communities of the gut have become a prominent focus for development of potential therapeutic approaches. In addition to polymicrobial interactions, the complex gut ecosystem also mediates interactions between the host and the microbiota. These interactions are complex and bidirectional; microbiota composition can be influenced by host immune response, disease-specific therapeutics, antimicrobial drugs, and overall ecosystems. However, the gut microbiota also influences host immune response to a drug or therapy by potentially transforming the drug's structure and altering bioavailability, activity, or toxicity. This is especially true in cases where the gut microbiota has produced a biofilm. The negative ramifications of biofilm formation include alteration of gut permeability, enhanced antimicrobial resistance, and alteration of host immune response effectiveness. Natural modulation of the gut microbiota, using probiotic and prebiotic approaches, may also be used to affect the host microbiome, a type of "natural" modulation of the host microbiota composition. In this review, we discuss potential bidirectional interactions between microbes and host, and we describe the changes in gut microbiota induced by probiotic and prebiotic approaches as well as their potential clinical consequences, including biofilm formation. We outline a systematic approach to designing probiotics capable of altering the host microbiota in disease states, using Crohn's disease as a model chronic disease. Understanding how the effective changes in the microbiome may enhance treatment efficacy may unlock the possibility of modulating the gut microbiome to improve treatment using a natural approach.
Collapse
Affiliation(s)
- Rachael Gowen
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio; University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Ahmed Gamal
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio; University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Luca Di Martino
- University Hospitals Cleveland Medical Center, Cleveland, Ohio; Department of Medicine, Case Western Reserve University, Cleveland, Ohio; Case Digestive Health Research Institute, Case Western Reserve University, Cleveland Ohio
| | - Thomas S McCormick
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio; University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Mahmoud A Ghannoum
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio; University Hospitals Cleveland Medical Center, Cleveland, Ohio.
| |
Collapse
|
50
|
Shirwaikar Thomas A, Hanauer S, Wang Y. Immune Checkpoint Inhibitor Enterocolitis vs Idiopathic Inflammatory Bowel Disease. Clin Gastroenterol Hepatol 2023; 21:878-890. [PMID: 36270617 DOI: 10.1016/j.cgh.2022.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 02/07/2023]
Abstract
Immune checkpoint inhibitors have revolutionized management of advanced malignancies. However, their use is frequently complicated by immune related adverse events (irAEs), immune checkpoint inhibitor enterocolitis (IMEC) being the most common toxicity. IMEC is a distinct form of bowel inflammation that is highly reminiscent of idiopathic inflammatory bowel disorders (Crohn's disease, ulcerative colitis, and microscopic colitis). In this review, we highlight the similarities and differences in the pathophysiology, clinical presentation, evaluation, and management of these overlapping immune inflammatory bowel disorders. IMEC is an inflammatory bowel disease-like irAE that occurs as an outcome of disruption of intestinal immune surveillance and gut dysbiosis. Clinical and endoscopic presentation of both entities is strikingly similar, which often guides management. Though well established in inflammatory bowel disease, little is known about the long term outcomes of IMEC.
Collapse
Affiliation(s)
- Anusha Shirwaikar Thomas
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Hanauer
- Division of Gastroenterology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yinghong Wang
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| |
Collapse
|