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Shin JH, Tillotson G, MacKenzie TN, Warren CA, Wexler HM, Goldstein EJC. Bacteroides and related species: The keystone taxa of the human gut microbiota. Anaerobe 2024; 85:102819. [PMID: 38215933 DOI: 10.1016/j.anaerobe.2024.102819] [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: 09/06/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
Microbial communities play a significant role in maintaining ecosystems in a healthy homeostasis. Presently, in the human gastrointestinal tract, there are certain taxonomic groups of importance, though there is no single species that plays a keystone role. Bacteroides spp. are known to be major players in the maintenance of eubiosis in the human gastrointestinal tract. Here we review the critical role that Bacteroides play in the human gut, their potential pathogenic role outside of the gut, and their various methods of adapting to the environment, with a focus on data for B. fragilis and B. thetaiotaomicron. Bacteroides are anaerobic non-sporing Gram negative organisms that are also resistant to bile acids, generally thriving in the gut and having a beneficial relationship with the host. While they are generally commensal organisms, some Bacteroides spp. can be opportunistic pathogens in scenarios of GI disease, trauma, cancer, or GI surgery, and cause infection, most commonly intra-abdominal infection. B. fragilis can develop antimicrobial resistance through multiple mechanisms in large part due to its plasticity and fluid genome. Bacteroidota (formerly, Bacteroidetes) have a very broad metabolic potential in the GI microbiota and can rapidly adapt their carbohydrate metabolism to the available nutrients. Gastrointestinal Bacteroidota species produce short-chain fatty acids such as succinate, acetate, butyrate, and occasionally propionate, as the major end-products, which have wide-ranging and many beneficial influences on the host. Bacteroidota, via bile acid metabolism, also play a role in in colonization-resistance of other organisms, including Clostridioides difficile, and maintenance of gut integrity.
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Affiliation(s)
- Jae Hyun Shin
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | | | | | - Cirle A Warren
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | - Hannah M Wexler
- GLAVAHCS, Los Angeles, CA, USA; David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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Seekatz AM, Safdar N, Khanna S. The role of the gut microbiome in colonization resistance and recurrent Clostridioides difficile infection. Therap Adv Gastroenterol 2022; 15:17562848221134396. [PMID: 36425405 PMCID: PMC9679343 DOI: 10.1177/17562848221134396] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 10/04/2022] [Indexed: 11/21/2022] Open
Abstract
The species composition of the human gut microbiota is related to overall health, and a healthy gut microbiome is crucial in maintaining colonization resistance against pathogens. Disruption of gut microbiome composition and functionality reduces colonization resistance and has been associated with several gastrointestinal and non-gastrointestinal diseases. One prime example is Clostridioides difficile infection (CDI) and subsequent recurrent infections that occur after the development of systemic antibiotic-related dysbiosis. Standard-of-care antibiotics used for both acute and recurrent infections do not address dysbiosis and often worsen the condition. Moreover, monoclonal antibodies, recommended in conjunction with standard-of-care antibiotics for the prevention of recurrent CDI in patients at high risk of recurrence, reduce recurrences but do not address the underlying dysbiosis. Fecal microbiota transplantation (FMT) is an evolving therapeutic strategy in which microbes are harvested from healthy donor stool and transplanted into the gut of a recipient to restore the gut microbiome. Although effective in the prevention of recurrent CDI, some existing challenges include screening and the standardization of stool acquisition and processing. Recent safety alerts by the US Food and Drug Administration raised concern about the possibility of transmission of multidrug-resistant organisms or severe acute respiratory syndrome coronavirus 2 via FMT. Increased knowledge that microbes are beneficial in restoring the gut microbiome has led to the clinical development of several newer biotherapeutic formulations that are more regulated than FMT, which may allow for improved restoration of the gut microbiome and prevention of CDI recurrence. This review focuses on mechanisms by which gut microbiome restoration could influence colonization resistance against the pathogen C. difficile. Plain language summary The Role of the Gut Microbiome in Clostridioides difficile Infection Introduction: A rich and diverse gut microbiome is key to immune system regulation and colonization resistance against pathogens.A disruption in the gut microbiome composition can make the gut more vulnerable to diseases such as Clostridioides difficile infection (CDI), caused by the bacterium C. difficile.CDI management presents a therapeutic dilemma, as it is usually treated with antibiotics that can treat the infection but also can damage the microbiome.Treatment of CDI using antibiotics can further reduce microbial diversity and deplete beneficial bacteria from the gut leading to a condition called dysbiosis.Antibiotic treatment can be followed by therapies that restore the gut microbiota, boost colonization resistance, and prevent the development of antimicrobial resistance.It is important to evaluate treatment options to determine their safety and effectiveness. Methods: The researchers provided an overview of the mechanisms that the gut microbiome uses to prevent colonization of the gut by pathogens.They subsequently reviewed the efficacy and shortcomings of the following treatments for CDI: - Antibiotics- Monoclonal antibodies- Fecal microbiota transplantation (FMT) Results: Commensal intestinal bacteria prevent colonization of the gut by pathogens using mechanisms such as: - Competition for key nutrients- Production of inhibitory bile acids- Short-chain fatty acid production- Lowering the luminal pH- Production of bacteriocinsAntibiotic therapy is recommended as a standard treatment for CDI. However, patients are vulnerable to recurrent CDI after discontinuation of the therapy.Monoclonal antibodies that inactivate C. difficile toxins may be recommended along with antibiotics to prevent recurrent CDI. However, this approach does not restore the microbiome.FMT is one method of microbial restoration, where stool is harvested from a healthy donor and transplanted into a patient's colon.Although FMT has shown some efficacy in the treatment of recurrent CDI, the procedure is not standardized.Safety concerns have been raised about the possibility of transmission of multidrug-resistant pathogens via FMT. Conclusion: Treatment methods that can efficiently restore the diversity of the gut microbiome are crucial in preventing recurrence of CDI.
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Affiliation(s)
| | - Nasia Safdar
- University of Wisconsin, Madison, WI, USA
- William S. Middleton Memorial VA Hospital, Madison, WI, USA
| | - Sahil Khanna
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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Risk Factors, Diagnosis, and Management of Clostridioides difficile Infection in Patients with Inflammatory Bowel Disease. Microorganisms 2022; 10:microorganisms10071315. [PMID: 35889034 PMCID: PMC9319314 DOI: 10.3390/microorganisms10071315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/10/2022] Open
Abstract
Clostridioides difficile infection (CDI) and inflammatory bowel disease (IBD) are two pathologies that share a bidirectional causal nexus, as CDI is known to have an aggravating effect on IBD and IBD is a known risk factor for CDI. The colonic involvement in IBD not only renders the host more prone to an initial CDI development but also to further recurrences. Furthermore, IBD flares, which are predominantly set off by a CDI, not only create a need for therapy escalation but also prolong hospital stay. For these reasons, adequate and comprehensive management of CDI is of paramount importance in patients with IBD. Microbiological diagnosis, correct evaluation of clinical status, and consideration of different treatment options (from antibiotics and fecal microbiota transplantation to monoclonal antibodies) carry pivotal importance. Thus, the aim of this article is to review the risk factors, diagnosis, and management of CDI in patients with IBD.
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Piotrowski M, Wultańska D, Pituch H. Effect of prebiotics on Bacteroides sp. adhesion and biofilm formation and synbiotic effect on Clostridioides difficile. Future Microbiol 2022; 17:363-375. [PMID: 35172601 DOI: 10.2217/fmb-2021-0206] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aim: The objective of this study was to determine the effect of standard and candidate prebiotics on the adhesion and biofilm formation of Bacteroides sp. in monoculture and co-culture with Clostridioides difficile. Materials & methods: The effect of seven prebiotics on the adhesion and biofilm formation of Bacteroides sp. to three human cell lines was determined. The effect of Bacteroides sp. and fructooligosaccharides (FOS) on the adhesion and biofilm formation of C. difficile was tested by the co-incubation assay. Results: Inulin, mannose and raffinose presented the best anti-adhesion properties against Bacteroides sp. Combination of Bacteroides sp. with FOS decreased the adhesion of C. difficile. Conclusion: The study shows the potential role of prebiotics and synbiotics in decreasing the burden of C. difficile infections.
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Affiliation(s)
- Michał Piotrowski
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, 02-091, Poland
| | - Dorota Wultańska
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, 02-091, Poland
| | - Hanna Pituch
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, 02-091, Poland
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5
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Abstract
Clostridioides difficile is a spore-forming, obligate anaerobe, and ubiquitous nosocomial pathogen. While C. difficile infection in adults causes a spectrum of disease, including pseudomembranous colitis and toxic megacolon, healthy infants are asymptomatically colonized at high rates. The mechanisms leading to high colonization rates and infant protection from C. difficile are currently unknown; however, the ecology and metabolic state of the intestinal microbiome are factors known to influence C. difficile pathogenesis. In this review, we will examine the aspects of the early-life microbiome that may contribute to the incidence of C. difficile and protection from disease manifestation in infants. We will also discuss whether features of the adult microbiota that enable and restrict C. difficile are prevalent during early-life colonization.
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Affiliation(s)
- Alexa K Semon
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Orlaith Keenan
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joseph P Zackular
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Corresponding Author: Joseph P. Zackular, PhD, Department of Pathology & Laboratory Medicine, University of Pennsylvania, Children’s Hospital of Philadelphia, 1211A Abramson Research Center, 3615 Civic Center Blvd, Philadelphia, PA 19104. E-mail:
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van Werkhoven CH, Ducher A, Berkell M, Mysara M, Lammens C, Torre-Cisneros J, Rodríguez-Baño J, Herghea D, Cornely OA, Biehl LM, Bernard L, Dominguez-Luzon MA, Maraki S, Barraud O, Nica M, Jazmati N, Sablier-Gallis F, de Gunzburg J, Mentré F, Malhotra-Kumar S, Bonten MJM, Vehreschild MJGT. Incidence and predictive biomarkers of Clostridioides difficile infection in hospitalized patients receiving broad-spectrum antibiotics. Nat Commun 2021; 12:2240. [PMID: 33854064 PMCID: PMC8046770 DOI: 10.1038/s41467-021-22269-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
Abstract
Trial enrichment using gut microbiota derived biomarkers by high-risk individuals can improve the feasibility of randomized controlled trials for prevention of Clostridioides difficile infection (CDI). Here, we report in a prospective observational cohort study the incidence of CDI and assess potential clinical characteristics and biomarkers to predict CDI in 1,007 patients ≥ 50 years receiving newly initiated antibiotic treatment with penicillins plus a beta-lactamase inhibitor, 3rd/4th generation cephalosporins, carbapenems, fluoroquinolones or clindamycin from 34 European hospitals. The estimated 90-day cumulative incidences of a first CDI episode is 1.9% (95% CI 1.1-3.0). Carbapenem treatment (Hazard Ratio (95% CI): 5.3 (1.7-16.6)), toxigenic C. difficile rectal carriage (10.3 (3.2-33.1)), high intestinal abundance of Enterococcus spp. relative to Ruminococcus spp. (5.4 (2.1-18.7)), and low Shannon alpha diversity index as determined by 16 S rRNA gene profiling (9.7 (3.2-29.7)), but not normalized urinary 3-indoxyl sulfate levels, predicts an increased CDI risk.
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Affiliation(s)
- Cornelis H van Werkhoven
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | | | - Matilda Berkell
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Mohamed Mysara
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Microbiology Unit, Environment Health and Safety, Belgian Nuclear Research Centre, SCK.CEN, Mol, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Julian Torre-Cisneros
- Maimonides Institute for Research in Biomedicine of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba (UCO), Cordoba, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain
- Departamento de Medicina, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
| | - Delia Herghea
- Oncology Institute Prof. Dr. I Chiricuta, Cluj Napoca, Romania
| | - Oliver A Cornely
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Chair Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Lena M Biehl
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Louis Bernard
- Centre hospitalo-universitaire de Tours, Tours, France
| | | | - Sofia Maraki
- University Hospital of Heraklion, Heraklion, Greece
| | - Olivier Barraud
- Université Limoges, INSERM U1092, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | - Maria Nica
- Infectious and Tropical Diseases Hospital "Dr. Victor Babes", Bucharest, Romania
| | - Nathalie Jazmati
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
- Labor Dr. Wisplinghoff, Cologne, Germany
| | | | | | | | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Maria J G T Vehreschild
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany.
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany.
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Nissen L, Casciano F, Chiarello E, Di Nunzio M, Bordoni A, Gianotti A. Colonic In Vitro Model Assessment of the Prebiotic Potential of Bread Fortified with Polyphenols Rich Olive Fiber. Nutrients 2021; 13:nu13030787. [PMID: 33673592 PMCID: PMC7997273 DOI: 10.3390/nu13030787] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
The use of olive pomace could represent an innovative and low-cost strategy to formulate healthier and value-added foods, and bakery products are good candidates for enrichment. In this work, we explored the prebiotic potential of bread enriched with Polyphenol Rich Fiber (PRF), a defatted olive pomace byproduct previously studied in the European Project H2020 EcoProlive. To this aim, after in vitro digestion, the PRF-enriched bread, its standard control, and fructo-oligosaccharides (FOS) underwent distal colonic fermentation using the in vitro colon model MICODE (multi-unit colon gut model). Sampling was done prior, over and after 24 h of fermentation, then metabolomic analysis by Solid Phase Micro Extraction Gas Chromatography Mass Spectrometry (SPME GCMS), 16S-rDNA genomic sequencing of colonic microbiota by MiSeq, and absolute quantification of main bacterial species by qPCR were performed. The results indicated that PRF-enriched bread generated positive effects on the host gut model: (i) surge in eubiosis; (ii) increased abundance of beneficial bacterial groups, such as Bifidobacteriaceae and Lactobacillales; (iii) production of certain bioactive metabolites, such as low organic fatty acids; (iv) reduction in detrimental compounds, such as skatole. Our study not only evidenced the prebiotic role of PRF-enriched bread, thereby paving the road for further use of olive by-products, but also highlighted the potential of the in vitro gut model MICODE in the critical evaluation of functionality of food prototypes as modulators of the gut microbiota.
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Affiliation(s)
- Lorenzo Nissen
- CIRI-Interdepartmental Centre of Agri-Food Industrial Research, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (M.D.N.); (A.B.); (A.G.)
- Correspondence: ; Tel.: +39-0547-338-146
| | - Flavia Casciano
- DiSTAL-Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (F.C.); (E.C.)
| | - Elena Chiarello
- DiSTAL-Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (F.C.); (E.C.)
| | - Mattia Di Nunzio
- CIRI-Interdepartmental Centre of Agri-Food Industrial Research, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (M.D.N.); (A.B.); (A.G.)
- DiSTAL-Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (F.C.); (E.C.)
| | - Alessandra Bordoni
- CIRI-Interdepartmental Centre of Agri-Food Industrial Research, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (M.D.N.); (A.B.); (A.G.)
- DiSTAL-Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (F.C.); (E.C.)
| | - Andrea Gianotti
- CIRI-Interdepartmental Centre of Agri-Food Industrial Research, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (M.D.N.); (A.B.); (A.G.)
- DiSTAL-Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Piazza G. Goidanich, 60, 47521 Cesena (FC), Italy; (F.C.); (E.C.)
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8
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Clostridioides difficile exploits toxin-mediated inflammation to alter the host nutritional landscape and exclude competitors from the gut microbiota. Nat Commun 2021; 12:462. [PMID: 33469019 PMCID: PMC7815924 DOI: 10.1038/s41467-020-20746-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/17/2020] [Indexed: 01/04/2023] Open
Abstract
Clostridioides difficile is a bacterial pathogen that causes a range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. difficile infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against C. difficile. Disease is mediated by two large toxins and the expression of their genes is induced upon nutrient depletion via the alternative sigma factor TcdR. Here, we use tcdR mutants in two strains of C. difficile and omics to investigate how toxin-induced inflammation alters C. difficile metabolism, tissue gene expression and the gut microbiota, and to determine how inflammation by the host may be beneficial to C. difficile. We show that C. difficile metabolism is significantly different in the face of inflammation, with changes in many carbohydrate and amino acid uptake and utilization pathways. Host gene expression signatures suggest that degradation of collagen and other components of the extracellular matrix by matrix metalloproteinases is a major source of peptides and amino acids that supports C. difficile growth in vivo. Lastly, the inflammation induced by C. difficile toxin activity alters the gut microbiota, excluding members from the genus Bacteroides that are able to utilize the same essential nutrients released from collagen degradation. The effects of antibiotics on the gut microbiota can lead to enhanced colonization of Clostridioides difficile (C. difficile) and toxin-mediated pathogenesis. Here, using defined toxin-mutant strains and a murine model, the authors provide insights into how toxin-induced inflammation alters C. difficile metabolism, host tissue gene expression and gut microbiota, together influencing a beneficial niche for infection.
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Liu H, Hong XL, Sun TT, Huang XW, Wang JL, Xiong H. Fusobacterium nucleatum exacerbates colitis by damaging epithelial barriers and inducing aberrant inflammation. J Dig Dis 2020; 21:385-398. [PMID: 32441482 DOI: 10.1111/1751-2980.12909] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 04/29/2020] [Accepted: 05/19/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Fusobacterium nucleatum (F. nucleatum) has been reported to be enriched in patients with inflammatory bowel disease (IBD). This study aimed to explore the role of F. nucleatum in IBD and its pathogenic mechanism. METHODS Several bacteria that have been reported to be associated with IBD or colorectal cancer were measured in the fecal samples of 91 patients with IBD and 43 healthy individuals. Mice with dextran sulfate sodium (DSS)-induced colitis and a Caco-2 cell line were used to explore the pathogenicity of F. nucleatum. Barrier damage was evaluated by a transmission electron microscope, the permeability of fluorescein isothiocyanate-dextran, transepithelial electrical resistance and immunofluorescence. Protein levels of the cell-cell junction and activation of the STAT3 signaling pathway were detected by immunohistochemistry and immunoblot. Cytokine secretion and T-cell differentiation were measured by quantitative real-time polymerase chain reaction and flow cytometry. RESULTS F. nucleatum was significantly enriched in the feces of patients with IBD and its abundance correlated with disease activity. Administration of F. nucleatum markedly exacerbated colitis in a DSS mouse model. Mechanistically, F. nucleatum damaged epithelial integrity and increased permeability by regulating the expression and distribution of tight junction proteins zonula occludens-1 and occludin. Moreover, F. nucleatum promoted the secretion of cytokines (tumor necrosis factor-α, interferon-γ, interleukin [IL]-1β, IL-6, and IL-17), activated the STAT3 signaling pathway, and induced CD4+ T cell proliferation and Th1 and Th17 subset differentiations. CONCLUSION F. nucleatum can damage the intestinal barrier and induce aberrant inflammation, which exacerbates colitis.
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Affiliation(s)
- Hua Liu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xia Lu Hong
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tian Tian Sun
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Wen Huang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Lin Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Xiong
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Chen J, Vitetta L. The Role of Butyrate in Attenuating Pathobiont-Induced Hyperinflammation. Immune Netw 2020; 20:e15. [PMID: 32395367 PMCID: PMC7192831 DOI: 10.4110/in.2020.20.e15] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/09/2020] [Accepted: 01/19/2020] [Indexed: 12/17/2022] Open
Abstract
An excessive hyperinflammatory response-caused septic shock is a major medical problem that is associated with pathogenic bacterial infections leading to high mortality rates. The intestinal microbiota and the associated elaborated metabolites such as short chain fatty acid butyrate have been shown to relieve pathogenic bacterial-caused acute inflammation. Butyrate can down-regulate inflammation by inhibiting the growth of pathobionts, increasing mucosal barrier integrity, encouraging obligate anaerobic bacterial dominance and decreasing oxygen availability in the gut. Butyrate can also decrease excessive inflammation through modulation of immune cells such as increasing functionalities of M2 macrophages and regulatory T cells and inhibiting infiltration by neutrophils. Therefore, various approaches can be used to increase butyrate to relieve pathogenic bacterial-caused hyperinflammation. In this review we summarize the roles of butyrate in attenuating pathogenic bacterial-caused hyperinflammatory responses and discuss the associated plausible mechanisms.
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Affiliation(s)
| | - Luis Vitetta
- Medlab Clinical Ltd, Sydney 2015, Australia
- The University of Sydney, Faculty of Medicine and Health, Sydney 2006, Australia
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11
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Insights into the Role of Human Gut Microbiota in Clostridioides difficile Infection. Microorganisms 2020; 8:microorganisms8020200. [PMID: 32023967 PMCID: PMC7074861 DOI: 10.3390/microorganisms8020200] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile infection (CDI) has emerged as a major health problem worldwide. A major risk factor for disease development is prior antibiotic use, which disrupts the normal gut microbiota by altering its composition and the gut’s metabolic functions, leading to the loss of colonization resistance and subsequent CDI. Data from human studies have shown that the presence of C. difficile, either as a colonizer or as a pathogen, is associated with a decreased level of gut microbiota diversity. The investigation of the gut’s microbial communities, in both healthy subjects and patients with CDI, elucidate the role of microbiota and improve the current biotherapeutics for patients with CDI. Fecal microbiota transplantation has a major role in managing CDI, aiming at re-establishing colonization resistance in the host gastrointestinal tract by replenishing the gut microbiota. New techniques, such as post-genomics, proteomics and metabolomics analyses, can possibly determine in the future the way in which C. difficile eradicates colonization resistance, paving the way for the development of new, more successful treatments and prevention. The aim of the present review is to present recent data concerning the human gut microbiota with a focus on its important role in health and disease.
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Yang M, Bose S, Lim SK, Kim H. Preventive Effects of Pyungwi-san against Dextran Sulfate Sodium- and Clostridium difficile-Induced Inflammatory Bowel Disease in Mice. Int J Mol Sci 2019; 20:ijms20246346. [PMID: 31888274 PMCID: PMC6940993 DOI: 10.3390/ijms20246346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 12/20/2022] Open
Abstract
Several lines of evidence indicate that inflammatory bowel disease (IBD) is associated with Clostridium difficile (CD) infection as a consequence of gut dysbiosis. Currently available treatments of IBD are either not very effective or have adverse effects. Pyungwi-san (PWS), a traditional Chinese herbal formulation, has long been used to treat gastrointestinal disorders. The present study was conducted to investigate the efficacy of PWS against dextran sulfate sodium (DSS) + CD-induced IBD in mice. The animals received DSS in drinking water for seven days to produce DSS-induced acute colitis. In the DSS + CD group, the DSS-fed animals were orally administered with CD spores twice during the DSS treatment period. We observed that exposure of DSS + CD-treated animals to PWS significantly decreased the disease activity index; prevented the shortening of colonic length and increases in spleen size and weight; restored colonic histological parameters by significantly increasing mucus thickness, crypt depth, and goblet cell numbers; protected the tight junction proteins; improved the profiles of pro-inflammatory and anti-inflammatory cytokines; and normalized the abundance ratio of the Firmicutes/Bacteroidetes in the gut. Thus, PWS exerted a number of protective effects on DSS + CD-induced colitis, which might be mediated via restoration of a balance in gut microbial communities.
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Affiliation(s)
- Meng Yang
- Department of Rehabilitation Medicine of Korean Medicine, Dongguk University, 814 Siksa-dong, Ilsandong-gu, Goyang-si 10326, Korea; (M.Y.); (S.-K.L.)
| | - Shambhunath Bose
- Scientific Consultant Board, BexPharm Korea Healthcare Ltd. 51, Seongsui-ro, Seongdong-gu, Seoul 04781, Korea;
| | - Soo-Kyoung Lim
- Department of Rehabilitation Medicine of Korean Medicine, Dongguk University, 814 Siksa-dong, Ilsandong-gu, Goyang-si 10326, Korea; (M.Y.); (S.-K.L.)
| | - Hojun Kim
- Department of Rehabilitation Medicine of Korean Medicine, Dongguk University, 814 Siksa-dong, Ilsandong-gu, Goyang-si 10326, Korea; (M.Y.); (S.-K.L.)
- Correspondence: ; Tel.: +82-31-961-9111; Fax: +82-31-961-9009
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Slater RT, Frost LR, Jossi SE, Millard AD, Unnikrishnan M. Clostridioides difficile LuxS mediates inter-bacterial interactions within biofilms. Sci Rep 2019; 9:9903. [PMID: 31289293 PMCID: PMC6616478 DOI: 10.1038/s41598-019-46143-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/21/2019] [Indexed: 12/18/2022] Open
Abstract
The anaerobic gut pathogen, Clostridioides difficile, forms adherent biofilms that may play an important role in recurrent C. difficile infections. The mechanisms underlying C. difficile community formation and inter-bacterial interactions are nevertheless poorly understood. C. difficile produces AI-2, a quorum sensing molecule that modulates biofilm formation across many bacterial species. We found that a strain defective in LuxS, the enzyme that mediates AI-2 production, is defective in biofilm development in vitro. Transcriptomic analyses of biofilms formed by wild type (WT) and luxS mutant (luxS) strains revealed a downregulation of prophage loci in the luxS mutant biofilms compared to the WT. Detection of phages and eDNA within biofilms may suggest that DNA release by phage-mediated cell lysis contributes to C. difficile biofilm formation. In order to understand if LuxS mediates C. difficile crosstalk with other gut species, C. difficile interactions with a common gut bacterium, Bacteroides fragilis, were studied. We demonstrate that C. difficile growth is significantly reduced when co-cultured with B. fragilis in mixed biofilms. Interestingly, the absence of C. difficile LuxS alleviates the B. fragilis-mediated growth inhibition. Dual species RNA-sequencing analyses from single and mixed biofilms revealed differential modulation of distinct metabolic pathways for C. difficile WT, luxS and B. fragilis upon co-culture, indicating that AI-2 may be involved in induction of selective metabolic responses in B. fragilis. Overall, our data suggest that C. difficile LuxS/AI-2 utilises different mechanisms to mediate formation of single and mixed species communities.
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Affiliation(s)
- Ross T Slater
- University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Lucy R Frost
- University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Sian E Jossi
- University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Andrew D Millard
- University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Meera Unnikrishnan
- University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom.
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14
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Deng H, Yang S, Zhang Y, Qian K, Zhang Z, Liu Y, Wang Y, Bai Y, Fan H, Zhao X, Zhi F. Bacteroides fragilis Prevents Clostridium difficile Infection in a Mouse Model by Restoring Gut Barrier and Microbiome Regulation. Front Microbiol 2018; 9:2976. [PMID: 30619112 PMCID: PMC6308121 DOI: 10.3389/fmicb.2018.02976] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/19/2018] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile is currently the leading cause of nosocomial infection. Antibiotics remain the first-line therapy for C. difficile-associated diseases (CDAD), despite the risks of resistance promotion and further gut microbiota perturbation. Notably, the abundance of Bacteroides fragilis was reported to be significantly decreased in CDAD patients. This study aimed to clarify the prophylactic effects of B. fragilis strain ZY-312 in a mouse model of C. difficile infection (CDI). The CDI mouse model was successfully created using C. difficile strain VPI 10463 spores, as confirmed by lethal diarrhea (12.5% survival rate), serious gut barrier disruption, and microbiota disruption. CDI model mice prophylactically treated with B. fragilis exhibited significantly higher survival rates (100% in low dosage group, 87.5% in high dosage group) and improved clinical manifestations. Histopathological analysis of colon and cecum tissue samples revealed an intact gut barrier with strong ZO-1 and Muc-2 expression. The bacterial diversity and relative abundance of gut microbiota were significantly improved. Interestingly, the relative abundance of Akkermansia muciniphila was positively correlated with B. fragilis treatment. In vitro experiments showed that B. fragilis inhibited C. difficile adherence, and attenuated the decrease in CDI-induced transepithelial electrical resistance, ZO-1 and MUC-2 loss, and apoptosis, suggesting that B. fragilis protected against CDI possibly by resisting pathogen colonization and improving gut barrier integrity and functions. In summary, B. fragilis exerted protective effects on a CDI mouse model by modulating gut microbiota and alleviating barrier destruction, thereby relieving epithelial stress and pathogenic colitis triggered by C. difficile. This study provides an alternative preventative measure for CDI and lays the foundations for further investigations of the relationships among opportunistic pathogens, commensal microbiota, and the gut barrier.
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Affiliation(s)
- Huimin Deng
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Siqi Yang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yucheng Zhang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kai Qian
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhaohui Zhang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yangyang Liu
- Guangzhou ZhiYi Biotechnology Co., Ltd., Guangzhou, China
| | - Ye Wang
- Guangzhou ZhiYi Biotechnology Co., Ltd., Guangzhou, China
| | - Yang Bai
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hongying Fan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xinmei Zhao
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fachao Zhi
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
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15
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Draper LA, Ryan FJ, Smith MK, Jalanka J, Mattila E, Arkkila PA, Ross RP, Satokari R, Hill C. Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation. MICROBIOME 2018; 6:220. [PMID: 30526683 PMCID: PMC6288847 DOI: 10.1186/s40168-018-0598-x] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/18/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Faecal microbiota transplantation (FMT) is used in the treatment of recurrent Clostridium difficile infection. Its success is typically attributed to the restoration of a diverse microbiota. Viruses (including bacteriophages) are the most numerically dominant and potentially the most diverse members of the microbiota, but their fate following FMT has not been well studied. RESULTS We studied viral transfer following FMT from 3 donors to 14 patients. Recipient viromes resembled those of their donors for up to 12 months. Tracking individual bacteriophage colonisation revealed that engraftment of individual bacteriophages was dependent on specific donor-recipient pairings. Specifically, multiple recipients from a single donor displayed highly individualised virus colonisation patterns. CONCLUSIONS The impact of viruses on long-term microbial dynamics is a factor that should be reviewed when considering FMT as a therapeutic option.
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Affiliation(s)
- L A Draper
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - F J Ryan
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Present Address: South Australian Health and Medical Research Institute, North Terrace, Adelaide, 5000, Australia
| | - M K Smith
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - J Jalanka
- Immunobiology Research Program and Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - E Mattila
- Departments of Gastroenterology and Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - P A Arkkila
- Departments of Gastroenterology and Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - R P Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - R Satokari
- Immunobiology Research Program and Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - C Hill
- APC Microbiome Institute, University College Cork, Cork, Ireland.
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16
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Zhu H, Zeng D, Wang Q, Wang N, Zeng B, Niu L, Ni X. Diarrhea-Associated Intestinal Microbiota in Captive Sichuan Golden Snub-Nosed Monkeys (Rhinopithecus roxellana). Microbes Environ 2018; 33:249-256. [PMID: 30047510 PMCID: PMC6167115 DOI: 10.1264/jsme2.me17163] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Diarrhea is often associated with marked alterations in the intestinal microbiota, termed dysbiosis; however, limited information is currently available on the intestinal microbiota in captive golden snub-nosed monkeys (Rhinopithecus roxellana) with diarrhea. We herein characterized the fecal microbiota in diarrhea and healthy monkeys using the Illumina MiSeq platform. The concentrations of fecal short-chain fatty acids (SCFAs) and copy numbers of virulence factor genes were also assessed using gas chromatography and quantitative PCR (qPCR), respectively. The results obtained showed that diarrhea monkeys harbored a distinctive microbiota from that of healthy monkeys and had 45% fewer Bacteroidetes. Among healthy subjects, old monkeys had the lowest relative abundance of Bacteroidetes. Linear discriminant analysis coupled with the effect size (LEfSe) and canonical correlation analysis (CCA) identified significant differences in microbial taxa between diarrhea and healthy monkeys. A PICRUSt analysis revealed that several pathogenic genes were enriched in diarrhea monkeys, while glycan metabolism genes were overrepresented in healthy monkeys. A positive correlation was observed between the abundance of nutrition metabolism-related genes and the individual digestive capacities of healthy monkeys. Consequently, the abundance of genes encoding heat stable enterotoxin was significantly higher in diarrhea monkeys than in healthy monkeys (P<0.05). In healthy subjects, adult monkeys had significant higher concentrations of butyrate and total SCFAs than old monkeys (P<0.05). In conclusion, the present study demonstrated that diarrhea had a microbial component and changes in the microbial structure were accompanied by altered systemic metabolic states. These results suggest that pathogens and malabsorption are the two main causes of diarrhea, which are closely related to the microbial structure and functions.
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Affiliation(s)
- Hui Zhu
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University.,Sichuan University of Science and Engineering
| | - Dong Zeng
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University
| | | | - Ning Wang
- Sichuan University of Science and Engineering.,Department of Parasitology, College of Veterinary, Sichuan Agricultural University
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University
| | - Lili Niu
- Chengdu Wildlife Institute, Chengdu Zoo
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University
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17
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Delgado ML, Singh P, Funk JA, Moore JA, Cannell EM, Kanesfsky J, Manning SD, Scribner KT. Intestinal Microbial Community Dynamics of White-Tailed Deer (Odocoileus virginianus) in an Agroecosystem. MICROBIAL ECOLOGY 2017; 74:496-506. [PMID: 28293696 DOI: 10.1007/s00248-017-0961-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/28/2017] [Indexed: 06/06/2023]
Abstract
The intestinal microbiota has important functions that contribute to host health. The compositional dynamics of microbial communities are affected by many factors, including diet and presence of pathogens. In contrast to humans and domestic mammals, the composition and seasonal dynamics of intestinal microbiota of wildlife species remain comparatively understudied. White-tailed deer (Odocoileus virginianus) is an ecologically and economically important wildlife species that inhabits agricultural ecosystems and is known to be a reservoir of enteric pathogens. Nevertheless, there is a lack of knowledge of white-tailed deer intestinal microbiota diversity and taxonomic composition. This study's first objective was to characterize and compare the intestinal microbiota of 66 fecal samples from white-tailed deer collected during two sampling periods (March and June) using 16S rDNA pyrosequencing. Associations between community diversity and composition and factors including season, sex, host genetic relatedness, and spatial location were quantified. Results revealed that white-tailed deer intestinal microbiota was predominantly comprised of phyla Firmicutes and Proteobacteria, whose relative frequencies varied significantly between sampling periods. The second objective was to examine the associations between the presence of Escherichia coli and Salmonella, and microbiota composition and diversity. Results indicated that relative abundance of some microbial taxa varied when a pathogen was present. This study provides insights into microbial compositional dynamics of a wildlife species inhabiting coupled natural and agricultural landscapes. Data focus attention on the high prevalence of Proteobacteria particularly during the summer and highlight the need for future research regarding the role of white-tailed deer as a natural pathogen reservoir in agroecosystems.
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Affiliation(s)
- M Lisette Delgado
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Rd, East Lansing, MI, 48824, USA.
| | - Pallavi Singh
- Department of Microbiology and Molecular Genetics, Michigan State University, 194 Food Safety & Toxicology Building, East Lansing, MI, 48824, USA
| | - Julie A Funk
- College of Veterinary Medicine, Michigan State University, 736 Wilson Rd, East Lansing, MI, 48824, USA
| | - Jennifer A Moore
- Department of Biology, Grand Valley State University, 1 Campus Drive, Allendale, MI, 49401, USA
| | - Emily M Cannell
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Rd, East Lansing, MI, 48824, USA
| | - Jeannette Kanesfsky
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Rd, East Lansing, MI, 48824, USA
| | - Shannon D Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, 194 Food Safety & Toxicology Building, East Lansing, MI, 48824, USA
| | - Kim T Scribner
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Rd, East Lansing, MI, 48824, USA
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18
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Modeling new immunoregulatory therapeutics as antimicrobial alternatives for treating Clostridium difficile infection. Artif Intell Med 2017; 78:1-13. [DOI: 10.1016/j.artmed.2017.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/06/2017] [Accepted: 05/06/2017] [Indexed: 12/14/2022]
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19
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Davis MY, Zhang H, Brannan LE, Carman RJ, Boone JH. Rapid change of fecal microbiome and disappearance of Clostridium difficile in a colonized infant after transition from breast milk to cow milk. MICROBIOME 2016; 4:53. [PMID: 27717398 PMCID: PMC5055705 DOI: 10.1186/s40168-016-0198-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/23/2016] [Indexed: 05/12/2023]
Abstract
BACKGROUND Clostridium difficile is the most common known cause of antibiotic-associated diarrhea. Upon the disturbance of gut microbiota by antibiotics, C. difficile establishes growth and releases toxins A and B, which cause tissue damage in the host. The symptoms of C. difficile infection disease range from mild diarrhea to pseudomembranous colitis and toxic megacolon. Interestingly, 10-50 % of infants are asymptomatic carriers of C. difficile. This longitudinal study of the C. difficile colonization in an infant revealed the dynamics of C. difficile presence in gut microbiota. METHODS Fifty fecal samples, collected weekly between 5.5 and 17 months of age from a female infant who was an asymptomatic carrier of C. difficile, were analyzed by 16S rRNA gene sequencing. RESULTS Colonization switching between toxigenic and non-toxigenic C. difficile strains as well as more than 100,000-fold fluctuations of C. difficile counts were observed. C. difficile toxins were detected during the testing period in some infant stool samples, but the infant never had diarrhea. Although fecal microbiota was stable during breast feeding, a dramatic and permanent change of microbiota composition was observed within 5 days of the transition from human milk to cow milk. A rapid decline and eventual disappearance of C. difficile coincided with weaning at 12.5 months. An increase in the relative abundance of Bacteroides spp., Blautia spp., Parabacteroides spp., Coprococcus spp., Ruminococcus spp., and Oscillospira spp. and a decrease of Bifidobacterium spp., Lactobacillus spp., Escherichia spp., and Clostridium spp. were observed during weaning. The change in microbiome composition was accompanied by a gradual increase of fecal pH from 5.5 to 7. CONCLUSIONS The bacterial groups that are less abundant in early infancy, and that increase in relative abundance after weaning, likely are responsible for the expulsion of C. difficile.
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Affiliation(s)
- Manli Y Davis
- TechLab, Inc., 2001 Kraft Drive, Blacksburg, VA, 24060, USA.
| | - Husen Zhang
- Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Lera E Brannan
- TechLab, Inc., 2001 Kraft Drive, Blacksburg, VA, 24060, USA
| | | | - James H Boone
- TechLab, Inc., 2001 Kraft Drive, Blacksburg, VA, 24060, USA.
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20
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McKenney ES, Kendall MM. Microbiota and pathogen 'pas de deux': setting up and breaking down barriers to intestinal infection. Pathog Dis 2016; 74:ftw051. [PMID: 27252177 PMCID: PMC5985477 DOI: 10.1093/femspd/ftw051] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/04/2016] [Accepted: 05/24/2016] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota plays essential roles in human health and disease. In this review, we focus on the role of the intestinal microbiota in promoting resistance to infection by bacterial pathogens as well as how pathogens overcome this barrier. We discuss how the resident microbiota restricts growth and colonization of invading pathogens by limiting availability of nutrients and through generation of a hostile environment. Additionally, we examine how microbiota-derived signaling molecules interfere with bacterial virulence. In turn, we discuss how pathogens exploit non-competitive metabolites to replicate in vivo as well as to precisely control virulence and cause disease. This bacterial two step of creating and overcoming challenges important in preventing and establishing infection highlights the complexities of elucidating interactions between the commensal bacteria and pathogens. Better understanding of microbiota-pathogen interplay will have significant implications for developing novel therapeutics to treat infectious diseases.
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Affiliation(s)
- Elizabeth S McKenney
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Melissa M Kendall
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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21
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Yuhashi K, Yagihara Y, Misawa Y, Sato T, Saito R, Okugawa S, Moriya K. Diagnosing Clostridium difficile-associated diarrhea using enzyme immunoassay: the clinical significance of toxin negativity in glutamate dehydrogenase-positive patients. Infect Drug Resist 2016; 9:93-9. [PMID: 27313472 PMCID: PMC4890683 DOI: 10.2147/idr.s105429] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Purpose The enzyme immunoassay (EIA) has lower sensitivity for Clostridium difficile toxins A and B than the polymerase chain reaction in the diagnosis of C. difficile-associated diarrhea (CDAD). Furthermore, toxin positivity with EIA performed on C. difficile isolates from stool cultures may be observed even in patients with EIA glutamate dehydrogenase (GDH)-positive and toxin-negative stool specimens. It is unclear whether such patients should be treated as having CDAD. Methods The present study retrospectively compared patient characteristics, treatment, and diarrhea duration among three groups of patients who underwent stool EIA testing for CDAD diagnosis: a toxin-positive stool group (positive stool group; n=39); a toxin-negative stool/toxin-positive isolate group (discrepant negative/positive group, n=14); and a dual toxin-negative stool and isolate group (dual negative group, n=15). All cases included were confirmed to be GDH positive on EIA test. Results Patients’ backgrounds and comorbidities were not significantly different among three groups. No difference was observed among the three groups with regard to antimicrobial drug use before diarrhea onset. Treatment was received by 82.1% of the positive stool group compared to 7.1% of the discrepant positive/negative group and 0% of the dual negative group, while mean diarrhea duration was 10.6 days compared to 7.9 days (P=0.6006) and 3.4 days (P=0.0312), respectively. Conclusion Even without treatment, patients with toxin-negative stool specimens had shorter diarrhea duration than those with toxin-positive stool specimens even with toxin-positive isolates. These findings may suggest a limited need for CDAD treatment for GDH-positive patients and toxin-negative stool specimens.
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Affiliation(s)
- Kazuhito Yuhashi
- Department of Infection Control and Prevention, Faculty of Medicine, The University of Tokyo
| | - Yuka Yagihara
- Department of Infection Control and Prevention, Faculty of Medicine, The University of Tokyo
| | - Yoshiki Misawa
- Department of Infection Control and Prevention, Faculty of Medicine, The University of Tokyo
| | - Tomoaki Sato
- Department of Infection Control and Prevention, Faculty of Medicine, The University of Tokyo
| | - Ryoichi Saito
- Department of Microbiology and Immunity, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Shu Okugawa
- Department of Infection Control and Prevention, Faculty of Medicine, The University of Tokyo
| | - Kyoji Moriya
- Department of Infection Control and Prevention, Faculty of Medicine, The University of Tokyo
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22
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Clooney AG, Bernstein CN, Leslie WD, Vagianos K, Sargent M, Laserna-Mendieta EJ, Claesson MJ, Targownik LE. A comparison of the gut microbiome between long-term users and non-users of proton pump inhibitors. Aliment Pharmacol Ther 2016; 43:974-84. [PMID: 26923470 DOI: 10.1111/apt.13568] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 01/17/2016] [Accepted: 02/02/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND Proton pump inhibitor (PPI) use is associated with an increased risk of Clostridium difficile infection (CDI), though the mechanism is unclear. PPI induced alterations to the gut microbiome may facilitate the emergence of CDI, though the effects of PPIs on gut microbiota are not well characterised. [Correction added on 10 March 2016, after first online publication: microflora has been changed to microbiota throughout the article.] AIM To compare the faecal microbiomes of long-term PPI users to those with no history of PPI use. METHODS We used a population-based database to identify individuals with ≥5 years of continuous PPI use along with non-PPI using controls. Stool samples were subjected to microbiological analysis, with hierarchical clustering at genus level, along with alpha and beta diversity measures comparing the two groups. Metadata was accounted for using quantile regression to eliminate potential confounding variables in taxonomic abundance comparisons. RESULTS Sixty-one subjects (32 PPI, 29 controls) were analysed. While no significant differences in alpha diversity were found between the PPI users and controls, a moderate shift of the PPI users away from the non-PPI user cluster in the beta diversity was observed. After controlling for pertinent confounders, we discovered a decrease in Bacteroidetes and an increase in Firmicutes at the phylum level. We also performed species classifications and found Holdemania filiformis and Pseudoflavonifractor capillosus to be increased and decreased in the PPI cohort, respectively. CONCLUSIONS Long-term PPIs use has an effect on the gut microbiome. The alteration in the ratio of Firmicutes to Bacteroidetes may pre-dispose to the development of CDI.
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Affiliation(s)
- A G Clooney
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - C N Bernstein
- Section of Gastroenterology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - W D Leslie
- Departments of Radiology and Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - K Vagianos
- Section of Gastroenterology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - M Sargent
- Section of Gastroenterology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - E J Laserna-Mendieta
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - M J Claesson
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - L E Targownik
- Section of Gastroenterology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
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23
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Costello SP, Conlon MA, Vuaran MS, Roberts-Thomson IC, Andrews JM. Faecal microbiota transplant for recurrent Clostridium difficile infection using long-term frozen stool is effective: clinical efficacy and bacterial viability data. Aliment Pharmacol Ther 2015; 42:1011-8. [PMID: 26264455 DOI: 10.1111/apt.13366] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/08/2015] [Accepted: 07/23/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Faecal microbial transplant (FMT) for recurrent Clostridium difficile infection (rCDI) is greatly facilitated by frozen stool banks. However, the effect of frozen storage of stool for greater than 2 months on the viability of stool bacteria is unknown and the efficacy of FMT is not clear. AIM To evaluate the viability of bacteria in stool frozen for up to 6 months, and the clinical efficacy of FMT with stool frozen for 2-10 months, for the treatment of rCDI. METHODS Viability of six representative groups of faecal bacteria after 2 and 6 months of storage at -80 °C, in normal saline (NS) or 10% glycerol were assessed by culture on plate media. The clinical outcomes of 16 consecutive patients with rCDI treated with aliquots of stool frozen in 10% glycerol and stored for 2-10 months were also examined. RESULTS Viability at both 2 and 6 months was similar to baseline, in specimens stored in 10% glycerol and at 2 months in stool stored in NS, but was reduced by >1 log at 6 months for Aerobes (P < 0.01), total Coliforms (P < 0.01) and Lactobacilli (P < 0.01) in NS. Using stool frozen for 2-10 months in 10% glycerol, the cure rate for rCDI was 88% with one FMT and 100% after repeat FMT in those who relapsed. CONCLUSION Stool for faecal microbial transplant to treat rCDI can be safely stored frozen in 10% glycerol for at least 6 months without loss of clinical efficacy or viability in the six bacterial groups tested.
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Affiliation(s)
- S P Costello
- IBD Service, Department of Gastroenterology and Hepatology, Royal Adelaide Hospital, Adelaide, SA, Australia.,Department of Gastroenterology, The Queen Elizabeth Hospital, Woodville, SA, Australia.,School of Medicine, Faculty of Health Sciences, University of Adelaide, SA, Australia
| | - M A Conlon
- CSIRO Food and Nutrition Flagship, Adelaide, SA, Australia
| | - M S Vuaran
- CSIRO Food and Nutrition Flagship, Adelaide, SA, Australia
| | - I C Roberts-Thomson
- Department of Gastroenterology, The Queen Elizabeth Hospital, Woodville, SA, Australia.,School of Medicine, Faculty of Health Sciences, University of Adelaide, SA, Australia
| | - J M Andrews
- IBD Service, Department of Gastroenterology and Hepatology, Royal Adelaide Hospital, Adelaide, SA, Australia.,School of Medicine, Faculty of Health Sciences, University of Adelaide, SA, Australia
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Vincent C, Manges AR. Antimicrobial Use, Human Gut Microbiota and Clostridium difficile Colonization and Infection. Antibiotics (Basel) 2015; 4:230-53. [PMID: 27025623 PMCID: PMC4790283 DOI: 10.3390/antibiotics4030230] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 12/20/2022] Open
Abstract
Clostridium difficile infection (CDI) is the most important cause of nosocomial diarrhea. Broad-spectrum antimicrobials have profound detrimental effects on the structure and diversity of the indigenous intestinal microbiota. These alterations often impair colonization resistance, allowing the establishment and proliferation of C. difficile in the gut. Studies involving animal models have begun to decipher the precise mechanisms by which the intestinal microbiota mediates colonization resistance against C. difficile and numerous investigations have described gut microbiota alterations associated with C. difficile colonization or infection in human subjects. Fecal microbiota transplantation (FMT) is a highly effective approach for the treatment of recurrent CDI that allows the restoration of a healthy intestinal ecosystem via infusion of fecal material from a healthy donor. The recovery of the intestinal microbiota after FMT has been examined in a few reports and work is being done to develop custom bacterial community preparations that could be used as a replacement for fecal material.
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Affiliation(s)
- Caroline Vincent
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada.
| | - Amee R Manges
- School of Population and Public Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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25
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Odagiri M, Schriewer A, Hanley K, Wuertz S, Misra PR, Panigrahi P, Jenkins MW. Validation of Bacteroidales quantitative PCR assays targeting human and animal fecal contamination in the public and domestic domains in India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 502:462-470. [PMID: 25285421 DOI: 10.1016/j.scitotenv.2014.09.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 09/13/2014] [Accepted: 09/13/2014] [Indexed: 06/03/2023]
Abstract
We compared host-associated Bacteroidales qPCR assays developed in the continental United States and Europe for the purpose of measuring the effect of improved sanitation on human fecal exposure in rural Indian communities where both human and animal fecal loading are high. Ten candidate Bacteroidales qPCR assays were tested against fecal samples (human, sewage, cow, buffalo, goat, sheep, dog and chicken) from a test set of 30 individual human, 5 sewage, and 60 pooled animal samples collected in coastal Odisha, India. The two universal/general Bacteroidales assays tested (BacUni, GenBac3) performed equally well, achieving 100% sensitivity on the test set. Across the five human-associated assays tested (HF183 Taqman, BacHum, HumM2, BacH, HF183 SYBR), we found low sensitivity (17 to 49%) except for HF183 SYBR (89%), and moderate to high cross-reactivity with dog (20 to 80%) and chicken fecal samples (60 to 100%). BacHum had the highest accuracy (67%), amplified all sewage samples within the range of quantification (ROQ), and did not cross-react with any fecal samples from cows, the most populous livestock animal in India. Of the ruminant- and cattle-associated assays tested (BacCow, CowM2), BacCow was more sensitive in detecting the full range of common Indian livestock animal fecal sources, while CowM2 only detected cow sources with 50% sensitivity. Neither assay cross-reacted with human sources. BacCan, the dog-associated assay tested, showed no cross-reactivity with human sources, and high sensitivity (90%) for dog fecal samples. Overall, our results indicate BacUni, BacHum, HumM2, BacCan and BacCow would be the most suitable MST assays to distinguish and quantify relative amounts of human-associated and livestock/domestic animal-associated contributions to fecal contamination in Odisha, India.
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Affiliation(s)
- Mitsunori Odagiri
- Department of Civil and Environmental Engineering, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Alexander Schriewer
- Department of Civil and Environmental Engineering, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Kaitlyn Hanley
- Department of Civil and Environmental Engineering, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Stefan Wuertz
- Department of Civil and Environmental Engineering, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA; Singapore Centre on Environmental Life Sciences Engineering (SCELSE), School of Biological Sciences, and School of Civil and Environmental Engineering, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
| | - Pravas R Misra
- Asian Institute of Public Health, Bhubaneswar, Odisha, India
| | - Pinaki Panigrahi
- Departments of Epidemiology and Pediatrics, Center for Global Health and Development, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Marion W Jenkins
- Department of Civil and Environmental Engineering, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA; Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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Bibbò S, Lopetuso LR, Ianiro G, Di Rienzo T, Gasbarrini A, Cammarota G. Role of microbiota and innate immunity in recurrent Clostridium difficile infection. J Immunol Res 2014; 2014:462740. [PMID: 24995345 PMCID: PMC4068057 DOI: 10.1155/2014/462740] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/20/2014] [Indexed: 12/17/2022] Open
Abstract
Recurrent Clostridium difficile infection represents a burdensome clinical issue whose epidemiology is increasing worldwide. The pathogenesis is not yet completely known. Recent observations suggest that the alteration of the intestinal microbiota and impaired innate immunity may play a leading role in the development of recurrent infection. Various factors can cause dysbiosis. The causes most involved in the process are antibiotics, NSAIDs, acid suppressing therapies, and age. Gut microbiota impairment can favor Clostridium difficile infection through several mechanisms, such as the alteration of fermentative metabolism (especially SCFAs), the alteration of bile acid metabolism, and the imbalance of antimicrobial substances production. These factors alter the intestinal homeostasis promoting the development of an ecological niche for Clostridium difficile and of the modulation of immune response. Moreover, the intestinal dysbiosis can promote a proinflammatory environment, whereas Clostridium difficile itself modulates the innate immunity through both toxin-dependent and toxin-independent mechanisms. In this narrative review, we discuss how the intestinal microbiota modifications and the modulation of innate immune response can lead to and exacerbate Clostridium difficile infection.
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Affiliation(s)
- Stefano Bibbò
- A. Gemelli Hospital, Division of Internal Medicine and Gastroenterology, Department of Internal Medicine, School of Medicine and Surgery, Catholic University, 8, 00168 Rome, Italy
| | - Loris Riccardo Lopetuso
- A. Gemelli Hospital, Division of Internal Medicine and Gastroenterology, Department of Internal Medicine, School of Medicine and Surgery, Catholic University, 8, 00168 Rome, Italy
| | - Gianluca Ianiro
- A. Gemelli Hospital, Division of Internal Medicine and Gastroenterology, Department of Internal Medicine, School of Medicine and Surgery, Catholic University, 8, 00168 Rome, Italy
| | - Teresa Di Rienzo
- A. Gemelli Hospital, Division of Internal Medicine and Gastroenterology, Department of Internal Medicine, School of Medicine and Surgery, Catholic University, 8, 00168 Rome, Italy
| | - Antonio Gasbarrini
- A. Gemelli Hospital, Division of Internal Medicine and Gastroenterology, Department of Internal Medicine, School of Medicine and Surgery, Catholic University, 8, 00168 Rome, Italy
| | - Giovanni Cammarota
- A. Gemelli Hospital, Division of Internal Medicine and Gastroenterology, Department of Internal Medicine, School of Medicine and Surgery, Catholic University, 8, 00168 Rome, Italy
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