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Zhu D, Sorg JA, Sun X. Clostridioides difficile Biology: Sporulation, Germination, and Corresponding Therapies for C. difficile Infection. Front Cell Infect Microbiol 2018; 8:29. [PMID: 29473021 PMCID: PMC5809512 DOI: 10.3389/fcimb.2018.00029] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/23/2018] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is a Gram-positive, spore-forming, toxin-producing anaerobe, and an important nosocomial pathogen. Due to the strictly anaerobic nature of the vegetative form, spores are the main morphotype of infection and transmission of the disease. Spore formation and their subsequent germination play critical roles in C. difficile infection (CDI) progress. Under suitable conditions, C. difficile spores will germinate and outgrow to produce the pathogenic vegetative form. During CDI, C. difficile produces toxins (TcdA and TcdB) that are required to initiate the disease. Meanwhile, it also produces spores that are responsible for the persistence and recurrence of C. difficile in patients. Recent studies have shed light on the regulatory mechanisms of C. difficile sporulation and germination. This review is to summarize recent advances on the regulation of sporulation/germination in C. difficile and the corresponding therapeutic strategies that are aimed at these important processes.
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Affiliation(s)
- Duolong Zhu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Joseph A Sorg
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
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202
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Mintz M, Khair S, Grewal S, LaComb JF, Park J, Channer B, Rajapakse R, Bucobo JC, Buscaglia JM, Monzur F, Chawla A, Yang J, Robertson CE, Frank DN, Li E. Longitudinal microbiome analysis of single donor fecal microbiota transplantation in patients with recurrent Clostridium difficile infection and/or ulcerative colitis. PLoS One 2018; 13:e0190997. [PMID: 29385143 PMCID: PMC5791968 DOI: 10.1371/journal.pone.0190997] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/22/2017] [Indexed: 12/14/2022] Open
Abstract
Background Studies of colonoscopic fecal microbiota transplant (FMT) in patients with recurrent CDI, indicate that this is a very effective treatment for preventing further relapses. In order to provide this service at Stony Brook University Hospital, we initiated an open-label prospective study of single colonoscopic FMT among patients with ≥ 2 recurrences of CDI, with the intention of monitoring microbial composition in the recipient before and after FMT, as compared with their respective donor. We also initiated a concurrent open label prospective trial of single colonoscopic FMT of patients with ulcerative colitis (UC) not responsive to therapy, after obtaining an IND permit (IND 15642). To characterize how FMT alters the fecal microbiota in patients with recurrent Clostridia difficile infections (CDI) and/or UC, we report the results of a pilot microbiome analysis of 11 recipients with a history of 2 or more recurrences of C. difficile infections without inflammatory bowel disease (CDI-only), 3 UC recipients with recurrent C. difficile infections (CDI + UC), and 5 UC recipients without a history of C. difficile infections (UC-only). Method V3V4 Illumina 16S ribosomal RNA (rRNA) gene sequencing was performed on the pre-FMT, 1-week post-FMT, and 3-months post-FMT recipient fecal samples along with those collected from the healthy donors. Fitted linear mixed models were used to examine the effects of Group (CDI-only, CDI + UC, UC-only), timing of FMT (Donor, pre-FMT, 1-week post-FMT, 3-months post-FMT) and first order Group*FMT interactions on the diversity and composition of fecal microbiota. Pairwise comparisons were then carried out on the recipient vs. donor and between the pre-FMT, 1-week post-FMT, and 3-months post-FMT recipient samples within each group. Results Significant effects of FMT on overall microbiota composition (e.g., beta diversity) were observed for the CDI-only and CDI + UC groups. Marked decreases in the relative abundances of the strictly anaerobic Bacteroidetes phylum, and two Firmicutes sub-phyla associated with butyrate production (Ruminococcaceae and Lachnospiraceae) were observed between the CDI-only and CDI + UC recipient groups. There were corresponding increases in the microaerophilic Proteobacteria phylum and the Firmicutes/Bacilli group in the CDI-only and CDI + UC recipient groups. At a more granular level, significant effects of FMT were observed for 81 genus-level operational taxonomic units (OTUs) in at least one of the three recipient groups (p<0.00016 with Bonferroni correction). Pairwise comparisons of the estimated pre-FMT recipient/donor relative abundance ratios identified 6 Gammaproteobacteria OTUs, including the Escherichia-Shigella genus, and 2 Fusobacteria OTUs with significantly increased relative abundance in the pre-FMT samples of all three recipient groups (FDR < 0.05), however the magnitude of the fold change was much larger in the CDI-only and CDI + UC recipients than in the UC-only recipients. Depletion of butyrate producing OTUs, such as Faecalibacterium, in the CDI-only and CDI + UC recipients, were restored after FMT. Conclusion The results from this pilot study suggest that the microbial imbalances in the CDI + UC recipients more closely resemble those of the CDI-only recipients than the UC-only recipients.
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Affiliation(s)
- Michael Mintz
- Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Shanawaj Khair
- Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Suman Grewal
- Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Joseph F. LaComb
- Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Jiyhe Park
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
| | - Breana Channer
- Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Ramona Rajapakse
- Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Juan Carlos Bucobo
- Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Jonathan M. Buscaglia
- Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Farah Monzur
- Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Anupama Chawla
- Department of Pediatrics, Stony Brook University, Stony Brook, New York, United States of America
| | - Jie Yang
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Charlie E. Robertson
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Daniel N. Frank
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Ellen Li
- Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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Abstract
Gut dysbiosis is associated with many non-communicable human diseases, but the mechanisms maintaining homeostasis remain incompletely understood. Recent insights suggest that during homeostasis, epithelial hypoxia limits oxygen availability in the colon, thereby maintaining a balanced microbiota that functions as a microbial organ, producing metabolites contributing to host nutrition, immune education and niche protection. Dysbiosis is characterized by a shift in the microbial community structure from obligate to facultative anaerobes, suggesting oxygen as an important ecological driver of microbial organ dysfunction. The ensuing disruption of gut homeostasis can lead to non- communicable disease because microbiota-derived metabolites are either depleted or generated at harmful concentrations. This Opinion article describes the concept that host control over the microbial ecosystem in the colon is critical for the composition and function of our microbial organ, which provides a theoretical framework for linking microorganisms to non-communicable diseases.
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Affiliation(s)
- Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, California 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, California 95616, USA
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Allegretti JR, Kassam Z, Osman M, Budree S, Fischer M, Kelly CR. The 5D framework: a clinical primer for fecal microbiota transplantation to treat Clostridium difficile infection. Gastrointest Endosc 2018; 87:18-29. [PMID: 28583769 DOI: 10.1016/j.gie.2017.05.036] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 05/24/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Jessica R Allegretti
- Brigham Women's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | | | - Majdi Osman
- Harvard Medical School, Boston, Massachusetts, USA; OpenBiome, Somerville, Massachusetts, USA; Boston Children's Hospital, Boston, Massachusetts, USA
| | - Shrish Budree
- OpenBiome, Somerville, Massachusetts, USA; University of Cape Town, Cape Town, South Africa, USA
| | | | - Colleen R Kelly
- Warren Alpert Medical School of Brown University, Miriam Hospital, and Lifespan Hospital System, Providence, Rhode Island, USA
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205
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Evolving Treatment Strategies for Severe Clostridium difficile Colitis: Defining the Therapeutic Window. HOT TOPICS IN ACUTE CARE SURGERY AND TRAUMA 2018. [DOI: 10.1007/978-3-319-59704-1_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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206
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Daquigan N, Seekatz AM, Greathouse KL, Young VB, White JR. High-resolution profiling of the gut microbiome reveals the extent of Clostridium difficile burden. NPJ Biofilms Microbiomes 2017; 3:35. [PMID: 29214047 PMCID: PMC5717231 DOI: 10.1038/s41522-017-0043-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 11/07/2017] [Accepted: 11/16/2017] [Indexed: 02/07/2023] Open
Abstract
Microbiome profiling through 16S rRNA gene sequence analysis has proven to be a useful research tool in the study of C. difficile infection (CDI); however, CDI microbiome studies typically report results at the genus level or higher, thus precluding identification of this pathogen relative to other members of the gut microbiota. Accurate identification of C. difficile relative to the overall gut microbiome may be useful in assessments of colonization in research studies or as a prognostic indicator for patients with CDI. To investigate the burden of C. difficile at the species level relative to the overall gut microbiome, we applied a high-resolution method for 16S rRNA sequence assignment to previously published gut microbiome studies of CDI and other patient populations. We identified C. difficile in 131 of 156 index cases of CDI (average abundance 1.78%), and 18 of 211 healthy controls (average abundance 0.008%). We further detected substantial levels of C. difficile in a subset of infants that persisted over the first two to 12 months of life. Correlation analysis of C. difficile burden compared to other detected species demonstrated consistent negative associations with C. scindens and multiple Blautia species. These analyses contribute insight into the relative burden of C. difficile in the gut microbiome for multiple patient populations, and indicate that high-resolution 16S rRNA gene sequence analysis may prove useful in the development and evaluation of new therapies for CDI.
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Affiliation(s)
| | - Anna Maria Seekatz
- Department of Internal Medicine/Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI USA
| | | | - Vincent B. Young
- Department of Internal Medicine/Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI USA
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207
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Konturek PC, Zopf Y. [Therapeutic modulation of intestinal microbiota in irritable bowel syndrome. From probiotics to fecal microbiota therapy]. MMW Fortschr Med 2017; 159:1-5. [PMID: 29204952 DOI: 10.1007/s15006-017-0338-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND An abnormal intestinal microbiota (dysbiosis) plays a central role in the pathogenesis of the irritable bowel syndrome. METHOD An overview of four current options for the treatment of irritable bowel syndrome, which are characterized by modulation of intestinal microbiota, is given. RESULTS AND CONCLUSIONS Probiotics have very different effects on the individual symptoms of the irritable bowel. The choice of the appropriate preparation should therefore be based on the clinical symptomatology. The antibiotic rifaximin is effective in selected patients. Some patients also benefit from the repetition of this therapy. A FODMAP-reduced diet has shown significant alleviation of irritable bowel symptoms in studies. The fecal microbiota therapy (FMT) is a promising treatment option. At present, however, there are no such placebo-controlled studies to assess the effectiveness of this method.
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Affiliation(s)
- P C Konturek
- Klinik für Innere Medizin II, Thüringen-Kliniken GmbH Saalfeld, Rainweg 68, 07318, Saalfeld, Deutschland.
| | - Yurdagül Zopf
- Medizinische Klinik 1, Universitätsklinikum Erlangen, Erlangen, Deutschland
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208
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Zamudio-Tiburcio Á, Bermúdez-Ruiz H, Lezama-Guzmán HR, Guevara-Ortigoza MDP, Islas-Solares E, Sosa-López FA. Rompiendo paradigmas. Trasplante de microbiota intestinal: reporte preliminar. CIR CIR 2017; 85 Suppl 1:6-12. [DOI: 10.1016/j.circir.2016.11.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/26/2016] [Indexed: 02/07/2023]
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209
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Cataldo MA, Granata G, Petrosillo N. Clostridium difficile infection: new approaches to prevention, non-antimicrobial treatment, and stewardship. Expert Rev Anti Infect Ther 2017; 15:1027-1040. [PMID: 28980505 DOI: 10.1080/14787210.2017.1387535] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Despite the large amount of scientific publications exploring the epidemiology and the clinical management of Clostridium difficile (CD) infection, some issues remain unsolved or need further studies. The aim of this review is to give an update on the hot topics on CD prevention, including stewardship programs, and on the non-microbiological treatment of CD infection. Areas covered: This article will review the importance of minimizing the CD spore shedding in the healthcare environment for potentially reducing CD transmission. Moreover, antimicrobial stewardship programs aimed to reduce CD incidence will be reviewed. Finally, new strategies for reducing CD infection recurrence will be described. Expert commentary: Besides the basic infection control and prevention practices, including hand hygiene, contact isolation and environmental cleaning, in the prevention of CD infection other issues should be addressed including minimizing the spread of CD in the healthcare setting, and implementing the best strategy for reducing CD infection occurrence, including tailored antimicrobial stewardship programs. Regarding new advancements in treatment and management of CDI episodes, non-antimicrobial approaches seem to be promising in reducing and managing recurrent CD infection.
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Affiliation(s)
- Maria Adriana Cataldo
- a Clinical and Research Department , National Institute for Infectious Diseases 'L. Spallanzani' , Rome , Italy
| | - Guido Granata
- a Clinical and Research Department , National Institute for Infectious Diseases 'L. Spallanzani' , Rome , Italy
| | - Nicola Petrosillo
- a Clinical and Research Department , National Institute for Infectious Diseases 'L. Spallanzani' , Rome , Italy
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210
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Kootte RS, Levin E, Salojärvi J, Smits LP, Hartstra AV, Udayappan SD, Hermes G, Bouter KE, Koopen AM, Holst JJ, Knop FK, Blaak EE, Zhao J, Smidt H, Harms AC, Hankemeijer T, Bergman JJGHM, Romijn HA, Schaap FG, Olde Damink SWM, Ackermans MT, Dallinga-Thie GM, Zoetendal E, de Vos WM, Serlie MJ, Stroes ESG, Groen AK, Nieuwdorp M. Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition. Cell Metab 2017; 26:611-619.e6. [PMID: 28978426 DOI: 10.1016/j.cmet.2017.09.008] [Citation(s) in RCA: 591] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 07/15/2017] [Accepted: 09/14/2017] [Indexed: 12/29/2022]
Abstract
The intestinal microbiota has been implicated in insulin resistance, although evidence regarding causality in humans is scarce. We therefore studied the effect of lean donor (allogenic) versus own (autologous) fecal microbiota transplantation (FMT) to male recipients with the metabolic syndrome. Whereas we did not observe metabolic changes at 18 weeks after FMT, insulin sensitivity at 6 weeks after allogenic FMT was significantly improved, accompanied by altered microbiota composition. We also observed changes in plasma metabolites such as γ-aminobutyric acid and show that metabolic response upon allogenic FMT (defined as improved insulin sensitivity 6 weeks after FMT) is dependent on decreased fecal microbial diversity at baseline. In conclusion, the beneficial effects of lean donor FMT on glucose metabolism are associated with changes in intestinal microbiota and plasma metabolites and can be predicted based on baseline fecal microbiota composition.
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Affiliation(s)
- Ruud S Kootte
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; Top Institute of Food and Nutrition, 6700 AN Wageningen, the Netherlands
| | - Evgeni Levin
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; Horaizon BV, 3062 ME Rotterdam, the Netherlands
| | - Jarkko Salojärvi
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland
| | - Loek P Smits
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Annick V Hartstra
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Shanti D Udayappan
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Gerben Hermes
- Top Institute of Food and Nutrition, 6700 AN Wageningen, the Netherlands; Laboratory of Microbiology, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - Kristien E Bouter
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Annefleur M Koopen
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Jens J Holst
- NNF Center for Basic Metabolic Research, Department of Biomedical Sciences, the Panum Institute, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Filip K Knop
- Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, 2900 Hellerup, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ellen E Blaak
- Top Institute of Food and Nutrition, 6700 AN Wageningen, the Netherlands; Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, 6229 ER Maastricht, the Netherlands
| | - Jing Zhao
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Hauke Smidt
- Top Institute of Food and Nutrition, 6700 AN Wageningen, the Netherlands; Laboratory of Microbiology, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - Amy C Harms
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Thomas Hankemeijer
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Jacques J G H M Bergman
- Department of Gastroenterology and Hepatology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Hans A Romijn
- Department of Internal Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Frank G Schaap
- Department of Surgery, Maastricht University Medical Center, 6229 ER Maastricht, the Netherlands
| | - Steven W M Olde Damink
- Department of Surgery, Maastricht University Medical Center, 6229 ER Maastricht, the Netherlands
| | - Mariette T Ackermans
- Department of Clinical Chemistry, Laboratory of Endocrinology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Geesje M Dallinga-Thie
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Erwin Zoetendal
- Top Institute of Food and Nutrition, 6700 AN Wageningen, the Netherlands; Laboratory of Microbiology, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, 6703 HB Wageningen, the Netherlands; Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, 00014 Helsinki, Finland
| | - Mireille J Serlie
- Department of Endocrinology and Metabolism, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Erik S G Stroes
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Albert K Groen
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; Top Institute of Food and Nutrition, 6700 AN Wageningen, the Netherlands
| | - Max Nieuwdorp
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; Top Institute of Food and Nutrition, 6700 AN Wageningen, the Netherlands; Department of Internal Medicine, VUMC, Free University, Amsterdam, the Netherlands; Wallenberg Laboratory, Sahlgrenska Hospital, University of Gothenburg, Gothenburg, Sweden.
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211
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Gleaning Insights from Fecal Microbiota Transplantation and Probiotic Studies for the Rational Design of Combination Microbial Therapies. Clin Microbiol Rev 2017; 30:191-231. [PMID: 27856521 DOI: 10.1128/cmr.00049-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Beneficial microorganisms hold promise for the treatment of numerous gastrointestinal diseases. The transfer of whole microbiota via fecal transplantation has already been shown to ameliorate the severity of diseases such as Clostridium difficile infection, inflammatory bowel disease, and others. However, the exact mechanisms of fecal microbiota transplant efficacy and the particular strains conferring this benefit are still unclear. Rationally designed combinations of microbial preparations may enable more efficient and effective treatment approaches tailored to particular diseases. Here we use an infectious disease, C. difficile infection, and an inflammatory disorder, the inflammatory bowel disease ulcerative colitis, as examples to facilitate the discussion of how microbial therapy might be rationally designed for specific gastrointestinal diseases. Fecal microbiota transplantation has already shown some efficacy in the treatment of both these disorders; detailed comparisons of studies evaluating commensal and probiotic organisms in the context of these disparate gastrointestinal diseases may shed light on potential protective mechanisms and elucidate how future microbial therapies can be tailored to particular diseases.
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212
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Li R, Wang H, Shi Q, Wang N, Zhang Z, Xiong C, Liu J, Chen Y, Jiang L, Jiang Q. Effects of oral florfenicol and azithromycin on gut microbiota and adipogenesis in mice. PLoS One 2017; 12:e0181690. [PMID: 28742883 PMCID: PMC5526540 DOI: 10.1371/journal.pone.0181690] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/04/2017] [Indexed: 12/11/2022] Open
Abstract
Certain antibiotics detected in urine are associated with childhood obesity. In the current experimental study, we investigated two representative antibiotics detected in urine, florfenicol and azithromycin, for their early effects on adipogenesis, gut microbiota, short-chain fatty acids (SCFAs), and bile acids in mice. Thirty C57BL/6 mice aged four weeks were randomly divided into three groups (florfenicol, azithromycin and control). The two experimental groups were administered florfenicol or azithromycin at 5 mg/kg/day for four weeks. Body weight was measured weekly. The composition of the gut microbiota, body fat, SCFAs, and bile acids in colon contents were measured at the end of the experiment. The composition of the gut microbiota was determined by sequencing the bacterial 16S rRNA gene. The concentration of SCFAs and bile acids was determined using gas chromatography and liquid chromatography coupled to tandem mass spectrometry, respectively. The composition of the gut microbiota indicated that the two antibiotics altered the gut microbiota composition and decreased its richness and diversity. At the phylum level, the ratio of Firmicutes/Bacteroidetes increased significantly in the antibiotic groups. At the genus level, there were declines in Christensenella, Gordonibacter and Anaerotruncus in the florfenicol group, in Lactobacillus in the azithromycin group, and in Alistipes, Desulfovibrio, Parasutterella and Rikenella in both the antibiotic groups. The decrease in Rikenella in the azithromycin group was particularly noticeable. The concentration of SCFAs and secondary bile acids decreased in the colon, but the concentration of primary bile acids increased. These findings indicated that florfenicol and azithromycin increased adipogenesis and altered gut microbiota composition, SCFA production, and bile acid metabolism, suggesting that exposure to antibiotics might be one risk factor for childhood obesity. More studies are needed to investigate the specific mechanisms.
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Affiliation(s)
- Rui Li
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, Shanghai, China
| | - Hexing Wang
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, Shanghai, China
| | - Qingfeng Shi
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, Shanghai, China
| | - Na Wang
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, Shanghai, China
| | - Zhijie Zhang
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, Shanghai, China
| | - Chenglong Xiong
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, Shanghai, China
| | - Jianxiang Liu
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, Shanghai, China
| | - Yue Chen
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Lufang Jiang
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, Shanghai, China
- * E-mail:
| | - Qingwu Jiang
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, Shanghai, China
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213
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Rojo D, Méndez-García C, Raczkowska BA, Bargiela R, Moya A, Ferrer M, Barbas C. Exploring the human microbiome from multiple perspectives: factors altering its composition and function. FEMS Microbiol Rev 2017; 41:453-478. [PMID: 28333226 PMCID: PMC5812509 DOI: 10.1093/femsre/fuw046] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023] Open
Abstract
Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.
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Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
| | | | - Beata Anna Raczkowska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), 46020 Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Paterna, 46980 Valencia, Spain
- These authors contributed equally to this work
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
- Corresponding author: Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain. Tel: (+34) 915854872; E-mail:
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
- These authors contributed equally to this work
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214
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Long SL, Gahan CGM, Joyce SA. Interactions between gut bacteria and bile in health and disease. Mol Aspects Med 2017; 56:54-65. [PMID: 28602676 DOI: 10.1016/j.mam.2017.06.002] [Citation(s) in RCA: 307] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 05/26/2017] [Accepted: 06/07/2017] [Indexed: 01/18/2023]
Abstract
Bile acids are synthesized from cholesterol in the liver and released into the intestine to aid the digestion of dietary lipids. The host enzymes that contribute to bile acid synthesis in the liver and the regulatory pathways that influence the composition of the total bile acid pool in the host have been well established. In addition, the gut microbiota provides unique contributions to the diversity of bile acids in the bile acid pool. Gut microbial enzymes contribute significantly to bile acid metabolism through deconjugation and dehydroxylation reactions to generate unconjugated bile acids and secondary bile acids. These microbial enzymes (which include bile salt hydrolase (BSH) and bile acid-inducible (BAI) enzymes) are essential for bile acid homeostasis in the host and represent a vital contribution of the gut microbiome to host health. Perturbation of the gut microbiota in disease states may therefore significantly influence bile acid signatures in the host, especially in the context of gastrointestinal or systemic disease. Given that bile acids are ligands for host cell receptors (including the FXR, TGR5 and Vitamin D Receptor) alterations to microbial enzymes and associated changes to bile acid signatures have significant consequences for the host. In this review we examine the contribution of microbial enzymes to the process of bile acid metabolism in the host and discuss the implications for microbe-host signalling in the context of C. difficile infection, inflammatory bowel disease and other disease states.
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Affiliation(s)
- Sarah L Long
- APC Microbiome Institute, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland
| | - Cormac G M Gahan
- APC Microbiome Institute, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland; School of Pharmacy, University College Cork, Cork, Ireland.
| | - Susan A Joyce
- APC Microbiome Institute, University College Cork, Cork, Ireland; School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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215
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Sandoval-Motta S, Aldana M, Martínez-Romero E, Frank A. The Human Microbiome and the Missing Heritability Problem. Front Genet 2017; 8:80. [PMID: 28659968 PMCID: PMC5468393 DOI: 10.3389/fgene.2017.00080] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 05/29/2017] [Indexed: 12/13/2022] Open
Abstract
The "missing heritability" problem states that genetic variants in Genome-Wide Association Studies (GWAS) cannot completely explain the heritability of complex traits. Traditionally, the heritability of a phenotype is measured through familial studies using twins, siblings and other close relatives, making assumptions on the genetic similarities between them. When this heritability is compared to the one obtained through GWAS for the same traits, a substantial gap between both measurements arise with genome wide studies reporting significantly smaller values. Several mechanisms for this "missing heritability" have been proposed, such as epigenetics, epistasis, and sequencing depth. However, none of them are able to fully account for this gap in heritability. In this paper we provide evidence that suggests that in order for the phenotypic heritability of human traits to be broadly understood and accounted for, the compositional and functional diversity of the human microbiome must be taken into account. This hypothesis is based on several observations: (A) The composition of the human microbiome is associated with many important traits, including obesity, cancer, and neurological disorders. (B) Our microbiome encodes a second genome with nearly a 100 times more genes than the human genome, and this second genome may act as a rich source of genetic variation and phenotypic plasticity. (C) Human genotypes interact with the composition and structure of our microbiome, but cannot by themselves explain microbial variation. (D) Microbial genetic composition can be strongly influenced by the host's behavior, its environment or by vertical and horizontal transmissions from other hosts. Therefore, genetic similarities assumed in familial studies may cause overestimations of heritability values. We also propose a method that allows the compositional and functional diversity of our microbiome to be incorporated to genome wide association studies.
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Affiliation(s)
- Santiago Sandoval-Motta
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
| | - Maximino Aldana
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico City, Mexico.,Instituto de Ciencias Físicas, Universidad Nacional Autónoma de MéxicoMorelos, Mexico
| | | | - Alejandro Frank
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico City, Mexico.,Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de MéxicoMexico City, Mexico.,Member of El Colegio NacionalMexico City, Mexico
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216
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Thanissery R, Winston JA, Theriot CM. Inhibition of spore germination, growth, and toxin activity of clinically relevant C. difficile strains by gut microbiota derived secondary bile acids. Anaerobe 2017; 45:86-100. [PMID: 28279860 PMCID: PMC5466893 DOI: 10.1016/j.anaerobe.2017.03.004] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/02/2017] [Accepted: 03/04/2017] [Indexed: 12/18/2022]
Abstract
The changing epidemiology of Clostridium difficile infection over the past decades presents a significant challenge in the management of C. difficile associated diseases. The gastrointestinal tract microbiota provides colonization resistance against C. difficile, and growing evidence suggests that gut microbial derived secondary bile acids (SBAs) play a role. We hypothesized that the C. difficile life cycle; spore germination and outgrowth, growth, and toxin production, of strains that vary by age and ribotype will differ in their sensitivity to SBAs. C. difficile strains R20291 and CD196 (ribotype 027), M68 and CF5 (017), 630 (012), BI9 (001) and M120 (078) were used to define taurocholate (TCA) mediated spore germination and outgrowth, growth, and toxin activity in the absence and presence of gut microbial derived SBAs (deoxycholate, isodeoxycholate, lithocholate, isolithocholate, ursodeoxycholate, ω-muricholate, and hyodeoxycholate) found in the human and mouse large intestine. C. difficile strains varied in their rates of germination, growth kinetics, and toxin activity without the addition of SBAs. C. difficile M120, a highly divergent strain, had robust germination, growth, but significantly lower toxin activity compared to other strains. Many SBAs were able to inhibit TCA mediated spore germination and outgrowth, growth, and toxin activity in a dose dependent manner, but the level of inhibition and resistance varied across all strains and ribotypes. This study illustrates how clinically relevant C. difficile strains can have different responses when exposed to SBAs present in the gastrointestinal tract.
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Affiliation(s)
- Rajani Thanissery
- Department of Population Health and Pathobiology, College of Veterinary Medicine, Research Building 424, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, United States.
| | - Jenessa A Winston
- Department of Population Health and Pathobiology, College of Veterinary Medicine, Research Building 424, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, United States.
| | - Casey M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, Research Building 424, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, United States.
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217
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Successful Resolution of Recurrent Clostridium difficile Infection using Freeze-Dried, Encapsulated Fecal Microbiota; Pragmatic Cohort Study. Am J Gastroenterol 2017; 112:940-947. [PMID: 28195180 PMCID: PMC5552199 DOI: 10.1038/ajg.2017.6] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 12/02/2016] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Fecal microbiota transplantation (FMT) is increasingly being used for treatment of recurrent Clostridium difficile infection (R-CDI) that cannot be cured with antibiotics alone. In addition, FMT is being investigated for a variety of indications where restoration or restructuring of the gut microbial community is hypothesized to be beneficial. We sought to develop a stable, freeze-dried encapsulated preparation of standardized fecal microbiota that can be used for FMT with ease and convenience in clinical practice and research. METHODS We systematically developed a lyophilization protocol that preserved the viability of bacteria across the taxonomic spectrum found in fecal microbiota and yielded physicochemical properties that enabled consistent encapsulation. We also treated a cohort of R-CDI patients with a range of doses of encapsulated microbiota and analyzed the associated changes in the fecal microbiome of the recipients. RESULTS The optimized lyophilized preparation satisfied all our preset goals for physicochemical properties, encapsulation ease, stability at different temperatures, and microbiota viability in vitro and in vivo (germ-free mice). The capsule treatment was administered to 49 patients. Overall, 43/49 (88%) of patients achieved a clinical success, defined as no recurrence of CDI over 2 months. Analysis of the fecal microbiome demonstrated near normalization of the fecal microbial community by 1 month following FMT treatment. The simplest protocol using the lowest dose (2.1-2.5 × 1011 bacteria in 2-3 capsules) without any colon purgative performed equally well in terms of clinical outcomes and microbiota engraftment. CONCLUSIONS A single administration of encapsulated, freeze-dried fecal microbiota from a healthy donor was highly successful in treating antibiotic-refractory R-CDI syndrome.
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218
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Wotzka SY, Nguyen BD, Hardt WD. Salmonella Typhimurium Diarrhea Reveals Basic Principles of Enteropathogen Infection and Disease-Promoted DNA Exchange. Cell Host Microbe 2017; 21:443-454. [PMID: 28407482 DOI: 10.1016/j.chom.2017.03.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/17/2017] [Accepted: 03/24/2017] [Indexed: 12/18/2022]
Abstract
Despite decades of research, efficient therapies for most enteropathogenic bacteria are still lacking. In this review, we focus on Salmonella enterica Typhimurium (S. Typhimurium), a frequent cause of acute, self-limiting food-borne diarrhea and a model that has revealed key principles of enteropathogen infection. We review the steps of gut infection and the mucosal innate-immune defenses limiting pathogen burdens, and we discuss how inflammation boosts gut luminal S. Typhimurium growth. We also discuss how S. Typhimurium-induced inflammation accelerates the transfer of plasmids and phages, which may promote the transmission of antibiotic resistance and facilitate emergence of pathobionts and pathogens with enhanced virulence. The targeted manipulation of the microbiota and vaccination might offer strategies to prevent this evolution. As gut luminal microbes impact various aspects of the host's physiology, improved strategies for preventing enteropathogen infection and disease-inflicted DNA exchange may be of broad interest well beyond the acute infection.
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Affiliation(s)
- Sandra Y Wotzka
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Bidong D Nguyen
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
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219
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Mooyottu S, Flock G, Upadhyay A, Upadhyaya I, Maas K, Venkitanarayanan K. Protective Effect of Carvacrol against Gut Dysbiosis and Clostridium difficile Associated Disease in a Mouse Model. Front Microbiol 2017; 8:625. [PMID: 28484429 PMCID: PMC5399026 DOI: 10.3389/fmicb.2017.00625] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 03/28/2017] [Indexed: 12/15/2022] Open
Abstract
This study investigated the effect of carvacrol (CR), a phytophenolic compound on antibiotic-associated gut dysbiosis and C. difficile infection in a mouse model. Five to six-week-old C57BL/6 mice were randomly divided into seven treatment groups (challenge and control) of eight mice each. Mice were fed with irradiated feed supplemented with CR (0, 0.05, and 0.1%); the challenge groups were made susceptible to C. difficile by orally administering an antibiotic cocktail in water and an intra-peritoneal injection of clindamycin. Both challenge and control groups were infected with 105CFU/ml of hypervirulent C. difficile (ATCC 1870) spores or PBS, and observed for clinical signs for 10 days. Respective control groups for CR, antibiotics, and their combination were included for investigating their effect on mouse enteric microflora. Mouse body weight and clinical and diarrhea scores were recorded daily post infection. Fecal samples were collected for microbiome analysis using rRNA sequencing in MiSeq platform. Carvacrol supplementation significantly reduced the incidence of diarrhea and improved the clinical and diarrhea scores in mice (p < 0.05). Microbiome analysis revealed a significant increase in Proteobacteria and reduction in the abundance of protective bacterial flora in antibiotic-treated and C. difficile-infected mice compared to controls (p < 0.05). However, CR supplementation positively altered the microbiome composition, as revealed by an increased abundance of beneficial bacteria, including Firmicutes, and significantly reduced the proportion of detrimental flora such as Proteobacteria, without significantly affecting the gut microbiome diversity compared to control. Results suggest that CR could potentially be used to control gut dysbiosis and reduce C. difficile infection.
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Affiliation(s)
| | - Genevieve Flock
- Department of Animal Science, University of ConnecticutStorrs, CT, USA
| | - Abhinav Upadhyay
- Department of Animal Science, University of ConnecticutStorrs, CT, USA
| | - Indu Upadhyaya
- Department of Animal Science, University of ConnecticutStorrs, CT, USA
| | - Kendra Maas
- Microbial Analysis, Resources, and Services, University of ConnecticutStorrs, CT, USA
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220
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Survival of the Fittest: How Bacterial Pathogens Utilize Bile To Enhance Infection. Clin Microbiol Rev 2017; 29:819-36. [PMID: 27464994 DOI: 10.1128/cmr.00031-16] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacterial pathogens have coevolved with humans in order to efficiently infect, replicate within, and be transmitted to new hosts to ensure survival and a continual infection cycle. For enteric pathogens, the ability to adapt to numerous host factors under the harsh conditions of the gastrointestinal tract is critical for establishing infection. One such host factor readily encountered by enteric bacteria is bile, an innately antimicrobial detergent-like compound essential for digestion and nutrient absorption. Not only have enteric pathogens evolved to resist the bactericidal conditions of bile, but these bacteria also utilize bile as a signal to enhance virulence regulation for efficient infection. This review provides a comprehensive and up-to-date analysis of bile-related research with enteric pathogens. From common responses to the unique expression of specific virulence factors, each pathogen has overcome significant challenges to establish infection in the gastrointestinal tract. Utilization of bile as a signal to modulate virulence factor expression has led to important insights for our understanding of virulence mechanisms for many pathogens. Further research on enteric pathogens exposed to this in vivo signal will benefit therapeutic and vaccine development and ultimately enhance our success at combating such elite pathogens.
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221
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Stoltz KL, Erickson R, Staley C, Weingarden AR, Romens E, Steer CJ, Khoruts A, Sadowsky MJ, Dosa PI. Synthesis and Biological Evaluation of Bile Acid Analogues Inhibitory to Clostridium difficile Spore Germination. J Med Chem 2017; 60:3451-3471. [PMID: 28402634 DOI: 10.1021/acs.jmedchem.7b00295] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Standard antibiotic-based strategies for the treatment of Clostridium difficile infections disrupt indigenous microbiota and commonly fail to eradicate bacterial spores, two key factors that allow recurrence of infection. As an alternative approach to controlling C. difficile infection, a series of bile acid derivatives have been prepared that inhibit taurocholate-induced spore germination. These analogues have been evaluated in a highly virulent NAP1 strain using optical density and phase-contrast microscopy assays. Heterocycle substitutions at C24 were well-tolerated and several tetrazole-containing derivatives were highly potent inhibitors in both assays, with complete inhibition of spore germination observed at 10-25 μM. To limit intestinal absorption, C7-sulfated analogues designed to avoid active and passive transport pathways were prepared. One of these derivatives, compound 21b, was found to be a potent inhibitor of C. difficile spore germination and poorly permeable in a Caco-2 model of intestinal epithelial absorption, suggesting that it is likely to be gut-restricted.
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Affiliation(s)
- Kristen L Stoltz
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, University of Minnesota , 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
| | - Raymond Erickson
- BioTechnology Institute, University of Minnesota , 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Christopher Staley
- BioTechnology Institute, University of Minnesota , 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Alexa R Weingarden
- BioTechnology Institute, University of Minnesota , 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States.,Department of Microbiology and Immunology, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Erin Romens
- BioTechnology Institute, University of Minnesota , 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Clifford J Steer
- Departments of Medicine and Genetics, Cell Biology, and Development, University of Minnesota , VFW Cancer Research Center, 406 Harvard Street, Minneapolis, Minnesota, United States
| | - Alexander Khoruts
- BioTechnology Institute, University of Minnesota , 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States.,Department of Medicine, Division of Gastroenterology, University of Minnesota , Minneapolis, Minnesota 55414, United States.,Center for Immunology, University of Minnesota , Minneapolis, Minnesota 55414, United States
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota , 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States.,Department of Soil, Water & Climate, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Peter I Dosa
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, University of Minnesota , 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
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222
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Affiliation(s)
- Alexander Khoruts
- Department of Medicine, Division of Gastroenterology, Center for Immunology and the BioTechnology Institute, University of Minnesota, Minneapolis, MN, USA,CONTACT Alexander Khoruts Department of Medicine, Division of Gastroenterology, Center for Immunology and the BioTechnology Institute, University of Minnesota, Minneapolis, MN 55414, USA
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223
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Ge X, Zhao W, Ding C, Tian H, Xu L, Wang H, Ni L, Jiang J, Gong J, Zhu W, Zhu M, Li N. Potential role of fecal microbiota from patients with slow transit constipation in the regulation of gastrointestinal motility. Sci Rep 2017; 7:441. [PMID: 28348415 PMCID: PMC5428802 DOI: 10.1038/s41598-017-00612-y] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/06/2017] [Indexed: 12/13/2022] Open
Abstract
The gut microbiota is involved in various physiological functions, and disturbances in the host-microbiome have been proven to contribute to the dysfunction of gut; however, whether microbiota participates in the pathogenesis of constipation remains unclear. In this study, we extracted and analyzed microbiota in feces from constipated donors who had undergone effective therapy with fecal microbiota transplantation, transplanted microbiota into pseudo-germ-free mice, and measured gut motility. These mice presented with lower pellet frequency and water percentage, smaller pellet size, delayed gastrointestinal transit time, and weaker spontaneous contractions of colonic smooth muscle. To determine the mechanism underlying delayed gut motility, microbial metabolites were measured. Short chain fatty acids and secondary bile acids were decreased in mice receiving microbiota from constipated donors. Moreover, the compositional changes of gut microbiota in constipated patients were identified, including the operational taxonomic unit, and the species richness and α diversity were much greater than those in healthy volunteers. These findings suggest that alterations of the microbiome might affect gut motility via altered microbial-derived metabolites in the development of constipation, and the restoration of disturbed microbiota might improve the clinical phenotype. This study indicates that regulating the intestinal environment may be a novel therapy strategy for constipation.
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Affiliation(s)
- Xiaolong Ge
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Wei Zhao
- Center of Reproductive Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Chao Ding
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Hongliang Tian
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Lizhi Xu
- Department of Medical Genetics, and Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Hongkan Wang
- First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Ling Ni
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Jun Jiang
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Jianfeng Gong
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China.
| | - Weiming Zhu
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China.
| | - Minsheng Zhu
- Model Animal Research Center and MOE Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing, 210002, China
| | - Ning Li
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China.
- Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University, Shanghai, 200072, China.
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224
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Cao H, Xu M, Dong W, Deng B, Wang S, Zhang Y, Wang S, Luo S, Wang W, Qi Y, Gao J, Cao X, Yan F, Wang B. Secondary bile acid-induced dysbiosis promotes intestinal carcinogenesis. Int J Cancer 2017; 140:2545-2556. [PMID: 28187526 DOI: 10.1002/ijc.30643] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 01/08/2017] [Accepted: 01/30/2017] [Indexed: 12/13/2022]
Abstract
The gut microbiota plays an important role in maintaining intestinal homeostasis. Dysbiosis is associated with intestinal tumorigenesis. Deoxycholic acid (DCA), a secondary bile acid increased by a western diet, correlates with intestinal carcinogenesis. However, evidence relating bile acids, intestinal microbiota and tumorigenesis are limited. In our study, we investigated the effect of DCA on induction of intestinal dysbiosis and its roles in intestinal carcinogenesis. Alteration of the composition of the intestinal microbiota was induced in DCA-treated APCmin/+ mice, which was accompanied by impaired intestinal barrier, gut low grade inflammation and tumor progression. The transfer of fecal microbiota from DCA-treated mice to another group of Apcmin/+ mice increased tumor multiplicity, induced inflammation and recruited M2 phenotype tumor-associated macrophages. Importantly, the fecal microbiota transplantation activated the tumor-associated Wnt/β-catenin signaling pathway. Moreover, microbiota depletion by a cocktail of antibiotics was sufficient to block DCA-induced intestinal carcinogenesis, further suggesting the role of dysbiosis in tumor development. Our study demonstrated that alteration of the microbial community induced by DCA promoted intestinal carcinogenesis.
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Affiliation(s)
- Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, People's Republic of China.,Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Mengque Xu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, People's Republic of China.,Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Wenxiao Dong
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, People's Republic of China
| | - Baoru Deng
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, People's Republic of China
| | - Sinan Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yujie Zhang
- Department of Pathology, General Hospital, Tianjin Medical University, Tianjin, People's Republic of China
| | - Shan Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, People's Republic of China
| | - Shenhui Luo
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, People's Republic of China
| | - Weiqiang Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yanrong Qi
- Department of Gastroenterology and Hepatology, Tianjin Haibin People's Hospital, Tianjin, People's Republic of China
| | - Jianxin Gao
- Department of Gastroenterology and Hepatology, Tianjin Haibin People's Hospital, Tianjin, People's Republic of China
| | - Xiaocang Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, People's Republic of China
| | - Fang Yan
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, People's Republic of China.,Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, People's Republic of China
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225
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Staley C, Vaughn BP, Graiziger CT, Singroy S, Hamilton MJ, Yao D, Chen C, Khoruts A, Sadowsky MJ. Community dynamics drive punctuated engraftment of the fecal microbiome following transplantation using freeze-dried, encapsulated fecal microbiota. Gut Microbes 2017; 8:276-288. [PMID: 28282270 PMCID: PMC5479395 DOI: 10.1080/19490976.2017.1299310] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Fecal microbiota transplantation (FMT) is a highly effective treatment of recurrent and recalcitrant Clostridium difficile infection (rCDI). In a recent study oral-delivery of encapsulated, freeze-dried donor material, resulted in comparable rates of cure to colonoscopic approaches. Here we characterize shifts in the fecal bacterial community structure of patients treated for rCDI using encapsulated donor material. Prior to FMT, patient fecal samples showed declines in diversity and abundance of Firmicutes and Bacteroidetes, with concurrent increases in members of the Proteobacteria, specifically Enterobacteriaceae. Moreover, patients who experienced recurrence of CDI within the 2-month clinical follow-up had greater abundances of Enterobacteriaceae and did not show resolution of dysbioses. Despite resolution of rCDI following oral-administration of encapsulated fecal microbiota, community composition was slow to return to a normal donor-like assemblage. Post-FMT taxa within the Firmicutes showed rapid increases in relative abundance and did not vary significantly over time. Conversely, Bacteroidetes taxa only showed significant increases in abundance after one month post-FMT, corresponding to significant increases in the community attributable to the donors. Changes in the associations among dominant OTUs were observed at days, weeks, and months post-FMT, suggesting shifts in community dynamics may be related to the timing of increases in abundance of specific taxa. Administration of encapsulated, freeze-dried, fecal microbiota to rCDI patients resulted in restoration of bacterial diversity and resolution of dysbiosis. However, shifts in the fecal microbiome were incremental rather than immediate, and may be driven by changes in community dynamics reflecting changes in the host environment.
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Affiliation(s)
- Christopher Staley
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA,CONTACT Christopher Staley BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN 55108
| | - Byron P. Vaughn
- Division of Gastroenterology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Carolyn T. Graiziger
- Division of Gastroenterology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Stephanie Singroy
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | | | - Dan Yao
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, Minnesota, USA
| | - Chi Chen
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, Minnesota, USA
| | - Alexander Khoruts
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA,Division of Gastroenterology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael J. Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA,Department of Soil, Water and Climate, University of Minnesota, St. Paul, Minnesota, USA
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226
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Hryckowian AJ, Pruss KM, Sonnenburg JL. The emerging metabolic view of Clostridium difficile pathogenesis. Curr Opin Microbiol 2017; 35:42-47. [PMID: 27997854 PMCID: PMC5474191 DOI: 10.1016/j.mib.2016.11.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/23/2016] [Accepted: 11/30/2016] [Indexed: 12/20/2022]
Abstract
It is widely accepted that Clostridium difficile exploits dysbiosis and leverages inflammation to thrive in the gut environment, where it can asymptomatically colonize humans or cause a toxin-mediated disease ranging in severity from frequent watery diarrhea to pseudomembranous colitis or toxic megacolon. Here, we synthesize recent findings from the gut microbiota and enteric pathogenesis fields to inform the next steps toward a better understanding of C. difficile infection (CDI). In this review, we present a model in which the lifestyle of C. difficile is dictated by the metabolic state of the distal gut ecosystem. Contributions by C. difficile (specifically the production and action of the large glycosylating toxins TcdA and TcdB), the microbiota, and the host dictate whether the gut environment is supportive to the pathogen. Mechanistic, metabolic pathway-focused approaches encompassing the roles of all of these players are helping to elucidate the molecular ecology of the distal gut underlying a diseased or healthy ecosystem. A new generation of therapeutic strategies that are more targeted (and palatable) than fecal microbiota transplants or broad-spectrum antibiotics will be fueled by insight into the interspecies (host-microbe and microbe-microbe) interactions that differentiate healthy from pathogen-infested microbiotas.
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Affiliation(s)
- Andrew J Hryckowian
- Department of Microbiology and Immunology, Stanford University, CA, United States
| | - Kali M Pruss
- Department of Microbiology and Immunology, Stanford University, CA, United States
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, CA, United States.
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227
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Mizuno S, Nanki K, Matsuoka K, Saigusa K, Ono K, Arai M, Sugimoto S, Kiyohara H, Nakashima M, Takeshita K, Naganuma M, Suda W, Hattori M, Kanai T. Single fecal microbiota transplantation failed to change intestinal microbiota and had limited effectiveness against ulcerative colitis in Japanese patients. Intest Res 2017; 15:68-74. [PMID: 28239315 PMCID: PMC5323309 DOI: 10.5217/ir.2017.15.1.68] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/03/2016] [Accepted: 10/14/2016] [Indexed: 02/07/2023] Open
Abstract
Background/Aims Recent developments in analytical techniques including next-generation sequencing have clarified the correlation between intestinal microbiota and inflammatory bowel disease. Fecal microbiota transplantation (FMT) for patients with ulcerative colitis (UC) is proposed as a potential approach to resolving their dysbiosis; however, its safety and efficacy have not been confirmed. This single-arm, open-label, non-randomized study aimed to evaluate the safety and efficacy of FMT for Japanese patients with UC as the first registered clinical trial in Japan. Methods We enrolled 10 patients with active UC despite medical therapy. The donors were the patients' relatives and were carefully screened for infectious diseases. Fecal material was administered via colonoscopy, and the primary endpoint was the presence or absence of serious adverse events related to FMT. The secondary endpoint was a change in partial Mayo score at 12 weeks post-FMT. Scores ≤2 were considered a clinical response. Fecal samples were collected to follow changes in gut microbiota, while extracted complementary DNA were analyzed by a next-generation sequencer. We obtained written informed consent from all patients and donors. This study was approved by our Institutional Review Board and is registered in the University hospital Medical Information Network (UMIN) Clinical Trials Registry (UMIN 000012814). Results Five patients with moderate disease and five with severe disease were enrolled. No severe adverse effects were observed. One patient achieved clinical response; however, none of the patients' microbiota diversity recovered to the donor levels. Conclusions The use of single FMT for UC was safe; however, we failed to show its clinical efficacy and potential to change the intestinal microbiota.
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Affiliation(s)
- Shinta Mizuno
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kosaku Nanki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Katsuyoshi Matsuoka
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keiichiro Saigusa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keiko Ono
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Mari Arai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shinya Sugimoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Hiroki Kiyohara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Moeko Nakashima
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kozue Takeshita
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.; Department of Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Makoto Naganuma
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Wataru Suda
- Department of Immunology, Keio University School of Medicine, Tokyo, Japan.; Laboratory of Metagenomics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Masahira Hattori
- Laboratory of Metagenomics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.; Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
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228
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Newman KM, Rank KM, Vaughn BP, Khoruts A. Treatment of recurrent Clostridium difficile infection using fecal microbiota transplantation in patients with inflammatory bowel disease. Gut Microbes 2017; 8:303-309. [PMID: 28102756 PMCID: PMC5479399 DOI: 10.1080/19490976.2017.1279377] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We recently compared results of fecal microbiota transplantation (FMT) in patients with refractory, recurrent Clostridium difficile infection (rCDI), with and without underlying inflammatory bowel disease (IBD). Here we extend this cohort and analyze outcomes in greater detail by subtype of IBD. We find that FMT is generally effective in breaking the cycle of CDI recurrence, but its effects on overall IBD progression are much less predictable. We discuss several challenges intrinsic to this complex clinical situation and outline the next steps that can address these challenges going forward.
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Affiliation(s)
- Krista M. Newman
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kevin M. Rank
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Byron P. Vaughn
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Alexander Khoruts
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA,Center for Immunology and BioTechnology Institute, University of Minnesota, Twin Cities Campus, Minneapolis, Minnesota, USA,CONTACT Dr. Alexander Khoruts 2101 6th St. SE, Walling Biomedical Sciences Building; Room 3–184, Minneapolis, MN 55414
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229
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Sadowsky MJ, Staley C, Heiner C, Hall R, Kelly CR, Brandt L, Khoruts A. Analysis of gut microbiota - An ever changing landscape. Gut Microbes 2017; 8:268-275. [PMID: 28051919 PMCID: PMC5479405 DOI: 10.1080/19490976.2016.1277313] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In the last two decades, the field of metagenomics has greatly expanded due to improvement in sequencing technologies allowing for a more comprehensive characterization of microbial communities. The use of these technologies has led to an unprecedented understanding of human, animal, and environmental microbiomes and have shown that the gut microbiota are comparable to an organ that is intrinsically linked with a variety of diseases. Characterization of microbial communities using next-generation sequencing-by-synthesis approaches have revealed important shifts in microbiota associated with debilitating diseases such as Clostridium difficile infection. But due to limitations in sequence read length, primer biases, and the quality of databases, genus- and species-level classification have been difficult. Third-generation technologies, such as Pacific Biosciences' single molecule, real-time (SMRT) approach, allow for unbiased, more specific identification of species that are likely clinically relevant. Comparison of Illumina next-generation characterization and SMRT sequencing of samples from patients treated for C. difficile infection revealed similarities in community composition at the phylum and family levels, but SMRT sequencing further allowed for species-level characterization - permitting a better understanding of the microbial ecology of this disease. Thus, as sequencing technologies continue to advance, new species-level insights can be gained in the study of complex and clinically-relevant microbial communities.
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Affiliation(s)
- Michael J. Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA,Department of Soil, Water & Climate, University of Minnesota, St. Paul, Minnesota, USA,CONTACT Michael J. Sadowsky , BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN 55108
| | - Christopher Staley
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | | | | | - Colleen R. Kelly
- Department of Medicine, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA,Women's Medicine Collaborative, The Miriam Hospital, Providence, Rhode Island, USA
| | - Lawrence Brandt
- Department of Medicine, Division of Gastroenterology, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY; USA
| | - Alexander Khoruts
- Department of Medicine, Division of Gastroenterology, University of Minnesota, Minneapolis, Minnesota, USA,Center for Immunology, University of Minnesota, Minneapolis, Minnesota, USA
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230
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Staley C, Weingarden AR, Khoruts A, Sadowsky MJ. Interaction of gut microbiota with bile acid metabolism and its influence on disease states. Appl Microbiol Biotechnol 2017; 101:47-64. [PMID: 27888332 PMCID: PMC5203956 DOI: 10.1007/s00253-016-8006-6] [Citation(s) in RCA: 353] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 01/18/2023]
Abstract
Primary bile acids serve important roles in cholesterol metabolism, lipid digestion, host-microbe interactions, and regulatory pathways in the human host. While most bile acids are reabsorbed and recycled via enterohepatic cycling, ∼5% serve as substrates for bacterial biotransformation in the colon. Enzymes involved in various transformations have been characterized from cultured gut bacteria and reveal taxa-specific distribution. More recently, bioinformatic approaches have revealed greater diversity in isoforms of these enzymes, and the microbial species in which they are found. Thus, the functional roles played by the bile acid-transforming gut microbiota and the distribution of resulting secondary bile acids, in the bile acid pool, may be profoundly affected by microbial community structure and function. Bile acids and the composition of the bile acid pool have historically been hypothesized to be associated with several disease states, including recurrent Clostridium difficile infection, inflammatory bowel diseases, metabolic syndrome, and several cancers. Recently, however, emphasis has been placed on how microbial communities in the dysbiotic gut may alter the bile acid pool to potentially cause or mitigate disease onset. This review highlights the current understanding of the interactions between the gut microbial community, bile acid biotransformation, and disease states, and addresses future directions to better understand these complex associations.
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Affiliation(s)
- Christopher Staley
- BioTechnology Institute, Center for Immunology University of Minnesota, Minneapolis, MN
| | - Alexa R Weingarden
- BioTechnology Institute, Center for Immunology University of Minnesota, Minneapolis, MN
| | - Alexander Khoruts
- BioTechnology Institute, Center for Immunology University of Minnesota, Minneapolis, MN
- Division of Gastroenterology, Department of Medicine, Center for Immunology University of Minnesota, Minneapolis, MN
| | - Michael J Sadowsky
- BioTechnology Institute, Center for Immunology University of Minnesota, Minneapolis, MN
- Department of Soil, Water and Climate, University of Minnesota, St. Paul, MN
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231
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Mathematical Modeling of the Effects of Nutrient Competition and Bile Acid Metabolism by the Gut Microbiota on Colonization Resistance Against Clostridium difficile. ASSOCIATION FOR WOMEN IN MATHEMATICS SERIES 2017. [DOI: 10.1007/978-3-319-60304-9_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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232
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Sandhu KV, Sherwin E, Schellekens H, Stanton C, Dinan TG, Cryan JF. Feeding the microbiota-gut-brain axis: diet, microbiome, and neuropsychiatry. Transl Res 2017; 179:223-244. [PMID: 27832936 DOI: 10.1016/j.trsl.2016.10.002] [Citation(s) in RCA: 304] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 09/08/2016] [Accepted: 10/06/2016] [Indexed: 02/07/2023]
Abstract
The microbial population residing within the human gut represents one of the most densely populated microbial niche in the human body with growing evidence showing it playing a key role in the regulation of behavior and brain function. The bidirectional communication between the gut microbiota and the brain, the microbiota-gut-brain axis, occurs through various pathways including the vagus nerve, the immune system, neuroendocrine pathways, and bacteria-derived metabolites. This axis has been shown to influence neurotransmission and the behavior that are often associated with neuropsychiatric conditions. Therefore, research targeting the modulation of this gut microbiota as a novel therapy for the treatment of various neuropsychiatric conditions is gaining interest. Numerous factors have been highlighted to influence gut microbiota composition, including genetics, health status, mode of birth, and environment. However, it is diet composition and nutritional status that has repeatedly been shown to be one of the most critical modifiable factors regulating the gut microbiota at different time points across the lifespan and under various health conditions. Thus the microbiota is poised to play a key role in nutritional interventions for maintaining brain health.
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Affiliation(s)
- Kiran V Sandhu
- APC Microbiome institute, University College Cork, Cork, Ireland
| | - Eoin Sherwin
- APC Microbiome institute, University College Cork, Cork, Ireland
| | - Harriët Schellekens
- APC Microbiome institute, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome institute, University College Cork, Cork, Ireland; Department of Psychiatry & Neurobehavioural Science, University College Cork, Cork, Ireland; Teagasc Moorepark Food Research Centre, Fermoy, Co, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome institute, University College Cork, Cork, Ireland; Department of Psychiatry & Neurobehavioural Science, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome institute, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
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233
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Complete Microbiota Engraftment Is Not Essential for Recovery from Recurrent Clostridium difficile Infection following Fecal Microbiota Transplantation. mBio 2016; 7:mBio.01965-16. [PMID: 27999162 PMCID: PMC5181777 DOI: 10.1128/mbio.01965-16] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Bacterial communities from subjects treated for recurrent Clostridium difficile infection (rCDI) by fecal microbiota transplantation (FMT), using either heterologous donor stool samples or autologous stool samples, were characterized by Illumina next-generation sequencing. As previously reported, the success of heterologous FMT (90%) was superior to that of autologous FMT (43%) (P = 0.019), and post-FMT intestinal bacterial communities differed significantly between treatment arms (P < 0.001). Subjects cured by autologous FMT typically had greater abundances of the Clostridium XIVa clade and Holdemania bacteria prior to treatment, and the relative abundances of these groups increased significantly after FMT compared to heterologous FMT and pre-FMT samples. The typical shift to post-FMT, donor-like assemblages, featuring high relative abundances of genera within the Bacteroidetes and Firmicutes phyla, was not observed in the autologous FMT subjects. Autologous FMT patient bacterial communities were significantly different in composition than those for heterologous FMT patients and donors (P < 0.001). The SourceTracker program, which employs a Bayesian algorithm to determine source contributions to sink communities, showed that patients initially treated by heterologous FMT had significantly higher percentages of engraftment (i.e., similarity to donor communities, mean value of 74%) compared to those who suffered recurrence following autologous FMT (1%) (P ≤ 0.013). The findings of this study suggest that complete donor engraftment may be not necessary if functionally critical taxa are present in subjects following antibiotic therapy. This study provides a detailed characterization of fecal bacterial communities in subjects who participated in a previously published randomized clinical trial to treat recurrent C. difficile infection (rCDI). Bacterial communities were characterized to determine differences between subjects who received fecal bacteria either from healthy donor stool samples or their own stool samples as “placebo” in order to determine which groups of bacteria were most important in achieving a cure. The results of this study suggested that bacteria associated with secondary bile acid metabolism could potentially provide resistance to infection and that complete transfer of healthy donor microorganisms was not necessary to resolve CDI following unsuccessful antibiotic treatment.
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234
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Studer N, Desharnais L, Beutler M, Brugiroux S, Terrazos MA, Menin L, Schürch CM, McCoy KD, Kuehne SA, Minton NP, Stecher B, Bernier-Latmani R, Hapfelmeier S. Functional Intestinal Bile Acid 7α-Dehydroxylation by Clostridium scindens Associated with Protection from Clostridium difficile Infection in a Gnotobiotic Mouse Model. Front Cell Infect Microbiol 2016; 6:191. [PMID: 28066726 PMCID: PMC5168579 DOI: 10.3389/fcimb.2016.00191] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/05/2016] [Indexed: 12/26/2022] Open
Abstract
Bile acids, important mediators of lipid absorption, also act as hormone-like regulators and as antimicrobial molecules. In all these functions their potency is modulated by a variety of chemical modifications catalyzed by bacteria of the healthy gut microbiota, generating a complex variety of secondary bile acids. Intestinal commensal organisms are well-adapted to normal concentrations of bile acids in the gut. In contrast, physiological concentrations of the various intestinal bile acid species play an important role in the resistance to intestinal colonization by pathogens such as Clostridium difficile. Antibiotic therapy can perturb the gut microbiota and thereby impair the production of protective secondary bile acids. The most important bile acid transformation is 7α-dehydroxylation, producing deoxycholic acid (DCA) and lithocholic acid (LCA). The enzymatic pathway carrying out 7α-dehydroxylation is restricted to a narrow phylogenetic group of commensal bacteria, the best-characterized of which is Clostridium scindens. Like many other intestinal commensal species, 7-dehydroxylating bacteria are understudied in vivo. Conventional animals contain variable and uncharacterized indigenous 7α-dehydroxylating organisms that cannot be selectively removed, making controlled colonization with a specific strain in the context of an undisturbed microbiota unfeasible. In the present study, we used a recently established, standardized gnotobiotic mouse model that is stably associated with a simplified murine 12-species “oligo-mouse microbiota” (Oligo-MM12). It is representative of the major murine intestinal bacterial phyla, but is deficient for 7α-dehydroxylation. We find that the Oligo-MM12 consortium carries out bile acid deconjugation, a prerequisite for 7α-dehydroxylation, and confers no resistance to C. difficile infection (CDI). Amendment of Oligo-MM12 with C. scindens normalized the large intestinal bile acid composition by reconstituting 7α-dehydroxylation. These changes had only minor effects on the composition of the native Oligo-MM12, but significantly decreased early large intestinal C. difficile colonization and pathogenesis. The delayed pathogenesis of C. difficile in C. scindens-colonized mice was associated with breakdown of cecal microbial bile acid transformation.
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Affiliation(s)
- Nicolas Studer
- Institute for Infectious Diseases, University of BernBern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of BernBern, Switzerland
| | - Lyne Desharnais
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne, Switzerland
| | - Markus Beutler
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich (LMU) Munich, Germany
| | - Sandrine Brugiroux
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich (LMU) Munich, Germany
| | - Miguel A Terrazos
- Institute for Infectious Diseases, University of Bern Bern, Switzerland
| | - Laure Menin
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne, Switzerland
| | | | - Kathy D McCoy
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern Bern, Switzerland
| | - Sarah A Kuehne
- Clostridia Research Group, Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC) Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham Nottingham, UK
| | - Nigel P Minton
- Clostridia Research Group, Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC) Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham Nottingham, UK
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich (LMU)Munich, Germany; German Center for Infection Research, Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Ludwig-Maximilians-University of Munich (LMU)Munich, Germany
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne, Switzerland
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235
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Abstract
Gut homeostasis plays an important role in maintaining animal and human health. The disruption of gut homeostasis has been shown to be associated with multiple diseases. The mutually beneficial relationship between the gut microbiota and the host has been demonstrated to maintain homeostasis of the mucosal immunity and preserve the integrity of the gut epithelial barrier. Currently, rapid progress in the understanding of the host-microbial interaction has redefined toxicological pathology of opioids and their pharmacokinetics. However, it is unclear how opioids modulate the gut microbiome and metabolome. Our study, showing opioid modulation of gut homeostasis in mice, suggests that medical interventions to ameliorate the consequences of drug use/abuse will provide potential therapeutic and diagnostic strategies for opioid-modulated intestinal infections. The study of morphine's modulation of the gut microbiome and metabolome will shed light on the toxicological pathology of opioids and its role in the susceptibility to infectious diseases.
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Affiliation(s)
- Fuyuan Wang
- 1 Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Sabita Roy
- 1 Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA.,2 Department of Surgery, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
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236
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Mattner J. Impact of Microbes on the Pathogenesis of Primary Biliary Cirrhosis (PBC) and Primary Sclerosing Cholangitis (PSC). Int J Mol Sci 2016; 17:ijms17111864. [PMID: 27834858 PMCID: PMC5133864 DOI: 10.3390/ijms17111864] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 02/07/2023] Open
Abstract
Primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC) represent the major clinical entities of chronic cholestatic liver diseases. Both disorders are characterized by portal inflammation and slowly progress to obliterative fibrosis and eventually liver cirrhosis. Although immune-pathogenic mechanisms have been implicated in the pathogenesis of PBC and PSC, neither disorder is considered to be a classical autoimmune disease, as PSC and PBC patients do not respond to immune-suppressants. Furthermore, the decreased bile flow resulting from the immune-mediated tissue assault and the subsequent accumulation of toxic bile products in PBC and PSC not only perpetuates biliary epithelial damage, but also alters the composition of the intestinal and biliary microbiota and its mutual interactions with the host. Consistent with the close association of PSC and inflammatory bowel disease (IBD), the polyclonal hyper IgM response in PBC and (auto-)antibodies which cross-react to microbial antigens in both diseases, an expansion of individual microbes leads to shifts in the composition of the intestinal or biliary microbiota and a subsequent altered integrity of epithelial layers, promoting microbial translocation. These changes have been implicated in the pathogenesis of both devastating disorders. Thus, we will discuss here these recent findings in the context of novel and alternative therapeutic options.
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MESH Headings
- Anti-Bacterial Agents/therapeutic use
- Antibodies, Bacterial/biosynthesis
- Bacterial Translocation
- Bile/drug effects
- Bile/microbiology
- Cholangiopancreatography, Endoscopic Retrograde
- Cholangitis, Sclerosing/diagnostic imaging
- Cholangitis, Sclerosing/drug therapy
- Cholangitis, Sclerosing/immunology
- Cholangitis, Sclerosing/microbiology
- Gastrointestinal Microbiome/drug effects
- Host-Pathogen Interactions
- Humans
- Immunoglobulin M/biosynthesis
- Liver Cirrhosis, Biliary/diagnostic imaging
- Liver Cirrhosis, Biliary/drug therapy
- Liver Cirrhosis, Biliary/immunology
- Liver Cirrhosis, Biliary/microbiology
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Affiliation(s)
- Jochen Mattner
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Wasserturmstr. 3/5, D-91054 Erlangen, Germany.
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237
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Rolhion N, Chassaing B. When pathogenic bacteria meet the intestinal microbiota. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150504. [PMID: 27672153 PMCID: PMC5052746 DOI: 10.1098/rstb.2015.0504] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2016] [Indexed: 12/25/2022] Open
Abstract
The intestinal microbiota is a large and diverse microbial community that inhabits the intestinal tract, containing about 100 trillion bacteria from 500-1000 distinct species that, collectively, provide multiple benefits to the host. The gut microbiota contributes to nutrient absorption and maturation of the immune system, and also plays a central role in protection of the host from enteric bacterial infection. On the other hand, many enteric pathogens have developed strategies in order to be able to outcompete the intestinal community, leading to infection and/or chronic diseases. This review will summarize findings describing the complex relationship occurring between the intestinal microbiota and enteric pathogens, as well as how future therapies can ultimately benefit from such discoveries.This article is part of the themed issue 'The new bacteriology'.
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Affiliation(s)
- Nathalie Rolhion
- Institut Pasteur, Unité des interactions Bactéries-Cellules, 75015 Paris, France Inserm, U604, 75015 Paris, France INRA, Unité sous contrat 2020, 75015 Paris, France
| | - Benoit Chassaing
- Institute for Biomedical Sciences, Center for Inflammation, Immunity, and Infection, Georgia State University, Atlanta, GA 30303, USA
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238
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Banerjee S, Sindberg G, Wang F, Meng J, Sharma U, Zhang L, Dauer P, Chen C, Dalluge J, Johnson T, Roy S. Opioid-induced gut microbial disruption and bile dysregulation leads to gut barrier compromise and sustained systemic inflammation. Mucosal Immunol 2016; 9:1418-1428. [PMID: 26906406 PMCID: PMC4996771 DOI: 10.1038/mi.2016.9] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/30/2015] [Indexed: 02/04/2023]
Abstract
Morphine and its pharmacological derivatives are the most prescribed analgesics for moderate to severe pain management. However, chronic use of morphine reduces pathogen clearance and induces bacterial translocation across the gut barrier. The enteric microbiome has been shown to have a critical role in the preservation of the mucosal barrier function and metabolic homeostasis. Here, we show for the first time, using bacterial 16s rDNA sequencing, that chronic morphine treatment significantly alters the gut microbial composition and induces preferential expansion of Gram-positive pathogenic and reduction in bile-deconjugating bacterial strains. A significant reduction in both primary and secondary bile acid levels was seen in the gut, but not in the liver with morphine treatment. Morphine-induced microbial dysbiosis and gut barrier disruption was rescued by transplanting placebo-treated microbiota into morphine-treated animals, indicating that microbiome modulation could be exploited as a therapeutic strategy for patients using morphine for pain management.
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Affiliation(s)
- Santanu Banerjee
- Department of Surgery, 515 Delaware St SE, Moos 11-204, University
of Minnesota, MN 55455, USA
| | - Gregory Sindberg
- Department of Veterinary Medicine, 515 Delaware St SE, Moos 11-204,
University of Minnesota, MN 55455, USA
| | - Fuyuan Wang
- Department of Veterinary Medicine, 515 Delaware St SE, Moos 11-204,
University of Minnesota, MN 55455, USA
| | - Jingjing Meng
- Department of Surgery, 515 Delaware St SE, Moos 11-204, University
of Minnesota, MN 55455, USA
| | - Umakant Sharma
- Department of Surgery, 515 Delaware St SE, Moos 11-204, University
of Minnesota, MN 55455, USA
| | - Li Zhang
- Department of Pharmacology, 515 Delaware St SE, Moos 11-204,
University of Minnesota, MN 55455, USA
| | - Patricia Dauer
- Department of Pharmacology, 515 Delaware St SE, Moos 11-204,
University of Minnesota, MN 55455, USA
| | - Chi Chen
- Department of Food Science and Nutrition, 515 Delaware St SE, Moos
11-204, University of Minnesota, MN 55455, USA
| | - Joseph Dalluge
- Department of Chemistry, 515 Delaware St SE, Moos 11-204, University
of Minnesota, MN 55455, USA
| | - Timothy Johnson
- Department of Veterinary Medicine, 515 Delaware St SE, Moos 11-204,
University of Minnesota, MN 55455, USA
| | - Sabita Roy
- Department of Surgery, 515 Delaware St SE, Moos 11-204, University
of Minnesota, MN 55455, USA,Department of Pharmacology, 515 Delaware St SE, Moos 11-204,
University of Minnesota, MN 55455, USA,To whom correspondence should be addressed. Prof. Sabita
Roy, Director, Division of Infection, Inflammation and Vascular Biology,
Department of Surgery and Pharmacology Telephone Number: 612-624-4615, Fax
Number 612 626-4900,
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239
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Ianiro G, Tilg H, Gasbarrini A. Antibiotics as deep modulators of gut microbiota: between good and evil. Gut 2016; 65:1906-1915. [PMID: 27531828 DOI: 10.1136/gutjnl-2016-312297] [Citation(s) in RCA: 398] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 12/11/2022]
Abstract
The recent increase in our knowledge of human gut microbiota has changed our view on antibiotics. Antibiotics are, indeed, no longer considered only beneficial, but also potentially harmful drugs, as their abuse appears to play a role in the pathogenesis of several disorders associated with microbiota impairment (eg, Clostridium difficile infection or metabolic disorders). Both drug-related factors (such as antibiotic class, timing of exposure or route of administration) and host-related factors appear to influence the alterations of human gut microbiota produced by antibiotics. Nevertheless, antibiotics are nowadays considered a reliable therapy for some non-communicable disorders, including IBS or hepatic encephalopathy. Moreover, some antibiotics can also act positively on gut microbiota, providing a so-called 'eubiotic' effect, by increasing abundance of beneficial bacteria. Therefore, antibiotics appear to change, for better or worse, the nature of several disorders, including IBS, IBD, metabolic disorders or liver disease. This reviews aims to address the potential of antibiotics in the development of major non-communicable disorders associated with the alteration of gut microbiota and on newly discovered therapeutic avenues of antibiotics beyond the cure of infectious diseases.
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Affiliation(s)
- Gianluca Ianiro
- Internal Medicine, Gastroenterology and Liver Unit, "Agostino Gemelli" University Hospital, Catholic University of Rome, Italy
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Endocrinology & Metabolism, Medical University Innsbruck, Innsbruck, Austria
| | - Antonio Gasbarrini
- Internal Medicine, Gastroenterology and Liver Unit, "Agostino Gemelli" University Hospital, Catholic University of Rome, Italy
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240
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Carlucci C, Petrof EO, Allen-Vercoe E. Fecal Microbiota-based Therapeutics for Recurrent Clostridium difficile Infection, Ulcerative Colitis and Obesity. EBioMedicine 2016; 13:37-45. [PMID: 27720396 PMCID: PMC5264253 DOI: 10.1016/j.ebiom.2016.09.029] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/21/2016] [Accepted: 09/29/2016] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiome is a complex ecosystem of fundamental importance to human health. Our increased understanding of gut microbial composition and functional interactions in health and disease states has spurred research efforts examining the gut microbiome as a valuable target for therapeutic intervention. This review provides updated insight into the state of the gut microbiome in recurrent Clostridium difficile infection (CDI), ulcerative colitis (UC), and obesity while addressing the rationale for the modulation of the gut microbiome using fecal microbiota transplant (FMT)-based therapies. Current microbiome-based therapeutics in pre-clinical or clinical development are discussed. We end by putting this within the context of the current regulatory framework surrounding FMT and related therapies. There is an increased understanding of gut microbial composition and functional interactions in health and disease states. FMT is effective for rCDI and has led to the development of fecal microbiota-based therapeutics for other indications. For stool-substitute therapies to enter mainstream medicine, further mechanistic studies, RCTs and regulations are needed.
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Affiliation(s)
- Christian Carlucci
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
| | - Elaine O Petrof
- Division of Infectious Diseases/GI Diseases Research Unit Wing, Department of Medicine, Kingston General Hospital, Queen's University, 76 Stuart Street, Kingston, Ontario K7L 2V7, Canada.
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
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241
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Khoruts A, Rank KM, Newman KM, Viskocil K, Vaughn BP, Hamilton MJ, Sadowsky MJ. Inflammatory Bowel Disease Affects the Outcome of Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection. Clin Gastroenterol Hepatol 2016; 14:1433-8. [PMID: 26905904 PMCID: PMC5552196 DOI: 10.1016/j.cgh.2016.02.018] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/18/2016] [Accepted: 02/03/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS A significant fraction of patients with recurrent Clostridium difficile infections (CDI) have inflammatory bowel disease (IBD). Fecal microbiota transplantation (FMT) can break the cycle of CDI recurrence and can be performed without evaluation of the colon. We evaluated the efficacy of colonoscopic FMT in patients with and without IBD, and whether we could identify IBD in patients during this procedure. METHODS We collected clinical meta-data and colonoscopy results from 272 consecutive patients that underwent FMT for recurrent CDI at the University of Minnesota from 2008 through 2015. Patients had at least 2 spontaneous relapses of CDI following their initial episode and did not clear the infection after 1 extended antibiotic regimen. We collected random mucosal biopsies from patients' right colons to identify lymphocytic or collagenous colitis during the FMT procedure. Failure or success in clearing CDI was determined within or at 2 months after the FMT. RESULTS Of patients undergoing FMT, 15% had established IBD and 2.6% were found to have IBD during the FMT procedure. A single colonoscopic FMT cleared CDI from 74.4% of patients with IBD and 92.1% of patients without IBD (P = .0018). Patients had similar responses to FMT regardless of immunosuppressive therapy. More than one-quarter of patients with IBD (25.6%) had a clinically significant flare of IBD after FMT. Lymphocytic colitis was documented in 7.4% of patients with endoscopically normal colon mucosa; only 3 of these patients (20%) required additional treatment for colitis after clearance of CDI. CONCLUSIONS Based on an analysis of 272 patients, FMT is somewhat less effective in clearing recurrent CDI from patients with IBD, compared with patients without IBD, regardless of immunosuppressive therapy. More than 25% of patients with IBD have a disease flare following FMT. Lymphocytic colitis did not affect the outcome of FMT, but a small fraction of these patients required pharmacologic treatment after the procedure.
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Affiliation(s)
- Alexander Khoruts
- Division of Gastroenterology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota; BioTechnology Institute, University of Minnesota, Minneapolis, Minnesota.
| | - Kevin M. Rank
- Division of Gastroenterology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Krista M. Newman
- Division of Gastroenterology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Kimberly Viskocil
- Division of Gastroenterology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Byron P. Vaughn
- Division of Gastroenterology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
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242
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Fecal microbiota transplant in patients with Clostridium difficile infection. J Trauma Acute Care Surg 2016; 81:756-64. [DOI: 10.1097/ta.0000000000001195] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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243
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Wang L, Urriola PE, Luo ZH, Rambo ZJ, Wilson ME, Torrison JL, Shurson GC, Chen C. Metabolomics revealed diurnal heat stress and zinc supplementation-induced changes in amino acid, lipid, and microbial metabolism. Physiol Rep 2016; 4:4/1/e12676. [PMID: 26755737 PMCID: PMC4760408 DOI: 10.14814/phy2.12676] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Heat stress (HS) dramatically disrupts the events in energy and nutrient metabolism, many of which requires zinc (Zn) as a cofactor. In this study, metabolic effects of HS and Zn supplementation were evaluated by examining growth performance, blood chemistry, and metabolomes of crossbred gilts fed with ZnNeg (no Zn supplementation), ZnIO (120 ppm ZnSO4), or ZnAA (60 ppm ZnSO4 + 60 ppm zinc amino acid complex) diets under diurnal HS or thermal‐neutral (TN) condition. The results showed that growth performance was reduced by HS but not by Zn supplementation. Among measured serum biochemicals, HS was found to increase creatinine but decrease blood urea nitrogen (BUN) level. Metabolomic analysis indicated that HS greatly affected diverse metabolites associated with amino acid, lipid, and microbial metabolism, including urea cycle metabolites, essential amino acids, phospholipids, medium‐chain dicarboxylic acids, fatty acid amides, and secondary bile acids. More importantly, many changes in these metabolite markers were correlated with both acute and adaptive responses to HS. Relative to HS‐induced metabolic effects, Zn supplementation‐associated effects were much more limited. A prominent observation was that ZnIO diet, potentially through its influences on microbial metabolism, yielded different responses to HS compared with two other diets, which included higher levels of short‐chain fatty acids (SCFAs) in cecal fluid and higher levels of lysine in the liver and feces. Overall, comprehensive metabolomic analysis identified novel metabolite markers associated with HS and Zn supplementation, which could guide further investigation on the mechanisms of these metabolic effects.
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Affiliation(s)
- Lei Wang
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, Minnesota
| | - Pedro E Urriola
- Department of Animal Science, University of Minnesota, Saint Paul, Minnesota
| | - Zhao-Hui Luo
- Department of Animal Science, University of Minnesota, Saint Paul, Minnesota
| | | | | | | | - Gerald C Shurson
- Department of Animal Science, University of Minnesota, Saint Paul, Minnesota
| | - Chi Chen
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, Minnesota
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244
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Abstract
This Review summarizes mechanistic investigations in faecal microbiota transplantation (FMT), which has increasingly been adapted into clinical practice as treatment for Clostridium difficile infection (CDI) that cannot be eliminated with antibiotics alone. Administration of healthy donor faecal microbiota in this clinical situation results in its engraftment and restoration of normal gut microbial community structure and functionality. In this Review, we consider several main mechanisms for FMT effectiveness in treatment of CDI, including direct competition of C. difficile with commensal microbiota delivered by FMT, restoration of secondary bile acid metabolism in the colon and repair of the gut barrier by stimulation of the mucosal immune system. Some of these mechanistic insights suggest possibilities for developing novel, next-generation CDI therapeutics. FMT might also have potential applications for non-CDI indications. The gut can become a reservoir of other potential antibiotic-resistant pathogens under pressure of antibiotic treatments, and restoration of normal microbial community structure by FMT might be a promising approach to protect against infections with these pathogens as well. Finally, FMT could be considered for multiple chronic diseases that are associated with some form of dysbiosis. However, considerable research is needed to optimize the FMT protocols for such applications before their therapeutic promise can be evaluated.
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Affiliation(s)
- Alexander Khoruts
- Department of Medicine, Division of Gastroenterology, Center for Immunology and BioTechnology Institute, Medical Biosciences Building, 2101 6th Street South East, University of Minnesota, Minneapolis, Minnesota 55414, USA
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate, BioTechnology Institute, and Microbial and Plant Genomics Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Avenue, St. Paul, Minnesota 55108, USA
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245
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Ursodeoxycholic Acid Inhibits Clostridium difficile Spore Germination and Vegetative Growth, and Prevents the Recurrence of Ileal Pouchitis Associated With the Infection. J Clin Gastroenterol 2016; 50:624-30. [PMID: 26485102 PMCID: PMC4834285 DOI: 10.1097/mcg.0000000000000427] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
GOALS To test whether ursodeoxycholic acid (UDCA) is inhibitory to Clostridium difficile and can be used in the treatment of C. difficile-associated ileal pouchitis. BACKGROUND The restoration of secondary bile metabolism may be the key mechanism for fecal microbiota transplantation (FMT) in treating recurrent C. difficile infections (RCDI). Therefore, it is possible that exogenous administration of inhibitory bile acids may be used directly as nonantibiotic therapeutics for this indication. The need for such a treatment alternative is especially significant in patients with refractory C. difficile-associated pouchitis, where the efficacy of FMT may be limited. STUDY We measured the ability of UDCA to suppress the germination and the vegetative growth of 11 clinical isolate strains of C. difficile from patients treated with FMT for RCDI. In addition, we used oral UDCA to treat a patient with RCDI pouchitis that proved refractory to multiple antibiotic treatments and FMT. RESULTS UDCA was found to be inhibitory to the germination and the vegetative growth of all C. difficile strains tested. Fecal concentrations of UDCA from the patient with RCDI pouchitis exceeded levels necessary to inhibit the germination and the growth of C. difficile in vitro. The patient has remained infection free for over 10 months after the initiation of UDCA. CONCLUSIONS UDCA can be considered as a therapeutic option in patients with C. difficile-associated pouchitis. Further studies need to be conducted to define the optimal dose and duration of such a treatment. In addition, bile acid derivatives inhibitory to C. difficile that are able to achieve high intracolonic concentrations may be developed as therapeutics for RCDI colitis.
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246
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Abt MC, McKenney PT, Pamer EG. Clostridium difficile colitis: pathogenesis and host defence. Nat Rev Microbiol 2016; 14:609-20. [PMID: 27573580 DOI: 10.1038/nrmicro.2016.108] [Citation(s) in RCA: 336] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Clostridium difficile is a major cause of intestinal infection and diarrhoea in individuals following antibiotic treatment. Recent studies have begun to elucidate the mechanisms that induce spore formation and germination and have determined the roles of C. difficile toxins in disease pathogenesis. Exciting progress has also been made in defining the role of the microbiome, specific commensal bacterial species and host immunity in defence against infection with C. difficile. This Review will summarize the recent discoveries and developments in our understanding of C. difficile infection and pathogenesis.
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Affiliation(s)
- Michael C Abt
- Immunology Program, Lucille Castori Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Peter T McKenney
- Immunology Program, Lucille Castori Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Eric G Pamer
- Immunology Program, Lucille Castori Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
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247
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Meehan AM, Tariq R, Khanna S. Challenges in management of recurrent and refractory Clostridium difficile infection. World J Clin Infect Dis 2016; 6:28-36. [DOI: 10.5495/wjcid.v6.i3.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 04/28/2016] [Accepted: 06/02/2016] [Indexed: 02/06/2023] Open
Abstract
Clostridium difficile infection (CDI) is the most common nosocomial infection in the United States and is associated with a high mortality. One quarter of patients treated for CDI have at least one recurrence. Spore persistence, impaired host immune response and alteration in the gastrointestinal microbiome due to antibiotic use are factors in recurrent disease. We review the etiology of recurrent CDI and best approaches to management including fecal microbiota transplantation.
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248
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Li M, Li Z, Wen S, Liu Y, Wang Y, Tang L. Transplantation of a bacterial consortium ameliorates trinitrobenzenesulfonic acid-induced colitis and intestinal dysbiosis in rats. Future Microbiol 2016; 11:887-902. [PMID: 27415182 DOI: 10.2217/fmb-2015-0002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AIM To investigate the effects of a defined bacterial consortium on trinitrobenzenesulfonic acid (TNBS)-induced colitis and intestinal dysbiosis in rats. MATERIALS & METHODS Rats with TNBS-induced colitis were treated with ceftriaxone and/or a mixture of ten bacterial strains isolated from mouse feces for continuous 24 days. Macroscopic and histopathological parameters in colonic tissue were compared, as were myeloperoxidase enzyme activity and cytokine levels. Patterns of intestinal microbiota were assessed by PCR-denaturing gradient gel electrophoresis, the abundance of selected microbial groups was evaluated by qPCR. RESULTS & CONCLUSION Transplantation of the bacterial consortium showed anti-inflammatory activity in the intestines of rats with TNBS-induced colitis and contributed to the rapid re-establishment of intestinal microbial equilibrium. A defined bacterial consortium may be a viable therapeutic option for the treatment inflammatory bowel disease.
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Affiliation(s)
- Ming Li
- Department of Microecology, School of Basic Medical Science, Dalian Medical University, China
| | - Zhenzhen Li
- Department of Microecology, School of Basic Medical Science, Dalian Medical University, China
| | - Shu Wen
- Department of Microecology, School of Basic Medical Science, Dalian Medical University, China
| | - Yinhui Liu
- Department of Microecology, School of Basic Medical Science, Dalian Medical University, China
| | - Ying Wang
- Department of Microecology, School of Basic Medical Science, Dalian Medical University, China
| | - Li Tang
- Department of Microecology, School of Basic Medical Science, Dalian Medical University, China
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249
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Han S, Shannahan S, Pellish R. Fecal Microbiota Transplant. J Intensive Care Med 2016; 31:577-86. [DOI: 10.1177/0885066615594344] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 05/14/2015] [Indexed: 12/16/2022]
Abstract
Clostridium difficile infection (CDI) has steadily increased in incidence since the 1990s, with an associated increase in recurrence and severity, which has in turn lead to more intensive care unit (ICU) admissions. The development of recurrent CDI, in particular, has been associated with increasing patient morbidity and mortality as well as an immense financial burden on the health care system. Recently, fecal microbiota transplantation (FMT) has received much publicity as an effective means of treatment for recurrent CDI. The goal of this review is to provide evidence-based recommendations for the diagnosis and management of CDI, with a particular focus on FMT and its utilization in the ICU.
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Affiliation(s)
- Samuel Han
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Sarah Shannahan
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Randall Pellish
- University of Massachusetts Medical School, Worcester, MA, USA
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250
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Bäumler AJ, Sperandio V. Interactions between the microbiota and pathogenic bacteria in the gut. Nature 2016; 535:85-93. [PMID: 27383983 PMCID: PMC5114849 DOI: 10.1038/nature18849] [Citation(s) in RCA: 832] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 04/22/2016] [Indexed: 02/07/2023]
Abstract
The microbiome has an important role in human health. Changes in the microbiota can confer resistance to or promote infection by pathogenic bacteria. Antibiotics have a profound impact on the microbiota that alters the nutritional landscape of the gut and can lead to the expansion of pathogenic populations. Pathogenic bacteria exploit microbiota-derived sources of carbon and nitrogen as nutrients and regulatory signals to promote their own growth and virulence. By eliciting inflammation, these bacteria alter the intestinal environment and use unique systems for respiration and metal acquisition to drive their expansion. Unravelling the interactions between the microbiota, the host and pathogenic bacteria will produce strategies for manipulating the microbiota against infectious diseases.
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Affiliation(s)
- Andreas J Bäumler
- Department of Medical Microbiology and Immunology, University of California, Davis, School of Medicine, Davis, California 95616, USA
| | - Vanessa Sperandio
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9048, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038, USA
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