1
|
Yin C, Zhong R, Zhang W, Liu L, Chen L, Zhang H. The Potential of Bile Acids as Biomarkers for Metabolic Disorders. Int J Mol Sci 2023; 24:12123. [PMID: 37569498 PMCID: PMC10418921 DOI: 10.3390/ijms241512123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/15/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
Bile acids (BAs) are well known to facilitate the absorption of dietary fat and fat-soluble molecules. These unique steroids also function by binding to the ubiquitous cell membranes and nuclear receptors. As chemical signals in gut-liver axis, the presence of metabolic disorders such as nonalcoholic fatty liver disease (NAFLD), type 2 diabetes mellitus (T2DM), and even tumors have been reported to be closely related to abnormal levels of BAs in the blood and fecal metabolites of patients. Thus, the gut microbiota interacting with BAs and altering BA metabolism are critical in the pathogenesis of numerous chronic diseases. This review intends to summarize the mechanistic links between metabolic disorders and BAs in gut-liver axis, and such stage-specific BA perturbation patterns may provide clues for developing new auxiliary diagnostic means.
Collapse
Affiliation(s)
| | | | | | | | - Liang Chen
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.Y.); (R.Z.)
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.Y.); (R.Z.)
| |
Collapse
|
2
|
Wang R. Clostridioides difficile infection: microbe-microbe interactions and live biotherapeutics. Front Microbiol 2023; 14:1182612. [PMID: 37228365 PMCID: PMC10203151 DOI: 10.3389/fmicb.2023.1182612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/03/2023] [Indexed: 05/27/2023] Open
Abstract
Clostridioides difficile is a gram-positive, spore-forming, obligate anaerobe that infects the colon. C. difficile is estimated to cause nearly half a million cases in the United States annually, with about 29,000 associated deaths. Unfortunately, the current antibiotic treatment is not ideal. While antibiotics can treat the infections, they also disrupt the gut microbiota that mediates colonization resistance against enteric pathogens, including C. difficile; disrupted gut microbiota provides a window of opportunity for recurrent infections. Therefore, therapeutics that restore the gut microbiota and suppress C. difficile are being evaluated for safety and efficacy. This review will start with mechanisms by which gut bacteria affect C. difficile pathogenesis, followed by a discussion on biotherapeutics for recurrent C. difficile infections.
Collapse
|
3
|
Saito Y, Sagae T. Defecation status, intestinal microbiota, and habitual diet are associated with the fecal bile acid composition: a cross-sectional study in community-dwelling young participants. Eur J Nutr 2023:10.1007/s00394-023-03126-8. [PMID: 36881180 DOI: 10.1007/s00394-023-03126-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023]
Abstract
PURPOSE Bile acid (BA) metabolism by intestinal bacteria is associated with the risk of gastrointestinal diseases; additionally, its control has become a modern strategy for treating metabolic diseases. This cross-sectional study investigated the influence of defecation status, intestinal microbiota, and habitual diet on fecal BA composition in 67 community-dwelling young participants. METHODS Feces were collected for intestinal microbiota and BA analyses; data about defecation status and dietary habits were collected using the Bristol stool form scales and a brief-type self-administered diet history questionnaire, respectively. The participants were categorized into four clusters based on their fecal BA composition, according to cluster analysis, and tertiles based on deoxycholic acid (DCA) and lithocholic acid (LCA) levels. RESULTS The high primary BA (priBA) cluster with high fecal cholic acid (CA) and chenodeoxycholic acid (CDCA) levels had the highest frequency of normal feces, whereas the second BA (secBA) cluster with high levels of fecal DCA and LCA had the lowest. Alternately, the high-priBA cluster had a distinct intestinal microbiota, with higher Clostridium subcluster XIVa and lower Clostridium cluster IV and Bacteroides. The low-secBA cluster with low fecal DCA and LCA levels had the lowest animal fat intake. Nevertheless, the insoluble fiber intake of the high-priBA cluster was significantly higher than that of the high-secBA cluster. CONCLUSION High fecal CA and CDCA levels were associated with distinct intestinal microbiota. Conversely, high levels of cytotoxic DCA and LCA were associated with increased animal fat intake and decreased frequency of normal feces and insoluble fiber intake. CLINICAL TRIAL REGISTRY University Hospital Medical Information Network (UMIN) Center system (UMIN000045639); date of registration: 15/11/2019.
Collapse
Affiliation(s)
- Yosuke Saito
- Department of Clinical Nutrition, Faculty of Health and Wellness Sciences, Hiroshima International University, 5-1-1, Hirokoshingai, Kure, Hiroshima, 737-0112, Japan.
- Department of Human Life Sciences, Sakura no Seibo Junior College, Fukushima, Japan.
| | - Toyoaki Sagae
- Department of Health and Nutrition, Yamagata Prefectural Yonezawa University of Nutrition Sciences, Yamagata, Japan
| |
Collapse
|
4
|
Aias M, Azrad M, Saad G, Leshem T, Hamo Z, Rahmoun LA, Peretz A. Different bile acids have versatile effects on sporulation, toxin levels and biofilm formation of different Clostridioides difficile strains. J Microbiol Methods 2023; 206:106692. [PMID: 36809809 DOI: 10.1016/j.mimet.2023.106692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 02/05/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023]
Abstract
Clostridioides difficile infection develops following ingestion of virulent stains by a susceptible host. Once germinated, toxins TcdA and TcdB, and in some of the strains binary toxin, are secreted, eliciting disease. Bile acids play a significant role in the process of spore germination and outgrowth, with cholate and its derivative enhancing colony formation, while chenodeoxycholate inhibit germination and outgrowth. This work investigated bile acids' impact on spore germination, toxin levels and biofilm formation in various strain types (STs). Thirty C. difficile isolates (A+ B+ CDT-\+) of different STs were exposed to increasing concentrations of the bile acids, cholic acid (CA), taurocholic acid (TCA) and chenodeoxycholic acid (CDCA). Following treatments, spore germination was determined. Toxin concentrations were semi-quantified using the C. Diff Tox A/B II™ kit. Biofilm formation was detected by the microplate assay with crystal violet. SYTO® 9 and propidium iodide staining were used for live and dead cell detection, respectively, inside the biofilm. Toxins levels were increased by 1.5-28-fold in response to CA and by 1.5-20-fold in response to TCA, and decreased by 1-37-fold due to CDCA exposure. CA had a concentration-dependent effect on biofilm formation, with the low concentration (0.1%) inducing- and the higher concentrations inhibiting biofilm formation, while CDCA significantly reduced biofilm production at all concentrations. There were no differences in the bile acids effects on different STs. Further investigation might identify a specific bile acids' combination with inhibitory effects on C. difficile toxin and biofilm production, which could modulate toxin formation to reduce the likelihood of developing CDI.
Collapse
Affiliation(s)
- Meral Aias
- Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Maya Azrad
- The Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya 1528001, Israel
| | - Gewa Saad
- Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Tamar Leshem
- The Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya 1528001, Israel
| | - Zohar Hamo
- The Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya 1528001, Israel
| | - Layan Abu Rahmoun
- Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Avi Peretz
- Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; The Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya 1528001, Israel.
| |
Collapse
|
5
|
Monma T, Iwamoto J, Ueda H, Tamamushi M, Kakizaki F, Konishi N, Yara S, Miyazaki T, Hirayama T, Ikegami T, Honda A. Evaluation of gut dysbiosis using serum and fecal bile acid profiles. World J Clin Cases 2022; 10:12484-12493. [PMID: 36579096 PMCID: PMC9791502 DOI: 10.12998/wjcc.v10.i34.12484] [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: 09/07/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 12/02/2022] Open
Abstract
Dysbiosis in the intestinal microflora can affect the gut production of microbial metabolites, and toxic substances can disrupt the barrier function of the intestinal wall, leading to the development of various diseases. Decreased levels of Clostridium subcluster XIVa (XIVa) are associated with the intestinal dysbiosis found in inflammatory bowel disease (IBD) and Clostridium difficile infection (CDI). Since XIVa is a bacterial group responsible for the conversion of primary bile acids (BAs) to secondary BAs, the proportion of intestinal XIVa can be predicted by determining the ratio of deoxycholic acid (DCA)/[DCA + cholic acid (CA)] in feces orserum. For example, serum DCA/(DCA+CA) was significantly lower in IBD patients than in healthy controls, even in the remission period. These results suggest that a low proportion of intestinal XIVa in IBD patients might be a precondition for IBD onset but not a consequence of intestinal inflammation. Another report showed that a reduced serum DCA/(DCA + CA) ratio could predict susceptibility to CDI. Thus, the BA profile, particularly the ratio of secondary to primary BAs, can serve as a surrogate marker of the intestinal dysbiosis caused by decreased XIVa.
Collapse
Affiliation(s)
- Tadakuni Monma
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Junichi Iwamoto
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Hajime Ueda
- Joint Research Center, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Makoto Tamamushi
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Fumio Kakizaki
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Naoki Konishi
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Shoichiro Yara
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Teruo Miyazaki
- Joint Research Center, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Takeshi Hirayama
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Tadashi Ikegami
- Department of Gastroenterology and Hepatology, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| | - Akira Honda
- Joint Research Center, Tokyo Medical University Ibaraki Medical Center, Inashiki-Gun 300-0395, Japan
| |
Collapse
|
6
|
Forster ER, Yang X, Tai AK, Hang HC, Shen A. Identification of a Bile Acid-Binding Transcription Factor in Clostridioides difficile Using Chemical Proteomics. ACS Chem Biol 2022; 17:3086-3099. [PMID: 36279369 PMCID: PMC10518218 DOI: 10.1021/acschembio.2c00463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Clostridioides difficile is a Gram-positive anaerobic bacterium that is the leading cause of hospital-acquired gastroenteritis in the US. In the gut milieu, C. difficile encounters microbiota-derived, growth-inhibiting bile acids that are thought to be a significant mechanism of colonization resistance. While the levels of certain bile acids in the gut correlate with susceptibility to C. difficile infection, their molecular targets in C. difficile remain unknown. In this study, we sought to use chemical proteomics to identify bile acid-interacting proteins in C. difficile. Using photoaffinity bile acid probes and chemical proteomics, we identified a previously uncharacterized MerR family protein, CD3583 (now BapR), as a putative bile acid-sensing transcription regulator. Our data indicate that BapR specifically binds to and is stabilized by lithocholic acid (LCA) in C. difficile. Although loss of BapR did not affect C. difficile's sensitivity to LCA, ΔbapR cells elongated more in the presence of LCA compared to wild-type cells. Transcriptomics revealed that BapR regulates several gene clusters, with the expression of the mdeA-cd3573 locus being specifically de-repressed in the presence of LCA in a BapR-dependent manner. Electrophoretic mobility shift assays revealed that BapR directly binds to the mdeA promoter region. Because mdeA is involved in amino acid-related sulfur metabolism and the mdeA-cd3573 locus encodes putative transporters, we propose that BapR senses a gastrointestinal tract-specific small molecule, LCA, as an environmental cue for metabolic adaptation.
Collapse
Affiliation(s)
- Emily R Forster
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, United States
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, United States
| | - Xinglin Yang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California 92037, United States
| | - Albert K Tai
- Department of Immunology, Tufts University School of Medicine, Boston, Massachusetts 02111, United States
- Data Intensive Studies Center, Tufts University, Medford, Massachusetts 02155, United States
| | - Howard C Hang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California 92037, United States
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
| | - Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, United States
| |
Collapse
|
7
|
Ramos RJ, Zhu C, Joseph DF, Thaker S, Lacomb JF, Markarian K, Lee HJ, Petrov JC, Monzur F, Buscaglia JM, Chawla A, Small-Harary L, Gathungu G, Morganstern JA, Yang J, Li J, Pamer EG, Robertson CE, Frank DN, Cross JR, Li E. Metagenomic and bile acid metabolomic analysis of fecal microbiota transplantation for recurrent Clostridiodes difficile and/or inflammatory bowel diseases. MEDICAL RESEARCH ARCHIVES 2022; 10:10.18103/mra.v10i10.3318. [PMID: 36618438 PMCID: PMC9817289 DOI: 10.18103/mra.v10i10.3318] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) is an effective treatment of recurrent Clostridioides difficile infections (rCDI), but has more limited efficacy in treating either ulcerative colitis (UC) or Crohn's disease (CD), two major forms of inflammatory bowel diseases (IBD). We hypothesize that FMT recipients with rCDI and/or IBD have baseline fecal bile acid (BA) compositions that differ significantly from that of their healthy donors and that FMT will normalize the BA compositions. AIM To study the effect of single colonoscopic FMT on microbial composition and function in four recipient groups: 1.) rCDI patients without IBD (rCDI-IBD); 2.) rCDI with IBD (rCDI+IBD); 3.) UC patients without rCDI (UC-rCDI); 4.) CD patients without rCDI (CD-rCDI). METHODS We performed 16S rRNA gene sequence, shotgun DNA sequence and quantitative bile acid metabolomic analyses on stools collected from 55 pairs of subjects and donors enrolled in two prospective single arm FMT clinical trials (Clinical Trials.gov ID NCT03268213, 479696, UC no rCDI ≥ 2x IND 1564 and NCT03267238, IND 16795). Fitted linear mixed models were used to examine the effects of four recipient groups, FMT status (Donor, pre-FMT, 1-week post-FMT, 3-months post-FMT) and first order Group*FMT interactions on microbial diversity and composition, bile acid metabolites and bile acid metabolizing enzyme gene abundance. RESULTS The pre-FMT stools collected from rCDI ± IBD recipients had reduced α-diversity compared to the healthy donor stools and was restored post-FMT. The α-diversity in the pre-FMT stools collected from UC-rCDI or CD-rCDI recipients did not differ significantly from donor stools. FMT normalized some recipient/donor ratios of genus level taxa abundance in the four groups. Fecal secondary BA levels, including some of the secondary BA epimers that exhibit in vitro immunomodulatory activities, were lower in rCDI±IBD and CD-rCDI but not UC-rCDI recipients compared to donors. FMT restored secondary BA levels. Metagenomic baiE gene and some of the eight bile salt hydrolase (BSH) phylotype abundances were significantly correlated with fecal BA levels. CONCLUSION Restoration of multiple secondary BA levels, including BA epimers implicated in immunoregulation, are associated with restoration of fecal baiE gene counts, suggesting that the 7-α-dehydroxylation step is rate-limiting.
Collapse
|
8
|
Functional and Metagenomic Evaluation of Ibezapolstat for Early Evaluation of Anti-Recurrence Effects in Clostridioides difficile Infection. Antimicrob Agents Chemother 2022; 66:e0224421. [PMID: 35862742 PMCID: PMC9380534 DOI: 10.1128/aac.02244-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reduction of Clostridioides difficile infection (CDI) recurrence is an essential endpoint for CDI-directed antibiotic development that is often not evaluated until Phase III trials. The purpose of this project was to use a functional and metagenomic approach to predict the potential anti-CDI recurrence effect of ibezapolstat, a DNA polymerase IIIC inhibitor, in clinical development for CDI. As part of the Phase I ibezapolstat clinical study, stool samples were collected from 22 healthy volunteers, who were given either ibezapolstat or vancomycin. Stool samples were evaluated for microbiome changes and bile acid concentrations. Ibezapolstat 450 mg and vancomycin, but not ibezapolstat 300 mg, showed statistically significant changes in alpha diversity over time compared to that of a placebo. Beta diversity changes confirmed that microbiota were significantly different between study groups. Vancomycin had a more wide-ranging effect on the microbiome, characterized by an increased proportion of Gammaproteobacteria. Ibezapolstat demonstrated an increased proportion of Actinobacteria, including the Bifidobacteriaceae family. Using a linear regression analysis, vancomycin was associated with significant increases in primary bile acids as well as primary:secondary bile acid ratios. An overabundance of Enterobacteriaceae was most highly correlated with primary bile acid concentrations (r = 0.63; P < 0.0001). Using Phase I healthy volunteer samples, beneficial changes suggestive of a lower risk of CDI recurrence were associated with ibezapolstat compared to vancomycin. This novel omics approach may allow for better and earlier prediction of anti-CDI recurrence effects for antibiotics in the clinical development pipeline.
Collapse
|
9
|
Kean IRL, Wagner J, Wijeyesekera A, De Goffau M, Thurston S, Clark JA, White DK, Ridout J, Agrawal S, Kayani R, O'Donnell R, Ramnarayan P, Peters MJ, Klein N, Holmes E, Parkhill J, Baker S, Pathan N. Profiling gut microbiota and bile acid metabolism in critically ill children. Sci Rep 2022; 12:10432. [PMID: 35729169 PMCID: PMC9213539 DOI: 10.1038/s41598-022-13640-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/26/2022] [Indexed: 11/08/2022] Open
Abstract
Broad-spectrum antimicrobial use during the treatment of critical illness influences gastrointestinal fermentation endpoints, host immune response and metabolic activity including the conversion of primary to secondary bile acids. We previously observed reduced fermentation capacity in the faecal microbiota of critically ill children upon hospital admission. Here, we further explore the timecourse of the relationship between the microbiome and bile acid profile in faecal samples collected from critically ill children. The microbiome was assayed by sequencing of the 16S rRNA gene, and faecal water bile acids were measured by liquid chromatography mass spectrometry. In comparison to admission faecal samples, members of the Lachnospiraceae recovered during the late-acute phase (days 8-10) of hospitalisation. Patients with infections had a lower proportion of Lachnospiraceae in their gut microbiota than controls and patients with primary admitting diagnoses. Keystone species linked to ecological recovery were observed to decline with the length of PICU admission. These species were further suppressed in patients with systemic infection, respiratory failure, and undergoing surgery. Bile acid composition recovers quickly after intervention for critical illness which may be aided by the compositional shift in Lachnospiraceae. Our findings suggest gut microbiota recovery can be readily assessed via measurement of faecal bile acids.
Collapse
Affiliation(s)
| | - Joseph Wagner
- The Peter Doherty Institute for Infection and Immunity, Melbourne Health, Melbourne, Australia
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Anisha Wijeyesekera
- Department of Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
| | - Marcus De Goffau
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Experimental Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Thurston
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - John A Clark
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Deborah K White
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Jenna Ridout
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
- EACH, Milton, Cambridge, United Kingdom
| | - Shruti Agrawal
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Riaz Kayani
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Roddy O'Donnell
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Padmanabhan Ramnarayan
- Paediatric Intensive Care Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- St Mary's Hospital, London, United Kingdom
| | - Mark J Peters
- Paediatric Intensive Care Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Nigel Klein
- Paediatric Intensive Care Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Elaine Holmes
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Julian Parkhill
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nazima Pathan
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| |
Collapse
|
10
|
Evaluation of the Risk of Clostridium difficile Infection Using a Serum Bile Acid Profile. Metabolites 2022; 12:metabo12040331. [PMID: 35448518 PMCID: PMC9032545 DOI: 10.3390/metabo12040331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 02/04/2023] Open
Abstract
Since intestinal secondary bile acids (BAs) prevent Clostridium difficile infection (CDI), the serum BA profile may be a convenient biomarker for CDI susceptibility in human subjects. To verify this hypothesis, we investigated blood samples from 71 patients of the Division of Gastroenterology and Hepatology at the time of admission (prior to antibiotic use and CDI onset). Twelve patients developed CDI during hospitalization, and the other 59 patients did not. The serum unconjugated deoxycholic acid (DCA)/[DCA + unconjugated cholic acid (CA)] ratio on admission was significantly lower in patients who developed CDI than in patients who did not develop CDI (p < 0.01) and in 46 healthy controls (p < 0.0001). Another unconjugated secondary BA ratio, 3β-hydroxy (3βOH)-BAs/(3βOH + 3αOH-BAs), was also significantly lower in patients who developed CDI than in healthy controls (p < 0.05) but was not significantly different between patients who developed and patients who did not develop CDI. A receiver operating characteristic (ROC) curve determined a cut-off point of DCA/(DCA + CA) < 0.349 that optimally discriminated on admission the high-risk patients who would develop CDI (sensitivity 91.7% and specificity 64.4%). In conclusion, a decreased serum DCA/(DCA + CA) ratio on admission strongly correlated with CDI onset during hospitalization in patients with gastrointestinal and hepatobiliary diseases. Serum BA composition could be a helpful biomarker for predicting susceptibility to CDI.
Collapse
|
11
|
Metabolic adaption to extracellular pyruvate triggers biofilm formation in Clostridioides difficile. THE ISME JOURNAL 2021; 15:3623-3635. [PMID: 34155333 PMCID: PMC8630010 DOI: 10.1038/s41396-021-01042-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Clostridioides difficile infections are associated with gut microbiome dysbiosis and are the leading cause of hospital-acquired diarrhoea. The infectious process is strongly influenced by the microbiota and successful infection relies on the absence of specific microbiota-produced metabolites. Deoxycholate and short-chain fatty acids are microbiota-produced metabolites that limit the growth of C. difficile and protect the host against this infection. In a previous study, we showed that deoxycholate causes C. difficile to form strongly adherent biofilms after 48 h. Here, our objectives were to identify and characterize key molecules and events required for biofilm formation in the presence of deoxycholate. We applied time-course transcriptomics and genetics to identify sigma factors, metabolic processes and type IV pili that drive biofilm formation. These analyses revealed that extracellular pyruvate induces biofilm formation in the presence of deoxycholate. In the absence of deoxycholate, pyruvate supplementation was sufficient to induce biofilm formation in a process that was dependent on pyruvate uptake by the membrane protein CstA. In the context of the human gut, microbiota-generated pyruvate is a metabolite that limits pathogen colonization. Taken together our results suggest that pyruvate-induced biofilm formation might act as a key process driving C. difficile persistence in the gut.
Collapse
|
12
|
Aguirre AM, Yalcinkaya N, Wu Q, Swennes A, Tessier ME, Roberts P, Miyajima F, Savidge T, Sorg JA. Bile acid-independent protection against Clostridioides difficile infection. PLoS Pathog 2021; 17:e1010015. [PMID: 34665847 PMCID: PMC8555850 DOI: 10.1371/journal.ppat.1010015] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/29/2021] [Accepted: 10/07/2021] [Indexed: 12/21/2022] Open
Abstract
Clostridioides difficile infections occur upon ecological / metabolic disruptions to the normal colonic microbiota, commonly due to broad-spectrum antibiotic use. Metabolism of bile acids through a 7α-dehydroxylation pathway found in select members of the healthy microbiota is regarded to be the protective mechanism by which C. difficile is excluded. These 7α-dehydroxylated secondary bile acids are highly toxic to C. difficile vegetative growth, and antibiotic treatment abolishes the bacteria that perform this metabolism. However, the data that supports the hypothesis that secondary bile acids protect against C. difficile infection is supported only by in vitro data and correlative studies. Here we show that bacteria that 7α-dehydroxylate primary bile acids protect against C. difficile infection in a bile acid-independent manner. We monoassociated germ-free, wildtype or Cyp8b1-/- (cholic acid-deficient) mutant mice and infected them with C. difficile spores. We show that 7α-dehydroxylation (i.e., secondary bile acid generation) is dispensable for protection against C. difficile infection and provide evidence that Stickland metabolism by these organisms consumes nutrients essential for C. difficile growth. Our findings indicate secondary bile acid production by the microbiome is a useful biomarker for a C. difficile-resistant environment but the microbiome protects against C. difficile infection in bile acid-independent mechanisms. Secondary bile acid production by the colonic microbiome strongly correlates with an environment that is resistant to C. difficile invasion. However, it remained unclear if these bile acids provided in vivo protection. Here, we show that members of the microbiome that generate secondary bile acids (e.g., C. scindens) protect against C. difficile disease independently of secondary bile acid generation. These results are important because efforts to restore colonization resistance (e.g., FMT or precision bacterial therapy) focus on restoring secondary bile acid generation. Instead, restoring the organisms that produce 5-aminovalerate or consume proline / glycine are more important.
Collapse
Affiliation(s)
- Andrea Martinez Aguirre
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Nazli Yalcinkaya
- Baylor College of Medicine & Texas Children’s Hospital, Houston, Texas, United States of America
| | - Qinglong Wu
- Baylor College of Medicine & Texas Children’s Hospital, Houston, Texas, United States of America
| | - Alton Swennes
- Baylor College of Medicine & Texas Children’s Hospital, Houston, Texas, United States of America
| | - Mary Elizabeth Tessier
- Baylor College of Medicine & Texas Children’s Hospital, Houston, Texas, United States of America
| | - Paul Roberts
- Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, United Kingdom
| | - Fabio Miyajima
- Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, United Kingdom
- Oswaldo Cruz Foundation, Ceara branch, Fortaleza, Brazil
| | - Tor Savidge
- Baylor College of Medicine & Texas Children’s Hospital, Houston, Texas, United States of America
| | - Joseph A. Sorg
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| |
Collapse
|
13
|
Sánchez-Pellicer P, Navarro-López V, González-Tamayo R, Llopis-Ruiz C, Núñez-Delegido E, Ruzafa-Costas B, Navarro-Moratalla L, Agüera-Santos J. Descriptive Study of Gut Microbiota in Infected and Colonized Subjects by Clostridiodes difficile. Microorganisms 2021; 9:microorganisms9081727. [PMID: 34442805 PMCID: PMC8401824 DOI: 10.3390/microorganisms9081727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022] Open
Abstract
Clostridiodes difficile can lead to a range of situations from the absence of symptoms (colonization) to severe diarrhea (infection). Disruption of gut microbiota provides an ideal environment for infection to occur. Comparison of gut microbiota of infected and colonized subjects could provide relevant information on susceptible groups or protectors to the development of infection, since the presence of certain genera could be related to the inhibition of transition from a state of colonization to infection. Through high-throughput sequencing of 16S rDNA gene, we performed alpha and beta diversity and composition studies on 15 infected patients (Group CDI), 15 colonized subjects (Group P), and 15 healthy controls (Group CTLR). A loss of alpha diversity and richness and a different structure have been evidenced in the CDI and P groups with respect to the CTRL group, but without significant differences between the first two. In CDI and P groups, there was a strong decrease in phylum Firmicutes and an expansion of potential pathogens. Likewise, there was a loss of inhibitory genus of C. difficile germination in infected patients that were partially conserved in colonized subjects. Therefore, infected and colonized subjects presented a gut microbiota that was completely different from that of healthy controls, although similar to each other. It is in composition where we found that colonized subjects, especially in minority genera, presented differences with respect to those infected.
Collapse
Affiliation(s)
- Pedro Sánchez-Pellicer
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
- Correspondence: (P.S.-P.); (V.N.-L.)
| | - Vicente Navarro-López
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
- Infectious Diseases Unit, University Hospital of Vinalopó, Carrer Tonico Sansano Mora, 14, 03293 Elche, Spain
- Correspondence: (P.S.-P.); (V.N.-L.)
| | - Ruth González-Tamayo
- Biochemistry Laboratory, Vega Baja Hospital, Carretera Orihuela-Almoradí s/n, 03314 San Bartolomé, Spain;
| | - Coral Llopis-Ruiz
- Microbiology Laboratory, University Hospital of Vinalopó, Carrer Tonico Sansano Mora, 14, 03293 Elche, Spain;
| | - Eva Núñez-Delegido
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
| | - Beatriz Ruzafa-Costas
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
| | - Laura Navarro-Moratalla
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
| | - Juan Agüera-Santos
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
| |
Collapse
|
14
|
Chiu CW, Tsai PJ, Lee CC, Ko WC, Hung YP. Application of Microbiome Management in Therapy for Clostridioides difficile Infections: From Fecal Microbiota Transplantation to Probiotics to Microbiota-Preserving Antimicrobial Agents. Pathogens 2021; 10:pathogens10060649. [PMID: 34073695 PMCID: PMC8225043 DOI: 10.3390/pathogens10060649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/02/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Oral vancomycin and metronidazole, though they are the therapeutic choice for Clostridioides difficile infections (CDIs), also markedly disturb microbiota, leading to a prolonged loss of colonization resistance to C. difficile after therapy; as a result, their use is associated with a high treatment failure rate and high recurrent rate. An alternative for CDIs therapy contains the delivery of beneficial (probiotic) microorganisms into the intestinal tract to restore the microbial balance. Recently, mixture regimens containing Lactobacillus species, Saccharomyces boulardii, or Clostridium butyricum have been extensively studied for the prophylaxis of CDIs. Fecal microbiota transplantation (FMT), the transfer of (processed) fecal material from healthy donors to patients for treating CDIs, combined with vancomycin was recommended as the primary therapy for multiple recurrent CDIs (rCDIs). Either probiotics or FMT have been utilized extensively in preventing or treating CDIs, aiming at less disturbance in the microbiota to prevent rCDIs after therapy cessation. Otherwise, many newly developed therapeutic agents have been developed and aim to preserve microbiota during CDI treatment to prevent disease recurrence and might be useful in clinical patients with rCDIs in the future.
Collapse
Affiliation(s)
- Chun-Wei Chiu
- Department of Internal Medicine, Tainan Hospital, Ministry of Health and Welfare, Tainan 700, Taiwan;
| | - Pei-Jane Tsai
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Medical College, Tainan 704, Taiwan;
| | - Ching-Chi Lee
- Clinical Medicine Research Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan 704, Taiwan
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Correspondence: (W.-C.K.); (Y.-P.H.)
| | - Yuan-Pin Hung
- Department of Internal Medicine, Tainan Hospital, Ministry of Health and Welfare, Tainan 700, Taiwan;
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan 704, Taiwan
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Correspondence: (W.-C.K.); (Y.-P.H.)
| |
Collapse
|
15
|
Contribution of Inhibitory Metabolites and Competition for Nutrients to Colonization Resistance against Clostridioides difficile by Commensal Clostridium. Microorganisms 2021; 9:microorganisms9020371. [PMID: 33673352 PMCID: PMC7918557 DOI: 10.3390/microorganisms9020371] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
Clostridioides difficile is an anaerobic pathogen that causes significant morbidity and mortality. Understanding the mechanisms of colonization resistance against C. difficile is important for elucidating the mechanisms by which C. difficile is able to colonize the gut after antibiotics. Commensal Clostridium play a key role in colonization resistance. They are able to modify bile acids which alter the C. difficile life cycle. Commensal Clostridium also produce other inhibitory metabolites including antimicrobials and short chain fatty acids. They also compete with C. difficile for vital nutrients such as proline. Understanding the mechanistic effects that these metabolites have on C. difficile and other gut pathogens is important for the development of new therapeutics against C. difficile infection (CDI), which are urgently needed.
Collapse
|
16
|
Faecal microbiota transplantation for Clostridioides difficile: mechanisms and pharmacology. Nat Rev Gastroenterol Hepatol 2021; 18:67-80. [PMID: 32843743 DOI: 10.1038/s41575-020-0350-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/07/2020] [Indexed: 12/14/2022]
Abstract
Faecal microbiota transplantation (FMT) has emerged as a remarkably successful treatment for recurrent Clostridioides difficile infection that cannot be cured with antibiotics alone. Understanding the complex biology and pathogenesis of C. difficile infection, which we discuss in this Perspective, is essential for understanding the potential mechanisms by which FMT cures this disease. Although FMT has already entered clinical practice, different microbiota-based products are currently in clinical trials and are vying for regulatory approval. However, all these therapeutics belong to an entirely new class of agents that require the development of a new branch of pharmacology. Characterization of microbiota therapeutics uses novel and rapidly evolving technologies and requires incorporation of microbial ecology concepts. Here, we consider FMT within a pharmacological framework, including its essential elements: formulation, pharmacokinetics and pharmacodynamics. From this viewpoint, multiple gaps in knowledge become apparent, identifying areas that require systematic research. This knowledge is needed to help clinical providers use microbiota therapeutics appropriately and to facilitate development of next-generation microbiota products with improved safety and efficacy. The discussion here is limited to FMT as a representative of microbiota therapeutics and recurrent C. difficile as the indication; however, consideration of the intrinsic basic principles is relevant to this entire class of microbiota-based therapeutics.
Collapse
|
17
|
Budi N, Safdar N, Rose WE. Treatment issues in recurrent Clostridioides difficile infections and the possible role of germinants. FEMS MICROBES 2020; 1:xtaa001. [PMID: 37333958 PMCID: PMC10117431 DOI: 10.1093/femsmc/xtaa001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/14/2020] [Indexed: 07/30/2023] Open
Abstract
Clostridioides difficile is the number one cause of hospital-acquired infections in the United States and one of the CDC's urgent-level pathogen threats. The inflammation caused by pathogenic C. difficile results in diarrhea and pseudomembranous colitis. Patients who undergo clinically successful treatment for this disease commonly experience recurrent infections. Current treatment options can eradicate the vegetative cell form of the bacteria but do not impact the spore form, which is impervious to antibiotics and resists conventional environmental cleaning procedures. Antibiotics used in treating C. difficile infections (CDI) often do not eradicate the pathogen and can prevent regeneration of the microbiome, leaving them vulnerable to recurrent CDI and future infections upon subsequent non-CDI-directed antibiotic therapy. Addressing the management of C. difficile spores in the gastrointestinal (GI) tract is important to make further progress in CDI treatment. Currently, no treatment options focus on reducing GI spores throughout CDI antibiotic therapy. This review focuses on colonization of the GI tract, current treatment options and potential treatment directions emphasizing germinant with antibiotic combinations to prevent recurrent disease.
Collapse
Affiliation(s)
- Noah Budi
- Corresponding author: School of Pharmacy, University of Wisconsin-Madison, Room 4123, 777 Highland Avenue, Madison, WI 53705, USA. Tel: +1-920-419-7704; E-mail:
| | - Nasia Safdar
- Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA, 53726
| | - Warren E Rose
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA, 53705
| |
Collapse
|
18
|
Qian X, Yanagi K, Kane AV, Alden N, Lei M, Snydman DR, Vickers RJ, Lee K, Thorpe CM. Ridinilazole, a narrow spectrum antibiotic for treatment of Clostridioides difficile infection, enhances preservation of microbiota-dependent bile acids. Am J Physiol Gastrointest Liver Physiol 2020; 319:G227-G237. [PMID: 32597706 PMCID: PMC7500266 DOI: 10.1152/ajpgi.00046.2020] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023]
Abstract
Antibiotic treatment is a standard therapy for Clostridioides difficile infection, but dysbiosis of the gut microbiota due to antibiotic exposure is also a major risk factor for the disease. Following an initial episode of C. difficile infection, a relentless cycle of recurrence can occur, where persistent treatment-related dysbiosis predisposes the patient to subsequent relapse. This study uses a longitudinal study design to compare the effects of a narrow-spectrum (ridinilazole) or broad-spectrum antibiotic (vancomycin) on intestinal bile acid profiles and their associations with gut bacteria over the course of C. difficile infection treatment. At the end of treatment (day 10), subjects receiving vancomycin showed a nearly 100-fold increase in the ratio of conjugated to secondary bile acids in their stool compared with baseline, whereas subjects receiving ridinilazole maintained this ratio near baseline levels. Correlation analysis detected significant positive associations between secondary bile acids and several Bacteroidales and Clostridiales families. These families were depleted in the vancomycin group but preserved at near-baseline abundance in the ridinilazole group. Enterobacteriaceae, which expanded to a greater extent in the vancomycin group, correlated negatively and positively with secondary and conjugated primary bile acids, respectively. Bile acid ratios at the end of treatment were significantly different between those who recurred and those who did not. These results indicate that a narrow-spectrum antibiotic maintains an intestinal bile acid profile associated with a lowered risk of recurrence.NEW & NOTEWORTHY This is the first study to demonstrate in humans the relationships between Clostridioides difficile antibiotic treatment choice and bile acid metabolism both during therapy and after treatment cessation. The results show a microbiota- and metabolome-preserving property of a novel narrow-spectrum agent that correlates with the agent's favorable sustained clinical response rates compared with broad-spectrum antibiotic treatment.
Collapse
Affiliation(s)
- Xi Qian
- Tufts Clinical and Translational Science Institute, Tufts University, Boston, Massachusetts
| | - Karin Yanagi
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts
| | | | - Nicholas Alden
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts
| | - Ming Lei
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts
| | - David R Snydman
- Tufts Clinical and Translational Science Institute, Tufts University, Boston, Massachusetts
- Tufts Medical Center, Boston, Massachusetts
- Tufts University School of Medicine, Boston, Massachusetts
| | | | - Kyongbum Lee
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts
| | - Cheleste M Thorpe
- Tufts Medical Center, Boston, Massachusetts
- Tufts University School of Medicine, Boston, Massachusetts
| |
Collapse
|
19
|
Solbach P, Chhatwal P, Woltemate S, Tacconelli E, Buhl M, Autenrieth IB, Vehreschild MJGT, Jazmati N, Gerhard M, Stein-Thoeringer CK, Rupp J, Ulm K, Ott A, Lasch F, Koch A, Manns MP, Suerbaum S, Bachmann O. Microbiota-associated risk factors for C. difficile acquisition in hospitalized patients: A prospective, multicentric study. Clin Infect Dis 2020; 73:e2625-e2634. [PMID: 32589701 DOI: 10.1093/cid/ciaa871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Asymptomatic C. difficile colonization is believed to predispose to subsequent C. difficile infection (CDI). While emerging insights into the role of the commensal microbiota in mediating colonization resistance against C. difficile have associated CDI with specific microbial components, corresponding prospectively collected data on colonization with C. difficile are largely unavailable. METHODS C. difficile status was assessed by GDH EIA and real-time PCR targeting the toxin A (tcdA) and B (tcdB) genes. 16S V3 and V4 gene sequencing results from fecal samples of patients tested positive for C. difficile were analyzed by assessing alpha and beta diversity, LefSe, and the Piphillin functional inference approach to estimate functional capacity. RESULTS 1506 patients were recruited into a prospective observational study (DRKS00005335) upon admission into one of five academic hospitals. 936 of them provided fecal samples on admission and at discharge and were thus available for longitudinal analysis. Upon hospital admission, 5.5% (83/1506) and 3.7% (56/1506) of patients were colonized with toxigenic (TCD) and non-toxigenic C. difficile (NTCD), respectively. During hospitalization, 1.7% (16/936) acquired TCD. Risk factors for acquisition of TCD included pre-existing lung diseases, lower GI endoscopy and antibiotics. Species protecting against hospital-related C. difficile acquisition included Gemmiger spp., Odoribacter splanchnicus, Ruminococcus bromii and other Ruminococcus spp.. Metagenomic pathway analysis identified steroid biosynthesis as the most underrepresented metabolic pathway in patients who later acquire C. difficile colonization. CONCLUSIONS Gemmiger spp., Odoribacter splanchnicus, Ruminococcus bromii and other Ruminococci were associated with a decreased risk of C. difficile acquisition.
Collapse
Affiliation(s)
- Philipp Solbach
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.,German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany.,Medical Department I, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Patrick Chhatwal
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Sabrina Woltemate
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Internal Medicine 1, Tübingen University Hospital, Tübingen, Germany and Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Italy.,German Center for Infection Research (DZIF), partner site Tübingen, Germany
| | - Michael Buhl
- German Center for Infection Research (DZIF), partner site Tübingen, Germany.,Institute of Medical Microbiology and Hygiene, Tübingen University Hospital, Tübingen, Germany
| | - Ingo B Autenrieth
- German Center for Infection Research (DZIF), partner site Tübingen, Germany.,Institute of Medical Microbiology and Hygiene, Tübingen University Hospital, Tübingen, Germany
| | - Maria J G T Vehreschild
- 1st Department of Internal Medicine, University Hospital Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany.,Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Nathalie Jazmati
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany; currently: Laboratory Dr. Wisplinghoff, Cologne, Germany
| | - Markus Gerhard
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Christoph K Stein-Thoeringer
- German Center for Infection Research (DZIF), partner site Munich, Germany.,Microbiome and Cancer Research Division, German Center for Cancer Research (DKFZ), Heidelberg, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Kurt Ulm
- Institute of Medical Informatics, Statistics and Epidemiology, Technische Universität München, Munich, Germany
| | - Armin Ott
- Institute of Medical Informatics, Statistics and Epidemiology, Technische Universität München, Munich, Germany
| | - Florian Lasch
- Institute for Biometry, Hannover Medical School, Hannover, Germany
| | - Armin Koch
- Institute for Biometry, Hannover Medical School, Hannover, Germany
| | - Michael P Manns
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.,German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany
| | - Sebastian Suerbaum
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany.,German Center for Infection Research (DZIF), partner site Munich, Germany.,Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Oliver Bachmann
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.,German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany
| |
Collapse
|
20
|
Reed AD, Nethery MA, Stewart A, Barrangou R, Theriot CM. Strain-Dependent Inhibition of Clostridioides difficile by Commensal Clostridia Carrying the Bile Acid-Inducible ( bai) Operon. J Bacteriol 2020; 202:e00039-20. [PMID: 32179626 PMCID: PMC7221253 DOI: 10.1128/jb.00039-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/06/2020] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is one of the leading causes of antibiotic-associated diarrhea. Gut microbiota-derived secondary bile acids and commensal Clostridia that carry the bile acid-inducible (bai) operon are associated with protection from C. difficile infection (CDI), although the mechanism is not known. In this study, we hypothesized that commensal Clostridia are important for providing colonization resistance against C. difficile due to their ability to produce secondary bile acids, as well as potentially competing against C. difficile for similar nutrients. To test this hypothesis, we examined the abilities of four commensal Clostridia carrying the bai operon (Clostridium scindens VPI 12708, C. scindens ATCC 35704, Clostridium hiranonis, and Clostridium hylemonae) to convert cholate (CA) to deoxycholate (DCA) in vitro, and we determined whether the amount of DCA produced was sufficient to inhibit the growth of a clinically relevant C. difficile strain. We also investigated the competitive relationships between these commensals and C. difficile using an in vitro coculture system. We found that inhibition of C. difficile growth by commensal Clostridia supplemented with CA was strain dependent, correlated with the production of ∼2 mM DCA, and increased the expression of bai operon genes. We also found that C. difficile was able to outcompete all four commensal Clostridia in an in vitro coculture system. These studies are instrumental in understanding the relationship between commensal Clostridia and C. difficile in the gut, which is vital for designing targeted bacterial therapeutics. Future studies dissecting the regulation of the bai operon in vitro and in vivo and how this affects CDI will be important.IMPORTANCE Commensal Clostridia carrying the bai operon, such as C. scindens, have been associated with protection against CDI; however, the mechanism for this protection is unknown. Herein, we show four commensal Clostridia that carry the bai operon and affect C. difficile growth in a strain-dependent manner, with and without the addition of cholate. Inhibition of C. difficile by commensals correlated with the efficient conversion of cholate to deoxycholate, a secondary bile acid that inhibits C. difficile germination, growth, and toxin production. Competition studies also revealed that C. difficile was able to outcompete the commensals in an in vitro coculture system. These studies are instrumental in understanding the relationship between commensal Clostridia and C. difficile in the gut, which is vital for designing targeted bacterial therapeutics.
Collapse
Affiliation(s)
- A D Reed
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - M A Nethery
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - A Stewart
- Molecular Education, Technology and Research Innovation Center, North Carolina State University, Raleigh, North Carolina, USA
| | - R Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - C M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| |
Collapse
|
21
|
Impact of deoxycholate on Clostridioides difficile growth, toxin production, and sporulation. Heliyon 2020; 6:e03717. [PMID: 32322715 PMCID: PMC7160582 DOI: 10.1016/j.heliyon.2020.e03717] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/27/2020] [Accepted: 03/30/2020] [Indexed: 12/15/2022] Open
Abstract
Purpose Bile acids play an important role in Clostridioides difficile life cycle. Deoxycholate (DCA), one of the most abundant secondary bile acids, is known to inhibit vegetative growth and toxin production. However, limited data are available on the role of DCA on C. difficile sporulation. Here, we investigated the phenotypic and genotypic impact of DCA on the growth, toxin production, and sporulation of C. difficile. Methodology Four genetically divergent C. difficile strains were cultured in nutrient-rich broth with and without DCA at various concentrations, and growth activity was evaluated for each strain. Cytotoxicity assays using culture supernatants from cells grown in nutrient-rich broth with and without 0.01% DCA were conducted. Sporulation efficiency was determined using sporulation media with and without 0.01% DCA. Transcript levels of tcdB and spo0A were analyzed using quantitative reverse-transcription polymerase chain reaction. Results We found that DCA led to growth reduction in a dose-depended manner and regulated toxin production by repressing tcdB expression during vegetative growth. To our knowledge, we have also provided the first evidence that DCA reduces C. difficile sporulation efficiency through the downregulation of spo0A expression during the sporulation stage. Conclusions DCA modulates C. difficile sporulation, vegetative growth, and toxin production.
Collapse
|
22
|
Sinha SR, Haileselassie Y, Nguyen LP, Tropini C, Wang M, Becker LS, Sim D, Jarr K, Spear ET, Singh G, Namkoong H, Bittinger K, Fischbach MA, Sonnenburg JL, Habtezion A. Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation. Cell Host Microbe 2020; 27:659-670.e5. [PMID: 32101703 DOI: 10.1016/j.chom.2020.01.021] [Citation(s) in RCA: 375] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 12/22/2019] [Accepted: 01/24/2020] [Indexed: 12/24/2022]
Abstract
Secondary bile acids (SBAs) are derived from primary bile acids (PBAs) in a process reliant on biosynthetic capabilities possessed by few microbes. To evaluate the role of BAs in intestinal inflammation, we performed metabolomic, microbiome, metagenomic, and transcriptomic profiling of stool from ileal pouches (surgically created resevoirs) in colectomy-treated patients with ulcerative colitis (UC) versus controls (familial adenomatous polyposis [FAP]). We show that relative to FAP, UC pouches have reduced levels of lithocholic acid and deoxycholic acid (normally the most abundant gut SBAs), genes required to convert PBAs to SBAs, and Ruminococcaceae (one of few taxa known to include SBA-producing bacteria). In three murine colitis models, SBA supplementation reduces intestinal inflammation. This anti-inflammatory effect is in part dependent on the TGR5 bile acid receptor. These data suggest that dysbiosis induces SBA deficiency in inflammatory-prone UC patients, which promotes a pro-inflammatory state within the intestine that may be treated by SBA restoration.
Collapse
Affiliation(s)
- Sidhartha R Sinha
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Yeneneh Haileselassie
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Linh P Nguyen
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carolina Tropini
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Min Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Laren S Becker
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Davis Sim
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karolin Jarr
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Estelle T Spear
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gulshan Singh
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hong Namkoong
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael A Fischbach
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Justin L Sonnenburg
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Aida Habtezion
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
23
|
Abbas A, Zackular JP. Microbe-microbe interactions during Clostridioides difficile infection. Curr Opin Microbiol 2020; 53:19-25. [PMID: 32088581 DOI: 10.1016/j.mib.2020.01.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 02/07/2023]
Abstract
Clostridioides difficile is the leading cause of hospital-acquired gastrointestinal infections and a major public health burden in the United States. C. difficile infection causes a spectrum of disease from mild diarrhea to severe complications such as pseudomembranous colitis, toxic megacolon and death. This broad range of disease is only partially explained by bacterial genetic factors, host genetics, comorbidities and previous drug exposures. Another important factor is the gut microbiome, the disruption of which results in a loss of colonization resistance to C. difficile. Here, we review how gut microbiota and their metabolites impact C. difficile virulence and influence disease.
Collapse
Affiliation(s)
- Arwa Abbas
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Joseph P Zackular
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
24
|
Savidge T, Sorg JA. Role of Bile in Infectious Disease: the Gall of 7α-Dehydroxylating Gut Bacteria. Cell Chem Biol 2019; 26:1-3. [PMID: 30658109 DOI: 10.1016/j.chembiol.2018.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Local antibiotics and quorum sensors produced by gut bacteria regulate microbiota community structure and guard against pathogens. In this issue of Cell Chemical Biology, Kang et al. (2019) guide us through a reciprocal host-antimicrobial interplay that redefines our understanding of Clostridioides (Clostridium) difficile pathogenesis.
Collapse
Affiliation(s)
- Tor Savidge
- Department of Pathology & Immunology, Baylor College of Medicine, Houston TX, 77030, USA; Texas Children's Microbiome Center, Texas Children's Hospital, Houston TX, 77030, USA.
| | - Joseph A Sorg
- Department of Biology, Texas A&M University, College Station TX, 77843, USA
| |
Collapse
|
25
|
Mullish BH, McDonald JAK, Pechlivanis A, Allegretti JR, Kao D, Barker GF, Kapila D, Petrof EO, Joyce SA, Gahan CGM, Glegola-Madejska I, Williams HRT, Holmes E, Clarke TB, Thursz MR, Marchesi JR. Microbial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent Clostridioides difficile infection. Gut 2019; 68:1791-1800. [PMID: 30816855 PMCID: PMC6839797 DOI: 10.1136/gutjnl-2018-317842] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/26/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Faecal microbiota transplant (FMT) effectively treats recurrent Clostridioides difficile infection (rCDI), but its mechanisms of action remain poorly defined. Certain bile acids affect C. difficile germination or vegetative growth. We hypothesised that loss of gut microbiota-derived bile salt hydrolases (BSHs) predisposes to CDI by perturbing gut bile metabolism, and that BSH restitution is a key mediator of FMT's efficacy in treating the condition. DESIGN Using stool collected from patients and donors pre-FMT/post-FMT for rCDI, we performed 16S rRNA gene sequencing, ultra performance liquid chromatography mass spectrometry (UPLC-MS) bile acid profiling, BSH activity measurement, and qPCR of bsh/baiCD genes involved in bile metabolism. Human data were validated in C. difficile batch cultures and a C57BL/6 mouse model of rCDI. RESULTS From metataxonomics, pre-FMT stool demonstrated a reduced proportion of BSH-producing bacterial species compared with donors/post-FMT. Pre-FMT stool was enriched in taurocholic acid (TCA, a potent C. difficile germinant); TCA levels negatively correlated with key bacterial genera containing BSH-producing organisms. Post-FMT samples demonstrated recovered BSH activity and bsh/baiCD gene copy number compared with pretreatment (p<0.05). In batch cultures, supernatant from engineered bsh-expressing E. coli and naturally BSH-producing organisms (Bacteroides ovatus, Collinsella aerofaciens, Bacteroides vulgatus and Blautia obeum) reduced TCA-mediated C. difficile germination relative to culture supernatant of wild-type (BSH-negative) E. coli. C. difficile total viable counts were ~70% reduced in an rCDI mouse model after administration of E. coli expressing highly active BSH relative to mice administered BSH-negative E. coli (p<0.05). CONCLUSION Restoration of gut BSH functionality contributes to the efficacy of FMT in treating rCDI.
Collapse
Affiliation(s)
- Benjamin H Mullish
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Julie A K McDonald
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Alexandros Pechlivanis
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Jessica R Allegretti
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital, Boston, Massachusetts, USA,Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - Dina Kao
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Grace F Barker
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Diya Kapila
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Elaine O Petrof
- Division of Infectious Diseases/ GI Diseases Research Unit Wing, Department of Medicine, Kingston General Hospital, Queen’s University, Kingston, Ontario, Canada
| | - Susan A Joyce
- APC Microbiome Institute, University College Cork, Cork, Ireland,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Cormac G M Gahan
- APC Microbiome Institute, University College Cork, Cork, Ireland,School of Pharmacy, University College Cork, Cork, Ireland
| | | | - Horace R T Williams
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Elaine Holmes
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Thomas B Clarke
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Mark R Thursz
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Julian R Marchesi
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK,School of Biosciences, Cardiff University, Cardiff, UK
| |
Collapse
|
26
|
Farowski F, Solbach P, Tsakmaklis A, Brodesser S, Cruz Aguilar MR, Cornely OA, Dettmer K, Higgins PG, Suerbaum S, Jazmati N, Oefner PJ, Vehreschild MJGT. Potential biomarkers to predict outcome of faecal microbiota transfer for recurrent Clostridioides difficile infection. Dig Liver Dis 2019; 51:944-951. [PMID: 30770201 DOI: 10.1016/j.dld.2019.01.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/15/2019] [Accepted: 01/17/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Faecal microbiota transplantation (FMT) has proven high clinical efficacy in the management of recurrent Clostridioides difficile infection (rCDI) with cure rates of over 80% after a single treatment. Nevertheless, the reasons for failure in the remaining 20% remain elusive. The aim of the present study was to investigate different potential predictors of response to FMT. METHODS Faecal specimens of sixteen patients undergoing FMT for rCDI, as well as samples from the respective donors were collected and analyzed by 16S rRNA gene profiling, bile acid-inducible (baiCD) gene specific qPCR, and liquid chromatography tandem-mass spectrometry (LC-MS/MS) to quantify the concentrations of primary and secondary bile acids. RESULTS Using the faecal concentration of the secondary bile acid lithocholic acid (LCA)within the patient specimens, we were able to predict response to FMT (accuracy 95.2%, sensitivity 100%, specificity 90.9%). By combining the faecal LCA concentration with the urinary pCS concentration, an accuracy of 100% was achieved. CONCLUSION LCA appears to be a promising marker candidate for prediction of clinical response to FMT. Other makers, such as urinary concentration of pCS, but not 3-IS, might be used to improve accuracy of prediction. Further studies are warranted to validate these candidate markers.
Collapse
Affiliation(s)
- Fedja Farowski
- Department I of Internal Medicine, University Hospital of Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany
| | - Philipp Solbach
- Hannover Medical School, Department of Gastroenterology, Hepatology and Endocrinology, Hannover, Germany; Hannover Medical School, Institute of Medical Microbiology and Hospital Epidemiology, Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Anastasia Tsakmaklis
- Department I of Internal Medicine, University Hospital of Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany
| | - Susanne Brodesser
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
| | | | - Oliver A Cornely
- Department I of Internal Medicine, University Hospital of Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
| | - Katja Dettmer
- Institute of Functional Genomics, University of Regensburg, Germany
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany
| | - Sebastian Suerbaum
- Hannover Medical School, Institute of Medical Microbiology and Hospital Epidemiology, Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany; Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Nathalie Jazmati
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany; Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Germany
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Germany
| | - Maria J G T Vehreschild
- Department I of Internal Medicine, University Hospital of Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany.
| | | |
Collapse
|
27
|
Reese AT, Carmody RN. Thinking Outside the Cereal Box: Noncarbohydrate Routes for Dietary Manipulation of the Gut Microbiota. Appl Environ Microbiol 2019; 85:e02246-18. [PMID: 30504210 PMCID: PMC6498178 DOI: 10.1128/aem.02246-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota is a diverse and dynamic ecological community that is increasingly recognized to play important roles in host metabolic, immunological, and behavioral functioning. As such, identifying new routes for manipulating the microbiota may provide valuable additional methods for improving host health. Dietary manipulations and prebiotic supplementation are active targets of research for altering the microbiota, but to date, this work has disproportionately focused on carbohydrates. However, many other resources can limit or shape microbial growth. Here, we provide a brief overview of the resource landscape in the mammalian gut and review relevant literature documenting associations between noncarbohydrate nutrients and the composition of the gut microbiota. To spur future work and accelerate translational applications, we propose that researchers take new approaches for studying the effects of diet on gut microbial communities, including more-careful consideration of media for in vitro experiments, measurement of absolute as well as relative abundances, concerted efforts to articulate how physiology may differ between humans and the animal models used in translational studies, and leveraging natural variation for additional insights. Finally, we close with a discussion of how to determine when or where to employ these potential dietary levers for manipulating the microbiota.
Collapse
Affiliation(s)
- Aspen T Reese
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Society of Fellows, Harvard University, Cambridge, Massachusetts, USA
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
28
|
Torcato IM, Kasal MR, Brito PH, Miller ST, Xavier KB. Identification of novel autoinducer-2 receptors in Clostridia reveals plasticity in the binding site of the LsrB receptor family. J Biol Chem 2019; 294:4450-4463. [PMID: 30696769 DOI: 10.1074/jbc.ra118.006938] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/26/2019] [Indexed: 12/22/2022] Open
Abstract
Autoinducer-2 (AI-2) is unique among quorum-sensing signaling molecules, as it is produced and recognized by a wide variety of bacteria and thus facilitates interspecies communication. To date, two classes of AI-2 receptors have been identified: the LuxP-type, present in the Vibrionales, and the LsrB-type, found in a number of phylogenetically distinct bacterial families. Recently, AI-2 was shown to affect the colonization levels of a variety of bacteria in the microbiome of the mouse gut, including members of the genus Clostridium, but no AI-2 receptor had been identified in this genus. Here, we identify a noncanonical, functional LsrB-type receptor in Clostridium saccharobutylicum. This novel LsrB-like receptor is the first one reported with variations in the binding-site amino acid residues that interact with AI-2. The crystal structure of the C. saccharobutylicum receptor determined at 1.35 Å resolution revealed that it binds the same form of AI-2 as the other known LsrB-type receptors, and isothermal titration calorimetry (ITC) assays showed that binding of AI-2 occurs at a submicromolar concentration. Using phylogenetic analysis, we inferred that the newly identified noncanonical LsrB receptor shares a common ancestor with known LsrB receptors and that noncanonical receptors are present in bacteria from different phyla. This led us to identify putative AI-2 receptors in bacterial species in which no receptors were known, as in bacteria belonging to the Spirochaetes and Actinobacteria phyla. Thus, this work represents a significant step toward understanding how AI-2-mediated quorum sensing influences bacterial interactions in complex biological niches.
Collapse
Affiliation(s)
- Inês M Torcato
- From the Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal.,the Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Meghann R Kasal
- the Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, and
| | - Patrícia H Brito
- From the Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal.,the Chronic Disease Research Center (CEDOC), NOVA Medical School, Universidade NOVA de Lisboa, Rua Câmara Pestana, 6, 1150-082 Lisboa, Portugal
| | - Stephen T Miller
- the Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, and
| | - Karina B Xavier
- From the Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal,
| |
Collapse
|
29
|
Kang JD, Myers CJ, Harris SC, Kakiyama G, Lee IK, Yun BS, Matsuzaki K, Furukawa M, Min HK, Bajaj JS, Zhou H, Hylemon PB. Bile Acid 7α-Dehydroxylating Gut Bacteria Secrete Antibiotics that Inhibit Clostridium difficile: Role of Secondary Bile Acids. Cell Chem Biol 2019; 26:27-34.e4. [PMID: 30482679 PMCID: PMC6338514 DOI: 10.1016/j.chembiol.2018.10.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/28/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022]
Abstract
Clostridium scindens biotransforms primary bile acids into secondary bile acids, and is correlated with inhibition of Clostridium difficile growth in vivo. The aim of the current study was to determine how C. scindens regulates C. difficile growth in vitro and if these interactions might relate to the regulation of gut microbiome structure in vivo. The bile acid 7α-dehydroxylating gut bacteria, C. scindens and C. sordellii, were found to secrete the tryptophan-derived antibiotics, 1-acetyl-β-carboline and turbomycin A, respectively. Both antibiotics inhibited growth of C. difficile and other gut bacteria. The secondary bile acids, deoxycholic acid and lithocholic acid, but not cholic acid, enhanced the inhibitory activity of these antibiotics. These antibiotics appear to inhibit cell division of C. difficile. The results help explain how endogenously synthesized antibiotics and secondary bile acids may regulate C. difficile growth and the structure of the gut microbiome in health and disease.
Collapse
Affiliation(s)
- Jason D Kang
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA; McGuire VA Medical Center, Richmond, VA, USA
| | - Christopher J Myers
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Spencer C Harris
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Genta Kakiyama
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA; McGuire VA Medical Center, Richmond, VA, USA
| | - In-Kyoung Lee
- NPChem, Co. and Division of Biotechnology, Chonbuk National University, Jeonju, Jeollabuk-do, Republic of Korea
| | - Bong-Sik Yun
- NPChem, Co. and Division of Biotechnology, Chonbuk National University, Jeonju, Jeollabuk-do, Republic of Korea
| | - Keiichi Matsuzaki
- Laboratory of Pharmacognosy and Natural Products Chemistry, School of Pharmacy, Nihon University, Chiba, Japan
| | - Megumi Furukawa
- Laboratory of Pharmacognosy and Natural Products Chemistry, School of Pharmacy, Nihon University, Chiba, Japan
| | - Hae-Ki Min
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Jasmohan S Bajaj
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA; McGuire VA Medical Center, Richmond, VA, USA
| | - Huiping Zhou
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA; McGuire VA Medical Center, Richmond, VA, USA
| | - Phillip B Hylemon
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA; McGuire VA Medical Center, Richmond, VA, USA.
| |
Collapse
|
30
|
Brown JRM, Flemer B, Joyce SA, Zulquernain A, Sheehan D, Shanahan F, O'Toole PW. Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection. BMC Gastroenterol 2018; 18:131. [PMID: 30153805 PMCID: PMC6114236 DOI: 10.1186/s12876-018-0860-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/15/2018] [Indexed: 12/12/2022] Open
Abstract
Background Alteration of the gut microbiota by repeated antibiotic treatment increases susceptibility to Clostridioides difficile infection. Faecal microbiota transplantation from donors with a normal microbiota effectively treats C. difficile infection. Methods The study involved 10 patients with recurrent C. difficile infection, nine of whom received transplants from individual donors and one who received a donor unit from a stool bank (OpenBiome). Results All individuals demonstrated enduring post-transplant resolution of C. difficile- associated diarrhoea. Faecal microbiota diversity of recipients significantly increased, and the composition of the microbiota resembled that of the donor. Patients with C. difficile infection exhibited significantly lower faecal levels of secondary/ bile acids and higher levels of primary bile acids. Levels of secondary bile acids were restored in all transplant recipients, but to a lower degree with the OpenBiome transplant. The abundance increased of bacterial genera known from previous studies to confer resistance to growth and germination of C. difficile. These were significantly negatively associated with primary bile acid levels and positively related with secondary bile acid levels. Although reduced levels of the short chain fatty acids, butyrate, propionate and acetate, have been previously reported, here we report elevations in SCFA, pyruvic and lactic fatty acids, saturated, ω-6, monounsaturated, ω-3 and ω-6 polyunsaturated fatty acids (PUFA) in C. difficile infection. This potentially indicates one or a combination of increased dietary FA intake, microbial modification of FAs or epithelial cell damage and inflammatory cell recruitment. No reversion to donor FA profile occurred post-FMT but ω-3 to ω-6 PUFA ratios were altered in the direction of the donor. Archaeal metabolism genes were found in some samples post FMT. Conclusion A consistent metabolic signature was identified in the post-transplant microbiota, with reduced primary bile acids and substantial restoration of secondary bile acid production capacity. Total FA levels were unchanged but the ratio of inflammatory to non-inflammatory FAs decreased. Electronic supplementary material The online version of this article (10.1186/s12876-018-0860-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jillian R-M Brown
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Burkhardt Flemer
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Susan A Joyce
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,School of Biochemistry and Cell Biology, University College Cork, National University of Ireland, Cork, Ireland
| | - Akbar Zulquernain
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
| | - Donal Sheehan
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
| | - Fergus Shanahan
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland.,Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland. .,School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
| |
Collapse
|