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Baumgartner M, Pfrunder-Cardozo KR, Hall AR. Microbial community composition interacts with local abiotic conditions to drive colonization resistance in human gut microbiome samples. Proc Biol Sci 2021; 288:20203106. [PMID: 33757361 PMCID: PMC8059542 DOI: 10.1098/rspb.2020.3106] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Biological invasions can alter ecosystem stability and function, and predicting what happens when a new species or strain arrives remains a major challenge in ecology. In the mammalian gastrointestinal tract, susceptibility of the resident microbial community to invasion by pathogens has important implications for host health. However, at the community level, it is unclear whether susceptibility to invasion depends mostly on resident community composition (which microbes are present), or also on local abiotic conditions (such as nutrient status). Here, we used a gut microcosm system to disentangle some of the drivers of susceptibility to invasion in microbial communities sampled from humans. We found resident microbial communities inhibited an invading Escherichia coli strain, compared to community-free control treatments, sometimes excluding the invader completely (colonization resistance). These effects were stronger at later time points, when we also detected altered community composition and nutrient availability. By separating these two components (microbial community and abiotic environment), we found taxonomic composition played a crucial role in suppressing invasion, but this depended critically on local abiotic conditions (adapted communities were more suppressive in nutrient-depleted conditions). This helps predict when resident communities will be most susceptible to invasion, with implications for optimizing treatments based on microbiota management.
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Affiliation(s)
- Michael Baumgartner
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Katia R Pfrunder-Cardozo
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Alex R Hall
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
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152
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Leslie JL, Jenior ML, Vendrov KC, Standke AK, Barron MR, O'Brien TJ, Unverdorben L, Thaprawat P, Bergin IL, Schloss PD, Young VB. Protection from Lethal Clostridioides difficile Infection via Intraspecies Competition for Cogerminant. mBio 2021; 12:e00522-21. [PMID: 33785619 PMCID: PMC8092246 DOI: 10.1128/mbio.00522-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile, a Gram-positive, spore-forming bacterium, is the primary cause of infectious nosocomial diarrhea. Antibiotics are a major risk factor for C. difficile infection (CDI), as they disrupt the gut microbial community, enabling increased germination of spores and growth of vegetative C. difficile To date, the only single-species bacterial preparation that has demonstrated efficacy in reducing recurrent CDI in humans is nontoxigenic C. difficile Using multiple infection models, we determined that precolonization with a less virulent strain is sufficient to protect from challenge with a lethal strain of C. difficile, surprisingly even in the absence of adaptive immunity. Additionally, we showed that protection is dependent on high levels of colonization by the less virulent strain and that it is mediated by exclusion of the invading strain. Our results suggest that reduction of amino acids, specifically glycine following colonization by the first strain of C. difficile, is sufficient to decrease germination of the second strain, thereby limiting colonization by the lethal strain.IMPORTANCE Antibiotic-associated colitis is often caused by infection with the bacterium Clostridioides difficile In this study, we found that reduction of the amino acid glycine by precolonization with a less virulent strain of C. difficile is sufficient to decrease germination of a second strain. This finding demonstrates that the axis of competition for nutrients can include multiple life stages. This work is important, as it is the first to identify a possible mechanism through which precolonization with C. difficile, a current clinical therapy, provides protection from reinfection. Furthermore, our work suggests that targeting nutrients utilized by all life stages could be an improved strategy for bacterial therapeutics that aim to restore colonization resistance in the gut.
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Affiliation(s)
- Jhansi L Leslie
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Matthew L Jenior
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kimberly C Vendrov
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alexandra K Standke
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Madeline R Barron
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Tricia J O'Brien
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lavinia Unverdorben
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Pariyamon Thaprawat
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ingrid L Bergin
- The Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick D Schloss
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
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153
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Dissecting Individual Interactions between Pathogenic and Commensal Bacteria within a Multispecies Gut Microbial Community. mSphere 2021; 6:6/2/e00013-21. [PMID: 33762315 PMCID: PMC8546675 DOI: 10.1128/msphere.00013-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Interactions of commensal bacteria within the gut microbiota and with invading pathogens are critical in determining the outcome of an infection. While murine studies have been valuable, we lack in vitro models to monitor community responses to pathogens at a single-species level. We have developed a multispecies community of nine representative gut species cultured together as a mixed biofilm and tracked numbers of individual species over time using a quantitative PCR (qPCR)-based approach. Introduction of the major nosocomial gut pathogen, Clostridioides difficile, to this community resulted in increased adhesion of commensals and inhibition of C. difficile multiplication. Interestingly, we observed an increase in individual Bacteroides species accompanying the inhibition of C. difficile. Furthermore, Bacteroides dorei reduced C. difficile growth within biofilms, suggesting a role for Bacteroides spp. in prevention of C. difficile colonization. We report here an in vitro tool with excellent applications for investigating bacterial interactions within a complex community. IMPORTANCE Studying interactions between bacterial species that reside in the human gut is crucial for gaining a better insight into how they provide protection from pathogen colonization. In vitro models of multispecies bacterial communities wherein behaviors of single species can be accurately tracked are key to such studies. Here, we have developed a synthetic, trackable, gut microbiota community which reduces growth of the human gut pathogen Clostridioides difficile. We report that Bacteroides spp. within this community respond by multiplying in the presence of this pathogen, resulting in reduction of C. difficile growth. Defined in vitro communities that can be tailored to include different species are well suited to functional genomic approaches and are valuable tools for understanding interbacterial interactions.
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154
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Le VVH, Biggs PJ, Wheeler D, Davies IG, Rakonjac J. Novel mechanisms of TolC-independent decreased bile-salt susceptibility in Escherichia coli. FEMS Microbiol Lett 2021; 367:5837082. [PMID: 32407499 DOI: 10.1093/femsle/fnaa083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/13/2020] [Indexed: 01/24/2023] Open
Abstract
Bile salts, including sodium deoxycholate (DOC), are secreted into the intestine to aid fat digestion and contribute to antimicrobial protection. Gram-negative pathogens such as Escherichia coli, however, are highly resistant to DOC, using multiple mechanisms of which the multidrug efflux pump AcrAB-TolC is the dominant one. Given that TolC-mediated efflux masks the interaction of DOC with potential targets, we sought to identify those targets by identifying genes whose mutations cause an increase in the MIC to DOC relative to the ∆tolC parental strain, that lacks TolC-associated functional efflux pumps. Using a mutant screen, we isolated twenty independent spontaneous mutants that had a higher MICDOC than the E. coli parental ∆tolC strain. Whole genome sequencing of these mutants mapped most mutations to the ptsI or cyaA gene. Analysis of knock-out mutants and complementation showed that elimination of PtsI, a component of the carbohydrate phosphotransferase system, or one of the two key proteins involved in cAMP synthesis and signaling, adenylate cyclase (CyaA) or cAMP receptor protein (Crp) causes low-level increased resistance of a ∆tolC E. coli strain to DOC.
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Affiliation(s)
- Vuong Van Hung Le
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,mEpilab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David Wheeler
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Ieuan G Davies
- New Zealand Pharmaceuticals Ltd., Palmerston North, New Zealand
| | - Jasna Rakonjac
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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155
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Blesl A, Stadlbauer V. The Gut-Liver Axis in Cholestatic Liver Diseases. Nutrients 2021; 13:nu13031018. [PMID: 33801133 PMCID: PMC8004151 DOI: 10.3390/nu13031018] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022] Open
Abstract
The gut-liver axis describes the physiological interplay between the gut and the liver and has important implications for the maintenance of health. Disruptions of this equilibrium are an important factor in the evolution and progression of many liver diseases. The composition of the gut microbiome, the gut barrier, bacterial translocation, and bile acid metabolism are the key features of this cycle. Chronic cholestatic liver diseases include primary sclerosing cholangitis, the generic term secondary sclerosing cholangitis implying the disease secondary sclerosing cholangitis in critically ill patients and primary biliary cirrhosis. Pathophysiology of these diseases is not fully understood but seems to be multifactorial. Knowledge about the alterations of the gut-liver axis influencing the pathogenesis and the outcome of these diseases has considerably increased. Therefore, this review aims to describe the function of the healthy gut-liver axis and to sum up the pathological changes in these cholestatic liver diseases. The review compromises the actual level of knowledge about the gut microbiome (including the mycobiome and the virome), the gut barrier and the consequences of increased gut permeability, the effects of bacterial translocation, and the influence of bile acid composition and pool size in chronic cholestatic liver diseases. Furthermore, therapeutic implications and future scientific objectives are outlined.
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Affiliation(s)
- Andreas Blesl
- Division for Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria;
- Correspondence:
| | - Vanessa Stadlbauer
- Division for Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria;
- Center for Biomarker Research in Medicine (CBmed), 8010 Graz, Austria
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156
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Bai X, Fu R, Duan Z, Liu Y, Zhu C, Fan D. Ginsenoside Rh4 alleviates antibiotic-induced intestinal inflammation by regulating the TLR4-MyD88-MAPK pathway and gut microbiota composition. Food Funct 2021; 12:2874-2885. [PMID: 33877243 DOI: 10.1039/d1fo00242b] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ginsenoside Rh4, as a bioactive component obtained from Panax notoginseng, has excellent pharmacological properties. However, its role in regulating gut microbiota and intestinal inflammation is still poorly understood. Thus, the aim of this study is to investigate the effect of Rh4 on gut microbiota, especially antibiotic-induced microbiota perturbation, and the underlying mechanisms. C57BL/6 mice were given different doses of Rh4 after the establishment of a gut microbiota disturbance model with antibiotics. Our data revealed that Rh4 administration could greatly improve the pathological phenotype, gut barrier disruption, and intestinal inflammation in mice that had been antibiotic-induced. Notably, it was found that Rh4 significantly inhibited the TLR4-MyD88-MAPK signaling pathway. In addition, Rh4 treatment could significantly increase the number of short chain fatty acids (SCFAs) and bile acids (BAs). These changes were accompanied with beneficial alterations in gut microbiota diversity and composition. In conclusion, Rh4 improves intestinal inflammation and induces potentially beneficial changes in the gut microbiota, which are conducive to revealing host-microbe interactions.
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Affiliation(s)
- Xue Bai
- Shaanxi Key Laboratory of Degradable Biomedical Materials and Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Taibai North Road 229, Xi'an, Shaanxi 710069, China.
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157
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Zhang X, Zheng J, Jiang N, Sun G, Bao X, Kong M, Cheng X, Lin A, Liu H. Modulation of gut microbiota and intestinal metabolites by lactulose improves loperamide-induced constipation in mice. Eur J Pharm Sci 2021; 158:105676. [PMID: 33310029 DOI: 10.1016/j.ejps.2020.105676] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
Lactulose is a common laxative and has been widely applied to clinical treatment for constipation. This study aimed to explore the improving effect of lactulose on constipation through the mediation of gut microbiota and intestinal metabolites. BALB/c mice with constipation induced by loperamide were orally treated with lactulose for four weeks. After the treatment, the constipation-related factors were determined. The effect of lactulose on the composition of gut microbiota was assessed by 16S rDNA gene sequencing. Gas chromatography or liquid chromatography-mass spectrometer (GC/LC-MS) analysis was used for the quantification of intestinal metabolites. The treatment of constipated mice with lactulose accelerated intestinal motility, suppressed inflammatory responses, protected gut barrier, and improved metabolisms of water and salt in the intestinal tract. These therapeutic effects were attributed to the reversed gut microbiota dysfunction, which conferred the benefit to the production of intestinal metabolites including bile acids, short-chain fatty acids, and tryptophan catabolites. Further, the depletion of intestinal flora from loperamide- or (loperamide + lactulose)-treated mice confirmed the significance of gut microbiota in the mediation of constipation. In summary, this study leads us to propose that lactulose may improve constipation through a prebiotic effect on gut microbiota and intestinal metabolites.
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Affiliation(s)
- Xiaoyu Zhang
- Clinical college of traditional Chinese medicine, Hubei University of Chinese Medicine, Wuhan 430060, PR China
| | - Junping Zheng
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, PR China
| | - Nan Jiang
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430061, PR China; Hubei Province Academy of Traditional Chinese Medicine, Wuhan 430074, PR China
| | - Guangjun Sun
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430061, PR China; Hubei Province Academy of Traditional Chinese Medicine, Wuhan 430074, PR China
| | - Xinkun Bao
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430061, PR China; Hubei Province Academy of Traditional Chinese Medicine, Wuhan 430074, PR China
| | - Mingwang Kong
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, PR China
| | - Xue Cheng
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, PR China
| | - Aizhen Lin
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430061, PR China; Hubei Province Academy of Traditional Chinese Medicine, Wuhan 430074, PR China.
| | - Hongtao Liu
- College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, PR China.
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158
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Jose S, Mukherjee A, Horrigan O, Setchell KDR, Zhang W, Moreno-Fernandez ME, Andersen H, Sharma D, Haslam DB, Divanovic S, Madan R. Obeticholic acid ameliorates severity of Clostridioides difficile infection in high fat diet-induced obese mice. Mucosal Immunol 2021; 14:500-510. [PMID: 32811993 PMCID: PMC7889747 DOI: 10.1038/s41385-020-00338-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/18/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
Severe Clostridiodes difficile infection (CDI) is life-threatening and responds poorly to treatment. Obesity is associated with development of severe CDI. Therefore, to define the mechanisms that exacerbate disease severity, we examined CDI pathogenesis in high-fat diet (HFD)-fed obese mice. Compared to control mice, HFD-fed mice failed to clear C. difficile bacteria which resulted in protracted diarrhea, weight loss and colonic damage. After infection, HFD-induced obese mice had an intestinal bile acid (BA) pool that was dominated by primary BAs which are known promoters of C. difficile spore germination, and lacked secondary BAs that inhibit C. difficile growth. Concurrently, synthesis of primary BAs from liver was significantly increased in C. difficile-infected HFD-fed mice. A key pathway that regulates hepatic BA synthesis is via feedback inhibition from intestinal Farnesoid X receptors (FXRs). Our data reveal that the proportion of FXR agonist BAs to FXR antagonist BAs in the intestinal lumen was significantly reduced in HFD-fed mice after CDI. Treatment of HFD-fed mice with an FXR agonist Obeticholic acid, resulted in decreased primary BA synthesis, fewer C. difficile bacteria and better CDI outcomes. Thus, OCA treatment holds promise as a therapy for severe CDI.
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Affiliation(s)
- Shinsmon Jose
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
| | - Anindita Mukherjee
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
| | - Olivia Horrigan
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
| | - Kenneth D R Setchell
- Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
| | - Wujuan Zhang
- Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Maria E Moreno-Fernandez
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Heidi Andersen
- Department of Pediatric Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Divya Sharma
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
| | - David B Haslam
- Department of Pediatric Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Senad Divanovic
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Rajat Madan
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45220, USA.
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Veterans Affairs Medical Center, Cincinnati, OH, 45220, USA.
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159
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Lower endoscopic delivery of freeze-dried intestinal microbiota results in more rapid and efficient engraftment than oral administration. Sci Rep 2021; 11:4519. [PMID: 33633264 PMCID: PMC7907225 DOI: 10.1038/s41598-021-84152-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
Fecal microbiota transplantation (FMT) is a highly effective treatment for recurrent Clostridioides difficile infection (rCDI). However, standardization of FMT products is essential for its broad implementation into clinical practice. We have developed an oral preparation of freeze-dried, encapsulated microbiota, which is ~ 80% clinically effective, but results in delayed engraftment of donor bacteria relative to administration via colonoscopy. Our objective was to measure the engraftment potential of freeze-dried microbiota without the complexity of variables associated with oral administration. We compared engraftment of identical preparations and doses of freeze-dried microbiota following colonoscopic (9 patients) versus oral administration (18 patients). Microbiota were characterized by sequencing of the 16S rRNA gene, and engraftment was determined using the SourceTracker algorithm. Oligotyping analysis was done to provide high-resolution patterns of microbiota engraftment. Colonoscopic FMT was associated with greater levels of donor engraftment within days following the procedure (ANOVA P = 0.035) and specific increases in the relative abundances of donor Lachnospiraceae, Bacteroidaceae, and Porphyromonadaceae (P ≤ 0.033). Lower relative abundances of Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae families were associated with clinical failures. These results suggest that further optimization of oral capsule FMT may improve its engraftment efficiency and clinical efficacy.
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160
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Castro-Córdova P, Mora-Uribe P, Reyes-Ramírez R, Cofré-Araneda G, Orozco-Aguilar J, Brito-Silva C, Mendoza-León MJ, Kuehne SA, Minton NP, Pizarro-Guajardo M, Paredes-Sabja D. Entry of spores into intestinal epithelial cells contributes to recurrence of Clostridioides difficile infection. Nat Commun 2021; 12:1140. [PMID: 33602902 PMCID: PMC7893008 DOI: 10.1038/s41467-021-21355-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 01/19/2021] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile spores produced during infection are important for the recurrence of the disease. Here, we show that C. difficile spores gain entry into the intestinal mucosa via pathways dependent on host fibronectin-α5β1 and vitronectin-αvβ1. The exosporium protein BclA3, on the spore surface, is required for both entry pathways. Deletion of the bclA3 gene in C. difficile, or pharmacological inhibition of endocytosis using nystatin, leads to reduced entry into the intestinal mucosa and reduced recurrence of the disease in a mouse model. Our findings indicate that C. difficile spore entry into the intestinal barrier can contribute to spore persistence and infection recurrence, and suggest potential avenues for new therapies.
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Affiliation(s)
- Pablo Castro-Córdova
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| | - Paola Mora-Uribe
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Rodrigo Reyes-Ramírez
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| | - Glenda Cofré-Araneda
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Josué Orozco-Aguilar
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| | - Christian Brito-Silva
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| | - María José Mendoza-León
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| | - Sarah A Kuehne
- School of Dentistry and Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Centre for Biomolecular Sciences, The University of Nottingham, Nottingham, UK
| | - Marjorie Pizarro-Guajardo
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Daniel Paredes-Sabja
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile.
- Department of Biology, Texas A&M University, College Station, TX, USA.
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161
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Velikova T, Krastev B, Lozenov S, Gencheva R, Peshevska-Sekulovska M, Nikolaev G, Peruhova M. Antibiotic-Related Changes in Microbiome: The Hidden Villain behind Colorectal Carcinoma Immunotherapy Failure. Int J Mol Sci 2021; 22:1754. [PMID: 33578709 PMCID: PMC7916407 DOI: 10.3390/ijms22041754] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/26/2021] [Accepted: 02/05/2021] [Indexed: 02/05/2023] Open
Abstract
The interplay between drugs and microbiota is critical for successful treatment. An accumulating amount of evidence has identified the significant impact of intestinal microbiota composition on cancer treatment response, particularly immunotherapy. The possible molecular pathways of the interaction between immune checkpoint inhibitors (ICIs) and the microbiome can be used to reverse immunotherapy tolerance in cancer by using various kinds of interventions on the intestinal bacteria. This paper aimed to review the data available on how the antibiotic-related changes in human microbiota during colorectal cancer (CRC) treatment can affect and determine ICI treatment outcomes. We also covered the data that support the potential intimate mechanisms of both local and systemic immune responses induced by changes in the intestinal microbiota. However, further better-powered studies are needed to thoroughly assess the clinical significance of antibiotic-induced alteration of the gut microbiota and its impact on CRC treatment by direct observations of patients receiving antibiotic treatment.
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Affiliation(s)
- Tsvetelina Velikova
- Department of Clinical Immunology, University Hospital Lozenetz, Sofia University St. Kliment Ohridski, Kozyak 1 Str., 1407 Sofia, Bulgaria
| | - Boris Krastev
- Clinic of Medical Oncology, MHAT Hospital for Women Health Nadezhda, 1330 Sofia, Bulgaria; (B.K.); (R.G.)
| | - Stefan Lozenov
- Laboratory for Control and Monitoring of the Antibiotic Resistance, National Centre for Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd, 1504 Sofia, Bulgaria;
| | - Radostina Gencheva
- Clinic of Medical Oncology, MHAT Hospital for Women Health Nadezhda, 1330 Sofia, Bulgaria; (B.K.); (R.G.)
| | - Monika Peshevska-Sekulovska
- Department of Gastroenterology, University Hospital Lozenetz, Sofia University St. Kliment Ohridski, Kozyak 1 Str., 1407 Sofia, Bulgaria; (M.P.-S.); (M.P.)
| | - Georgi Nikolaev
- Faculty of Biology, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria;
| | - Milena Peruhova
- Department of Gastroenterology, University Hospital Lozenetz, Sofia University St. Kliment Ohridski, Kozyak 1 Str., 1407 Sofia, Bulgaria; (M.P.-S.); (M.P.)
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162
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Host immunity modulates the efficacy of microbiota transplantation for treatment of Clostridioides difficile infection. Nat Commun 2021; 12:755. [PMID: 33531483 PMCID: PMC7854624 DOI: 10.1038/s41467-020-20793-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/21/2020] [Indexed: 01/30/2023] Open
Abstract
Fecal microbiota transplantation (FMT) is a successful therapeutic strategy for treating recurrent Clostridioides difficile infection. Despite remarkable efficacy, implementation of FMT therapy is limited and the mechanism of action remains poorly understood. Here, we demonstrate a critical role for the immune system in supporting FMT using a murine C. difficile infection system. Following FMT, Rag1 heterozygote mice resolve C. difficile while littermate Rag1-/- mice fail to clear the infection. Targeted ablation of adaptive immune cell subsets reveal a necessary role for CD4+ Foxp3+ T-regulatory cells, but not B cells or CD8+ T cells, in FMT-mediated resolution of C. difficile infection. FMT non-responsive mice exhibit exacerbated inflammation, impaired engraftment of the FMT bacterial community and failed restoration of commensal bacteria-derived secondary bile acid metabolites in the large intestine. These data demonstrate that the host's inflammatory immune status can limit the efficacy of microbiota-based therapeutics to treat C. difficile infection.
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163
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Rüb AM, Tsakmaklis A, Gräfe SK, Simon MC, Vehreschild MJ, Wuethrich I. Biomarkers of human gut microbiota diversity and dysbiosis. Biomark Med 2021; 15:137-148. [PMID: 33442994 DOI: 10.2217/bmm-2020-0353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022] Open
Abstract
The association of gut microbiota dysbiosis with various human diseases is being substantiated with increasing evidence. Metabolites derived from both, microbiota and the human host play a central role in disease susceptibility and disease progression by extensively modulating host physiology and metabolism. Several of these metabolites have the potential to serve as diagnostic biomarkers for monitoring disease states in conjunction with intestinal microbiota dysbiosis. In this narrative review we evaluate the potential of trimethylamine-N-oxide, short-chain fatty acids, 3-indoxyl sulfate, p-cresyl sulfate, secondary bile acids, hippurate, human β-defensin-2, chromogranin A, secreted immunoglobulins and zonulin to serve as biomarkers for metabolite profiling and diagnostic suitability for dysbiosis and disease.
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Affiliation(s)
- Alina M Rüb
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Anastasia Tsakmaklis
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Stefanie K Gräfe
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Marie-Christine Simon
- Department of Nutrition & Food Sciences, Nutrition & Microbiota, University of Bonn, Bonn, Germany
| | - Maria Jgt Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Irene Wuethrich
- Department of Biosystems Science & Engineering, ETH Zurich, Basel, Switzerland
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164
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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: 78] [Impact Index Per Article: 26.0] [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.
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165
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Pike CM, Theriot CM. Mechanisms of Colonization Resistance Against Clostridioides difficile. J Infect Dis 2020; 223:S194-S200. [PMID: 33326565 DOI: 10.1093/infdis/jiaa408] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Clostridioides difficile is an urgent antimicrobial-resistant bacterium, causing mild to moderate and sometimes life-threatening disease. Commensal gut microbes are critical for providing colonization resistance against C difficile and can be leveraged as non-antibiotic alternative therapeutics for the prevention and treatment of C difficile infection.
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Affiliation(s)
- Colleen M Pike
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Casey M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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166
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Thanissery R, McLaren MR, Rivera A, Reed AD, Betrapally NS, Burdette T, Winston JA, Jacob M, Callahan BJ, Theriot CM. Clostridioides difficile carriage in animals and the associated changes in the host fecal microbiota. Anaerobe 2020; 66:102279. [PMID: 33022384 PMCID: PMC10760528 DOI: 10.1016/j.anaerobe.2020.102279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/31/2020] [Accepted: 09/27/2020] [Indexed: 02/08/2023]
Abstract
The relationship between the gut microbiota and Clostridioides difficile, and its role in the severity of C. difficile infection in humans is an area of active research. Intestinal carriage of toxigenic and non-toxigenic C. difficile strains, with and without clinical signs, is reported in animals, however few studies have looked at the risk factors associated with C. difficile carriage and the role of the host gut microbiota. Here, we isolated and characterized C. difficile strains from different animal species (predominantly canines (dogs), felines (cats), and equines (horses)) that were brought in for tertiary care at North Carolina State University Veterinary Hospital. C. difficile strains were characterized by toxin gene profiling, fluorescent PCR ribotyping, and antimicrobial susceptibility testing. 16S rRNA gene sequencing was done on animal feces to investigate the relationship between the presence of C. difficile and the gut microbiota in different hosts. Here, we show that C. difficile was recovered from 20.9% of samples (42/201), which included 33 canines, 2 felines, and 7 equines. Over 69% (29/42) of the isolates were toxigenic and belonged to 14 different ribotypes including ones known to cause CDI in humans. The presence of C. difficile results in a shift in the fecal microbial community structure in both canines and equines. Commensal Clostridium hiranonis was negatively associated with C. difficile in canines. Further experimentation showed a clear antagonistic relationship between the two strains in vitro, suggesting that commensal Clostridia might play a role in colonization resistance against C. difficile in different hosts.
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Affiliation(s)
- R Thanissery
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - M R McLaren
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - A Rivera
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - A D Reed
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - N S Betrapally
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - T Burdette
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - J A Winston
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - M Jacob
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - B J Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - C M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.
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167
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Zubeldia-Varela E, Barber D, Barbas C, Perez-Gordo M, Rojo D. Sample pre-treatment procedures for the omics analysis of human gut microbiota: Turning points, tips and tricks for gene sequencing and metabolomics. J Pharm Biomed Anal 2020; 191:113592. [PMID: 32947167 DOI: 10.1016/j.jpba.2020.113592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/29/2020] [Accepted: 08/23/2020] [Indexed: 02/06/2023]
Abstract
The connection between gut microbiota and human health is becoming increasingly relevant and the number of groups working in this field is constantly growing. In this context, from high-throughput gene sequencing to metabolomics analysis, the omics technologies have contributed enormously to unveil the secret crosstalk between us and our microbes. All the omics technologies produce a great amount of information, and processing this information is time-consuming and expensive. For this reason, a correct experimental design and a careful pre-analytical planning are crucial. To study the human gut microbiota, faeces are the sample of choice. Faecal material is complex, and procedures for collecting and preserving faeces are not well-established. Furthermore, increasing evidence suggests that multiple confounding factors, such as antibiotics consumption, mode of delivery, diet, aging and several diseases and disorders can alter the composition and functionality of the microbiota. This review is focused on the discussion of critical general issues during the pre-analytical planning, from patient handling to faeces sampling, including collection procedures, transport, storage conditions and possible pre-treatments, which are critical for a successful research in omics with a special attention to metabolomics and gene sequencing. We also point out that the adoption of standard operating procedures in the field is needed to guarantee accuracy and reproducibility of results.
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Affiliation(s)
- Elisa Zubeldia-Varela
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Domingo Barber
- Institute of Applied and Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Marina Perez-Gordo
- Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Institute of Applied and Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - David Rojo
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain.
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168
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Zaher S. Nutrition and the gut microbiome during critical illness: A new insight of nutritional therapy. Saudi J Gastroenterol 2020; 26:300487. [PMID: 33208559 PMCID: PMC8019138 DOI: 10.4103/sjg.sjg_352_20] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/16/2020] [Accepted: 08/16/2020] [Indexed: 12/13/2022] Open
Abstract
Changes in the microbiome in response to environmental influences can affect the overall health. Critical illness is considered one of the major environmental factors that can potentially influence the normal gut homeostasis. It is associated with pathophysiological effects causing damage to the intestinal microbiome. Alteration of intestinal microbial composition during critical illness may subsequently compromise the integrity of the intestinal epithelial barrier and intestinal mucosa absorptive function. Many factors can impact the microbiome of critically ill patients including ischemia, hypoxia and hypotension along with the iatrogenic effects of therapeutic agents and the lack of enteral feeds. Factors related to disease state and medication are inevitable and they are part of the intensive care unit (ICU) exposure. However, a nutritional intervention targeting gut microbiota might have the potential to improve clinical outcomes in the critically ill population given the extensive vascular and lymphatic links between the intestines and other organs. Although nutrition is considered an integral part of the treatment plan of critically ill patients, still the role of nutritional intervention is restricted to improve nitrogen balance. What is dismissed is whether the nutrients we provide are adequate and how they are processed and utilised by the host and the microbiota. Therefore, the goal of nutrition therapy during critical illness should be extended to provide good quality feeds with balanced macronutrient content to feed up the entire body including the microbiota and host cells. The main aim of this review is to examine the current literature on the effect of critical illness on the gut microbiome and to highlight the role of nutrition as a factor affecting the intestinal microbiome-host relationship during critical illness.
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Affiliation(s)
- Sara Zaher
- Department of Clinical Nutrition, Faculty of Applied Medical Sciences, Taibah University, Saudi Arabia
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169
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Engevik MA, Danhof HA, Shrestha R, Chang-Graham AL, Hyser JM, Haag AM, Mohammad MA, Britton RA, Versalovic J, Sorg JA, Spinler JK. Reuterin disrupts Clostridioides difficile metabolism and pathogenicity through reactive oxygen species generation. Gut Microbes 2020; 12:1788898. [PMID: 32804011 PMCID: PMC7524292 DOI: 10.1080/19490976.2020.1795388] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/16/2020] [Accepted: 07/06/2020] [Indexed: 02/03/2023] Open
Abstract
Antibiotic resistance is one of the world's greatest public health challenges and adjunct probiotic therapies are strategies that could lessen this burden. Clostridioides difficile infection (CDI) is a prime example where adjunct probiotic therapies could decrease disease incidence through prevention. Human-derived Lactobacillus reuteri is a probiotic that produces the antimicrobial compound reuterin known to prevent C. difficile colonization of antibiotic-treated fecal microbial communities. However, the mechanism of inhibition is unclear. We show that reuterin inhibits C. difficile outgrowth from spores and vegetative cell growth, however, no effect on C. difficile germination or sporulation was observed. Consistent with published studies, we found that exposure to reuterin stimulated reactive oxygen species (ROS) in C. difficile, resulting in a concentration-dependent reduction in cell viability that was rescued by the antioxidant glutathione. Sublethal concentrations of reuterin enhanced the susceptibility of vegetative C. difficile to vancomycin and metronidazole treatment and reduced toxin synthesis by C. difficile. We also demonstrate that reuterin is protective against C. difficile toxin-mediated cellular damage in the human intestinal enteroid model. Overall, our results indicate that ROS are essential mediators of reuterin activity and show that reuterin production by L. reuteri is compatible as a therapeutic in a clinically relevant model.
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Affiliation(s)
- Melinda A. Engevik
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Heather A. Danhof
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Ritu Shrestha
- Department of Biology, Texas A&M University, College Station, TX, USA
| | | | - Joseph M. Hyser
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony M. Haag
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Mahmoud A. Mohammad
- Department of Pediatrics, Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Robert A. Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Joseph A. Sorg
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Jennifer K. Spinler
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
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170
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Wallace MJ, Fishbein SRS, Dantas G. Antimicrobial resistance in enteric bacteria: current state and next-generation solutions. Gut Microbes 2020; 12:1799654. [PMID: 32772817 PMCID: PMC7524338 DOI: 10.1080/19490976.2020.1799654] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Antimicrobial resistance is one of the largest threats to global health and imposes substantial burdens in terms of morbidity, mortality, and economic costs. The gut is a key conduit for the genesis and spread of antimicrobial resistance in enteric bacterial pathogens. Distinct bacterial species that cause enteric disease can exist as invasive enteropathogens that immediately evoke gastrointestinal distress, or pathobionts that can arise from established bacterial commensals to inflict dysbiosis and disease. Furthermore, various environmental reservoirs and stressors facilitate the evolution and transmission of resistance. In this review, we present a comprehensive discussion on circulating resistance profiles and gene mobilization strategies of the most problematic species of enteric bacterial pathogens. Importantly, we present emerging approaches toward surveillance of pathogens and their resistance elements as well as promising treatment strategies that can circumvent common resistance mechanisms.
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Affiliation(s)
- M. J. Wallace
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - S. R. S. Fishbein
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - G. Dantas
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA,CONTACT G. Dantas Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO
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171
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Shao H, Zhang C, Xiao N, Tan Z. Gut microbiota characteristics in mice with antibiotic-associated diarrhea. BMC Microbiol 2020; 20:313. [PMID: 33059603 PMCID: PMC7559773 DOI: 10.1186/s12866-020-01999-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/07/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Antibiotic-associated diarrhea (AAD), defined as diarrhea that occurs in association with the administration of antibiotics and without another clear etiology, is one of the most common adverse drug events of antibiotics therapy. We established a diarrhea model induced by gentamycin and cefradine to investigate the microbiota characteristics in the intestinal lumen of mice with AAD and provide insights into noteworthy bacteria related to gentamicin and cefradine-associated diarrhea. RESULTS The number of OTUs in the model group and the normal group was 983 and 2107, respectively, and 872 identical OTUs were shared between two groups. Species richness and species diversity of intestinal microbe were altered by antibiotics administration. PCoA showed a clear separation between AAD and health control. The dominant phyla of AAD mice were Firmicutes (52.63%) and Proteobacteria (46.37%). Among the genus with top 20 abundance, the relative abundance of 7 genera, Ruminococcus, Blautia, Enterococcus, Eubacterium, Clostridium, Coprococcus, and Aerococcus, were enriched in the model group. Based upon the LEfSe analysis, Enterococcus, Eubacterium, Ruminococcus, and Blautia were identified as potential biomarkers for AAD. CONCLUSIONS The bacterial diversity of the intestinal lumen was diminished after gentamicin and cefradine administration. The alterations in the abundance and composition of gut microbiota further led to the dysfunction of gut microbiota. More specifically, gentamicin and cefradine significantly increased the abundance of the opportunistic pathogens, of which Enterococcus and Clostridium were the most prominent and most worthy of attention.
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Affiliation(s)
- Haoqing Shao
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China.,Hunan Key Laboratory of TCM Prescription and Syndromes Translational Medicine, Changsha, Hunan, China
| | - Chenyang Zhang
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China.,Hunan Key Laboratory of TCM Prescription and Syndromes Translational Medicine, Changsha, Hunan, China
| | - Nenqun Xiao
- School of Pharmaceutical Science, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Zhoujin Tan
- Hunan Key Laboratory of TCM Prescription and Syndromes Translational Medicine, Changsha, Hunan, China. .,School of Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China.
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172
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Pereira FC, Wasmund K, Cobankovic I, Jehmlich N, Herbold CW, Lee KS, Sziranyi B, Vesely C, Decker T, Stocker R, Warth B, von Bergen M, Wagner M, Berry D. Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization. Nat Commun 2020; 11:5104. [PMID: 33037214 PMCID: PMC7547075 DOI: 10.1038/s41467-020-18928-1] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 09/18/2020] [Indexed: 12/18/2022] Open
Abstract
Many intestinal pathogens, including Clostridioides difficile, use mucus-derived sugars as crucial nutrients in the gut. Commensals that compete with pathogens for such nutrients are therefore ecological gatekeepers in healthy guts, and are attractive candidates for therapeutic interventions. Nevertheless, there is a poor understanding of which commensals use mucin-derived sugars in situ as well as their potential to impede pathogen colonization. Here, we identify mouse gut commensals that utilize mucus-derived monosaccharides within complex communities using single-cell stable isotope probing, Raman-activated cell sorting and mini-metagenomics. Sequencing of cell-sorted fractions reveals members of the underexplored family Muribaculaceae as major mucin monosaccharide foragers, followed by members of Lachnospiraceae, Rikenellaceae, and Bacteroidaceae families. Using this information, we assembled a five-member consortium of sialic acid and N-acetylglucosamine utilizers that impedes C. difficile's access to these mucosal sugars and impairs pathogen colonization in antibiotic-treated mice. Our findings underscore the value of targeted approaches to identify organisms utilizing key nutrients and to rationally design effective probiotic mixtures.
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Affiliation(s)
- Fátima C Pereira
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Kenneth Wasmund
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Iva Cobankovic
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Straße 38, 1090, Vienna, Austria
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Craig W Herbold
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Kang Soo Lee
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Barbara Sziranyi
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Cornelia Vesely
- Medical University of Vienna, Center for Anatomy and Cell Biology, Division of Cell and Developmental Biology, Vienna, Austria
| | - Thomas Decker
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Roman Stocker
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Benedikt Warth
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Währinger Straße 38, 1090, Vienna, Austria
| | - Martin von Bergen
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Permoserstraße 15, 04318, Leipzig, Germany
| | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220, Aalborg, Denmark
| | - David Berry
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Althanstrasse 14, 1090, Vienna, Austria.
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
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173
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Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic. mSystems 2020; 5:5/5/e00340-20. [PMID: 33024048 PMCID: PMC7542558 DOI: 10.1128/msystems.00340-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We are just beginning to understand the unintended effects of antibiotics on our microbiomes and health. In this study, we aimed to define an approach by which one could obtain a comprehensive picture of (i) how antibiotics spatiotemporally impact commensal microbes throughout the gut and (ii) how these changes influence host chemistry throughout the body. We found that just a single dose of antibiotic altered host chemistry in a variety of organs and that microbiome alterations were not uniform throughout the gut. As technological advances increase the feasibility of whole-organism studies, we argue that using these approaches can provide further insight on both the wide-ranging effects of antibiotics on health and how to restore microbial communities to mitigate these effects. Antibiotics are a mainstay of modern medicine, but as they kill their target pathogen(s), they often affect the commensal microbiota. Antibiotic-induced microbiome dysbiosis is a growing research focus and health concern, often assessed via analysis of fecal samples. However, such analysis does not inform how antibiotics influence the microbiome across the whole host or how such changes subsequently alter host chemistry. In this study, we investigated the acute (1 day postadministration) and delayed (6 days postadministration) effects of a single parenteral dose of two common antibiotics, ampicillin or vancomycin, on the global metabolome and microbiome of mice across 77 different body sites from 25 different organs. The broader-spectrum agent ampicillin had the greatest impact on the microbiota in the lower gastrointestinal tract (cecum and colon), where microbial diversity is highest. In the metabolome, the greatest effects were seen 1 day posttreatment, and changes in metabolite abundances were not confined to the gut. The local abundance of ampicillin and its metabolites correlated with increased metabolome effect size and a loss of alpha diversity versus control mice. Additionally, small peptides were elevated in the lower gastrointestinal tract of mice 1 day after antibiotic treatment. While a single parenteral dose of antibiotic did not drastically alter the microbiome, nevertheless, changes in the metabolome were observed both within and outside the gut. This study provides a framework for how whole-organism -omics approaches can be employed to understand the impact of antibiotics on the entire host. IMPORTANCE We are just beginning to understand the unintended effects of antibiotics on our microbiomes and health. In this study, we aimed to define an approach by which one could obtain a comprehensive picture of (i) how antibiotics spatiotemporally impact commensal microbes throughout the gut and (ii) how these changes influence host chemistry throughout the body. We found that just a single dose of antibiotic altered host chemistry in a variety of organs and that microbiome alterations were not uniform throughout the gut. As technological advances increase the feasibility of whole-organism studies, we argue that using these approaches can provide further insight on both the wide-ranging effects of antibiotics on health and how to restore microbial communities to mitigate these effects.
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174
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The Great ESKAPE: Exploring the Crossroads of Bile and Antibiotic Resistance in Bacterial Pathogens. Infect Immun 2020; 88:IAI.00865-19. [PMID: 32661122 DOI: 10.1128/iai.00865-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Throughout the course of infection, many pathogens encounter bactericidal conditions that threaten the viability of the bacteria and impede the establishment of infection. Bile is one of the most innately bactericidal compounds present in humans, functioning to reduce the bacterial burden in the gastrointestinal tract while also aiding in digestion. It is becoming increasingly apparent that pathogens successfully resist the bactericidal conditions of bile, including bacteria that do not normally cause gastrointestinal infections. This review highlights the ability of Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, Enterobacter (ESKAPE), and other enteric pathogens to resist bile and how these interactions can impact the sensitivity of bacteria to various antimicrobial agents. Given that pathogen exposure to bile is an essential component to gastrointestinal transit that cannot be avoided, understanding how bile resistance mechanisms align with antimicrobial resistance is vital to our ability to develop new, successful therapeutics in an age of widespread and increasing antimicrobial resistance.
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175
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Arsenic Accumulation of Realgar Altered by Disruption of Gut Microbiota in Mice. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:8380473. [PMID: 32908570 PMCID: PMC7450324 DOI: 10.1155/2020/8380473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/20/2020] [Indexed: 12/21/2022]
Abstract
Objective To investigate the influence of gut microbiota on arsenic accumulation of realgar in mice. Methods Mice were treated with antibiotics to form a mouse model of gut microbial disruption. Antibiotic-treated and normally raised mice were given 15 mg/kg, 150 mg/kg, and 750 mg/kg realgar by gavage and 0.2 mg/kg and 1 mg/kg arsenic solution by subcutaneous injection for 7 days. The concentration of arsenic in mice whole blood was determined by inductively coupled plasma mass spectrometry (ICP-MS). Arsenic accumulation in antibiotic-treated mice and normally raised mice was compared. Results After exposure to low dose (15 mg/kg) and middle dose (150 mg/kg) of realgar, significantly, more arsenic was accumulated in the whole blood of antibiotic-treated mice compared to normally raised counterparts, which indicated that the disruption of gut microbiota could lead to higher arsenic load of realgar in mice. The homeostasis of gut microbiota was supposed to be disrupted by high dose (750 mg/kg) of realgar because after exposure to high dose of realgar, there was no significant difference in arsenic accumulation between antibiotic-treated and normally raised mice. Furthermore, arsenic solution was administered by subcutaneous injection to mice to investigate the influence of gut microbial differences on arsenic accumulation in addition to the absorption process, and there was no significant difference in arsenic accumulation between mice with these two different statuses of gut microbiota. Conclusions Gut microbiota disruption could increase arsenic accumulation of realgar in mice.
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176
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Jones SM, Gaier A, Enomoto H, Ishii P, Pilla R, Price J, Suchodolski J, Steiner JM, Papich MG, Messenger K, Tolbert MK. The effect of combined carprofen and omeprazole administration on gastrointestinal permeability and inflammation in dogs. J Vet Intern Med 2020; 34:1886-1893. [PMID: 32893926 PMCID: PMC7517840 DOI: 10.1111/jvim.15897] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022] Open
Abstract
Background Proton pump inhibitors (eg, omeprazole) commonly are administered concurrently with nonsteroidal anti‐inflammatory drugs (NSAIDs; eg, carprofen) as prophylaxis to decrease the risk of gastrointestinal (GI) injury. However, evidence to support this practice is weak, and it might exacerbate dysbiosis and inflammation. Hypothesis/Objectives To evaluate the effect of carprofen alone or combined with omeprazole in dogs. We hypothesized that coadministration of omeprazole and carprofen would significantly increase GI permeability and dysbiosis index (DI) compared to no treatment or carprofen alone. Animals Six healthy adult colony beagle dogs. Methods Gastrointestinal permeability and inflammation were assessed by serum lipopolysaccharide (LPS) concentration, plasma iohexol concentration, fecal DI, and fecal calprotectin concentration in a prospective, 3‐period design. In the first 7‐day period, dogs received no intervention (baseline). During the 2nd period, dogs received 4 mg/kg of carprofen q24h PO for 7 days. In the 3rd period, dogs received 4 mg/kg of carprofen q24h and 1 mg/kg of omeprazole q12h PO for 7 days. Gastrointestinal permeability testing was performed at the end of each period. Data were analyzed using repeated measures mixed model analysis of variance with Tukey‐Kramer post hoc tests (P < .05). Results Serum LPS and plasma iohexol concentrations did not differ between treatments. Fecal calprotectin concentrations differed between treatments (P = .03). The DI varied over time based on the treatment received (P = .03). Coadministration of omeprazole and carprofen significantly increased fecal calprotectin concentration and DI compared to baseline and carprofen alone. Conclusions and Clinical Importance Omeprazole prophylaxis induces fecal dysbiosis and increases intestinal inflammatory markers when coadministered with carprofen to otherwise healthy dogs with no other risk factors for GI bleeding.
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Affiliation(s)
- Susan M Jones
- College of Veterinary Medicine, Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Ann Gaier
- College of Veterinary Medicine, Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Hiroko Enomoto
- College of Veterinary Medicine, Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Patricia Ishii
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Rachel Pilla
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Josh Price
- Office of Information and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jan Suchodolski
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Joerg M Steiner
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Mark G Papich
- College of Veterinary Medicine, Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Kristen Messenger
- College of Veterinary Medicine, Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - M Katherine Tolbert
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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177
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Lawler AJ, Lambert PA, Worthington T. A Revised Understanding of Clostridioides difficile Spore Germination. Trends Microbiol 2020; 28:744-752. [DOI: 10.1016/j.tim.2020.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/17/2020] [Accepted: 03/25/2020] [Indexed: 12/17/2022]
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178
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Shao H, Zhang C, Wang C, Tan Z. Intestinal mucosal bacterial diversity of antibiotic-associated diarrhea (AAD) mice treated with Debaryomyces hansenii and Qiweibaizhu powder. 3 Biotech 2020; 10:392. [PMID: 32832342 DOI: 10.1007/s13205-020-02383-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/06/2020] [Indexed: 02/08/2023] Open
Abstract
The aim was to investigate the combined effect of Debaryomyces hansenii and Qiweibaizhu powder (QWBZP) on the bacterial diversity of the intestinal mucosa of antibiotic-associated diarrhea (AAD) mice, for the potential treatment of diarrhea, especially which is induced by administration of antibiotics. Eighteen (18) mice were randomly assigned to three equal groups of six mice, namely Normal (mn group), Placebo control (mm group) and D. hansenii and QWBZP (DQ) treatment (mdq group). Mice were gavaged with a solution (23.33 mL·kg-1·day-1) consisting of gentamicin and cefradine to establish AAD. The DQ treatment group was gavaged with DQ for 4 days, and sterile water was used as a placebo control. The metagenome DNA of the intestinal mucosal microbiota was extracted, and the 16S rRNA gene was sequenced. Analysis showed that there were 288 OTUs for the normal group, 443 for the placebo control group, and 229 for the DQ treatment group. Phylogenetically, the gut microbiota of the DQ treatment group and the normal group were closer to each other than to the placebo control group. Both the DQ and placebo-treated groups included Stenotrophomonas, Robinsoniella, Bacteroidales S24-7 group norank, Citrobacter, and Glutamicibacter, but their abundances were significantly higher in the DQ treatment group than in the placebo control group. This suggested that the combined use of D. hansenii and QWBZP overcame the influence of dysbacteriosis and could lead to the recovery of intestinal mucosal microbiota homeostasis. This positive effect is likely related to short-chain fatty acid (SCFA)-producing bacteria, such as members of Micrococcaceae, Lachnospiraceae, and Bacteroidales S24-7 group, which could play beneficial roles in protecting the mucosal barrier and stimulating the immune response in mice.
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179
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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.
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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
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180
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Pilla R, Gaschen FP, Barr JW, Olson E, Honneffer J, Guard BC, Blake AB, Villanueva D, Khattab MR, AlShawaqfeh MK, Lidbury JA, Steiner JM, Suchodolski JS. Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs. J Vet Intern Med 2020; 34:1853-1866. [PMID: 32856349 PMCID: PMC7517498 DOI: 10.1111/jvim.15871] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 07/17/2020] [Accepted: 07/28/2020] [Indexed: 12/27/2022] Open
Abstract
Background Metronidazole has a substantial impact on the gut microbiome. However, the recovery of the microbiome after discontinuation of administration, and the metabolic consequences of such alterations have not been investigated to date. Objectives To describe the impact of 14‐day metronidazole administration, alone or in combination with a hydrolyzed protein diet, on fecal microbiome, metabolome, bile acids (BAs), and lactate production, and on serum metabolome in healthy dogs. Animals Twenty‐four healthy pet dogs. Methods Prospective, nonrandomized controlled study. Dogs fed various commercial diets were divided in 3 groups: control group (no intervention, G1); group receiving hydrolyzed protein diet, followed by metronidazole administration (G2); and group receiving metronidazole only (G3). Microbiome composition was evaluated with sequencing of 16S rRNA genes and quantitative polymerase chain reaction (qPCR)‐based dysbiosis index. Untargeted metabolomics analysis of fecal and serum samples was performed, followed by targeted assays for fecal BAs and lactate. Results No changes were observed in G1, or G2 during diet change. Metronidazole significantly changed microbiome composition in G2 and G3, including decreases in richness (P < .001) and in key bacteria such as Fusobacteria (q < 0.001) that did not fully resolve 4 weeks after metronidazole discontinuation. Fecal dysbiosis index was significantly increased (P < .001). Those changes were accompanied by increased fecal total lactate (P < .001), and decreased secondary BAs deoxycholic acid and lithocholic acid (P < .001). Conclusion and Clinical Importance Our results indicate a minimum 4‐week effect of metronidazole on fecal microbiome and metabolome, supporting a cautious approach to prescription of metronidazole in dogs.
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Affiliation(s)
- Rachel Pilla
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
| | - Frederic P Gaschen
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - James W Barr
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
| | - Erin Olson
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Julia Honneffer
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
| | - Blake C Guard
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
| | - Amanda B Blake
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
| | - Dean Villanueva
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
| | - Mohammad R Khattab
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
| | - Mustafa K AlShawaqfeh
- School of Electrical Engineering and Information Technology, German-Jordanian University, Amman, Jordan
| | - Jonathan A Lidbury
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
| | - Jörg M Steiner
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
| | - Jan S Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, Texas, USA
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181
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Gutierrez D, Weinstock A, Antharam VC, Gu H, Jasbi P, Shi X, Dirks B, Krajmalnik-Brown R, Maldonado J, Guinan J, Thangamani S. Antibiotic-induced gut metabolome and microbiome alterations increase the susceptibility to Candida albicans colonization in the gastrointestinal tract. FEMS Microbiol Ecol 2020; 96:5643884. [PMID: 31769789 PMCID: PMC6934136 DOI: 10.1093/femsec/fiz187] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Antibiotic-induced alterations in the gut ecosystem increases the susceptibility to Candida albicans, yet the mechanisms involved remains poorly understood. Here we show that mice treated with the broad-spectrum antibiotic cefoperazone promoted the growth, morphogenesis and gastrointestinal (GI) colonization of C. albicans. Using metabolomics, we revealed that the cecal metabolic environment of the mice treated with cefoperazone showed a significant alteration in intestinal metabolites. Levels of carbohydrates, sugar alcohols and primary bile acids increased, whereas carboxylic acids and secondary bile acids decreased in antibiotic treated mice susceptible to C. albicans. Furthermore, using in-vitro assays, we confirmed that carbohydrates, sugar alcohols and primary bile acids promote, whereas carboxylic acids and secondary bile acids inhibit the growth and morphogenesis of C. albicans. In addition, in this study we report changes in the levels of gut metabolites correlated with shifts in the gut microbiota. Taken together, our in-vivo and in-vitro results indicate that cefoperazone-induced metabolome and microbiome alterations favor the growth and morphogenesis of C. albicans, and potentially play an important role in the GI colonization of C. albicans.
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Affiliation(s)
- Daniel Gutierrez
- College of Veterinary Medicine, Midwestern University, 19555 N. 59th Ave. Glendale, AZ 85308, USA
| | - Anthony Weinstock
- Arizona College of Osteopathic Medicine, Midwestern University, 19555 N. 59th Ave. Glendale, AZ 85308, USA
| | - Vijay C Antharam
- Department of Chemistry, School of Science and Human Development, Methodist University, 5400 Ramsey St, Fayetteville, NC 28311, USA
| | - Haiwei Gu
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Phoenix, AZ 85259, USA
| | - Paniz Jasbi
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Phoenix, AZ 85259, USA
| | - Xiaojian Shi
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Phoenix, AZ 85259, USA
| | - Blake Dirks
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85280, USA
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85280, USA.,School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287, USA.,Biodesign Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Juan Maldonado
- Biodesign Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jack Guinan
- College of Veterinary Medicine, Midwestern University, 19555 N. 59th Ave. Glendale, AZ 85308, USA
| | - Shankar Thangamani
- Department of Pathology and Population Medicine, College of Veterinary Medicine, Midwestern University, 19555 N. 59th Ave. Glendale, AZ 85308, USA
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182
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Stephen-Victor E, Crestani E, Chatila TA. Dietary and Microbial Determinants in Food Allergy. Immunity 2020; 53:277-289. [PMID: 32814026 PMCID: PMC7467210 DOI: 10.1016/j.immuni.2020.07.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/13/2020] [Accepted: 07/27/2020] [Indexed: 12/16/2022]
Abstract
The steep rise in food allergy (FA) has evoked environmental factors involved in disease pathogenesis, including the gut microbiota, diet, and their metabolites. Early introduction of solid foods synchronizes with the "weaning reaction," a time during which the microbiota imprints durable oral tolerance. Recent work has shown that children with FA manifest an early onset dysbiosis with the loss of Clostridiales species, which promotes the differentiation of ROR-γt+ regulatory T cells to suppress FA. This process can be reversed in pre-clinical mouse models by targeted bacteriotherapy. Here, we review the dominant tolerance mechanisms enforced by the microbiota to suppress FA and discuss therapeutic intervention strategies that act to recapitulate the early life window of opportunity in stemming the FA epidemic.
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Affiliation(s)
- Emmanuel Stephen-Victor
- Division of Immunology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Elena Crestani
- Division of Immunology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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183
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Perino A, Demagny H, Velazquez-Villegas L, Schoonjans K. Molecular Physiology of Bile Acid Signaling in Health, Disease, and Aging. Physiol Rev 2020; 101:683-731. [PMID: 32790577 DOI: 10.1152/physrev.00049.2019] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Over the past two decades, bile acids (BAs) have become established as important signaling molecules that enable fine-tuned inter-tissue communication from the liver, their site of production, over the intestine, where they are modified by the gut microbiota, to virtually any organ, where they exert their pleiotropic physiological effects. The chemical variety of BAs, to a large extent determined by the gut microbiome, also allows for a complex fine-tuning of adaptive responses in our body. This review provides an overview of the mechanisms by which BA receptors coordinate several aspects of physiology and highlights new therapeutic strategies for diseases underlying pathological BA signaling.
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Affiliation(s)
- Alessia Perino
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne (EPFL), Switzerland
| | - Hadrien Demagny
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne (EPFL), Switzerland
| | - Laura Velazquez-Villegas
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne (EPFL), Switzerland
| | - Kristina Schoonjans
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne (EPFL), Switzerland
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184
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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.
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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
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185
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Identification of Simplified Microbial Communities That Inhibit Clostridioides difficile Infection through Dilution/Extinction. mSphere 2020; 5:5/4/e00387-20. [PMID: 32727857 PMCID: PMC7392540 DOI: 10.1128/msphere.00387-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The gastrointestinal microbiome plays an important role in limiting susceptibility to infection with Clostridioides difficile To better understand the ecology of bacteria important for C. difficile colonization resistance, we developed an experimental platform to simplify complex communities of fecal bacteria through dilution and rapidly screen for their ability to resist C. difficile colonization after challenge, as measured by >100-fold reduction in levels of C. difficile in challenged communities. We screened 76 simplified communities diluted from cultures of six fecal donors and identified 24 simplified communities that inhibited C. difficile colonization in vitro Sequencing revealed that simplified communities were composed of 19 to 67 operational taxonomic units (OTUs) and could be partitioned into four distinct community types. One simplified community could be further simplified from 56 to 28 OTUs through dilution and retain the ability to inhibit C. difficile We tested the efficacy of seven simplified communities in a humanized microbiota mouse model. We found that four communities were able to significantly reduce the severity of the initial C. difficile infection and limit susceptibility to disease relapse. Analysis of fecal microbiomes from treated mice demonstrated that simplified communities accelerated recovery of indigenous bacteria and led to stable engraftment of 19 to 22 OTUs from simplified communities. Overall, the insights gained through the identification and characterization of these simplified communities increase our understanding of the microbial dynamics of C. difficile infection and recovery.IMPORTANCEClostridioides difficile is the leading cause of antibiotic-associated diarrhea and a significant health care burden. Fecal microbiota transplantation is highly effective at treating recurrent C. difficile disease; however, uncertainties about the undefined composition of fecal material and potential long-term unintended health consequences remain. These concerns have motivated studies to identify new communities of microbes with a simpler composition that will be effective at treating disease. This work describes a platform for rapidly identifying and screening new simplified communities for efficacy in treating C. difficile infection. Four new simplified communities of microbes with potential for development of new therapies to treat C. difficile disease are identified. While this platform was developed and validated to model infection with C. difficile, the underlying principles described in the paper could be easily modified to develop therapeutics to treat other gastrointestinal diseases.
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186
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Cabral DJ, Wurster JI, Korry BJ, Penumutchu S, Belenky P. Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin. mSystems 2020; 5:e00317-20. [PMID: 32723789 PMCID: PMC7394352 DOI: 10.1128/msystems.00317-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/08/2020] [Indexed: 02/07/2023] Open
Abstract
Dietary composition and antibiotic use have major impacts on the structure and function of the gut microbiome, often resulting in dysbiosis. Despite this, little research has been done to explore the role of host diet as a determinant of antibiotic-induced microbiome disruption. Here, we utilize a multi-omic approach to characterize the impact of Western-style diet consumption on ciprofloxacin-induced changes to gut microbiome structure and transcriptional activity. We found that Western diet consumption dramatically increased Bacteroides abundances and shifted the community toward the metabolism of simple sugars and mucus glycoproteins. Mice consuming a Western-style diet experienced a greater expansion of Firmicutes following ciprofloxacin treatment than those eating a control diet. Transcriptionally, we found that ciprofloxacin reduced the abundance of tricarboxylic acid (TCA) cycle transcripts on both diets, suggesting that carbon metabolism plays a key role in the response of the gut microbiome to this antibiotic. Despite this, we observed extensive diet-dependent differences in the impact of ciprofloxacin on microbiota function. In particular, at the whole-community level we detected an increase in starch degradation, glycolysis, and pyruvate fermentation following antibiotic treatment in mice on the Western diet, which we did not observe in mice on the control diet. Similarly, we observed diet-specific changes in the transcriptional activity of two important commensal bacteria, Akkermansia muciniphila and Bacteroides thetaiotaomicron, involving diverse cellular processes such as nutrient acquisition, stress responses, and capsular polysaccharide (CPS) biosynthesis. These findings demonstrate that host diet plays a role in determining the impacts of ciprofloxacin on microbiome composition and microbiome function.IMPORTANCE Due to the growing incidence of disorders related to antibiotic-induced dysbiosis, it is essential to determine how our "Western"-style diet impacts the response of the microbiome to antibiotics. While diet and antibiotics have profound impacts on gut microbiome composition, little work has been done to examine their combined effects. Previous work has shown that nutrient availability, influenced by diet, plays an important role in determining the extent of antibiotic-induced disruption to the gut microbiome. Thus, we hypothesize that the Western diet will shift microbiota metabolism toward simple sugar and mucus degradation and away from polysaccharide utilization. Because of bacterial metabolism's critical role in antibiotic susceptibility, this change in baseline metabolism will impact how the structure and function of the microbiome are impacted by ciprofloxacin exposure. Understanding how diet modulates antibiotic-induced microbiome disruption will allow for the development of dietary interventions that can alleviate many of the microbiome-dependent complications of antibiotic treatment.
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Affiliation(s)
- Damien J Cabral
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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187
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Marion S, Desharnais L, Studer N, Dong Y, Notter MD, Poudel S, Menin L, Janowczyk A, Hettich RL, Hapfelmeier S, Bernier-Latmani R. Biogeography of microbial bile acid transformations along the murine gut. J Lipid Res 2020; 61:1450-1463. [PMID: 32661017 DOI: 10.1194/jlr.ra120001021] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bile acids, which are synthesized from cholesterol by the liver, are chemically transformed along the intestinal tract by the gut microbiota, and the products of these transformations signal through host receptors, affecting overall host health. These transformations include bile acid deconjugation, oxidation, and 7α-dehydroxylation. An understanding of the biogeography of bile acid transformations in the gut is critical because deconjugation is a prerequisite for 7α-dehydroxylation and because most gut microorganisms harbor bile acid transformation capacity. Here, we used a coupled metabolomic and metaproteomic approach to probe in vivo activity of the gut microbial community in a gnotobiotic mouse model. Results revealed the involvement of Clostridium scindens in 7α-dehydroxylation, of the genera Muribaculum and Bacteroides in deconjugation, and of six additional organisms in oxidation (the genera Clostridium, Muribaculum, Bacteroides, Bifidobacterium, Acutalibacter, and Akkermansia). Furthermore, the bile acid profile in mice with a more complex microbiota, a dysbiosed microbiota, or no microbiota was considered. For instance, conventional mice harbor a large diversity of bile acids, but treatment with an antibiotic such as clindamycin results in the complete inhibition of 7α-dehydroxylation, underscoring the strong inhibition of organisms that are capable of carrying out this process by this compound. Finally, a comparison of the hepatic bile acid pool size as a function of microbiota revealed that a reduced microbiota affects host signaling but not necessarily bile acid synthesis. In this study, bile acid transformations were mapped to the associated active microorganisms, offering a systematic characterization of the relationship between microbiota and bile acid composition.
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Affiliation(s)
- Solenne Marion
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Lyne Desharnais
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Studer
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Yuan Dong
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Matheus D Notter
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Suresh Poudel
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Laure Menin
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Andrew Janowczyk
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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188
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Romo JA, Markey L, Kumamoto CA. Lipid Species in the GI Tract are Increased by the Commensal Fungus Candida albicans and Decrease the Virulence of Clostridioides difficile. J Fungi (Basel) 2020; 6:E100. [PMID: 32635220 PMCID: PMC7557729 DOI: 10.3390/jof6030100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/18/2020] [Accepted: 06/30/2020] [Indexed: 12/12/2022] Open
Abstract
Prior antibiotic treatment is a risk factor for Clostridioides difficile infection (CDI); the commensal gut microbiota plays a key role in determining host susceptibility to the disease. Previous studies demonstrate that the pre-colonization of mice with a commensal fungus, Candida albicans, protects against a lethal challenge with C. difficile spores. The results reported here demonstrate that the cecum contents of antibiotic-treated mice with C. albicans colonization contained different levels of several lipid species, including non-esterified, unsaturated long-chain fatty acids compared to non-C. albicans-colonized mice. Mice fed olive oil for one week and challenged with C. difficile spores showed enhanced survival compared to PBS-fed mice. The amount of olive oil administered was not sufficient to cause weight gain or to result in significant changes to the bacterial microbiota, in contrast to the effects of a high-fat diet. Furthermore, the direct exposure of C. difficile bacteria in laboratory culture to the unsaturated fatty acid oleic acid, the major fatty acid found in olive oil, reduced the transcription of genes encoding the toxins and reduced the survival of bacteria in the post-exponential phase. Therefore, the effects of C. albicans on the metabolite milieu contributed to the attenuation of C. difficile virulence.
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Affiliation(s)
- Jesus A. Romo
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - Laura Markey
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences and Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA;
| | - Carol A. Kumamoto
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
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189
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Smith AB, Soto Ocana J, Zackular JP. From Nursery to Nursing Home: Emerging Concepts in Clostridioides difficile Pathogenesis. Infect Immun 2020; 88:IAI.00934-19. [PMID: 32122939 PMCID: PMC7309631 DOI: 10.1128/iai.00934-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Clostridioides difficile is a Gram-positive, spore-forming, anaerobic bacterium that infects the human gastrointestinal tract, causing a wide range of disorders that vary in severity from mild diarrhea to toxic megacolon and/or death. Over the past decade, incidence, severity, and costs associated with C. difficile infection (CDI) have increased dramatically in both the pediatric and adult populations. The factors driving this rapidly evolving epidemiology remain largely unknown but are likely due in part to previously unappreciated host, microbiota, and environmental factors. In this review, we will cover the risks and challenges of CDI in adult and pediatric populations and examine asymptomatic colonization in infants. We will also discuss the emerging role of diet, pharmaceutical drugs, and pathogen-microbiota interactions in C. difficile pathogenesis, as well as the impact of host-microbiota interactions in the manifestation of C. difficile-associated disease. Finally, we highlight new areas of research and novel strategies that may shed light on this complex infection and provide insights into the future of microbiota-based therapeutics for CDI.
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Affiliation(s)
- Alexander B Smith
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joshua Soto Ocana
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joseph P Zackular
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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190
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Blake S, Thanissery R, Rivera AJ, Hixon MS, Lin M, Theriot CM, Janda KD. Salicylanilide Analog Minimizes Relapse of Clostridioides difficile Infection in Mice. J Med Chem 2020; 63:6898-6908. [PMID: 32482070 DOI: 10.1021/acs.jmedchem.0c00123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Clostridioides difficile infection (CDI) causes serious and sometimes fatal symptoms like diarrhea and pseudomembranous colitis. Although antibiotics for CDI exist, they are either expensive or cause recurrence of the infection due to their altering the colonic microbiota, which is necessary to suppress the infection. Here, we leverage a class of known membrane-targeting compounds that we previously showed to have broad inhibitory activity across multiple Clostridioides difficile strains while preserving the microbiome to develop an efficacious agent. A new series of salicylanilides was synthesized, and the most potent analog was selected through an in vitro inhibitory assay to evaluate its pharmacokinetic parameters and potency in a CDI mouse model. The results revealed reduced recurrence of CDI and diminished disturbance of the microbiota in mice compared to standard-of-care vancomycin, thus paving the way for novel therapy that can potentially target the cell membrane of C. difficile to minimize relapse in the recovering patient.
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Affiliation(s)
- Steven Blake
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Rajani Thanissery
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Alissa J Rivera
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Mark S Hixon
- Mark S. Hixon Consulting, LLC., 11273 Spitfire Road, San Diego, California 92126, United States
| | - Mingliang Lin
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Casey M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Kim D Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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191
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Dethloff F, Vargas F, Elijah E, Quinn R, Park DI, Herzog DP, Müller MB, Gentry EC, Knight R, Gonzalez A, Dorrestein PC, Turck CW. Paroxetine Administration Affects Microbiota and Bile Acid Levels in Mice. Front Psychiatry 2020; 11:518. [PMID: 32581888 PMCID: PMC7287167 DOI: 10.3389/fpsyt.2020.00518] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
Recent interest in the role of microbiota in health and disease has implicated gut microbiota dysbiosis in psychiatric disorders including major depressive disorder. Several antidepressant drugs that belong to the class of selective serotonin reuptake inhibitors have been found to display antimicrobial activities. In fact, one of the first antidepressants discovered serendipitously in the 1950s, the monoamine-oxidase inhibitor Iproniazid, was a drug used for the treatment of tuberculosis. In the current study we chronically treated DBA/2J mice for 2 weeks with paroxetine, a selective serotonin reuptake inhibitor, and collected fecal pellets as a proxy for the gut microbiota from the animals after 7 and 14 days. Behavioral testing with the forced swim test revealed significant differences between paroxetine- and vehicle-treated mice. Untargeted mass spectrometry and 16S rRNA profiling of fecal pellet extracts showed several primary and secondary bile acid level, and microbiota alpha diversity differences, respectively between paroxetine- and vehicle-treated mice, suggesting that microbiota functions are altered by the drug. In addition to their lipid absorbing activities bile acids have important signaling activities and have been associated with gastrointestinal diseases and colorectal cancer. Antidepressant drugs like paroxetine should therefore be used with caution to prevent undesirable side effects.
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Affiliation(s)
- Frederik Dethloff
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA , United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
- Division of Biological Science, University of California, San Diego, La Jolla, CA, United States
| | - Emmanuel Elijah
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA , United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Robert Quinn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA , United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Dong Ik Park
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - David P. Herzog
- Laboratory of Translational Psychiatry, Department of Psychiatry and Psychotherapy & Focus Program Translational Neuroscience, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Marianne B. Müller
- Laboratory of Translational Psychiatry, Department of Psychiatry and Psychotherapy & Focus Program Translational Neuroscience, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Emily C. Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA , United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Rob Knight
- Department of Pediatrics, Bioengineering and Computer Science and Engineering, and Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
| | - Antonio Gonzalez
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA , United States
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Christoph W. Turck
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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192
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Opioid system influences gut-brain axis: Dysbiosis and related alterations. Pharmacol Res 2020; 159:104928. [PMID: 32504837 DOI: 10.1016/j.phrs.2020.104928] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/24/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023]
Abstract
Opioid drugs are widely used to treat chronic pain, but their misuse can lead to tolerance, dependence, and addiction and have created a significant public health problem. In addition, food-derived opioid peptides, known as exorphins, like gluten exorphins have been shown to have harmful effects in certain pathologies like celiac disease, for example. Several studies support the involvement of the opioid system in the development of disorders such as autism spectrum syndrome. Moreover, bidirectional communication between the intestine and brain has been shown to be altered in various neurodegenerative diseases including Alzheimer´s and Parkinson´s. The presence of opioid receptors in both the digestive tract and the central nervous system (CNS) suggests that opioid drugs and exorphins may modulate the gut-brain axis. Morphine, for example, has shown a dysbiotic effect on the bacterial microbiota in addition to inducing an increase in intestinal permeability facilitating bacterial translocation. Furthermore, certain components of bacteria can modify the expression of opioid receptors at the central level increasing sensitivity to pain. Strategies based on use of probiotics have resulted in improvements in symptoms of autism and Parkinson´s disease. In this manuscript, we review the role of the opioid system in disorders and CNS pathologies and the involvement of the gut-brain axis.
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193
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Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function. mSystems 2020; 5:5/3/e00176-20. [PMID: 32487741 PMCID: PMC8534727 DOI: 10.1128/msystems.00176-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Dietary high protein and low carbohydrate levels compromise colonic microbiota and bile acid metabolism, which underlies a detrimental gut environment. However, it remains unclear if the diet-induced changes in colonic health are due to a change in hindgut nutrient availability and what key intermediates link the microbe-epithelium dialogue. To specifically alter the hindgut nutrient substrate availability, here we used a cecally cannulated pig model to infuse corn starch and casein hydrolysate directly into the cecum to generate a stepwise change of carbohydrate/nitrogenous compound (C/N) ratio. Pigs were cecally infused daily with either saline (Control), corn starch (Starch), or casein hydrolysate (Casein) (n = 8 per group), respectively, for 19 days. After infusion, C/N ratios in colonic digesta were 16.33, 12.56, and 8.54 for the starch, control, and casein groups, respectively (P < 0.05). Relative to the control group, casein infusion showed greater abundance of the bacteria (Eubacterium) capable of bile acid 7α-dehydroxylation (baiJ), higher levels of expression of bacterial genes encoding the baiJ enzyme, and higher levels of secondary bile acid (deoxycholic acid [DCA] and lithocholic acid [LCA]), while the starch infusion showed the opposite effect. Correspondingly, casein infusion downregulated expression of genes encoding tight junction proteins (ZO-1 and OCLD) and upregulated expression of genes encoding epidermal growth factor receptor (EGFR). The ratio of C/N was linearly related with the concentrations of DCA and LCA and gene expression levels of ZO-1, occludin, and EGFR. Caco-2 cell experiments further showed that DCA and LCA downregulated expression of genes involved in barrier function (ZO-1 and OCLD) and upregulated the gene expression of EGFR and Src. Inhibition of EGFR and Src could abolish DCA- and LCA-induced downregulation of ZO-1, indicating that DCA and LCA impair gut barrier function via enhancing the EGFR-Src pathway. These results suggest that the ratio of C/N in the large intestine is an important determinant of microbial metabolism and gut barrier function in the colon. The findings provide evidence that microbe-related secondary bile acid metabolism may mediate the interplay between microbes and gut barrier function. IMPORTANCE High-fiber or high-protein diets could alter gut microbiota and health in the large intestine, but factors involved in the effects remain unclear. The present study for the first time demonstrates that the starch- and casein-induced C/N ratio in the hindgut is an important factor. Using the cannulated pig model, we found that the distinct C/N ratio induced by cecal infusion of corn starch or casein hydrolysate was linearly correlated with microbial metabolites (secondary bile acids) and tight junction proteins (ZO-1 and OCLD). Cell culture study further demonstrates that the gut microbial metabolites (DCA and LCA) could impair the intestinal barrier function via the EGFR-Src pathway. These suggest that DCA and LCA were key metabolites mediating microbe-epithelium dialogue when the hindgut C/N ratios were altered by cecal infusion of corn starch or casein hydrolysate. These findings provide new insight into the impact of C/N ratio in the large intestine on colonic health and provide a new framework for therapeutic strategy in gut health through targeted manipulation of hindgut microbiota by increasing the carbohydrate level in the large intestine.
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194
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Adams LA, Wang Z, Liddle C, Melton PE, Ariff A, Chandraratna H, Tan J, Ching H, Coulter S, de Boer B, Christophersen CT, O'Sullivan TA, Morrison M, Jeffrey GP. Bile acids associate with specific gut microbiota, low-level alcohol consumption and liver fibrosis in patients with non-alcoholic fatty liver disease. Liver Int 2020; 40:1356-1365. [PMID: 32243703 DOI: 10.1111/liv.14453] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 03/20/2020] [Accepted: 03/24/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Bile acids (BAs) are synthesized by the liver and modified by gut bacteria, and may play an intermediary role between the gut microbiome and liver in promoting fibrosis in non-alcoholic fatty liver disease (NAFLD). We investigated the associations between serum and faecal BAs, gut microbiome and fibrosis in patients with and without NAFLD and examined the impact of diet and alcohol consumption on these relationships. METHODS Adult patients (n = 122) underwent liver biopsy and BAs characterization by high-performance liquid chromatography/mass spectrometry. Gut microbiome composition was analysed using next-generation 16S rRNA sequencing. Diet and alcohol intake were determined by 3-day food diary. RESULTS Serum and faecal BA concentrations increased progressively among non-NAFLD controls (n = 55), NAFLD patients with no/mild fibrosis (F0-2, n = 58) and NAFLD with advanced fibrosis (F3/4, n = 9). Progressive increases in serum BAs were driven by primary conjugated BAs including glycocholic acid [GCA] and secondary conjugated BAs. In contrast, faecal BA increase was driven by secondary unconjugated BAs (predominately deoxycholic acid [DCA]). Serum GCA levels and faecal DCA levels correlated with the abundance of Bacteroidaceae and Lachnospiraceae, and stool secondary BAs with an unclassifiable family of the order Bacteroidales (Bacteroidales;other). These bacterial taxa were also associated with advanced fibrosis. Modest alcohol consumption was positively correlated with faecal DCA levels and relative abundance of Lachnospiracaea and Bacteroidales;other. CONCLUSIONS Higher serum and faecal BA levels are associated with advanced fibrosis in NAFLD. Specific gut bacteria link alterations in BA profiles and advanced fibrosis, and may be influenced by low-level alcohol consumption.
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Affiliation(s)
- Leon A Adams
- Medical School, Faculty of Medical and Health Sciences, The University of Western Australia, Perth, WA, Australia.,Department of Hepatology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Zhengyi Wang
- Medical School, Faculty of Medical and Health Sciences, The University of Western Australia, Perth, WA, Australia.,Department of Hepatology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Chris Liddle
- Storr Liver Centre, The Westmead Institute, University of Sydney, Westmead, NSW, Australia
| | - Phillip E Melton
- Curtin/UWA Centre for Genetic Origins of Health and Disease, Curtin University and University of Western Australia, Perth, WA, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, WA, Australia
| | - Amir Ariff
- Curtin/UWA Centre for Genetic Origins of Health and Disease, Curtin University and University of Western Australia, Perth, WA, Australia
| | | | - Jeremy Tan
- Department of Upper GI and Bariatric Surgery, Singapore General Hospital, Singapore, Singapore
| | - Helena Ching
- Medical School, Faculty of Medical and Health Sciences, The University of Western Australia, Perth, WA, Australia
| | - Sally Coulter
- Storr Liver Centre, The Westmead Institute, University of Sydney, Westmead, NSW, Australia
| | - Bastiaan de Boer
- Department of Anatomy, PathWest Laboratory Medical WA, Pathwest, WA, Australia
| | - Claus T Christophersen
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.,WA Human Microbiome Collaboration Centre, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Therese A O'Sullivan
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Mark Morrison
- Faculty of Medicine, The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Gary P Jeffrey
- Medical School, Faculty of Medical and Health Sciences, The University of Western Australia, Perth, WA, Australia.,Department of Hepatology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
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Saccharomyces boulardii CNCM I-745: A Non-bacterial Microorganism Used as Probiotic Agent in Supporting Treatment of Selected Diseases. Curr Microbiol 2020; 77:1987-1996. [PMID: 32472262 PMCID: PMC7415030 DOI: 10.1007/s00284-020-02053-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/23/2020] [Indexed: 02/07/2023]
Abstract
The yeast Saccharomyces boulardii CNCM I-745 is a unique, non-bacterial microorganism classified as a probiotic agent. In this review article, at first, we briefly summarized the mechanisms responsible for its probiotic properties, e.g. adhesion to and elimination of enteropathogenic microorganisms and their toxins; extracellular cleavage of pathogens’ virulent factors; trophic and anti-inflammatory effects on the intestinal mucosa. The efficacy of S. boulardii administration was tested in variety of human diseases. We discussed the results of S. boulardii CNCM I-745 use in the treatment or prevention of Helicobacter pylori infections, diarrhoea (Clostridium difficile infections, antibiotic-associated diarrhoea, and traveller’s diarrhoea), inflammatory bowel diseases, irritable bowel syndrome, candidiasis, dyslipidemia, and small intestine bacterial overgrowth in patients with multiple sclerosis. In case of limited number of studies regarding this strain, we also presented studies demonstrating properties and efficacy of other strains of S. boulardii. Administration of S. boulardii CNCMI I-745 during antibiotic therapy has certain advantage over bacterial probiotics, because—due to its fungal natural properties—it is intrinsically resistant to the antibiotics and cannot promote the spread of antimicrobial resistance. Even though cases of fungemia following S. boulardii CNCM I-745 administration were reported, it should be treated as a widely available and safe probiotic strain.
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196
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Mahnic A, Auchtung JM, Poklar Ulrih N, Britton RA, Rupnik M. Microbiota in vitro modulated with polyphenols shows decreased colonization resistance against Clostridioides difficile but can neutralize cytotoxicity. Sci Rep 2020; 10:8358. [PMID: 32433519 DOI: 10.1038/s41598-020-65253-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/21/2020] [Indexed: 01/01/2023] Open
Abstract
While the knowledge on gut microbiota - C. difficile interactions has improved over the years, the understanding of the underlying mechanisms providing colonization resistance as well as preventative measures against the infection remain incomplete. In this study the antibiotic clindamycin and polyphenol extracts from pomegranate and blueberries were used individually and in combination to modulate fecal microbial communities in minibioreactor arrays (MBRA). Modulated communities were inoculated with C. difficile (ribotype 027). Subsequent 7-day periodical monitoring included evaluation of C. difficile growth and activity of toxins TcdA and TcdB as well as analysis of MBRA bacterial community structure (V3V4 16 S metagenomics). Polyphenols affected multiple commensal bacterial groups and showed different synergistic and antagonistic effects in combination with clindamycin. Exposure to either clindamycin or polyphenols led to the loss of colonization resistance against C. difficile. The successful growth of C. difficile was most significantly correlated with the decrease in Collinsella and Lachnospiraceae. Additionally, we demonstrated that Clostridium sporogenes decreased the activity of both C. difficile toxins TcdA and TcdB. The feature was shown to be common among distinct C. sporogenes strains and could potentially be applicable as a non-antibiotic agent for the alleviation of C. difficile infection.
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Affiliation(s)
- Aleksander Mahnic
- National Laboratory for Health, Environment and Food, Prvomajska 1, 2000, Maribor, Slovenia
| | - Jennifer M Auchtung
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Nataša Poklar Ulrih
- University of Ljubljana, Biotechnical Faculty, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Robert A Britton
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Prvomajska 1, 2000, Maribor, Slovenia. .,University of Maribor, Faculty of Medicine, Taborska 8, 2000, Maribor, Slovenia.
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197
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Ursodeoxycholic Acid (UDCA) Mitigates the Host Inflammatory Response during Clostridioides difficile Infection by Altering Gut Bile Acids. Infect Immun 2020; 88:IAI.00045-20. [PMID: 32205405 DOI: 10.1128/iai.00045-20] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/18/2020] [Indexed: 12/14/2022] Open
Abstract
Clostridioides difficile infection (CDI) is associated with increasing morbidity and mortality posing an urgent threat to public health. Recurrence of CDI after successful treatment with antibiotics is high, thus necessitating discovery of novel therapeutics against this enteric pathogen. Administration of the secondary bile acid ursodeoxycholic acid (UDCA; ursodiol) inhibits the life cycles of various strains of C. difficile in vitro, suggesting that the FDA-approved formulation of UDCA, known as ursodiol, may be able to restore colonization resistance against C. difficile in vivo However, the mechanism(s) by which ursodiol is able to restore colonization resistance against C. difficile remains unknown. Here, we confirmed that ursodiol inhibits C. difficile R20291 spore germination and outgrowth, growth, and toxin activity in a dose-dependent manner in vitro In a murine model of CDI, exogenous administration of ursodiol resulted in significant alterations in the bile acid metabolome with little to no changes in gut microbial community structure. Ursodiol pretreatment resulted in attenuation of CDI pathogenesis early in the course of disease, which coincided with alterations in the cecal and colonic inflammatory transcriptome, bile acid-activated receptors nuclear farnesoid X receptor (FXR) and transmembrane G-protein-coupled membrane receptor 5 (TGR5), which are able to modulate the innate immune response through signaling pathways such as NF-κB. Although ursodiol pretreatment did not result in a consistent decrease in the C. difficile life cycle in vivo, it was able to attenuate an overly robust inflammatory response that is detrimental to the host during CDI. Ursodiol remains a viable nonantibiotic treatment and/or prevention strategy against CDI. Likewise, modulation of the host innate immune response via bile acid-activated receptors FXR and TGR5 represents a new potential treatment strategy for patients with CDI.
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198
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Jukes CA, Ijaz UZ, Buckley A, Spencer J, Irvine J, Candlish D, Li JV, Marchesi JR, Douce G. Bile salt metabolism is not the only factor contributing to Clostridioides ( Clostridium) difficile disease severity in the murine model of disease. Gut Microbes 2020; 11:481-496. [PMID: 31793403 PMCID: PMC7524298 DOI: 10.1080/19490976.2019.1678996] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Susceptibility of patients to antibiotic-associated C. difficile disease is intimately associated with specific changes to gut microbiome composition. In particular, loss of microbes that modify bile salt acids (BSA) play a central role; primary bile acids stimulate spore germination whilst secondary bile acids limit C. difficile vegetative growth. To determine the relative contribution of bile salt (BS) metabolism on C. difficile disease severity, we treated mice with three combinations of antibiotics prior to infection. Mice given clindamycin alone became colonized but displayed no tissue pathology while severe disease, exemplified by weight loss and inflammatory tissue damage occurred in animals given a combination of five antibiotics and clindamycin. Animals given only the five antibiotic cocktails showed only transient colonization and no disease. C. difficile colonization was associated with a reduction in bacterial diversity, an inability to amplify bile salt hydrolase (BSH) sequences from fecal DNA and a relative increase in primary bile acids (pBA) in cecal lavages from infected mice. Further, the link between BSA modification and the microbiome was confirmed by the isolation of strains of Lactobacillus murinus that modified primary bile acids in vitro, thus preventing C. difficile germination. Interestingly, BSH activity did not correlate with disease severity which appeared linked to alternations in mucin, which may indirectly lead to increased exposure of the epithelial surface to inflammatory signals. These data confirm the role of microbial metabolic activity in protection of the gut and highlights the need for greater understanding the function of bacterial communities in disease prevention.
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Affiliation(s)
- Caitlin A. Jukes
- Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, Glasgow, UK
| | - Umer Zeeshan Ijaz
- School of Engineering, College of Science and Engineering, University of Glasgow, Glasgow, UK
| | - Anthony Buckley
- Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, Glasgow, UK,Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - Janice Spencer
- Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, Glasgow, UK,School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
| | - June Irvine
- Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, Glasgow, UK
| | - Denise Candlish
- Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jia V. Li
- Faculty of Medicine, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Julian R. Marchesi
- Faculty of Medicine, Department of Surgery & Cancer, Imperial College London, London, UK,School of Biosciences, Cardiff University, Cardiff, UK,CONTACT Julian R. Marchesi Faculty of Medicine, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Gillian Douce
- Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, Glasgow, UK,Gillian Douce Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, UK
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199
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Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HR. The ' in vivo lifestyle' of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice. Gut Microbes 2020; 11:381-404. [PMID: 31177942 PMCID: PMC7524365 DOI: 10.1080/19490976.2019.1618173] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The formation of secondary bile acids by gut microbes is a current topic of considerable biomedical interest. However, a detailed understanding of the biology of anaerobic bacteria in the genus Clostridium that are capable of generating secondary bile acids is lacking. We therefore sought to determine the transcriptional responses of two prominent secondary bile acid producing bacteria, Clostridium hylemonae and Clostridium hiranonis to bile salts (in vitro) and the cecal environment of gnotobiotic mice. The genomes of C. hylemonae DSM 15053 and C. hiranonis DSM 13275 were closed, and found to encode 3,647 genes (3,584 protein-coding) and 2,363 predicted genes (of which 2,239 are protein-coding), respectively, and 1,035 orthologs were shared between C. hylemonae and C. hiranonis. RNA-Seq analysis was performed in growth medium alone, and in the presence of cholic acid (CA) and deoxycholic acid (DCA). Growth with CA resulted in differential expression (>0.58 log2FC; FDR < 0.05) of 197 genes in C. hiranonis and 118 genes in C. hylemonae. The bile acid-inducible operons (bai) from each organism were highly upregulated in the presence of CA but not DCA. We then colonized germ-free mice with human gut bacterial isolates capable of metabolizing taurine-conjugated bile acids. This consortium included bile salt hydrolase-expressing Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Parabacteroides distasonis DSM 20701, as well as taurine-respiring Bilophila wadsworthia DSM 11045, and deoxycholic/lithocholic acid generating Clostridium hylemonae DSM 15053 and Clostridium hiranonis DSM 13275. Butyrate and iso-bile acid-forming Blautia producta ATCC 27340 was also included. The Bacteroidetes made up 84.71% of 16S rDNA cecal reads, B. wadsworthia, constituted 14.7%, and the clostridia made up <.75% of 16S rDNA cecal reads. Bile acid metabolomics of the cecum, serum, and liver indicate that the synthetic community were capable of functional bile salt deconjugation, oxidation/isomerization, and 7α-dehydroxylation of bile acids. Cecal metatranscriptome analysis revealed expression of genes involved in metabolism of taurine-conjugated bile acids. The in vivo transcriptomes of C. hylemonae and C. hiranonis suggest fermentation of simple sugars and utilization of amino acids glycine and proline as electron acceptors. Genes predicted to be involved in trimethylamine (TMA) formation were also expressed.
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Affiliation(s)
- Jason M. Ridlon
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA,CONTACT Jason M. Ridlon, Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology
| | - Saravanan Devendran
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - João Mp Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Heidi Doden
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Patricia G. Wolf
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gabriel V. Pereira
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lindsey Ly
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alyssa Volland
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, Japan
| | | | - Tsuyoshi Murai
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
| | - Takao Kurosawa
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
| | - George E. Chlipala
- UIC Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Stefan J. Green
- UIC Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Alvaro G. Hernandez
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J. Fields
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christy L. Wright
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Genta Kakiyama
- Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Isaac Cann
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Purna Kashyap
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA,Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Vance McCracken
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA,Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA
| | - H. Rex Gaskins
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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200
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Engevik MA, Danhof HA, Chang-Graham AL, Spinler JK, Engevik KA, Herrmann B, Endres BT, Garey KW, Hyser JM, Britton RA, Versalovic J. Human intestinal enteroids as a model of Clostridioides difficile-induced enteritis. Am J Physiol Gastrointest Liver Physiol 2020; 318:G870-G888. [PMID: 32223302 PMCID: PMC7272722 DOI: 10.1152/ajpgi.00045.2020] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Clostridioides difficile is an important nosocomial pathogen that produces toxins to cause life-threatening diarrhea and colitis. Toxins bind to epithelial receptors and promote the collapse of the actin cytoskeleton. C. difficile toxin activity is commonly studied in cancer-derived and immortalized cell lines. However, the biological relevance of these models is limited. Moreover, no model is available for examining C. difficile-induced enteritis, an understudied health problem. We hypothesized that human intestinal enteroids (HIEs) express toxin receptors and provide a new model to dissect C. difficile cytotoxicity in the small intestine. We generated biopsy-derived jejunal HIE and Vero cells, which stably express LifeAct-Ruby, a fluorescent label of F-actin, to monitor actin cytoskeleton rearrangement by live-cell microscopy. Imaging analysis revealed that toxins from pathogenic C. difficile strains elicited cell rounding in a strain-dependent manner, and HIEs were tenfold more sensitive to toxin A (TcdA) than toxin B (TcdB). By quantitative PCR, we paradoxically found that HIEs expressed greater quantities of toxin receptor mRNA and yet exhibited decreased sensitivity to toxins when compared with traditionally used cell lines. We reasoned that these differences may be explained by components, such as mucins, that are present in HIEs cultures, that are absent in immortalized cell lines. Addition of human-derived mucin 2 (MUC2) to Vero cells delayed cell rounding, indicating that mucus serves as a barrier to toxin-receptor binding. This work highlights that investigation of C. difficile infection in that HIEs can provide important insights into the intricate interactions between toxins and the human intestinal epithelium.NEW & NOTEWORTHY In this article, we developed a novel model of Clostridioides difficile-induced enteritis using jejunal-derived human intestinal enteroids (HIEs) transduced with fluorescently tagged F-actin. Using live-imaging, we identified that jejunal HIEs express high levels of TcdA and CDT receptors, are more sensitive to TcdA than TcdB, and secrete mucus, which delays toxin-epithelial interactions. This work also optimizes optically clear C. difficile-conditioned media suitable for live-cell imaging.
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Affiliation(s)
- Melinda A. Engevik
- 1Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas,2Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Heather A. Danhof
- 3Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, Texas,4Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | | | - Jennifer K. Spinler
- 1Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas,2Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Kristen A. Engevik
- 3Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, Texas,4Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Beatrice Herrmann
- 1Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas,2Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Bradley T. Endres
- 5Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas
| | - Kevin W. Garey
- 5Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas
| | - Joseph M. Hyser
- 1Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas,2Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Robert A. Britton
- 3Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, Texas,4Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - James Versalovic
- 1Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas,2Department of Pathology, Texas Children’s Hospital, Houston, Texas
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