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Huang X, Johnson AE, Auchtung TA, McCullough HC, Lerma AI, Haidacher SJ, Hoch KM, Horvath TD, Haag AM, Auchtung JM. Clostridioides difficile colonization is not mediated by bile salts and requires Stickland fermentation of proline in an in vitro model of infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603937. [PMID: 39071387 PMCID: PMC11275744 DOI: 10.1101/2024.07.17.603937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Treatment with antibiotics is a major risk factor for Clostridioides difficile infection, likely due to depletion of the gastrointestinal microbiota. Two microbiota-mediated mechanisms thought to limit C. difficile colonization include conversion of conjugated primary bile salts into secondary bile salts toxic to C. difficile growth, and competition between the microbiota and C. difficile for limiting nutrients. Using a continuous flow model of the distal colon, we investigated how treatment with six clinically-used antibiotics influenced susceptibility to C. difficile infection in 12 different microbial communities cultivated from healthy individuals. Antibiotic treatment reduced microbial richness; disruption varied by antibiotic class and microbiota composition, but did not correlate with C. difficile susceptibility. Antibiotic treatment also disrupted microbial bile salt metabolism, increasing levels of the primary bile salt, cholate, and decreasing levels of the secondary bile salt, deoxycholate. However, decreased levels of deoxycholate did not correlate with increased C. difficile susceptibility. Further, bile salts were not required to inhibit C. difficile colonization. We tested whether amino acid fermentation contributed to persistence of C. difficile in antibiotic-treated communities. C. difficile mutants unable to use proline as an electron acceptor in Stickland fermentation due to disruption of proline reductase (Δ prdB ) had significantly lower levels of colonization than wild-type strains in four of six antibiotic-treated communities tested. This data provides further support for the importance of bile salt-independent mechanisms in regulating colonization of C. difficile . IMPORTANCE C. difficile is one of the leading causes of hospital-acquired infections and antibiotic-associated diarrhea. Several potential mechanisms through which the microbiota can limit C. difficile infection have been identified and are potential targets for new therapeutics. However, it is unclear which mechanisms of C. difficile inhibition represent the best targets for development of new therapeutics. These studies demonstrate that in a complex in vitro model of C. difficile infection, colonization resistance is independent of microbial bile salt metabolism. Instead, the ability of C. difficile to colonize is dependent upon its ability to metabolize proline, although proline-dependent colonization is context-dependent and is not observed in all disrupted communities. Altogether, these studies support the need for further work to understand how bile-independent mechanisms regulate C. difficile colonization.
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Vorländer D, Schultz G, Hoffmann K, Rasch D, Dohnt K. PETR: A novel peristaltic mixed tubular bioreactor simulating human colonic conditions. Biotechnol Bioeng 2024; 121:1118-1143. [PMID: 38151924 DOI: 10.1002/bit.28636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/29/2023]
Abstract
A novel bioreactor simulating human colonic conditions for in vitro cultivation of intestinal microbiota is presented. The PEristaltic mixed Tubular bioReactor (PETR) is modular designed and periodically kneaded to simulate intestinal peristalsis. The reactor is introduced, characterized from a bioprocess engineer's perspective and discussed in its ability to mimic colon conditions. PETR provides physiological temperature and appropriate anaerobic conditions, simulates intestinal peristalsis, and has a mean residence time of 32.8 ± 0.8 h comparable to the adult human colon. The single-tube design enables a time-constant and longitudinally progressive pH gradient from 5.5 to 7.0. Using a dialysis liquid containing high molecular weight polyethylene glycol, the integrated dialysis system efficiently absorbs short chain fatty acids (up to 60%) and water (on average 850 mL d-1 ). Cultivation of a typical gut bacterium (Bifidobacterium animalis) was performed to demonstrate the applicability for controlled microbiota cultivation. PETR is unique in combining simulation of the entire colon, peristaltic mixing, dialytic water and metabolite absorption, and a progressive pH gradient in a single-tube design. PETR is a further step to precise replication of colonic conditions in vitro for reliable and reproducible microbiota research, such as studying the effect of food compounds, prebiotics or probiotics, or the development and treatment of infections with enteric pathogens, but also for further medical applications such as drug delivery studies or to study the effect of drugs on and their degradation by the microbiota.
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Affiliation(s)
- David Vorländer
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Gábor Schultz
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Kristin Hoffmann
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Detlev Rasch
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Katrin Dohnt
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
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3
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Vuotto C, Donelli G, Buckley A, Chilton C. Clostridioides difficile Biofilm. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:249-272. [PMID: 38175479 DOI: 10.1007/978-3-031-42108-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides difficile infection (CDI), previously Clostridium difficile infection, is a symptomatic infection of the large intestine caused by the spore-forming anaerobic, gram-positive bacterium Clostridioides difficile. CDI is an important healthcare-associated disease worldwide, characterized by high levels of recurrence, morbidity, and mortality. CDI is observed at a higher rate in immunocompromised patients after antimicrobial therapy, with antibiotics disrupting the commensal microbiota and promoting C. difficile colonization of the gastrointestinal tract.A rise in clinical isolates resistant to multiple antibiotics and the reduced susceptibility to the most commonly used antibiotic molecules have made the treatment of CDI more complicated, allowing the persistence of C. difficile in the intestinal environment.Gut colonization and biofilm formation have been suggested to contribute to the pathogenesis and persistence of C. difficile. In fact, biofilm growth is considered as a serious threat because of the related antimicrobial tolerance that makes antibiotic therapy often ineffective. This is the reason why the involvement of C. difficile biofilm in the pathogenesis and recurrence of CDI is attracting more and more interest, and the mechanisms underlying biofilm formation of C. difficile as well as the role of biofilm in CDI are increasingly being studied by researchers in the field.Findings on C. difficile biofilm, possible implications in CDI pathogenesis and treatment, efficacy of currently available antibiotics in treating biofilm-forming C. difficile strains, and some antimicrobial alternatives under investigation will be discussed here.
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Affiliation(s)
- Claudia Vuotto
- Microbial Biofilm Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy.
| | | | - Anthony Buckley
- Microbiome and Nutritional Sciences Group, School of Food Science & Nutrition, University of Leeds, Leeds, UK
| | - Caroline Chilton
- Healthcare Associated Infection Research Group, Section of Molecular Gastroenterology, Leeds Institute for Medical Research at St James, University of Leeds, Leeds, UK
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4
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Sidner B, Lerma A, Biswas B, Do TVT, Yu Y, Ronish LA, McCullough H, Auchtung JM, Piepenbrink KH. Flagellin is essential for initial attachment to mucosal surfaces by Clostridioides difficile. Microbiol Spectr 2023; 11:e0212023. [PMID: 37823657 PMCID: PMC10714722 DOI: 10.1128/spectrum.02120-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 09/04/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Clostridioides difficile is one of the leading causes of hospital-acquired infections worldwide and presents challenges in treatment due to recurrent gastrointestinal disease after treatment with antimicrobials. The mechanisms by which C. difficile colonizes the gut represent a key gap in knowledge, including its association with host cells and mucosa. Our results show the importance of flagellin for specific adhesion to mucosal hydrogels and can help to explain prior observations of adhesive defects in flagellin and pilin mutants.
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Affiliation(s)
- Ben Sidner
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Armando Lerma
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Baishakhi Biswas
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Thi Van Thanh Do
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Yafan Yu
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Leslie A. Ronish
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Hugh McCullough
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jennifer M. Auchtung
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Kurt H. Piepenbrink
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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5
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Bosnjak M, Karpe AV, Van TTH, Kotsanas D, Jenkin GA, Costello SP, Johanesen P, Moore RJ, Beale DJ, Srikhanta YN, Palombo EA, Larcombe S, Lyras D. Multi-omics analysis of hospital-acquired diarrhoeal patients reveals biomarkers of enterococcal proliferation and Clostridioides difficile infection. Nat Commun 2023; 14:7737. [PMID: 38007555 PMCID: PMC10676382 DOI: 10.1038/s41467-023-43671-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 11/16/2023] [Indexed: 11/27/2023] Open
Abstract
Hospital-acquired diarrhoea (HAD) is common, and often associated with gut microbiota and metabolome dysbiosis following antibiotic administration. Clostridioides difficile is the most significant antibiotic-associated diarrhoeal (AAD) pathogen, but less is known about the microbiota and metabolome associated with AAD and C. difficile infection (CDI) with contrasting antibiotic treatment. We characterised faecal microbiota and metabolome for 169 HAD patients (33 with CDI and 133 non-CDI) to determine dysbiosis biomarkers and gain insights into metabolic strategies C. difficile might use for gut colonisation. The specimen microbial community was analysed using 16 S rRNA gene amplicon sequencing, coupled with untargeted metabolite profiling using gas chromatography-mass spectrometry (GC-MS), and short-chain fatty acid (SCFA) profiling using GC-MS. AAD and CDI patients were associated with a spectrum of dysbiosis reflecting non-antibiotic, short-term, and extended-antibiotic treatment. Notably, extended antibiotic treatment was associated with enterococcal proliferation (mostly vancomycin-resistant Enterococcus faecium) coupled with putative biomarkers of enterococcal tyrosine decarboxylation. We also uncovered unrecognised metabolome dynamics associated with concomitant enterococcal proliferation and CDI, including biomarkers of Stickland fermentation and amino acid competition that could distinguish CDI from non-CDI patients. Here we show, candidate metabolic biomarkers for diagnostic development with possible implications for CDI and vancomycin-resistant enterococci (VRE) treatment.
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Affiliation(s)
- Marijana Bosnjak
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Avinash V Karpe
- Environment, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, Queensland, Australia
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora, Victoria, Australia
| | - Despina Kotsanas
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Grant A Jenkin
- Department of Infectious Diseases, Monash Health, Clayton, Victoria, Australia
| | - Samuel P Costello
- Department of Gastroenterology, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia
| | - Priscilla Johanesen
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Robert J Moore
- School of Science, RMIT University, Bundoora, Victoria, Australia
| | - David J Beale
- Environment, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, Queensland, Australia
| | - Yogitha N Srikhanta
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Sarah Larcombe
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Dena Lyras
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia.
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6
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Motta-Romero HA, Perez-Donado CE, Auchtung JM, Rose DJ. Toxicity of cadmium on dynamic human gut microbiome cultures and the protective effect of cadmium-tolerant bacteria autochthonous to the gut. CHEMOSPHERE 2023; 338:139581. [PMID: 37474038 DOI: 10.1016/j.chemosphere.2023.139581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
Cadmium (Cd) is a heavy metal toxic to the gut microbiome. In this study, we cultivated two human gut microbiomes (A and B) in bioreactors with Cd at 0 and 20 ppm for 7 days to investigate effects of Cd on the gut microbiome and to isolate Cd-tolerant bacteria autochthonous to the gut. Cd showed profound toxicity, abolishing butyrate production, depleting microbes in microbiome B, and simplifying microbiome A to a small Cd-tolerant community after 2 d of incubation. When spiked into the Cd-sensitive microbiome B, the Cd-tolerant community from microbiome A and isolates from that community worked synergistically with microbiome B to enhance butyrate production and maintained this synergism at Cd concentrations up to 5 ppm. Bacteria isolated from this Cd-tolerant community included Enterococcus faecium, Enterobacter cloacae, Lactococcus lactis, and Lactobacillus taiwanensis species. This work demonstrates a straightforward method for identifying Cd-tolerant bacteria autochthonous to the human gut that synergize with the microbiome to protect against Cd-related loss of butyrate production.
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Affiliation(s)
- Hollman A Motta-Romero
- Department of Food Science and Technology, University of Nebraska Lincoln, NE, USA; Nebraska Food for Health Center, University of Nebraska Lincoln, NE, USA
| | - Carmen E Perez-Donado
- Department of Food Science and Technology, University of Nebraska Lincoln, NE, USA; Nebraska Food for Health Center, University of Nebraska Lincoln, NE, USA
| | - Jennifer M Auchtung
- Department of Food Science and Technology, University of Nebraska Lincoln, NE, USA; Nebraska Food for Health Center, University of Nebraska Lincoln, NE, USA
| | - Devin J Rose
- Department of Food Science and Technology, University of Nebraska Lincoln, NE, USA; Nebraska Food for Health Center, University of Nebraska Lincoln, NE, USA; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
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7
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Larsen IS, Chenaux M, Collins FWJ, Mandic A, Hansen LBS, Lauridsen CAS, Haller RF, Elvig-Jørgensen S, Horwell E, Christiansen J, Silva A, Vehreschild MJGT, Cutting SM, Roggenbuck-Wedemeyer M, Kristensen NN. Bacillus velezensis DSM 33864 reduces Clostridioides difficile colonization without disturbing commensal gut microbiota composition. Sci Rep 2023; 13:14941. [PMID: 37696924 PMCID: PMC10495459 DOI: 10.1038/s41598-023-42128-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/05/2023] [Indexed: 09/13/2023] Open
Abstract
Up to 25% of the US population harbor Clostridioides difficile in the gut. Following antibiotic disruption of the gut microbiota, C. difficile can act as an opportunistic pathogen and induce potentially lethal infections. Consequently, reducing the colonization of C. difficile in at-risk populations is warranted, prompting us to identify and characterize a probiotic candidate specifically targeting C. difficile colonization. We identified Bacillus velezensis DSM 33864 as a promising strain to reduce C. difficile levels in vitro. We further investigated the effects of B. velezensis DSM 33864 in an assay including human fecal medium and in healthy or clindamycin-treated mouse models of C. difficile colonization. The addition of B. velezensis DSM 33864 to human fecal samples was shown to reduce the colonization of C. difficile in vitro. This was supported in vivo where orally administered B. velezensis DSM 33864 spores reduced C. difficile levels in clindamycin-treated mice. The commensal microbiota composition or post-antibiotic reconstitution was not impacted by B. velezensis DSM 33864 in human fecal samples, short-, or long-term administration in mice. In conclusion, oral administration of B. velezensis DSM 33864 specifically reduced C. difficile colonization in vitro and in vivo without adversely impacting the commensal gut microbiota composition.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ed Horwell
- Bioscience Innovation Centre, Sporegen Ltd., 2 Royal College Street, London, NW1 0NH, UK
| | | | | | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Simon M Cutting
- Bioscience Innovation Centre, Sporegen Ltd., 2 Royal College Street, London, NW1 0NH, UK
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
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8
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Wang K, Zhang Z, Hang J, Liu J, Guo F, Ding Y, Li M, Nie Q, Lin J, Zhuo Y, Sun L, Luo X, Zhong Q, Ye C, Yun C, Zhang Y, Wang J, Bao R, Pang Y, Wang G, Gonzalez FJ, Lei X, Qiao J, Jiang C. Microbial-host-isozyme analyses reveal microbial DPP4 as a potential antidiabetic target. Science 2023; 381:eadd5787. [PMID: 37535747 DOI: 10.1126/science.add5787] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 06/14/2023] [Indexed: 08/05/2023]
Abstract
A mechanistic understanding of how microbial proteins affect the host could yield deeper insights into gut microbiota-host cross-talk. We developed an enzyme activity-screening platform to investigate how gut microbiota-derived enzymes might influence host physiology. We discovered that dipeptidyl peptidase 4 (DPP4) is expressed by specific bacterial taxa of the microbiota. Microbial DPP4 was able to decrease the active glucagon like peptide-1 (GLP-1) and disrupt glucose metabolism in mice with a leaky gut. Furthermore, the current drugs targeting human DPP4, including sitagliptin, had little effect on microbial DPP4. Using high-throughput screening, we identified daurisoline-d4 (Dau-d4) as a selective microbial DPP4 inhibitor that improves glucose tolerance in diabetic mice.
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Affiliation(s)
- Kai Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Zhiwei Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Jing Hang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
| | - Jia Liu
- Department of Endocrinology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Fusheng Guo
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yong Ding
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Meng Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Qixing Nie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Jun Lin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Yingying Zhuo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Lulu Sun
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xi Luo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Qihang Zhong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
| | - Chuan Ye
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Chuyu Yun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Yi Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Jue Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
| | - Rui Bao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yanli Pang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
| | - Guang Wang
- Department of Endocrinology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jie Qiao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Beijing Advanced Innovation Center for Genomics, Beijing, China
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, China
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9
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Sidner B, Lerma A, Biswas B, Ronish LA, McCullough H, Auchtung JM, Piepenbrink KH. Flagellin is essential for initial attachment to mucosal surfaces by Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541533. [PMID: 37292962 PMCID: PMC10245794 DOI: 10.1101/2023.05.19.541533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mucins are glycoproteins which can be found in host cell membranes and as a gelatinous surface formed from secreted mucins. Mucosal surfaces in mammals form a barrier to invasive microbes, particularly bacteria, but are a point of attachment for others. Clostridioides difficile is anaerobic bacterium which colonizes the mammalian GI tract and is a common cause of acute GI inflammation leading to a variety of negative outcomes. Although C. difficile toxicity stems from secreted toxins, colonization is a prerequisite for C. difficile disease. While C. difficile is known to associate with the mucus layer and underlying epithelium, the mechanisms underlying these interactions that facilitate colonization are less well-understood. To understand the molecular mechanisms by which C. difficile interacts with mucins, we used ex vivo mucosal surfaces to test the ability of C. difficile to bind to mucins from different mammalian tissues. We found significant differences in C. difficile adhesion based upon the source of mucins, with highest levels of binding observed to mucins purified from the human colonic adenocarcinoma line LS174T and lowest levels of binding to porcine gastric mucin. We also observed that defects in adhesion by mutants deficient in flagella, but not type IV pili. These results imply that interactions between host mucins and C. difficile flagella facilitate the initial host attachment of C. difficile to host cells and secreted mucus.
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10
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Jiang J, Li K, Wang Y, Wu Z, Ma H, Zheng S, Li Z. Screening, Identification and Physiological Characteristics of Lactobacillus rhamnosus M3 (1) against Intestinal Inflammation. Foods 2023; 12:foods12081628. [PMID: 37107423 PMCID: PMC10138118 DOI: 10.3390/foods12081628] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/30/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The probiotic role of lactic acid bacteria (LAB) in regulating intestinal microbiota to promote human health has been widely reported. However, the types and quantities of probiotics used in practice are still limited. Therefore, isolating and screening LAB with potential probiotic functions from various habitats has become a hot topic. In this study, 104 strains of LAB were isolated from and identified in traditionally fermented vegetables, fresh milk, healthy infant feces, and other environments. The antibacterial properties-resistance to acid, bile salts, and digestive enzymes-and adhesion ability of the strains were determined, and the biological safety of LAB with better performance was studied. Three LAB with good comprehensive performance were obtained. These bacteria had broad-spectrum antibacterial properties and good acid resistance and adhesion ability. They exhibited some tolerance to pig bile salt, pepsin, and trypsin and showed no hemolysis. They were sensitive to the selected antibiotics, which met the required characteristics and safety evaluation criteria for probiotics. An in vitro fermentation experiment and milk fermentation performance test of Lactobacillus rhamnosus (L. rhamnosus) M3 (1) were carried out to study its effect on the intestinal flora and fermentation performance in patients with inflammatory bowel disease (IBD). Studies have shown that this strain can effectively inhibit the growth of harmful microorganisms and produce a classic, pleasant flavor. It has probiotic potential and is expected to be used as a microecological agent to regulate intestinal flora and promote intestinal health. It can also be used as an auxiliary starter to enhance the probiotic value of fermented milk.
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Affiliation(s)
- Jiayan Jiang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Ke Li
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yuanliang Wang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Zhongqin Wu
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Huiqin Ma
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Shilin Zheng
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Zongjun Li
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
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11
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MBRA-2: a Modified Chemostat System to Culture Biofilms. Microbiol Spectr 2023; 11:e0292822. [PMID: 36475832 PMCID: PMC9927502 DOI: 10.1128/spectrum.02928-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Culture-dependent approaches for investigating microbial ecology aim to model the nutrient content of specific environments by simplifying the system for high-resolution molecular analysis. These in vitro systems are enticing due to their increased throughput compared to animal models, flexibility in modulating nutrient content and community composition, scaling of culture volume to isolate biological molecules, and control of environmental parameters, such as temperature, humidity, and nutrient flow. However, different devices are used to investigate homogenous, planktonic microbial communities and heterogeneous biofilms. Here, we present the minibioreactor array 2 (MBRA-2) with media rails, a benchtop multireactor system derived from the MBRA system that enables researchers to use the same system to grow planktonic and biofilm cultures. We simplified flow through the system and reduced contamination, leakage, and time required for array assembly by designing and implementing a reusable media rail to replace the branched tubing traditionally used to convey media through chemostat arrays. Additionally, we altered the structure of the six-bioreactor strip to incorporate a removable lid to provide easy access to the bioreactor wells, enabling biofilm recovery and thorough cleaning for reuse. Using Pseudomonas aeruginosa, a model biofilm-producing organism, we show that the technical improvements of the MBRA-2 for biofilms growth does not disrupt the function of the bioreactor array. IMPORTANCE The MBRA-2 with media rails provides an accessible system for investigators to culture heterogenous, suspended biofilms under constant flow.
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12
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Horvat S, Mahnic A, Makuc D, Pečnik K, Plavec J, Rupnik M. Children gut microbiota exhibits a different composition and metabolic profile after in vitro exposure to Clostridioides difficile and increases its sporulation. Front Microbiol 2022; 13:1042526. [PMID: 36569098 PMCID: PMC9780542 DOI: 10.3389/fmicb.2022.1042526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile (Clostridium difficile) infection (CDI) is one of the main public health concerns in adults, while children under 2 years of age are often colonized asymptomatically. In both adults and children, CDI is strongly associated with disturbances in gut microbiota. In this study, an in-vitro model of children gut microbiota was challenged with vegetative cells or a conditioned media of six different toxigenic C. difficile strains belonging to the ribotypes 027, 078, and 176. In the presence of C. difficile or conditioned medium the children gut microbiota diversity decreased and all main phyla (Bacteroidetes, Firmicutes, and Proteobacteria) were affected. The NMR metabolic spectra divided C. difficile exposed children gut microbiota into three clusters. The grouping correlated with nine metabolites (short chain fatty acids, ethanol, phenolic acids and tyramine). All strains were able to grow in the presence of children gut microbiota and showed a high sporulation rate of up to 57%. This high sporulation rate in combination with high asymptomatic carriage in children could contribute to the understanding of the reported role of children in C. difficile transmissions.
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Affiliation(s)
- Sabina Horvat
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Aleksander Mahnic
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia,Centre for Medical Microbiology, National Laboratory of Health, Environment and Food, Maribor, Slovenia
| | - Damjan Makuc
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Klemen Pečnik
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Maja Rupnik
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia,Centre for Medical Microbiology, National Laboratory of Health, Environment and Food, Maribor, Slovenia,*Correspondence: Maja Rupnik,
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13
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Zaytsoff SJM, Montina T, Boras VF, Brassard J, Moote PE, Uwiera RRE, Inglis GD. Microbiota Transplantation in Day-Old Broiler Chickens Ameliorates Necrotic Enteritis via Modulation of the Intestinal Microbiota and Host Immune Responses. Pathogens 2022; 11:pathogens11090972. [PMID: 36145404 PMCID: PMC9503007 DOI: 10.3390/pathogens11090972] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
A microbiota transplant (MT) originating from mature adult chicken ceca and propagated in bioreactors was administered to day-old broiler chicks to ascertain the degree to which, and how, the MT affects Clostridium perfringens (Cp)-incited necrotic enteritis (NE). Using a stress predisposition model of NE, birds administered the MT and challenged with Cp showed fewer necrotic lesions, and exhibited a substantially higher α- and β-diversity of bacteria in their jejunum and ceca. Birds challenged with Cp and not administered the MT showed decreased Lactobacillus and increased Clostridium sensu strico 1 in the jejunum. In ceca, Megamonas, a genus containing butyrate-producing bacteria, was only present in birds administered the MT, and densities of this genus were increased in birds challenged with Cp. Metabolite profiles in cecal digesta were altered in birds administered the MT and challenged with the pathogen; 59 metabolites were differentially abundant following MT treatment, and the relative levels of short chain fatty acids, butyrate, valerate, and propionate, were decreased in birds with NE. Birds administered the MT and challenged with Cp showed evidence of enhanced restoration of intestinal barrier functions, including elevated mRNA of MUC2B, MUC13, and TJP1. Likewise, birds administered the MT exhibited higher mRNA of IL2, IL17A, and IL22 at 2-days post-inoculation with Cp, indicating that these birds were better immunologically equipped to respond to pathogen challenge. Collectively, study findings demonstrated that administering a MT containing a diverse mixture of microorganisms to day-old birds ameliorated NE in broilers by increasing bacterial diversity and promoting positive immune responses.
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Affiliation(s)
- Sarah J. M. Zaytsoff
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Tony Montina
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Valerie F. Boras
- Chinook Regional Hospital, Alberta Health Services, Lethbridge, AB T1J 1W5, Canada
| | - Julie Brassard
- Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC J2S 8E3, Canada
| | - Paul E. Moote
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Richard R. E. Uwiera
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - G. Douglas Inglis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
- Correspondence:
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14
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Singh V, Son H, Lee G, Lee S, Unno T, Shin JH. Role, Relevance, and Possibilities of In vitro fermentation models in human dietary, and gut-microbial studies. Biotechnol Bioeng 2022; 119:3044-3061. [PMID: 35941765 DOI: 10.1002/bit.28206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 08/03/2022] [Indexed: 11/11/2022]
Abstract
Dietary studies play a crucial role in determining the health-benefiting effects of most food substances, including prebiotics, probiotics, functional foods, and bioactive compounds. Such studies involve gastrointestinal digestion and colonic fermentation of dietary substances. In colonic fermentation, any digested food is further metabolized in the gut by the residing colonic microbiota, causing a shift in the gut microenvironment and production of various metabolites, such as short-chain fatty acids (SCFA). These diet-induced shifts in the microbial community and metabolite production, which can be assessed through in vitro fermentation models using a donor's fecal microbiota, are well known to impact the health of the host. Although in vivo or animal experiments are the gold standard in dietary studies, recent advancements using different in vitro systems, like artificial colon (ARCOL), mini bioreactor array (MBRA), TNO in vitro model of the colon (TIM), Simulator of the Human Intestinal Microbial Ecosystem (SHIME), M-SHIME, CoMiniGut, and Dynamic Gastrointestinal Simulator (SIMGI) make it easy to study the dietary impact in terms of the gut microbiota and metabolites. Such a continuous in vitro system can have multiple compartments corresponding to different parts of the colon, i.e., proximal, transverse, and distal colon, making the findings physiologically more significant. Further, post-fermentation samples can be analyzed using metagenomic, metabolomic, qPCR and flow cytometry approaches. Moreover, studies have shown that in vitro results are in accordance with the in vivo findings, supporting their relevance in dietary studies and giving confidence that shifts in metabolites are only due to microbes. This review meticulously describes the recent advancements in various fermentation models and their relevance in dietary studies. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Vineet Singh
- Department of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - HyunWoo Son
- Department of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - GyuDae Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Sunwoo Lee
- Department of Biotechnology,, School of Life Sciences, SARI, Jeju National University, Jeju, South Korea
| | - Tatsuya Unno
- Department of Biotechnology,, School of Life Sciences, SARI, Jeju National University, Jeju, South Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, South Korea
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15
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Jin Z, Ng A, Maurice CF, Juncker D. The Mini Colon Model: a benchtop multi-bioreactor system to investigate the gut microbiome. Gut Microbes 2022; 14:2096993. [PMID: 35844189 PMCID: PMC9291644 DOI: 10.1080/19490976.2022.2096993] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In vitro fermentation systems allow for the investigation of gut microbial communities with precise control of various physiological parameters while decoupling confounding factors from the human host. Current systems, such as the SHIME and Robogut, are large in footprint, lack multiplexing, and have low experimental throughput. Alternatives which address these shortcomings, such as the Mini Bioreactor Array system, are often reliant on expensive specialized equipment, which hinders wide replication across labs. Here, we present the Mini Colon Model (MiCoMo), a low-cost, benchtop multi-bioreactor system that simulates the human colon environment with physiologically relevant conditions. The device consists of triplicate bioreactors working independently of an anaerobic chamber and equipped with automated pH, temperature, and fluidic control. We conducted 14-d experiments and found that MiCoMo was able to support a stable complex microbiota community with a Shannon Index of 3.17 ± 0.65, from individual fecal samples after only 3-5 d of inoculation. MiCoMo also retained inter-sample microbial differences by developing closely related communities unique to each donor, while maintaining both minimal variations between replicate reactors (average Bray-Curtis similarity 0.72 ± 0.13) andday-to-day variations (average Bray-Curtis similarity 0.81±0.10) after this short stabilization period. Together, these results establish MiCoMo as an accessible system for studying gut microbial communities with high throughput and multiplexing capabilities.
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Affiliation(s)
- Zijie Jin
- Department of Biomedical Engineering, McGill University, Montreal, QuebecCanada,McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Andy Ng
- Department of Biomedical Engineering, McGill University, Montreal, QuebecCanada,McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Corinne F. Maurice
- Department of Microbiology and Immunology, McGill University, Montreal, QCCanada,CONTACT Corinne F. Maurice Life Sciences Complex Room 332, Bellini Building 3649 Promenade Sir William Osler Montreal, QC, H3G 0B1, Canada
| | - David Juncker
- Department of Biomedical Engineering, McGill University, Montreal, QuebecCanada,McGill Genome Centre, McGill University, Montreal, QC, Canada,David JunckerMcgill Genome Center, 740 Dr. Penfield Ave, Room 6500Montreal, QC, H3A 0G1, Canada
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16
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Hobson CA, Vigue L, Naimi S, Chassaing B, Magnan M, Bonacorsi S, Gachet B, El Meouche I, Birgy A, Tenaillon O. MiniBioReactor Array (MBRA) in vitro gut model: a reliable system to study microbiota-dependent response to antibiotic treatment. JAC Antimicrob Resist 2022; 4:dlac077. [PMID: 35795241 PMCID: PMC9252984 DOI: 10.1093/jacamr/dlac077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 06/14/2022] [Indexed: 11/18/2022] Open
Abstract
Background Antimicrobial drugs are mostly studied for their impact on emergence of bacterial antibiotic resistance, but their impact on the gut microbiota is also of tremendous interest. In vitro gut models are important tools to study such complex drug–microbiota interactions in humans. Methods The MiniBioReactor Array (MBRA) in vitro microbiota system; a single-stage continuous flow culture model, hosted in an anaerobic chamber; was used to evaluate the impact of three concentrations of a third-generation cephalosporin (ceftriaxone) on faecal microbiota from two healthy donors (treatment versus control: three replicates per condition). We conducted 16S microbiome profiling and analysed microbial richness, diversity and taxonomic changes. β-Lactamase activities were evaluated and correlated with the effects observed in the MBRA in vitro system. Results The MBRA preserved each donor’s specificities, and differences between the donors were maintained through time. Before treatment, all faecal cultures belonging to the same donor were comparable in composition, richness, and diversity. Treatment with ceftriaxone was associated with a decrease in α-diversity, and an increase in β-diversity index, in a concentration-dependent manner. The maximum effect on diversity was observed after 72 h of treatment. Importantly, one donor had a stronger microbiota β-lactamase activity that was associated with a reduced impact of ceftriaxone on microbiota composition. Conclusions MBRA can reliably mimic the intestinal microbiota and its modifications under antibiotic selective pressure. The impact of the treatment was donor- and concentration-dependent. We hypothesize these results could be explained, at least in part, by the differences in β-lactamase activity of the microbiota itself. Our results support the relevance and promise of the MBRA system to study drug–microbiota interactions.
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Affiliation(s)
- C A Hobson
- IAME, UMR 1137, INSERM, Université de Paris, AP-HP , Paris , France
| | - L Vigue
- IAME, UMR 1137, INSERM, Université de Paris, AP-HP , Paris , France
| | - S Naimi
- INSERM U1016, Team ‘Mucosal Microbiota in Chronic Inflammatory diseases’, CNRS UMR 8104, Université de Paris , Paris , France
| | - B Chassaing
- INSERM U1016, Team ‘Mucosal Microbiota in Chronic Inflammatory diseases’, CNRS UMR 8104, Université de Paris , Paris , France
| | - M Magnan
- IAME, UMR 1137, INSERM, Université de Paris, AP-HP , Paris , France
| | - S Bonacorsi
- IAME, UMR 1137, INSERM, Université de Paris, AP-HP , Paris , France
- Laboratoire de Microbiologie, Hôpital Robert Debré, AP-HP , 75019 Paris , France
| | - B Gachet
- IAME, UMR 1137, INSERM, Université de Paris, AP-HP , Paris , France
| | - I El Meouche
- IAME, UMR 1137, INSERM, Université de Paris, AP-HP , Paris , France
| | - A Birgy
- IAME, UMR 1137, INSERM, Université de Paris, AP-HP , Paris , France
- Laboratoire de Microbiologie, Hôpital Robert Debré, AP-HP , 75019 Paris , France
| | - O Tenaillon
- IAME, UMR 1137, INSERM, Université de Paris, AP-HP , Paris , France
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17
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Hernalsteens S, Huang S, Cong HH, Chen XD. The final fate of food: On the establishment of in vitro colon models. Food Res Int 2021; 150:110743. [PMID: 34865762 DOI: 10.1016/j.foodres.2021.110743] [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: 06/04/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 02/07/2023]
Abstract
The search for life/health quality has driven the search for a better understanding of food components on the overall individual health, which turns to be intrinsically related to the digestive system. In vitro digestion models are considered an alternative for the in vivo studies for a variety of practical reasons, but further research is still needed concerning the colon model establishment. An effective in vitro colon model should consider all unit operations and transport phenomena, together with chemical and biochemical reactions, material handling and reactor design. Due to the different techniques and dependence on the donor microbiota, it is difficult to obtain a standard protocol with results reproductible in time and space. Furthermore, the colon model should be fed with a representative substrate, thus what happens in upper digestion tract and absorption prior to colon is also of crucial importance. Essentially, there are two ways to think about how to achieve a good and useful in vitro colon model: a complex biomimetic system that provides results comparable with the in vivo studies or a simple system, that despite the fact it could not give physiologically relevant data, it is sufficient to understand the fate of some specific components.
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Affiliation(s)
- Saartje Hernalsteens
- College of Chemistry, Chemical Engineering and Materials Science - Soochow University, China.
| | | | - Hai Hua Cong
- College of Food Science and Engineering - Dalian Ocean University, China
| | - Xiao Dong Chen
- College of Chemistry, Chemical Engineering and Materials Science - Soochow University, China.
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18
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Leggieri PA, Liu Y, Hayes M, Connors B, Seppälä S, O'Malley MA, Venturelli OS. Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. Annu Rev Biomed Eng 2021; 23:169-201. [PMID: 33781078 PMCID: PMC8277735 DOI: 10.1146/annurev-bioeng-082120-022836] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. The spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review, we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps.
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Affiliation(s)
- Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Yiyi Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Madeline Hayes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Bryce Connors
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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19
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Wongkuna S, Janvilisri T, Phanchana M, Harnvoravongchai P, Aroonnual A, Aimjongjun S, Malaisri N, Chankhamhaengdecha S. Temporal Variations in Patterns of Clostridioides difficile Strain Diversity and Antibiotic Resistance in Thailand. Antibiotics (Basel) 2021; 10:antibiotics10060714. [PMID: 34199301 PMCID: PMC8231780 DOI: 10.3390/antibiotics10060714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 01/04/2023] Open
Abstract
Clostridioides difficile has been recognized as a life-threatening pathogen that causes enteric diseases, including antibiotic-associated diarrhea and pseudomembranous colitis. The severity of C. difficile infection (CDI) correlates with toxin production and antibiotic resistance of C. difficile. In Thailand, the data addressing ribotypes, toxigenic, and antimicrobial susceptibility profiles of this pathogen are scarce and some of these data sets are limited. In this study, two groups of C. difficile isolates in Thailand, including 50 isolates collected from 2006 to 2009 (THA group) and 26 isolates collected from 2010 to 2012 (THB group), were compared for toxin genes and ribotyping profiles. The production of toxins A and B were determined on the basis of toxin gene profiles. In addition, minimum inhibitory concentration of eight antibiotics were examined for all 76 C. difficile isolates. The isolates of the THA group were categorized into 27 A−B+CDT− (54%) and 23 A-B-CDT- (46%), while the THB isolates were classified into five toxigenic profiles, including six A+B+CDT+ (23%), two A+B+CDT− (8%), five A−B+CDT+ (19%), seven A−B+CDT− (27%), and six A−B−CDT− (23%). By visually comparing them to the references, only five ribotypes were identified among THA isolates, while 15 ribotypes were identified within THB isolates. Ribotype 017 was the most common in both groups. Interestingly, 18 unknown ribotyping patterns were identified. Among eight tcdA-positive isolates, three isolates showed significantly greater levels of toxin A than the reference strain. The levels of toxin B in 3 of 47 tcdB-positive isolates were significantly higher than that of the reference strain. Based on the antimicrobial susceptibility test, metronidazole showed potent efficiency against most isolates in both groups. However, high MIC values of cefoxitin (MICs 256 μg/mL) and chloramphenicol (MICs ≥ 64 μg/mL) were observed with most of the isolates. The other five antibiotics exhibited diverse MIC values among two groups of isolates. This work provides evidence of temporal changes in both C. difficile strains and patterns of antimicrobial resistance in Thailand.
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Affiliation(s)
- Supapit Wongkuna
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.W.); (T.J.)
| | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.W.); (T.J.)
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Phurt Harnvoravongchai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (P.H.); (N.M.)
| | - Amornrat Aroonnual
- Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Sathid Aimjongjun
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Natamon Malaisri
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (P.H.); (N.M.)
| | - Surang Chankhamhaengdecha
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (P.H.); (N.M.)
- Correspondence:
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20
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Roupar D, Berni P, Martins JT, Caetano AC, Teixeira JA, Nobre C. Bioengineering approaches to simulate human colon microbiome ecosystem. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.04.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Engevik MA, Engevik AC, Engevik KA, Auchtung JM, Chang-Graham AL, Ruan W, Luna RA, Hyser JM, Spinler JK, Versalovic J. Mucin-Degrading Microbes Release Monosaccharides That Chemoattract Clostridioides difficile and Facilitate Colonization of the Human Intestinal Mucus Layer. ACS Infect Dis 2021; 7:1126-1142. [PMID: 33176423 DOI: 10.1021/acsinfecdis.0c00634] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
It is widely accepted that the pathogen Clostridioides difficile exploits an intestinal environment with an altered microbiota, but the details of these microbe-microbe interactions are unclear. Adherence and colonization of mucus has been demonstrated for several enteric pathogens and it is possible that mucin-associated microbes may be working in concert with C. difficile. We showed that C. difficile ribotype-027 adheres to MUC2 glycans and using fecal bioreactors, we identified that C. difficile associates with several mucin-degrading microbes. C. difficile was found to chemotax toward intestinal mucus and its glycan components, demonstrating that C. difficile senses the mucus layer. Although C. difficile lacks the glycosyl hydrolases required to degrade mucin glycans, coculturing C. difficile with the mucin-degrading Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Ruminococcus torques allowed C. difficile to grow in media that lacked glucose but contained purified MUC2. Collectively, these studies expand our knowledge on how intestinal microbes support C. difficile.
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Affiliation(s)
- Melinda A. Engevik
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Amy C. Engevik
- Department of Surgery, Vanderbilt University School of Medicine, Nashville Tennessee 37232, United States
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville Tennessee 37232, United States
| | - Kristen A. Engevik
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Jennifer M. Auchtung
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Food Science and Technology, University of Nebraska—Lincoln, Lincoln Nebraska 68588, United States
| | - Alexandra L. Chang-Graham
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Wenly Ruan
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Ruth Ann Luna
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Joseph M. Hyser
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Jennifer K. Spinler
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
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22
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Teichmann J, Cockburn DW. In vitro Fermentation Reveals Changes in Butyrate Production Dependent on Resistant Starch Source and Microbiome Composition. Front Microbiol 2021; 12:640253. [PMID: 33995299 PMCID: PMC8117019 DOI: 10.3389/fmicb.2021.640253] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/06/2021] [Indexed: 12/31/2022] Open
Abstract
One of the primary benefits associated with dietary resistant starch (RS) is the production of butyrate by the gut microbiome during fermentation of this fiber in the large intestine. The ability to degrade RS is a relatively rare trait among microbes in the gut, seemingly confined to only a few species, none of which are butyrate producing organisms. Thus, production of butyrate during RS fermentation requires a network of interactions between RS degraders and butyrate producers. This is further complicated by the fact that there are multiple types of RS that differ in their structural properties and impacts on the microbiome. Human dietary intervention trials with RS have shown increases in fecal butyrate levels at the population level but with individual to individual differences. This suggests that interindividual differences in microbiome composition dictate butyrate response, but the factors driving this are still unknown. Furthermore, it is unknown whether a lack of increase in butyrate production upon supplementation with one RS is indicative of a lack of butyrate production with any RS. To shed some light on these issues we have undertaken an in vitro fermentation approach in an attempt to mimic RS fermentation in the colon. Fecal samples from 10 individuals were used as the inoculum for fermentation with 10 different starch sources. Butyrate production was heterogeneous across both fecal inocula and starch source, suggesting that a given microbiome is best suited to produce butyrate only from a subset of RS sources that differs between individuals. Interestingly, neither the total amount of RS degraders nor butyrate producers seemed to be limiting for any individual, rather the membership of these sub-populations was more important. While none of the RS degrading organisms were correlated with butyrate levels, Ruminococcus bromii was strongly positively correlated with many of the most important butyrate producers in the gut, though total butyrate production was strongly influenced by factors such as pH and lactate levels. Together these results suggest that the membership of the RS degrader and butyrate producer communities rather than their abundances determine the RS sources that will increase butyrate levels for a given microbiome.
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Affiliation(s)
- June Teichmann
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
| | - Darrell W Cockburn
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
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Badilla-Lobo A, Rodríguez C. Microbiological features, epidemiology, and clinical presentation of Clostridioidesdifficile strains from MLST Clade 2: A narrative review. Anaerobe 2021; 69:102355. [PMID: 33711422 DOI: 10.1016/j.anaerobe.2021.102355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 02/06/2023]
Abstract
Clostridioides difficile is an emerging One Health pathogen and a common etiologic agent of diarrhea, both in healthcare settings and the community. This bacterial species is highly diverse, and its global population has been classified in eight clades by multilocus sequence typing (MLST). The C. difficile MLST Clade 2 includes the NAP1/RT027/ST01 strain, which is highly recognized due to its epidemicity and association with severe disease presentation and mortality. By contrast, the remaining 83 sequence types (STs) that compose this clade have received much less attention. In response to this shortcoming, we reviewed articles published in English between 1999 and 2020 and collected information for 27 Clade 2 STs, with an emphasis on STs 01, 67, 41 and 188/231/365. Our analysis provides evidence of large phenotypic differences that preclude support of the rather widespread notion that ST01 and Clade 2 strains are "hypervirulent". Moreover, it revealed a profound lack of (meta)data for nearly 70% of the Clade 2 STs that have been identified in surveillance efforts. Targeted studies aiming to relate wet-lab and bioinformatics results to patient and clinical parameters should be performed to gain a more in-depth insight into the biology of this intriguing group of C. difficile isolates.
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Affiliation(s)
- Adriana Badilla-Lobo
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, and Master's Program in Microbiology, Parasitology, Clinical Chemistry and Immunology, Universidad de Costa Rica, Costa Rica
| | - César Rodríguez
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, and Master's Program in Microbiology, Parasitology, Clinical Chemistry and Immunology, Universidad de Costa Rica, Costa Rica.
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24
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Engevik MA, Danhof HA, Auchtung J, Endres BT, Ruan W, Bassères E, Engevik AC, Wu Q, Nicholson M, Luna RA, Garey KW, Crawford SE, Estes MK, Lux R, Yacyshyn MB, Yacyshyn B, Savidge T, Britton RA, Versalovic J. Fusobacteriumnucleatum Adheres to Clostridioides difficile via the RadD Adhesin to Enhance Biofilm Formation in Intestinal Mucus. Gastroenterology 2021; 160:1301-1314.e8. [PMID: 33227279 PMCID: PMC7956072 DOI: 10.1053/j.gastro.2020.11.034] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/02/2020] [Accepted: 11/13/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS Although Clostridioides difficile infection (CDI) is known to involve the disruption of the gut microbiota, little is understood regarding how mucus-associated microbes interact with C difficile. We hypothesized that select mucus-associated bacteria would promote C difficile colonization and biofilm formation. METHODS To create a model of the human intestinal mucus layer and gut microbiota, we used bioreactors inoculated with healthy human feces, treated with clindamycin and infected with C difficile with the addition of human MUC2-coated coverslips. RESULTS C difficile was found to colonize and form biofilms on MUC2-coated coverslips, and 16S rRNA sequencing showed a unique biofilm profile with substantial cocolonization with Fusobacterium species. Consistent with our bioreactor data, publicly available data sets and patient stool samples showed that a subset of patients with C difficile infection harbored high levels of Fusobacterium species. We observed colocalization of C difficile and F nucleatum in an aggregation assay using adult patients and stool of pediatric patients with inflammatory bowel disease and in tissue sections of patients with CDI. C difficile strains were found to coaggregate with F nucleatum subspecies in vitro; an effect that was inhibited by blocking or mutating the adhesin RadD on Fusobacterium and removal of flagella on C difficile. Aggregation was shown to be unique between F nucleatum and C difficile, because other gut commensals did not aggregate with C difficile. Addition of F nucleatum also enhanced C difficile biofilm formation and extracellular polysaccharide production. CONCLUSIONS Collectively, these data show a unique interaction of between pathogenic C difficile and F nucleatum in the intestinal mucus layer.
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Affiliation(s)
- Melinda A. Engevik
- Department of Pathology & Immunology, Baylor College of
Medicine,Texas Children’s Microbiome Center, Department of
Pathology, Texas Children's Hospital
| | - Heather A. Danhof
- Department of Molecular Virology and Microbiology, Baylor
College of Medicine
| | - Jennifer Auchtung
- Department of Molecular Virology and Microbiology, Baylor
College of Medicine,Department of Food Science and Technology, University of
Nebraska-Lincoln
| | - Bradley T. Endres
- Department of Pharmacy Practice and Translational Research,
University of Houston College of Pharmacy
| | - Wenly Ruan
- Department of Pathology & Immunology, Baylor College of
Medicine,Texas Children’s Microbiome Center, Department of
Pathology, Texas Children's Hospital
| | - Eugénie Bassères
- Department of Pharmacy Practice and Translational Research,
University of Houston College of Pharmacy
| | - Amy C. Engevik
- Department of Surgical Sciences, Vanderbilt University
Medical Center
| | - Qinglong Wu
- Department of Pathology & Immunology, Baylor College of
Medicine,Texas Children’s Microbiome Center, Department of
Pathology, Texas Children's Hospital
| | | | - Ruth Ann Luna
- Department of Pathology & Immunology, Baylor College of
Medicine,Texas Children’s Microbiome Center, Department of
Pathology, Texas Children's Hospital
| | - Kevin W. Garey
- Department of Pharmacy Practice and Translational Research,
University of Houston College of Pharmacy
| | - Sue E. Crawford
- Department of Molecular Virology and Microbiology, Baylor
College of Medicine
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor
College of Medicine,Department of Surgical Sciences, Vanderbilt University
Medical Center
| | - Renate Lux
- Department of Periodontics, University of California Los
Angeles School of Dentistry
| | - Mary Beth Yacyshyn
- Department of Medicine Division of Digestive Diseases
University of Cincinnati College of Medicine
| | - Bruce Yacyshyn
- Department of Medicine Division of Digestive Diseases
University of Cincinnati College of Medicine
| | - Tor Savidge
- Department of Pathology & Immunology, Baylor College of
Medicine,Texas Children’s Microbiome Center, Department of
Pathology, Texas Children's Hospital
| | - Robert A. Britton
- Department of Molecular Virology and Microbiology, Baylor
College of Medicine
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of
Medicine,Texas Children’s Microbiome Center, Department of
Pathology, Texas Children's Hospital
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25
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The Initial Gut Microbiota and Response to Antibiotic Perturbation Influence Clostridioides difficile Clearance in Mice. mSphere 2020; 5:5/5/e00869-20. [PMID: 33087520 PMCID: PMC7580958 DOI: 10.1128/msphere.00869-20] [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: 12/11/2022] Open
Abstract
Clostridioides difficile is a leading nosocomial infection. Although perturbation to the gut microbiota is an established risk, there is variation in who becomes asymptomatically colonized, develops an infection, or has adverse infection outcomes. Mouse models of C. difficile infection (CDI) are widely used to answer a variety of C. difficile pathogenesis questions. However, the interindividual variation between mice from the same breeding facility is less than what is observed in humans. Therefore, we challenged mice from 6 different breeding colonies with C. difficile. We found that the starting microbial community structures and C. difficile persistence varied by the source of mice. Interestingly, a subset of the bacteria that varied across sources were associated with how long C. difficile was able to colonize. By increasing the interindividual diversity of the starting communities, we were able to better model human diversity. This provided a more nuanced perspective of C. difficile pathogenesis. The gut microbiota has a key role in determining susceptibility to Clostridioides difficile infections (CDIs). However, much of the mechanistic work examining CDIs in mouse models uses animals obtained from a single source. We treated mice from 6 sources (2 University of Michigan colonies and 4 commercial vendors) with clindamycin, followed by a C. difficile challenge, and then measured C. difficile colonization levels throughout the infection. The microbiota were profiled via 16S rRNA gene sequencing to examine the variation across sources and alterations due to clindamycin treatment and C. difficile challenge. While all mice were colonized 1 day postinfection, variation emerged from days 3 to 7 postinfection with animals from some sources colonized with C. difficile for longer and at higher levels. We identified bacteria that varied in relative abundance across sources and throughout the experiment. Some bacteria were consistently impacted by clindamycin treatment in all sources of mice, including Lachnospiraceae, Ruminococcaceae, and Enterobacteriaceae. To identify bacteria that were most important to colonization regardless of the source, we created logistic regression models that successfully classified mice based on whether they cleared C. difficile by 7 days postinfection using community composition data at baseline, post-clindamycin treatment, and 1 day postinfection. With these models, we identified 4 bacterial taxa that were predictive of whether C. difficile cleared. They varied across sources (Bacteroides) or were altered by clindamycin (Porphyromonadaceae) or both (Enterobacteriaceae and Enterococcus). Allowing for microbiota variation across sources better emulates human interindividual variation and can help identify bacterial drivers of phenotypic variation in the context of CDIs. IMPORTANCEClostridioides difficile is a leading nosocomial infection. Although perturbation to the gut microbiota is an established risk, there is variation in who becomes asymptomatically colonized, develops an infection, or has adverse infection outcomes. Mouse models of C. difficile infection (CDI) are widely used to answer a variety of C. difficile pathogenesis questions. However, the interindividual variation between mice from the same breeding facility is less than what is observed in humans. Therefore, we challenged mice from 6 different breeding colonies with C. difficile. We found that the starting microbial community structures and C. difficile persistence varied by the source of mice. Interestingly, a subset of the bacteria that varied across sources were associated with how long C. difficile was able to colonize. By increasing the interindividual diversity of the starting communities, we were able to better model human diversity. This provided a more nuanced perspective of C. difficile pathogenesis.
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26
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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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27
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Abstract
The microfluidics field is at a critical crossroads. The vast majority of microfluidic devices are presently manufactured using micromolding processes that work very well for a reduced set of biocompatible materials, but the time, cost, and design constraints of micromolding hinder the commercialization of many devices. As a result, the dissemination of microfluidic technology-and its impact on society-is in jeopardy. Digital manufacturing (DM) refers to a family of computer-centered processes that integrate digital three-dimensional (3D) designs, automated (additive or subtractive) fabrication, and device testing in order to increase fabrication efficiency. Importantly, DM enables the inexpensive realization of 3D designs that are impossible or very difficult to mold. The adoption of DM by microfluidic engineers has been slow, likely due to concerns over the resolution of the printers and the biocompatibility of the resins. In this article, we review and discuss the various printer types, resolution, biocompatibility issues, DM microfluidic designs, and the bright future ahead for this promising, fertile field.
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Affiliation(s)
- Arman Naderi
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA;
| | - Nirveek Bhattacharjee
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA;
| | - Albert Folch
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA;
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28
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Piironen K, Haapala M, Talman V, Järvinen P, Sikanen T. Cell adhesion and proliferation on common 3D printing materials used in stereolithography of microfluidic devices. LAB ON A CHIP 2020; 20:2372-2382. [PMID: 32500123 DOI: 10.1039/d0lc00114g] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Three-dimensional (3D) printing has recently emerged as a cost-effective alternative for rapid prototyping of microfluidic devices. The feature resolution of stereolithography-based 3D printing is particularly well suited for manufacturing of continuous flow cell culture platforms. Poor cell adhesion or material-induced cell death may, however, limit the introduction of new materials to microfluidic cell culture. In this work, we characterized four commercially available materials commonly used in stereolithography-based 3D printing with respect to long-term (2 month) cell survival on native 3D printed surfaces. Cell proliferation rates, along with material-induced effects on apoptosis and cell survival, were examined in mouse embryonic fibroblasts. Additionally, the feasibility of Dental SG (material with the most favored properties) for culturing of human hepatocytes and human-induced pluripotent stem cells was evaluated. The strength of cell adhesion to Dental SG was further examined over a shear force gradient of 1-89 dyne per cm2 by using a custom-designed microfluidic shear force assay incorporating a 3D printed, tilted and tapered microchannel sealed with a polydimethylsiloxane lid. According to our results, autoclavation of the devices prior to cell seeding played the most important role in facilitating long-term cell survival on the native 3D printed surfaces with the shear force threshold in the range of 3-8 dyne per cm2.
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Affiliation(s)
- Kati Piironen
- Faculty of Pharmacy, Drug Research Program, Division of Pharmaceutical Chemistry and Technology, University of Helsinki, Viikinkaari 5E, FI-00014, Finland.
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29
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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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30
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Vitucci JC, Pulse M, Tabor-Simecka L, Simecka J. Epidemic ribotypes of Clostridium (now Clostridioides) difficile are likely to be more virulent than non-epidemic ribotypes in animal models. BMC Microbiol 2020; 20:27. [PMID: 32024477 PMCID: PMC7003423 DOI: 10.1186/s12866-020-1710-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/21/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Clostridioides difficile infections have become more frequently diagnosed and associated with greater disease severity, which has resulted in an increase burden on the healthcare system. These increases are attributed to the increased prevalence of hypervirulent strains encompassing select ribotypes. These epidemic ribotypes were characterized as hypervirulent due to higher in vitro spore and toxin production, as well as increased incidence, severity and mortality within patients. However, it is unclear whether epidemic ribotypes are truly more virulent than non-epidemic ribotypes in vivo. Furthermore, there is conflicting evidence about the ability of a strain's in vitro phenotype to be predictive of their in vivo virulence. The goals of the current studies were to determine if epidemic ribotypes are more virulent than other ribotypes in animal models, and whether the in vitro virulence phenotype of an isolate or ribotype predict in vivo virulence. RESULTS To determine if epidemic strains were truly more virulent than other non-epidemic strains, the in vivo virulence of 13 C. difficile isolates (7 non-epidemic and 6 epidemic ribotype isolates) were determined in murine and hamster models of CDI. The isolates of epidemic ribotype of C. difficile were found to be more virulent in both the murine and hamster models than non-epidemic isolates. In particular, the group of epidemic ribotypes of C. difficile had lower LD50 values in hamsters. The increased severity of disease was associated with higher levels of Toxin A and Toxin B production found in fecal samples, but not numbers of organisms recovered. The isolates were further characterized for their in vitro virulence phenotypes, e.g. toxin production, growth rates, spore formation and adherence of spores to intestinal epithelial cell lines. Although there were higher levels of toxins produced and greater adherence for the group of epidemic ribotypes, the in vitro profiles of individual isolates were not always predictive of their in vivo virulence. CONCLUSIONS Overall, the group of epidemic ribotypes of C. difficile were more virulent in vivo despite individual isolates having similar phenotypes to the non-epidemic isolates in vitro.
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Affiliation(s)
- John C Vitucci
- Department of Pharmaceutical Sciences and UNTHSC Preclinical Services, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Mark Pulse
- Department of Pharmaceutical Sciences and UNTHSC Preclinical Services, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | | | - Jerry Simecka
- Department of Pharmaceutical Sciences and UNTHSC Preclinical Services, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA.
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Clostridioides (Clostridium) Difficile in Food-Producing Animals, Horses and Household Pets: A Comprehensive Review. Microorganisms 2019; 7:microorganisms7120667. [PMID: 31835413 PMCID: PMC6955671 DOI: 10.3390/microorganisms7120667] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 02/06/2023] Open
Abstract
Clostridioides (Clostridium) difficile is ubiquitous in the environment and is also considered as a bacterium of great importance in diarrhea-associated disease for humans and different animal species. Food animals and household pets are frequently found positive for toxigenic C. difficile without exposing clinical signs of infection. Humans and animals share common C. difficile ribotypes (RTs) suggesting potential zoonotic transmission. However, the role of animals for the development of human infection due to C. difficile remains unclear. One major public health issue is the existence of asymptomatic animals that carry and shed the bacterium to the environment, and infect individuals or populations, directly or through the food chain. C. difficile ribotype 078 is frequently isolated from food animals and household pets as well as from their environment. Nevertheless, direct evidence for the transmission of this particular ribotype from animals to humans has never been established. This review will summarize the current available data on epidemiology, clinical presentations, risk factors and laboratory diagnosis of C. difficile infection in food animals and household pets, outline potential prevention and control strategies, and also describe the current evidence towards a zoonotic potential of C. difficile infection.
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32
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Emele MF, Joppe FM, Riedel T, Overmann J, Rupnik M, Cooper P, Kusumawati RL, Berger FK, Laukien F, Zimmermann O, Bohne W, Groß U, Bader O, Zautner AE. Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes. Front Microbiol 2019; 10:2087. [PMID: 31552001 PMCID: PMC6747054 DOI: 10.3389/fmicb.2019.02087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 08/23/2019] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile, a Gram-positive spore-forming bacterium, is the leading cause of nosocomial diarrhea worldwide and therefore a substantial burden to the healthcare system. During the past decade, hypervirulent PCR-ribotypes (RT) e.g., RT027 or RT176 emerged rapidly all over the world, associated with both, increased severity and mortality rates. It is thus of great importance to identify epidemic strains such as RT027 and RT176 as fast as possible. While commonly used diagnostic methods, e.g., multilocus sequence typing (MLST) or PCR-ribotyping, are time-consuming, proteotyping offers a fast, inexpensive, and reliable alternative solution. In this study, we established a MALDI-TOF-based typing scheme for C. difficile. A total of 109 ribotyped strains representative for five MLST clades were analyzed by MALDI-TOF. MLST, based on whole genome sequences, and PCR-ribotyping were used as reference methods. Isoforms of MS-detectable biomarkers, typically ribosomal proteins, were related with the deduced amino acid sequences and added to the C. difficile proteotyping scheme. In total, we were able to associate nine biomarkers with their encoding genes and include them in our proteotyping scheme. The discriminatory capacity of the C. difficile proteotyping scheme was mainly based on isoforms of L28-M (2 main isoforms), L35-M (4 main isoforms), and S20-M (2 main isoforms) giving rise to at least 16 proteotyping-derived types. In our test population, five of these 16 proteotyping-derived types were detected. These five proteotyping-derived types did not correspond exactly to the included five MLST-based C. difficile clades, nevertheless the subtyping depth of both methods was equivalent. Most importantly, proteotyping-derived clade B contained only isolates of the hypervirulent RT027 and RT176. Proteotyping is a stable and easy-to-perform intraspecies typing method and a promising alternative to currently used molecular techniques. It is possible to distinguish the group of RT027 and RT176 isolates from non-RT027/non-RT176 isolates using proteotyping, providing a valuable diagnostic tool.
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Affiliation(s)
- Matthias F Emele
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Felix M Joppe
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Thomas Riedel
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Braunschweig, Germany
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | | | - R Lia Kusumawati
- Department of Microbiology, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Fabian K Berger
- National Reference Center for Clostridioides (Clostridium) difficile, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Friederike Laukien
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Ortrud Zimmermann
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Wolfgang Bohne
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Uwe Groß
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Oliver Bader
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Andreas E Zautner
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
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Vernon JJ, Wilcox MH, Freeman J. Effect of fluoroquinolone resistance mutation Thr-82→Ile on Clostridioides difficile fitness. J Antimicrob Chemother 2018; 74:877-884. [DOI: 10.1093/jac/dky535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/31/2018] [Accepted: 11/22/2018] [Indexed: 01/19/2023] Open
Affiliation(s)
- J J Vernon
- Healthcare-Associated Infections Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Old Medical School, Leeds General Infirmary, Leeds, UK
| | - M H Wilcox
- Healthcare-Associated Infections Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Old Medical School, Leeds General Infirmary, Leeds, UK
- Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
| | - J Freeman
- Healthcare-Associated Infections Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Old Medical School, Leeds General Infirmary, Leeds, UK
- Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
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Increased sporulation underpins adaptation of Clostridium difficile strain 630 to a biologically-relevant faecal environment, with implications for pathogenicity. Sci Rep 2018; 8:16691. [PMID: 30420658 PMCID: PMC6232153 DOI: 10.1038/s41598-018-35050-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/24/2018] [Indexed: 02/07/2023] Open
Abstract
Clostridium difficile virulence is driven primarily by the processes of toxinogenesis and sporulation, however many in vitro experimental systems for studying C. difficile physiology have arguably limited relevance to the human colonic environment. We therefore created a more physiologically–relevant model of the colonic milieu to study gut pathogen biology, incorporating human faecal water (FW) into growth media and assessing the physiological effects of this on C. difficile strain 630. We identified a novel set of C. difficile–derived metabolites in culture supernatants, including hexanoyl– and pentanoyl–amino acid derivatives by LC-MSn. Growth of C. difficile strain 630 in FW media resulted in increased cell length without altering growth rate and RNA sequencing identified 889 transcripts as differentially expressed (p < 0.001). Significantly, up to 300–fold increases in the expression of sporulation–associated genes were observed in FW media–grown cells, along with reductions in motility and toxin genes’ expression. Moreover, the expression of classical stress–response genes did not change, showing that C. difficile is well–adapted to this faecal milieu. Using our novel approach we have shown that interaction with FW causes fundamental changes in C. difficile biology that will lead to increased disease transmissibility.
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35
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Horvat S, Rupnik M. Interactions Between Clostridioides difficile and Fecal Microbiota in in Vitro Batch Model: Growth, Sporulation, and Microbiota Changes. Front Microbiol 2018; 9:1633. [PMID: 30087660 PMCID: PMC6066498 DOI: 10.3389/fmicb.2018.01633] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/29/2018] [Indexed: 12/14/2022] Open
Abstract
Disturbance in gut microbiota is crucial for the development of Clostridioides difficile infection (CDI). Different mechanisms through which gut microbiota influences C. difficile colonization are known. However, C. difficile could also affect gut microbiota balance as previously demonstrated by cultivation of fecal microbiota in C. difficile conditioned medium. In current study, the interactions of C. difficile cells with gut microbiota were addressed. Three different strains (ribotypes 027, 014/020, and 010) were co-cultivated with two types of fecal microbiota (healthy and dysbiotic) using in vitro batch model. While all strains showed higher sporulation frequency in the presence of dysbiotic fecal microbiota, the growth was strain dependent. C. difficile either proliferated to comparable levels in the presence of dysbiotic and healthy fecal microbiota or grew better in co-culture with dysbiotic microbiota. In co-cultures with any C. difficile strain fecal microbiota showed decreased richness and diversity. Dysbiotic fecal microbiota was more affected after co-culture with C. difficile than healthy microbiota. Altogether, 62 OTUs were significantly changed in co-cultures of dysbiotic microbiota/C. difficile and 45 OTUs in co-cultures of healthy microbiota/C. difficile. However, the majority of significantly changed OTUs in both types of microbiota belonged to the phylum Firmicutes with Lachnospiraceae and Ruminococcaceae origin.
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Affiliation(s)
- Sabina Horvat
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Maja Rupnik
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Centre for Medical Microbiology, National Laboratory for Health, Environment and Food, Maribor, Slovenia
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36
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Antibiotic susceptibility and resistance profiles of Romanian Clostridioides difficile isolates. REV ROMANA MED LAB 2018. [DOI: 10.2478/rrlm-2018-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
This study investigated the antibiotic susceptibility patterns and genetic resistance markers of 35 C. difficile strains isolated from patients with C. difficile infection. Vancomycin, metronidazole, tigecycline, teicoplanin, rifampicin, moxifloxacin, cefotaxime, tetracycline, erythromycin, clindamycin, chloramphenicol, linezolid and imipenem MICs were determined for toxigenic strains belonging to PCR ribotypes (PR) 012 (2), 014 (4), 017 (3), 018 (2), 027 (17), 046 (2), 087 (3) and 115 (2). Results showed vancomycin, metronidazole, tigecycline and teicoplanin to be active against all isolates. High resistance rates were noticed against cefotaxime (n = 35), clindamycin (n = 33), imipenem (n = 31), moxifloxacin (n = 25), erythromycin (n = 25) and rifampicin (n = 22). Linezolid-resistance was found in three isolates (PR 017/2, PR 012/1), showing complex resistance (7-9 antibiotics). PR 012, 017, 018, 027 and 046 isolates (n = 26) were resistant to 5-9 antibiotics. Twelve resistance profiles (2-9 antibiotics) were detected. Rifampicin-moxifloxacin-cefotaxime-erythromycin-clindamycin-imipenem-resistance was predominant, being expressed by 18 strains (PR 027/17, PR 018/1). PCR results suggested tetracycline-resistance to be induced by the gene tetM. Three tetM-positive isolates (PRs 012, 046), were also tndX-positive, suggesting the presence of a Tn5397-like element. Only two MLSB-resistant strains (PR 012) had the ermB gene and chloramphenicol-resistance determinant catD was not detected, leaving room for further investigating resistance mechanisms. Multidrug resistance could be attributed to most analysed strains, underlining, once more, the impact of wide-spectrum antimicrobial over prescription, still a tendency in our country, on transmission of antimicrobial resistance and emergence of epidemic C. difficile strains generating outbreaks.
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Abstract
Each year in the United States, billions of dollars are spent combating almost half a million Clostridium difficile infections (CDIs) and trying to reduce the ∼29,000 patient deaths in which C. difficile has an attributed role. In Europe, disease prevalence varies by country and level of surveillance, though yearly costs are estimated at €3 billion. One factor contributing to the significant health care burden of C. difficile is the relatively high frequency of recurrent CDIs. Recurrent CDI, i.e., a second episode of symptomatic CDI occurring within 8 weeks of successful initial CDI treatment, occurs in ∼25% of patients, with 35 to 65% of these patients experiencing multiple episodes of recurrent disease. Using microbial communities to treat recurrent CDI, either as whole fecal transplants or as defined consortia of bacterial isolates, has shown great success (in the case of fecal transplants) or potential promise (in the case of defined consortia of isolates). This review will briefly summarize the epidemiology and physiology of C. difficile infection, describe our current understanding of how fecal microbiota transplants treat recurrent CDI, and outline potential ways that knowledge can be used to rationally design and test alternative microbe-based therapeutics.
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Pham VT, Mohajeri MH. The application of in vitro human intestinal models on the screening and development of pre- and probiotics. Benef Microbes 2018; 9:725-742. [PMID: 29695182 DOI: 10.3920/bm2017.0164] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The importance of the gut microbiota community on host's health and disease has long been recognised and is well documented. The development of pro- and prebiotic interventions offers an opportunity for the modulation of the gut microbiota towards long lasting health. In vitro fermentation models were developed as a powerful tool to study the impact of pro- and prebiotics on the gut microbiota under tightly controlled conditions, which allow dynamic sampling over time in reactors mimicking different colon regions. These models have been further evolved to suit specific experimental purposes, e.g. including immobilised faecal microbiota, peristaltic movement, mucin microcosm and the ability to perform treatments in parallel. In this review we discuss the advantages, disadvantages and technical considerations of the most frequently used models. We further focus on recent advances in the application of these models in prebiotics and probiotics research and outline their predictability for clinical research.
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Affiliation(s)
- V T Pham
- 1 DSM Nutritional Products Ltd., R&D Human Nutrition and Health, P.O. Box 2676, 4002 Basel, Switzerland
| | - M H Mohajeri
- 1 DSM Nutritional Products Ltd., R&D Human Nutrition and Health, P.O. Box 2676, 4002 Basel, Switzerland.,2 University of Zurich, Winterthurerstr. 190, 8057 Zürich, Switzerland
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39
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Lepowsky E, Tasoglu S. Emerging Anti-Fouling Methods: Towards Reusability of 3D-Printed Devices for Biomedical Applications. MICROMACHINES 2018; 9:E196. [PMID: 30424129 PMCID: PMC6187557 DOI: 10.3390/mi9040196] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/07/2018] [Accepted: 04/19/2018] [Indexed: 12/21/2022]
Abstract
Microfluidic devices are used in a myriad of biomedical applications such as cancer screening, drug testing, and point-of-care diagnostics. Three-dimensional (3D) printing offers a low-cost, rapid prototyping, efficient fabrication method, as compared to the costly-in terms of time, labor, and resources-traditional fabrication method of soft lithography of poly(dimethylsiloxane) (PDMS). Various 3D printing methods are applicable, including fused deposition modeling, stereolithography, and photopolymer inkjet printing. Additionally, several materials are available that have low-viscosity in their raw form and, after printing and curing, exhibit high material strength, optical transparency, and biocompatibility. These features make 3D-printed microfluidic chips ideal for biomedical applications. However, for developing devices capable of long-term use, fouling-by nonspecific protein absorption and bacterial adhesion due to the intrinsic hydrophobicity of most 3D-printed materials-presents a barrier to reusability. For this reason, there is a growing interest in anti-fouling methods and materials. Traditional and emerging approaches to anti-fouling are presented in regard to their applicability to microfluidic chips, with a particular interest in approaches compatible with 3D-printed chips.
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Affiliation(s)
- Eric Lepowsky
- Department of Mechanical Engineering, University of Connecticut, Storrs, CT 06269, USA.
| | - Savas Tasoglu
- Department of Mechanical Engineering, University of Connecticut, Storrs, CT 06269, USA.
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA.
- Institute for Collaboration on Health, Intervention, and Policy, University of Connecticut, Storrs, CT 06269, USA.
- The Connecticut Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, CT 06269, USA.
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40
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Blanco N, Walk S, Malani AN, Rickard A, Benn M, Eisenberg M, Zhang M, Foxman B. Clostridium difficile shows no trade-off between toxin and spore production within the human host. J Med Microbiol 2018. [PMID: 29533173 DOI: 10.1099/jmm.0.000719] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE This study aimed to describe the correlation between Clostridium difficile spore and toxin levels within the human host. In addition, we assessed whether overgrowth of Candida albicans modified this association. METHODOLOGY We measured toxin, spore and Candida albicans levels among 200 successively collected stool samples that tested positive for C. difficile, and PCR ribotyped these C. difficile isolates. Analysis of variance and linear regression were used to test the association between spore and toxin levels. Kruskal-Wallis tests and t-tests were used to compare the association between spore or toxin levels and host, specimen, or pathogen characteristics. RESULTS C. difficile toxin and spore levels were positively associated (P<0.001); this association did not vary significantly with C. albicans overgrowth [≥5 logs of C. albicans colony-forming units (c.f.u.) g-1]. However, ribotypes 027 and 078-126 were significantly associated with higher levels of toxin and spores, and C. albicans overgrowth. CONCLUSION The strong positive association observed between in vivo levels of C. difficile toxin and spores suggests that patients with more severe C. difficile infections may have increased spore production, enhancing C. difficile transmission. Although, on average, spore levels were higher in toxin-positive samples than in toxin-negative/PCR-positive samples, spores were found in almost all toxin-negative samples. The ubiquity of spore production among toxin-negative and formed stool samples emphasizes the importance of following infection prevention and control measures for all C. difficile-positive patients during their entire hospital stay.
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Affiliation(s)
- Natalia Blanco
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Seth Walk
- Department of Microbiology and Immunology, College of Letters & Science, Montana State, Bozeman, Montana, USA
| | - Anurag N Malani
- Department of Infection Prevention and Control, Department of Internal Medicine, Division of Infectious Diseases, St Joseph Mercy Health System, Ann Arbor, Michigan, USA
| | - Alexander Rickard
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Michele Benn
- Department of Pathology, Microbiology Laboratory, St Joseph Mercy Health System, Ann Arbor, Michigan, USA
| | - Marisa Eisenberg
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Min Zhang
- Department of Infection Prevention and Control, Department of Internal Medicine, Division of Infectious Diseases, St Joseph Mercy Health System, Ann Arbor, Michigan, USA.,Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Betsy Foxman
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
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41
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Gomez EJ, Montgomery S, Alby K, Robinson DP, Roundtree SS, Blecker-Shelly D, Sullivan KV. Poor yield of Clostridium difficile testing algorithms using glutamate dehydrogenase antigen and C. difficile toxin enzyme immunoassays in a pediatric population with declining prevalence of clostridium difficile strain BI/NAP1/027. Diagn Microbiol Infect Dis 2018; 91:229-232. [PMID: 29567127 DOI: 10.1016/j.diagmicrobio.2018.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 02/14/2018] [Accepted: 02/21/2018] [Indexed: 01/05/2023]
Abstract
We compared the performance of algorithmic Clostridium difficile infection (CDI) diagnosis with four molecular tests in children. Stool samples in patients 1-18 years old were tested with an algorithm (C. Diff Quik Chek Complete (QCC) reflexed to illumigene C. difficile); AmpliVue C. difficile (ACD); Lyra Direct C. difficile (Lyra); BD MAX C diff (BDM); and Xpert C. difficile (XCD). The gold standard was positivity by two tests. Sensitivity, specificity, positive predictive value, and negative predictive value were 85%, 99%, 93%, 97% for the algorithm; 21%, 99%, 78%, 87% for QCC's toxin component; 94%, 99%, 94%, 99% for ACD; 88%, 99%, 94%, 98% for Lyra; 94%, 100%, 100%, 99% for BDM, and 94%, 99%, 94% and 99% for XCD. 9.6% of samples were ribotype 027. Algorithms may detect CDI with lower sensitivity compared to molecular methods in children. This may be related to low prevalence of NAP-1/ribotype 027.
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Affiliation(s)
- Emily J Gomez
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, USA, 19103; Author's location has changed to Clinical Laboratory, Abington-Jefferson Health, 1200 Old York Rd, Abington, PA, USA, 19001
| | - Sandra Montgomery
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, USA, 19103
| | - Kevin Alby
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Spruce St., Philadelphia, PA, USA, 20104
| | - Diana P Robinson
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, USA, 19103
| | - Sylvester S Roundtree
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, USA, 19103
| | - Deborah Blecker-Shelly
- Department of Pathology and Laboratory Medicine, Penn Medicine Princeton Medical Center, 1 Plainsboro Rd, Plainsboro Township, NJ, USA, 08536
| | - Kaede V Sullivan
- Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine at Temple University, Temple University Health System, 3401 N Broad St., Philadelphia, PA, USA, 19140.
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43
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Collins J, Robinson C, Danhof H, Knetsch C, van Leeuwen H, Lawley T, Auchtung J, Britton. R. Dietary trehalose enhances virulence of epidemic Clostridium difficile. Nature 2018; 553:291-294. [PMID: 29310122 PMCID: PMC5984069 DOI: 10.1038/nature25178] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 11/28/2017] [Indexed: 12/24/2022]
Abstract
Clostridium difficile disease has recently increased to become a dominant nosocomial pathogen in North America and Europe, although little is known about what has driven this emergence. Here we show that two epidemic ribotypes (RT027 and RT078) have acquired unique mechanisms to metabolize low concentrations of the disaccharide trehalose. RT027 strains contain a single point mutation in the trehalose repressor that increases the sensitivity of this ribotype to trehalose by more than 500-fold. Furthermore, dietary trehalose increases the virulence of a RT027 strain in a mouse model of infection. RT078 strains acquired a cluster of four genes involved in trehalose metabolism, including a PTS permease that is both necessary and sufficient for growth on low concentrations of trehalose. We propose that the implementation of trehalose as a food additive into the human diet, shortly before the emergence of these two epidemic lineages, helped select for their emergence and contributed to hypervirulence.
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Affiliation(s)
- J. Collins
- Baylor College of Medicine, Department of Molecular Virology and
Microbiology
| | - C. Robinson
- University of Oregon, Institute for Molecular Biology
| | - H. Danhof
- Baylor College of Medicine, Department of Molecular Virology and
Microbiology
| | - C.W. Knetsch
- Leiden University Medical Centre, Department of Medical
Microbiology, The Netherlands
| | - H.C. van Leeuwen
- Leiden University Medical Centre, Department of Medical
Microbiology, The Netherlands
| | - T.D. Lawley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
United Kingdom
| | - J.M. Auchtung
- Baylor College of Medicine, Department of Molecular Virology and
Microbiology
| | - R.A. Britton.
- Baylor College of Medicine, Department of Molecular Virology and
Microbiology
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In vitro models of the human microbiota and microbiome. Emerg Top Life Sci 2017; 1:373-384. [DOI: 10.1042/etls20170045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 01/05/2023]
Abstract
Gut microbiome studies have been gaining popularity over the years, especially with the development of new technologies (e.g. metataxonomics, metagenomics, metatranscriptomics, and metabonomics) that makes it easier for researchers to characterize the composition and functionality of these complex microbial communities. The goal of these studies is to identify a microorganism, group of microbes, or microbial metabolite which correlates with a disease state (e.g. inflammatory bowel disease, colorectal cancer, and obesity). Many of these are cross-sectional studies, where fecal samples from a group of diseased individuals are compared with those from a group of healthy individuals at a single time point. However, there are a wide range of variables that can affect the gut microbiota of humans which make mechanistic studies challenging. Longitudinal studies are required for research to more reliably correlate interventions or disease status to microbiota composition and functionality. However, longitudinal studies in humans and animals are difficult, expensive, and time-consuming. This review will discuss in vitro gut fermentation models and how they can be used to perform longitudinal studies that complement in vivo microbiome studies. Gut fermentation models support the growth of stable, reproducible, and diverse microbial communities in a tightly controlled environment set to mimic the conditions microbes encounter in the gastrointestinal tract. Gut fermentation models will make it easier for researchers to perform mechanistic studies and aid in the development of novel treatments that are both targeted and maintained over time.
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Evaluating the effect of Clostridium difficile conditioned medium on fecal microbiota community structure. Sci Rep 2017; 7:16448. [PMID: 29180685 PMCID: PMC5703886 DOI: 10.1038/s41598-017-15434-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 10/26/2017] [Indexed: 01/05/2023] Open
Abstract
Clostridium difficile infection (CDI) is typically associated with disturbed gut microbiota and changes related to decreased colonization resistance against C. difficile are well described. However, nothing is known about possible effects of C. difficile on gut microbiota restoration during or after CDI. In this study, we have mimicked such a situation by using C. difficile conditioned medium of six different C. difficile strains belonging to PCR ribotypes 027 and 014/020 for cultivation of fecal microbiota. A marked decrease of microbial diversity was observed in conditioned medium of both tested ribotypes. The majority of differences occurred within the phylum Firmicutes, with a general decrease of gut commensals with putative protective functions (i.e. Lactobacillus, Clostridium_XIVa) and an increase in opportunistic pathogens (i.e. Enterococcus). Bacterial populations in conditioned medium differed between the two C. difficile ribotypes, 027 and 014/020 and are likely associated with nutrient availability. Fecal microbiota cultivated in medium conditioned by E. coli, Salmonella Enteritidis or Staphylococcus epidermidis grouped together and was clearly different from microbiota cultivated in C. difficile conditioned medium suggesting that C. difficile effects are specific. Our results show that the changes observed in microbiota of CDI patients are partially directly influenced by C. difficile.
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Shaffer M, Armstrong AJS, Phelan VV, Reisdorph N, Lozupone CA. Microbiome and metabolome data integration provides insight into health and disease. Transl Res 2017; 189:51-64. [PMID: 28764956 PMCID: PMC5659916 DOI: 10.1016/j.trsl.2017.07.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/28/2017] [Accepted: 07/08/2017] [Indexed: 02/07/2023]
Abstract
For much of our history, the most basic information about the microbial world has evaded characterization. Next-generation sequencing has led to a rapid increase in understanding of the structure and function of host-associated microbial communities in diverse diseases ranging from obesity to autism. Through experimental systems such as gnotobiotic mice only colonized with known microbes, a causal relationship between microbial communities and disease phenotypes has been supported. Now, microbiome research must move beyond correlations and general demonstration of causality to develop mechanistic understandings of microbial influence, including through their metabolic activities. Similar to the microbiome field, advances in technologies for cataloguing small molecules have broadened our understanding of the metabolites that populate our bodies. Integration of microbial and metabolomics data paired with experimental validation has promise for identifying microbial influence on host physiology through production, modification, or degradation of bioactive metabolites. Realization of microbial metabolic activities that affect health is hampered by gaps in our understanding of (1) biological properties of microbes and metabolites, (2) which microbial enzymes/pathways produce which metabolites, and (3) the effects of metabolites on hosts. Capitalizing on known mechanistic relationships and filling gaps in our understanding has the potential to enable translational microbiome research across disease contexts.
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Affiliation(s)
- Michael Shaffer
- Department of Medicine, University of Colorado Denver, Aurora, Colo; Computational Bioscience Program, University of Colorado Denver, Aurora, Colo
| | - Abigail J S Armstrong
- Department of Medicine, University of Colorado Denver, Aurora, Colo; Department of Immunology and Microbiology, University of Colorado Denver, Aurora, Colo
| | - Vanessa V Phelan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colo
| | - Nichole Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colo
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47
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Next-Generation Probiotics Targeting Clostridium difficile through Precursor-Directed Antimicrobial Biosynthesis. Infect Immun 2017; 85:IAI.00303-17. [PMID: 28760934 PMCID: PMC5607411 DOI: 10.1128/iai.00303-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/24/2017] [Indexed: 12/18/2022] Open
Abstract
Integration of antibiotic and probiotic therapy has the potential to lessen the public health burden of antimicrobial-associated diseases. Clostridium difficile infection (CDI) represents an important example where the rational design of next-generation probiotics is being actively pursued to prevent disease recurrence. Because intrinsic resistance to clinically relevant antibiotics used to treat CDI (vancomycin, metronidazole, and fidaxomicin) is a desired trait in such probiotic species, we screened several bacteria and identified Lactobacillus reuteri to be a promising candidate for adjunct therapy. Human-derived L. reuteri bacteria convert glycerol to the broad-spectrum antimicrobial compound reuterin. When supplemented with glycerol, strains carrying the pocR gene locus were potent reuterin producers, with L. reuteri 17938 inhibiting C. difficile growth at a level on par with the level of growth inhibition by vancomycin. Targeted pocR mutations and complementation studies identified reuterin to be the precursor-induced antimicrobial agent. Pathophysiological relevance was demonstrated when the codelivery of L. reuteri with glycerol was effective against C. difficile colonization in complex human fecal microbial communities, whereas treatment with either glycerol or L. reuteri alone was ineffective. A global unbiased microbiome and metabolomics analysis independently confirmed that glycerol precursor delivery with L. reuteri elicited changes in the composition and function of the human microbial community that preferentially targets C. difficile outgrowth and toxicity, a finding consistent with glycerol fermentation and reuterin production. Antimicrobial resistance has thus been successfully exploited in the natural design of human microbiome evasion of C. difficile, and this method may provide a prototypic precursor-directed probiotic approach. Antibiotic resistance and substrate bioavailability may therefore represent critical new determinants of probiotic efficacy in clinical trials.
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48
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von Martels JZH, Sadaghian Sadabad M, Bourgonje AR, Blokzijl T, Dijkstra G, Faber KN, Harmsen HJM. The role of gut microbiota in health and disease: In vitro modeling of host-microbe interactions at the aerobe-anaerobe interphase of the human gut. Anaerobe 2017; 44:3-12. [PMID: 28062270 DOI: 10.1016/j.anaerobe.2017.01.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/16/2016] [Accepted: 01/02/2017] [Indexed: 02/07/2023]
Abstract
The microbiota of the gut has many crucial functions in human health. Dysbiosis of the microbiota has been correlated to a large and still increasing number of diseases. Recent studies have mostly focused on analyzing the associations between disease and an aberrant microbiota composition. Functional studies using (in vitro) gut models are required to investigate the precise interactions that occur between specific bacteria (or bacterial mixtures) and gut epithelial cells. As most gut bacteria are obligate or facultative anaerobes, studying their effect on oxygen-requiring human gut epithelial cells is technically challenging. Still, several (anaerobic) bacterial-epithelial co-culture systems have recently been developed that mimic host-microbe interactions occurring in the human gut, including 1) the Transwell "apical anaerobic model of the intestinal epithelial barrier", 2) the Host-Microbiota Interaction (HMI) module, 3) the "Human oxygen-Bacteria anaerobic" (HoxBan) system, 4) the human gut-on-a-chip and 5) the HuMiX model. This review discusses the role of gut microbiota in health and disease and gives an overview of the characteristics and applications of these novel host-microbe co-culture systems.
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Affiliation(s)
- Julius Z H von Martels
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Mehdi Sadaghian Sadabad
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tjasso Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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49
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Rashid SJ, Barylski J, Hargreaves KR, Millard AA, Vinner GK, Clokie MRJ. Two Novel Myoviruses from the North of Iraq Reveal Insights into Clostridium difficile Phage Diversity and Biology. Viruses 2016; 8:v8110310. [PMID: 27854339 PMCID: PMC5127024 DOI: 10.3390/v8110310] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 12/18/2022] Open
Abstract
Bacteriophages (phages) are increasingly being explored as therapeutic agents to combat bacterial diseases, including Clostridium difficile infections. Therapeutic phages need to be able to efficiently target and kill a wide range of clinically relevant strains. While many phage groups have yet to be investigated in detail, those with new and useful properties can potentially be identified when phages from newly studied geographies are characterised. Here, we report the isolation of C. difficile phages from soil samples from the north of Iraq. Two myoviruses, CDKM15 and CDKM9, were selected for detailed sequence analysis on the basis of their broad and potentially useful host range. CDKM9 infects 25/80 strains from 12/20 C. difficile ribotypes, and CDKM15 infects 20/80 strains from 9/20 ribotypes. Both phages can infect the clinically relevant ribotypes R027 and R001. Phylogenetic analysis based on whole genome sequencing revealed that the phages are genetically distinct from each other but closely related to other long-tailed myoviruses. A comparative genomic analysis revealed key differences in the genes predicted to encode for proteins involved in bacterial infection. Notably, CDKM15 carries a clustered regularly interspaced short palindromic repeat (CRISPR) array with spacers that are homologous to sequences in the CDKM9 genome and of phages from diverse localities. The findings presented suggest a possible shared evolutionary past for these phages and provides evidence of their widespread dispersal.
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Affiliation(s)
- Srwa J Rashid
- Department of Infection, Immunity and Inflammation, Medical Sciences Building, University of Leicester, University Road, Leicester, LE1 9HN, UK.
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan 61-712, Poland.
| | | | - Andrew A Millard
- Microbiology & Infection Unit, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
| | - Gurinder K Vinner
- Department of Chemical Engineering, Loughborough University, Loughborough, LE11 3TU, UK.
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, Medical Sciences Building, University of Leicester, University Road, Leicester, LE1 9HN, UK.
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50
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Moono P, Foster NF, Hampson DJ, Knight DR, Bloomfield LE, Riley TV. Clostridium difficile Infection in Production Animals and Avian Species: A Review. Foodborne Pathog Dis 2016; 13:647-655. [PMID: 27602596 DOI: 10.1089/fpd.2016.2181] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Clostridium difficile is the leading cause of antibiotic-associated diarrhea and colitis in hospitalized humans. Recently, C. difficile infection (CDI) has been increasingly recognized as a cause of neonatal enteritis in food animals such as pigs, resulting in stunted growth, delays in weaning, and mortality, as well as colitis in large birds such as ostriches. C. difficile is a strictly anaerobic spore-forming bacterium, which produces two toxins A (TcdA) and B (TcdB) as its main virulence factors. The majority of strains isolated from animals produce an additional binary toxin (C. difficile transferase) that is associated with increased virulence. C. difficile is ubiquitous in the environment and has a wide host range. This review summarizes the epidemiology, clinical presentations, risk factors, and laboratory diagnosis of CDI in animals. Increased awareness by veterinarians and animal owners of the significance of clinical disease caused by C. difficile in livestock and avians is needed. Finally, this review provides an overview on methods for controlling environmental contamination and potential therapeutics available.
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Affiliation(s)
- Peter Moono
- 1 Microbiology & Immunology, School of Pathology and Laboratory Medicine, The University of Western Australia , Nedlands, WA, Australia
| | - Niki F Foster
- 2 Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre , Nedlands, WA, Australia
| | - David J Hampson
- 3 School of Veterinary & Life Sciences, Murdoch University , Murdoch, WA, Australia
| | - Daniel R Knight
- 1 Microbiology & Immunology, School of Pathology and Laboratory Medicine, The University of Western Australia , Nedlands, WA, Australia
| | - Lauren E Bloomfield
- 4 Healthcare Associated Infection Unit, Department of Health, Communicable Disease Control Directorate, Shenton Park, WA, Australia
| | - Thomas V Riley
- 1 Microbiology & Immunology, School of Pathology and Laboratory Medicine, The University of Western Australia , Nedlands, WA, Australia .,2 Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre , Nedlands, WA, Australia .,3 School of Veterinary & Life Sciences, Murdoch University , Murdoch, WA, Australia .,4 Healthcare Associated Infection Unit, Department of Health, Communicable Disease Control Directorate, Shenton Park, WA, Australia .,5 School of Medical & Health Sciences, Edith Cowan University , Joondalup, WA, Australia
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