1
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Guo C, Liu J, Wei Y, Du W, Li S. Comparison of the gastrointestinal bacterial microbiota between dairy cows with and without mastitis. Front Microbiol 2024; 15:1332497. [PMID: 38585704 PMCID: PMC10996066 DOI: 10.3389/fmicb.2024.1332497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/14/2024] [Indexed: 04/09/2024] Open
Abstract
Mastitis causes significant losses in the global dairy industry, and the health of animals has been linked to their intestinal microbiota. To better understand the relationship between gastrointestinal microbiota and mastitis in dairy cows, we collected blood, rumen fluid, and fecal samples from 23 dairy cows, including 13 cows with mastitis and 10 healthy cows. Using ELISA kit and high-throughput sequencing, we found that cows with mastitis had higher concentrations of TNF-α, IL-1, and LPS than healthy cows (p < 0.05), but no significant differences in microbiota abundance or diversity (p > 0.05). Principal coordinate analysis (PCOA) revealed significant differences in rumen microbial structure between the two groups (p < 0.05), with Moryella as the signature for rumen in cows with mastitis. In contrast, fecal microbial structure showed no significant differences (p > 0.05), with Aeriscardovia, Lactococcus, and Bacillus as the signature for feces in healthy cows. Furthermore, the results showed distinct microbial interaction patterns in the rumen and feces of cows with mastitis compared to healthy cows. Additionally, we observed correlations between the microbiota in both the rumen and feces of cows and blood inflammatory indicators. Our study sheds new light on the prevention of mastitis in dairy cows by highlighting the relationship between gastrointestinal microbiota and mastitis.
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Affiliation(s)
- Chunyan Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Jinzhong Vocational and Technical College, Jinzhong, China
| | - Jingjing Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yong Wei
- Xinjiang Agricultural University, Urumuqi, China
| | - Wen Du
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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2
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Wu R, Xiong R, Li Y, Chen J, Yan R. Gut microbiome, metabolome, host immunity associated with inflammatory bowel disease and intervention of fecal microbiota transplantation. J Autoimmun 2023; 141:103062. [PMID: 37246133 DOI: 10.1016/j.jaut.2023.103062] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/30/2023]
Abstract
Gut dysbiosis has been associated with inflammatory bowel disease (IBD), one of the most common gastrointestinal diseases. The microbial communities play essential roles in host physiology, with profound effects on immune homeostasis, directly or via their metabolites and/or components. There are increasing clinical trials applying fecal microbiota transplantation (FMT) with Crohn's disease (CD) and ulcerative colitis (UC). The restoration of dysbiotic gut microbiome is considered as one of the mechanisms of FMT therapy. In this work, latest advances in the alterations in gut microbiome and metabolome features in IBD patients and experimental mechanistic understanding on their contribution to the immune dysfunction were reviewed. Then, the therapeutic outcomes of FMT on IBD were summarized based on clinical remission, endoscopic remission and histological remission of 27 clinical trials retrieved from PubMed which have been registered on ClinicalTrials.gov with the results been published in the past 10 years. Although FMT is established as an effective therapy for both subtypes of IBD, the promising outcomes are not always achieved. Among the 27 studies, only 11 studies performed gut microbiome profiling, 5 reported immune response alterations and 3 carried out metabolome analysis. Generally, FMT partially restored typical changes in IBD, resulted in increased α-diversity and species richness in responders and similar but less pronounced shifts of patient microbial and metabolomics profiles toward donor profiles. Measurements of immune responses to FMT mainly focused on T cells and revealed divergent effects on pro-/anti-inflammatory functions. The very limited information and the extremely confounding factors in the designs of the FMT trials significantly hindered a reasonable conclusion on the mechanistic involvement of gut microbiota and metabolites in clinical outcomes and an analysis of the inconsistencies.
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Affiliation(s)
- Rongrong Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Rui Xiong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Yan Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Junru Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Ru Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
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3
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Anand A, Parveen Shaikh N, Aggarwal Y, Fatima U, Chapagain S, Chidurala R, Vaghela J, Surana A, Parikh C, Patel RH. Vowst's FDA approval is a boon for the prevention of recurrent Clostridioides difficile infection. Ann Med Surg (Lond) 2023; 85:5852-5854. [PMID: 38098563 PMCID: PMC10718391 DOI: 10.1097/ms9.0000000000001410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/09/2023] [Indexed: 12/17/2023] Open
Affiliation(s)
- Ayush Anand
- B.P. Koirala Institute of Health Sciences, Dharan
- Global Consortium of Medical Education and Research, Pune, India
| | - Nameera Parveen Shaikh
- Batumi Shota Rustaveli State University, Batumi, Georgia
- Global Consortium of Medical Education and Research, Pune, India
| | - Yash Aggarwal
- Government Institute of Medical Sciences, Greater Noida
- Global Consortium of Medical Education and Research, Pune, India
| | - Umaima Fatima
- Shadan Institute of Medical Sciences, Hyderabad, Telangana
- Global Consortium of Medical Education and Research, Pune, India
| | - Sanskriti Chapagain
- Devdaha Medical College and Research Institute, Rupandehi, Nepal
- Global Consortium of Medical Education and Research, Pune, India
| | - Rahul Chidurala
- Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
- Global Consortium of Medical Education and Research, Pune, India
| | | | - Arihant Surana
- Department of Internal Medicine, Saint Vincent Hospital, Worcester, Massachusetts
| | - Charmy Parikh
- Department of Internal Medicine, Carle BroMenn Medical Center, Normal, Illinois
| | - Raj H. Patel
- Department of Internal Medicine, St. Mary Medical Center, Pennsylvania, USA
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4
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Poto R, Laniro G, de Paulis A, Spadaro G, Marone G, Gasbarrini A, Varricchi G. Is there a role for microbiome-based approach in common variable immunodeficiency? Clin Exp Med 2023; 23:1981-1998. [PMID: 36737487 PMCID: PMC9897624 DOI: 10.1007/s10238-023-01006-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023]
Abstract
Common variable immunodeficiency (CVID) is a primary immunodeficiency characterized by low levels of serum immunoglobulins and increased susceptibility to infections, autoimmune disorders and cancer. CVID embraces a plethora of heterogeneous manifestations linked to complex immune dysregulation. While CVID is thought to be due to genetic defects, the exact cause of this immune disorder is unknown in the large majority of cases. Compelling evidences support a linkage between the gut microbiome and the CVID pathogenesis, therefore a potential for microbiome-based treatments to be a therapeutic pathway for this disorder. Here we discuss the potential of treating CVID patients by developing a gut microbiome-based personalized approach, including diet, prebiotics, probiotics, postbiotics and fecal microbiota transplantation. We also highlight the need for a better understanding of microbiota-host interactions in CVID patients to prime the development of improved preventive strategies and specific therapeutic targets.
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Affiliation(s)
- Remo Poto
- Department of Translational Medical Sciences, University of Naples Federico II, 80131, Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80131, Naples, Italy
- World Allergy Organization (WAO), Center of Excellence, 80131, Naples, Italy
- Department of Oncology and Molecular Medicine, Istituto Superiore Di Sanità (ISS), Rome, Italy
| | - Gianluca Laniro
- Digestive Disease Center, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of Rome, Rome, Italy
| | - Amato de Paulis
- Department of Translational Medical Sciences, University of Naples Federico II, 80131, Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80131, Naples, Italy
- World Allergy Organization (WAO), Center of Excellence, 80131, Naples, Italy
| | - Giuseppe Spadaro
- Department of Translational Medical Sciences, University of Naples Federico II, 80131, Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80131, Naples, Italy
- World Allergy Organization (WAO), Center of Excellence, 80131, Naples, Italy
| | - Gianni Marone
- Department of Translational Medical Sciences, University of Naples Federico II, 80131, Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80131, Naples, Italy
- World Allergy Organization (WAO), Center of Excellence, 80131, Naples, Italy
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, 80131, Naples, Italy
| | - Antonio Gasbarrini
- Digestive Disease Center, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy
- Department of Translational Medicine and Surgery, Catholic University of Rome, Rome, Italy
| | - Gilda Varricchi
- Department of Translational Medical Sciences, University of Naples Federico II, 80131, Naples, Italy.
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, 80131, Naples, Italy.
- World Allergy Organization (WAO), Center of Excellence, 80131, Naples, Italy.
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, 80131, Naples, Italy.
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5
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Zhu J, Lyu J, Zhao R, Liu G, Wang S. Gut macrobiotic and its metabolic pathways modulate cardiovascular disease. Front Microbiol 2023; 14:1272479. [PMID: 37822750 PMCID: PMC10562559 DOI: 10.3389/fmicb.2023.1272479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023] Open
Abstract
Thousands of microorganisms reside in the human gut, and extensive research has demonstrated the crucial role of the gut microbiota in overall health and maintaining homeostasis. The disruption of microbial populations, known as dysbiosis, can impair the host's metabolism and contribute to the development of various diseases, including cardiovascular disease (CVD). Furthermore, a growing body of evidence indicates that metabolites produced by the gut microbiota play a significant role in the pathogenesis of cardiovascular disease. These bioactive metabolites, such as short-chain fatty acids (SCFAs), trimethylamine (TMA), trimethylamine N-oxide (TMAO), bile acids (BAs), and lipopolysaccharides (LPS), are implicated in conditions such as hypertension and atherosclerosis. These metabolites impact cardiovascular function through various pathways, such as altering the composition of the gut microbiota and activating specific signaling pathways. Targeting the gut microbiota and their metabolic pathways represents a promising approach for the prevention and treatment of cardiovascular diseases. Intervention strategies, such as probiotic drug delivery and fecal transplantation, can selectively modify the composition of the gut microbiota and enhance its beneficial metabolic functions, ultimately leading to improved cardiovascular outcomes. These interventions hold the potential to reshape the gut microbial community and restore its balance, thereby promoting cardiovascular health. Harnessing the potential of these microbial metabolites through targeted interventions offers a novel avenue for tackling cardiovascular health issues. This manuscript provides an in-depth review of the recent advances in gut microbiota research and its impact on cardiovascular health and offers a promising avenue for tackling cardiovascular health issues through gut microbiome-targeted therapies.
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Affiliation(s)
- Junwen Zhu
- Department of Cardiology, The Affiliated Wenling Hospital of Wenzhou Medical University (The First People’s Hospital of Wenling), Zhejiang, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Jin Lyu
- Department of Pathology, The First People’s Hospital of Foshan, Foshan, Guangdong, China
| | - Ruochi Zhao
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Affiliated First Hospital of Ningbo University, Ningbo, China
| | - Gang Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Shuangshuang Wang
- Department of Cardiology, The Affiliated Wenling Hospital of Wenzhou Medical University (The First People’s Hospital of Wenling), Zhejiang, China
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6
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McFarland LV, Goldstein EJC, Kullar R. Microbiome-Related and Infection Control Approaches to Primary and Secondary Prevention of Clostridioides difficile Infections. Microorganisms 2023; 11:1534. [PMID: 37375036 DOI: 10.3390/microorganisms11061534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Clostridioides difficile infections (CDIs) have decreased in the past years, but since 2021, some hospitals have reported an increase in CDI rates. CDI remains a global concern and has been identified as an urgent threat to healthcare. Although multiple treatment options are available, prevention strategies are more limited. As CDI is an opportunistic infection that arises after the normally protective microbiome has been disrupted, preventive measures aimed at restoring the microbiome have been tested. Our aim is to update the present knowledge on these various preventive strategies published in the past five years (2018-2023) to guide clinicians and healthcare systems on how to best prevent CDI. A literature search was conducted using databases (PubMed, Google Scholar, and clinicaltrials.gov) for phase 2-3 clinical trials for the primary or secondary prevention of CDI and microbiome and probiotics. As the main factor for Clostridium difficile infections is the disruption of the normally protective intestinal microbiome, strategies aimed at restoring the microbiome seem most rational. Some strains of probiotics, the use of fecal microbial therapy, and live biotherapeutic products offer promise to fill this niche; although, more large randomized controlled trials are needed that document the shifts in the microbiome population.
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Affiliation(s)
| | | | - Ravina Kullar
- Expert Stewardship Inc., Newport Beach, CA 92663, USA
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7
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Yadegar A, Pakpoor S, Ibrahim FF, Nabavi-Rad A, Cook L, Walter J, Seekatz AM, Wong K, Monaghan TM, Kao D. Beneficial effects of fecal microbiota transplantation in recurrent Clostridioides difficile infection. Cell Host Microbe 2023; 31:695-711. [PMID: 37167952 DOI: 10.1016/j.chom.2023.03.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Fecal microbiota transplantation (FMT) is highly effective in preventing recurrent Clostridioides difficile infection (rCDI). However, the mechanisms underpinning its clinical efficacy are incompletely understood. Herein, we provide an overview of rCDI pathogenesis followed by a discussion of potential mechanisms of action focusing on the current understanding of trans-kingdom microbial, metabolic, immunological, and epigenetic mechanisms. We then outline the current research gaps and offer methodological recommendations for future studies to elevate the quality of research and advance knowledge translation. By combining interventional trials with multiomics technology and host and environmental factors, analyzing longitudinally collected biospecimens will generate results that can be validated with animal and other models. Collectively, this will confirm causality and improve translation, ultimately to develop targeted therapies to replace FMT.
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Affiliation(s)
- Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sepideh Pakpoor
- School of Engineering, University of British Columbia, Kelowna, BC, Canada
| | - Fathima F Ibrahim
- National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK; Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Ali Nabavi-Rad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Laura Cook
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jens Walter
- School of Microbiology, Department of Medicine and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Anna M Seekatz
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Karen Wong
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Tanya M Monaghan
- National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK; Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK.
| | - Dina Kao
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada.
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8
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Lahtinen P, Jalanka J, Mattila E, Tillonen J, Bergman P, Satokari R, Arkkila P. Fecal microbiota transplantation for the maintenance of remission in patients with ulcerative colitis: A randomized controlled trial. World J Gastroenterol 2023; 29:2666-2678. [PMID: 37213403 PMCID: PMC10198050 DOI: 10.3748/wjg.v29.i17.2666] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/06/2023] [Accepted: 04/11/2023] [Indexed: 05/23/2023] Open
Abstract
BACKGROUND Fecal microbial transplantation (FMT) is a promising new method for treating active ulcerative colitis (UC), but knowledge regarding FMT for quiescent UC is scarce.
AIM To investigate FMT for the maintenance of remission in UC patients.
METHODS Forty-eight UC patients were randomized to receive a single-dose FMT or autologous transplant via colonoscopy. The primary endpoint was set to the maintenance of remission, a fecal calprotectin level below 200 μg/g, and a clinical Mayo score below three throughout the 12-mo follow-up. As secondary endpoints, we recorded the patient’s quality of life, fecal calprotectin, blood chemistry, and endoscopic findings at 12 mo.
RESULTS The main endpoint was achieved by 13 out of 24 (54%) patients in the FMT group and by 10 out of 24 (41%) patients in the placebo group (log-rank test, P = 0.660). Four months after FMT, the quality-of-life scores decreased in the FMT group compared to the placebo group (P = 0.017). In addition, the disease-specific quality of life measure was higher in the placebo group than in the FMT group at the same time point (P = 0.003). There were no differences in blood chemistry, fecal calprotectin, or endoscopic findings among the study groups at 12 mo. The adverse events were infrequent, mild, and distributed equally between the groups.
CONCLUSION There were no differences in the number of relapses between the study groups at the 12-mo follow-up. Thus, our results do not support the use of a single-dose FMT for the maintenance of remission in UC.
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Affiliation(s)
- Perttu Lahtinen
- Department of Gastroenterology, Päijät-Häme Central Hospital, Lahti 15610, Finland
- Department of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Jonna Jalanka
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Eero Mattila
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki 00029, Uusimaa, Finland
| | - Jyrki Tillonen
- Department of Gastroenterology, Päijät-Häme Central Hospital, Lahti 15610, Finland
| | - Paula Bergman
- Department of Bioinformatics, Helsinki University Hospital, Helsinki 00014, Finland
| | - Reetta Satokari
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Perttu Arkkila
- Department of Gastroenterology, University Helsinki, Center Hospital, Helsinki 00029, Uusimaa, Finland
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9
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King WL, Richards SC, Kaminsky LM, Bradley BA, Kaye JP, Bell TH. Leveraging microbiome rediversification for the ecological rescue of soil function. ENVIRONMENTAL MICROBIOME 2023; 18:7. [PMID: 36691096 PMCID: PMC9872425 DOI: 10.1186/s40793-023-00462-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attempts to rediversify agricultural soils rely on either targeted microbial introductions or retaining natural lands as biodiversity reservoirs. As many soil functions are provided by a combination of microbial taxa, rather than outsized impacts by single taxa, such functions may benefit more from diverse microbiome additions than additions of individual commercial strains. In this study, we measured the impact of soil microbial diversity loss and rediversification (i.e. rescue) on nitrification by quantifying ammonium and nitrate pools. We manipulated microbial assemblages in two distinct soil types, an agricultural and a forest soil, with a dilution-to-extinction approach and performed a microbiome rediversification experiment by re-introducing microorganisms lost from the dilution. A microbiome water control was included to act as a reference point. We assessed disruption and potential restoration of (1) nitrification, (2) bacterial and fungal composition through 16S rRNA gene and fungal ITS amplicon sequencing and (3) functional genes through shotgun metagenomic sequencing on a subset of samples. RESULTS Disruption of nitrification corresponded with diversity loss, but nitrification was successfully rescued in the rediversification experiment when high diversity inocula were introduced. Bacterial composition clustered into groups based on high and low diversity inocula. Metagenomic data showed that genes responsible for the conversion of nitrite to nitrate and taxa associated with nitrogen metabolism were absent in the low diversity inocula microcosms but were rescued with high diversity introductions. CONCLUSIONS In contrast to some previous work, our data suggest that soil functions can be rescued by diverse microbiome additions, but that the concentration of the microbial inoculum is important. By understanding how microbial rediversification impacts soil microbiome performance, we can further our toolkit for microbial management in human-controlled systems in order to restore depleted microbial functions.
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Affiliation(s)
- William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 317 Buckhout Lab, University Park, PA, 16802, USA
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 317 Buckhout Lab, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Laura M Kaminsky
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 317 Buckhout Lab, University Park, PA, 16802, USA
| | - Brosi A Bradley
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jason P Kaye
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 317 Buckhout Lab, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, PA, 16802, USA.
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10
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Bhute SS, Mefferd CC, Phan JR, Ahmed M, Fox-King AE, Alarcia S, Villarama JV, Abel-Santos E, Hedlund BP. A High-Carbohydrate Diet Prolongs Dysbiosis and Clostridioides difficile Carriage and Increases Delayed Mortality in a Hamster Model of Infection. Microbiol Spectr 2022; 10:e0180421. [PMID: 35708337 PMCID: PMC9431659 DOI: 10.1128/spectrum.01804-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/21/2022] [Indexed: 12/20/2022] Open
Abstract
Studies using mouse models of Clostridioides difficile infection (CDI) have demonstrated a variety of relationships between dietary macronutrients on antibiotic-associated CDI; however, few of these effects have been examined in more susceptible hamster models of CDI. In this study, we investigated the effect of a high-carbohydrate diet previously shown to protect mice from CDI on the progression and resolution of CDI in a hamster disease model, with 10 animals per group. Hamsters fed the high-carbohydrate diet developed distinct diet-specific microbiomes during antibiotic treatment and CDI, with lower diversity, persistent C. difficile carriage, and delayed microbiome restoration. In contrast to CDI protection in mice, most hamsters fed a high-carbohydrate diet developed fulminant CDI including several cases of late-onset CDI, that were not observed in hamsters fed a standard lab diet. We speculate that prolonged high-carbohydrate diet-specific dysbiosis in these animals allowed C. difficile to persist in the gut of the animals where they could proliferate postvancomycin treatment, leading to delayed CDI onset. This study, along with similar studies in mouse models of CDI, suggests some high-carbohydrate diets may promote antibiotic-associated dysbiosis and long-term C. difficile carriage, which may later convert to symptomatic CDI. IMPORTANCE The effects of diet on CDI are not completely known. Here, we used a high-carbohydrate diet previously shown to protect mice against CDI to assess its effect on a hamster model of CDI and paradoxically found that it promoted dysbiosis, C. difficile carriage, and higher mortality. A common thread in both mouse and hamster experimental models was that the high-carbohydrate diet promoted dysbiosis and long-term carriage of C. difficile, which may have converted to fulminant CDI only in the highly susceptible hamster model system. If diets high in carbohydrates also promote dysbiosis and C. difficile carriage in humans, then these diets might paradoxically increase chances of CDI relapse despite their protective effects against primary CDI.
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Affiliation(s)
- Shrikant S. Bhute
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Chrisabelle C. Mefferd
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- School of Public Health, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Jacqueline R. Phan
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Muneeba Ahmed
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- College of Osteopathic Medicine, Touro University, Nevada, Henderson, Nevada, USA
| | - Amelia E. Fox-King
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- College of Osteopathic Medicine, Touro University, Nevada, Henderson, Nevada, USA
| | - Stephanie Alarcia
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Jacob V. Villarama
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Kirk Kerkorian School of Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Ernesto Abel-Santos
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
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Ermolenko E, Simanenkova A, Voropaeva L, Lavrenova N, Kotyleva M, Minasian S, Chernikova A, Timkina N, Gladyshev N, Dmitriev A, Suvorov A, Galagudza M, Karonova T. Metformin Influence on the Intestinal Microbiota and Organism of Rats with Metabolic Syndrome. Int J Mol Sci 2022; 23:6837. [PMID: 35743280 PMCID: PMC9224185 DOI: 10.3390/ijms23126837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 01/27/2023] Open
Abstract
Metformin is a first-line drug for DM2 treatment and prevention, but its complex effect on impaired glucose tolerance (IGT), including its influence on myocardial resistance to ischemia-reperfusion injury, is not completely studied. We aimed to evaluate the influence of metformin on the intestinal microbiota (IM), metabolism, and functional and morphological characteristics of myocardium in rats with IGT. IGT was modelled in SPF Wistar rats with a high-fat diet and streptozotocin and nicotinamide injection. Rats were divided into three groups: IGT (without treatment), IGT MET (metformin therapy), and CRL (without IGT induction and treatment). IGT group was characterized by: higher body weight, increased serum glucose and total cholesterol levels, atherogenic coefficient, impairment in the functional parameters of the isolated heart during perfusion, and larger myocardium infarction (MI) size in comparison with the CRL group. IM of IGT rats differed from that of CRL: an increase of Bacteroides, Acinetobacter, Akkermansia, Roseburia, and a decrease of Lactobacillus genera representation. Metformin therapy led to the diminishing of metabolic syndrome (MS) symptoms, which correlated with IM restoration, especially with the growth of Akkermansia spp. and decline of Roseburia populations and their influence on other members of IM. The obtained results allow us to consider from a new point of view the expediency of probiotic A. muciniphila use for MS treatment.
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Affiliation(s)
- Elena Ermolenko
- Federal State Budgetary Institution “Institute of Experimental Medicine”, 197376 Saint Petersburg, Russia; (L.V.); (N.L.); (M.K.); (N.G.); (A.D.); or (A.S.)
| | - Anna Simanenkova
- Almazov National Medical Research Centre, 197341 Saint Petersburg, Russia; (A.S.); (S.M.); (A.C.); (N.T.); (M.G.); (T.K.)
| | - Lyubov Voropaeva
- Federal State Budgetary Institution “Institute of Experimental Medicine”, 197376 Saint Petersburg, Russia; (L.V.); (N.L.); (M.K.); (N.G.); (A.D.); or (A.S.)
| | - Nadezhda Lavrenova
- Federal State Budgetary Institution “Institute of Experimental Medicine”, 197376 Saint Petersburg, Russia; (L.V.); (N.L.); (M.K.); (N.G.); (A.D.); or (A.S.)
| | - Maryna Kotyleva
- Federal State Budgetary Institution “Institute of Experimental Medicine”, 197376 Saint Petersburg, Russia; (L.V.); (N.L.); (M.K.); (N.G.); (A.D.); or (A.S.)
| | - Sarkis Minasian
- Almazov National Medical Research Centre, 197341 Saint Petersburg, Russia; (A.S.); (S.M.); (A.C.); (N.T.); (M.G.); (T.K.)
| | - Alena Chernikova
- Almazov National Medical Research Centre, 197341 Saint Petersburg, Russia; (A.S.); (S.M.); (A.C.); (N.T.); (M.G.); (T.K.)
| | - Natalya Timkina
- Almazov National Medical Research Centre, 197341 Saint Petersburg, Russia; (A.S.); (S.M.); (A.C.); (N.T.); (M.G.); (T.K.)
| | - Nikita Gladyshev
- Federal State Budgetary Institution “Institute of Experimental Medicine”, 197376 Saint Petersburg, Russia; (L.V.); (N.L.); (M.K.); (N.G.); (A.D.); or (A.S.)
| | - Alexander Dmitriev
- Federal State Budgetary Institution “Institute of Experimental Medicine”, 197376 Saint Petersburg, Russia; (L.V.); (N.L.); (M.K.); (N.G.); (A.D.); or (A.S.)
| | - Alexander Suvorov
- Federal State Budgetary Institution “Institute of Experimental Medicine”, 197376 Saint Petersburg, Russia; (L.V.); (N.L.); (M.K.); (N.G.); (A.D.); or (A.S.)
| | - Michael Galagudza
- Almazov National Medical Research Centre, 197341 Saint Petersburg, Russia; (A.S.); (S.M.); (A.C.); (N.T.); (M.G.); (T.K.)
| | - Tatiana Karonova
- Almazov National Medical Research Centre, 197341 Saint Petersburg, Russia; (A.S.); (S.M.); (A.C.); (N.T.); (M.G.); (T.K.)
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12
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King WL, Kaminsky LM, Gannett M, Thompson GL, Kao‐Kniffin J, Bell TH. Soil salinization accelerates microbiome stabilization in iterative selections for plant performance. THE NEW PHYTOLOGIST 2022; 234:2101-2110. [PMID: 34614202 PMCID: PMC9297847 DOI: 10.1111/nph.17774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/29/2021] [Indexed: 06/01/2023]
Abstract
Climate change-related soil salinization increases plant stress and decreases productivity. Soil microorganisms are thought to reduce salt stress through multiple mechanisms, so diverse assemblages could improve plant growth under such conditions. Previous studies have shown that microbiome selection can promote desired plant phenotypes, but with high variability. We hypothesized that microbiome selection would be more consistent in saline soils by increasing potential benefits to the plants. In both salt-amended and untreated soils, we transferred forward Brassica rapa root microbiomes (from high-biomass or randomly selected pots) across six planting generations while assessing bacterial (16S rRNA) and fungal (ITS) composition in detail. Uniquely, we included an add-back control (re-adding initial frozen soil microbiome) as a within-generation reference for microbiome and plant phenotype selection. We observed inconsistent effects of microbiome selection on plant biomass across generations, but microbial composition consistently diverged from the add-back control. Although salt amendment strongly impacted microbial composition, it did not increase the predictability of microbiome effects on plant phenotype, but it did increase the rate at which microbiome selection plateaued. These data highlight a disconnect in the trajectories of microbiomes and plant phenotypes during microbiome selection, emphasizing the role of standard controls to explain microbiome selection outcomes.
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Affiliation(s)
- William L. King
- Department of Plant Pathology and Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Laura M. Kaminsky
- Department of Plant Pathology and Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA16802USA
- School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Maria Gannett
- School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Grant L. Thompson
- School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
- Department of HorticultureIowa State UniversityAmesIA50011USA
| | - Jenny Kao‐Kniffin
- School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Terrence H. Bell
- Department of Plant Pathology and Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA16802USA
- School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
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Wu Z, Xu Q, Gu S, Chen Y, Lv L, Zheng B, Wang Q, Wang K, Wang S, Xia J, Yang L, Bian X, Jiang X, Zheng L, Li L. Akkermansia muciniphila Ameliorates Clostridioides difficile Infection in Mice by Modulating the Intestinal Microbiome and Metabolites. Front Microbiol 2022; 13:841920. [PMID: 35663882 PMCID: PMC9159907 DOI: 10.3389/fmicb.2022.841920] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Clostridioides difficile is a common cause of nosocomial infection. Antibiotic-induced dysbiosis in the intestinal microbiota is a core cause of C. difficile infection (CDI). Akkermansia muciniphila plays an active role in maintaining gastrointestinal balance and might offer the protective effects on CDI as probiotics. Here, we investigated the effects and mechanisms of A. muciniphila on CDI. C57BL/6 mice (n = 29) were administered A. muciniphila Muc T (3 × 109 CFUs, 0.2 mL) or phosphate-buffered saline (PBS) by oral gavage for 2 weeks. Mice were pretreated with an antibiotic cocktail and subsequently challenged with the C. difficile strain VPI 10463. A. muciniphila treatment prevented weight loss in mice and reduced the histological injury of the colon. And it also alleviated inflammation and improved the barrier function of the intestine. The administration effects of A. muciniphila may be associated with an increase in short-chain fatty acid production and the maintenance of bile acids' steady-state. Our results provide evidence that administration of A. muciniphila to CDI mice, with an imbalance in the microbial community structure, lead to a decrease in abundance of members of the Enterobacteriaceae and Enterococcaceae. In short, A. muciniphila shows a potential anti-CDI role by modulating gut microbiota and the metabolome.
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Affiliation(s)
- Zhengjie Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiaomai Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Silan Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiangqiang Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kaicen Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuting Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiafeng Xia
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liya Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyuan Bian
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xianwan Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lisi Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Bacterial Research Platform, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
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14
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Van Daele E, Kamphorst K, Vlieger AM, Hermes G, Milani C, Ventura M, Belzer C, Smidt H, van Elburg RM, Knol J. Effect of antibiotics in the first week of life on faecal microbiota development. Arch Dis Child Fetal Neonatal Ed 2022; 107:fetalneonatal-2021-322861. [PMID: 35534183 PMCID: PMC9606546 DOI: 10.1136/archdischild-2021-322861] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 03/17/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Infants are frequently exposed to antibiotics (AB) in the first week of life for suspected bacterial infections. Little is known about the effect of AB on the developing intestinal microbiota. Therefore, we studied intestinal microbiota development with and without AB exposure in the first week of life in term born infants. METHODS We analysed the faecal microbiota from birth until 2.5 years of age by 16S rRNA gene amplicon sequencing in a cohort with 56 term born infants, exposed to AB in the first week of life (AB+) (AB for 2-3 days (AB2, n=20), AB for 7 days (AB7, n=36)), compared with 126 healthy controls (AB-). The effects of AB and duration were examined in relation to delivery and feeding mode. RESULTS AB+ was associated with significantly increased relative abundance of Enterobacteriaceae at 3 weeks and 1 year and a decrease of Bifidobacteriaceae, from 1 week until 3 months of age only in vaginally delivered, but not in C-section born infants. Similar deviations were noted in AB7, but not in AB2. After AB, breastfed infants had lower relative abundance of potentially pathogenic Enterobacteriaceae compared with formula fed infants and recovered 2 weeks faster towards controls. CONCLUSIONS AB exposure in the first week of life alters faecal microbiota development with deviations in the relative abundance of individual taxa until 1 year of age. These alterations can have long-term health consequences, which emphasises the need for future studies aiming at restoring intestinal microbiota after AB administration.
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Affiliation(s)
- Emmy Van Daele
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Kim Kamphorst
- Pediatrics, Amsterdam Gastroenterology, Metabolism & Nutrition, Amsterdam Reproduction & Development, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
- Pediatrics, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - Arine M Vlieger
- Pediatrics, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - Gerben Hermes
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma Department of Chemical Life Sciences and Environmental Sustainability, Parma, Emilia-Romagna, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Emilia-Romagna, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma Department of Chemical Life Sciences and Environmental Sustainability, Parma, Emilia-Romagna, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Emilia-Romagna, Italy
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ruurd M van Elburg
- Pediatrics, Amsterdam Gastroenterology, Metabolism & Nutrition, Amsterdam Reproduction & Development Amsterdam, Amsterdam UMC Locatie AMC, Amsterdam, North Holland, The Netherlands
| | - Jan Knol
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Nutricia Research BV, Utrecht, The Netherlands
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15
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Fomite Transmission Follows Invasion Ecology Principles. mSystems 2022; 7:e0021122. [PMID: 35502902 PMCID: PMC9238404 DOI: 10.1128/msystems.00211-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The invasion ecology principles illustrated in many ecosystems have not yet been explored in the context of fomite transmission. We hypothesized that invaders in fomite transmission are trackable, are neutrally distributed between hands and environmental surfaces, and exhibit a proximity effect. To test this hypothesis, a surrogate invader, Lactobacillus delbrueckii subsp. bulgaricus, was spread by a root carrier in an office housing more than 20 participants undertaking normal activities, and the microbiotas on skin and environmental surfaces were analyzed before and after invasion. First, we found that the invader was trackable. Its identity and emission source could be determined using microbial-interaction networks, and the root carrier could be identified using a rank analysis. Without prior information, L. bulgaricus could be identified as the invader emitted from a source that exclusively contained the invader, and the probable root carrier could be located. In addition to the single-taxon invasion by L. bulgaricus, multiple-taxon invasion was observed, as genera from sputum/saliva exhibited co-occurrence relationships on skin and environmental surfaces. Second, the invader had a below-neutral distribution in a neutral community model, suggesting that hands accrued heavier invader contamination than environmental surfaces. Third, a proximity effect was observed on a surface touch network. Invader contamination on surfaces decreased with increasing geodesic distance from the hands of the carrier, indicating that the carrier’s touching behaviors were the main driver of fomite transmission. Taken together, these results demonstrate the invasion ecology principles in fomite transmission and provide a general basis for the management of ecological fomite transmission. IMPORTANCE Fomite transmission contributes to the spread of many infectious diseases. However, pathogens in fomite transmission typically are either investigated individually without considering the context of native microbiotas or investigated in a nondiscriminatory way from the dispersal of microbiotas. In this study, we adopted an invasion ecology framework in which we considered pathogens as invaders, the surface environment as an ecosystem, and human behaviors as the driver of microbial dispersal. With this approach, we assessed the ability of quantitative ecological theories to track and forecast pathogen movements in fomite transmission. By uncovering the relationships between the invader and native microbiotas and between human behaviors and invader/microbiota dispersal, we demonstrated that fomite transmission follows idiosyncratic invasion ecology principles. Our findings suggest that attempts to manage fomite transmission for public health purposes should focus on the microbial communities and anthropogenic factors involved, in addition to the pathogens.
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16
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Hiippala K, Khan I, Ronkainen A, Boulund F, Vähä-Mäkilä H, Suutarinen M, Seifert M, Engstrand L, Satokari R. Novel strain of Pseudoruminococcus massiliensis possesses traits important in gut adaptation and host-microbe interactions. Gut Microbes 2022; 14:2013761. [PMID: 34965174 PMCID: PMC8726730 DOI: 10.1080/19490976.2021.2013761] [Citation(s) in RCA: 0] [Impact Index Per Article: 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
Fecal microbiota transplantation (FMT) is an efficient treatment for recurrent Clostridioides difficile infection and currently investigated as a treatment for other intestinal and systemic diseases. Better understanding of the species potentially transferred in FMT is needed. We isolated from a healthy fecal donor a novel strain E10-96H of Pseudoruminococcus massiliensis, a recently described strictly anaerobic species currently represented only by the type strain. The whole genome sequence of E10-96H had over 98% similarity with the type strain. E10-96H carries 20 glycoside hydrolase encoding genes, degrades starch in vitro and thus may contribute to fiber degradation, cross-feeding of other species and butyrate production in the intestinal ecosystem. The strain carries pilus-like structures, harbors pilin genes in its genome and adheres to enterocytes in vitro but does not provoke a proinflammatory response. P. massiliensis seems to have commensal behavior with the host epithelium, and its role in intestinal ecology should be studied further.
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Affiliation(s)
- Kaisa Hiippala
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Imran Khan
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Aki Ronkainen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Fredrik Boulund
- Centre for Translational Microbiome Research, Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Helena Vähä-Mäkilä
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Maiju Suutarinen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Maike Seifert
- Centre for Translational Microbiome Research, Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Lars Engstrand
- Centre for Translational Microbiome Research, Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Reetta Satokari
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland,CONTACT Reetta Satokari Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Bonanomi G, Idbella M, Abd-ElGawad AM. Microbiota Management for Effective Disease Suppression: A Systematic Comparison between Soil and Mammals Gut. SUSTAINABILITY 2021; 13:7608. [DOI: 10.3390/su13147608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Both soil and the human gut support vast microbial biodiversity, in which the microbiota plays critical roles in regulating harmful organisms. However, the functional link between microbiota taxonomic compositions and disease suppression has not been explained yet. Here, we provide an overview of pathogen regulation in soil and mammals gut, highlighting the differences and the similarities between the two systems. First, we provide a review of the ecological mechanisms underlying the regulation of soil and pathogens, as well as the link between disease suppression and soil health. Particular emphasis is thus given to clarifying how soil and the gut microbiota are associated with organic amendment and the human diet, respectively. Moreover, we provide several insights into the importance of organic amendment and diet composition in shaping beneficial microbiota as an efficient way to support crop productivity and human health. This review also discusses novel ways to functionally characterize organic amendments and the proper operational combining of such materials with beneficial microbes for stirring suppressive microbiota against pathogens. Furthermore, specific examples are given to describe how agricultural management practices, including the use of antibiotics and fumigants, hinder disease suppression by disrupting microbiota structure, and the potentiality of entire microbiome transplant. We conclude by discussing general strategies to promote soil microbiota biodiversity, the connection with plant yield and health, and their possible integration through a “One Health” framework.
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Gopalakrishnan V, Dozier EA, Glover MS, Novick S, Ford M, Morehouse C, Warrener P, Caceres C, Hess S, Sellman BR, Cohen TS. Engraftment of Bacteria after Fecal Microbiota Transplantation Is Dependent on Both Frequency of Dosing and Duration of Preparative Antibiotic Regimen. Microorganisms 2021; 9:1399. [PMID: 34209573 PMCID: PMC8306289 DOI: 10.3390/microorganisms9071399] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 01/04/2023] Open
Abstract
The gut microbiota has emerged as a key mediator of human physiology, and germ-free mice have been essential in demonstrating a role for the microbiome in disease. Preclinical models using conventional mice offer the advantage of working with a mature immune system. However, optimal protocols for fecal microbiota transplant (FMT) engraftment in conventional mice are yet to be established. Conventional BALB/c mice were randomized to receive 3-day (3d) or 3-week (3w) antibiotic (ABX) regimen in their drinking water followed by 1 or 5-daily FMTs from a human donor. Fecal samples were collected longitudinally and characterized using 16S ribosomal RNA (rRNA) sequencing. Semi-targeted metabolomic profiling of fecal samples was also done with liquid chromatography-mass spectrometry (LC-MS). Lastly, we sought to confirm our findings in BKS mice. Recovery of baseline diversity scores were greatest in the 3d groups, driven by re-emergence of mouse commensal microbiota, whereas the most resemblance to donor microbiota was seen in the 3w + 5-FMT group. Amplicon sequence variants (ASVs) that were linked to the input material (human ASVs) engrafted to a significantly greater extent when compared to mouse ASVs in the 3-week groups but not the 3-day groups. Lastly, comparison of metabolomic profiles revealed distinct functional profiles by ABX regimen. These results indicate successful model optimization and emphasize the importance of ABX duration and frequency of FMT dosing; the most stable and reliable colonization by donor ASVs was seen in the 3wk + 5-FMT group.
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Affiliation(s)
- Vancheswaran Gopalakrishnan
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Elizabeth Ashley Dozier
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Matthew S. Glover
- Dynamic Omics, Antibody Discovery & Protein Engineering, R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (M.S.G.); (S.H.)
| | - Steven Novick
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA;
| | - Michael Ford
- Animal Sciences and Technologies, R & D, AstraZeneca, Gaithersburg, MD 20878, USA;
| | - Christopher Morehouse
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Paul Warrener
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Carolina Caceres
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Sonja Hess
- Dynamic Omics, Antibody Discovery & Protein Engineering, R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (M.S.G.); (S.H.)
| | - Bret R. Sellman
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Taylor S. Cohen
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
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Nutritional and therapeutic approaches for protecting human gut microbiota from psychotropic treatments. Prog Neuropsychopharmacol Biol Psychiatry 2021; 108:110182. [PMID: 33232785 DOI: 10.1016/j.pnpbp.2020.110182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/05/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023]
Abstract
Emerging evidence highlighted the essential role played by the microbiota-gut-brain axis in maintaining human homeostasis, including nutrition, immunity, and metabolism. Much recent work has linked the gut microbiota to many psychiatric and neurodegenerative disorders such as depression, schizophrenia, and Alzheimer's disease. Shared gut microbiota alterations or dysbiotic microbiota have been identified in these separate disorders relative to controls. Much attention has focused on the bidirectional interplay between the gut microbiota and the brain, establishing gut dysbiotic status as a critical factor in psychiatric disorders. Still, the antibiotic-like effect of psychotropic drugs, medications used for the treatment of these disorders, on gut microbiota is largely neglected. In this review, we summarize the current findings on the impact of psychotropics on gut microbiota and how their antimicrobial potency can trigger dysbiosis. We also discuss the potential therapeutic strategies, including probiotics, prebiotics, and fecal transplantation, to attenuate the dysbiosis related to psychotropics intake.
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Fecal microbiota transplantation in human metabolic diseases: From a murky past to a bright future? Cell Metab 2021; 33:1098-1110. [PMID: 34077717 DOI: 10.1016/j.cmet.2021.05.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/26/2021] [Accepted: 05/05/2021] [Indexed: 12/15/2022]
Abstract
Fecal microbiota transplantation (FMT) is gaining considerable traction as a therapeutic approach to influence the course of a plethora of chronic conditions, ranging from metabolic syndrome and malignancies to auto-immune and neurological diseases, and helped to establish the contribution of the gut microbiome to these conditions. Although FMT procedures have yielded important mechanistic insights, their use in clinical practice may be limited due to practical objections in the setting of metabolic diseases. While its applicability is established to treat recurrent Clostridiodes difficile, FMT is emerging in ulcerative colitis and various other diseases. A particularly new insight is that FMTs may not only alter insulin sensitivity but may also alter the course of type 1 diabetes by attenuating underlying auto-immunity. In this review, we will outline the major principles and pitfalls of FMT and where optimization of study design and the procedure itself will further advance the field of cardiometabolic medicine.
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Cronin P, Joyce SA, O’Toole PW, O’Connor EM. Dietary Fibre Modulates the Gut Microbiota. Nutrients 2021; 13:nu13051655. [PMID: 34068353 PMCID: PMC8153313 DOI: 10.3390/nu13051655] [Citation(s) in RCA: 251] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 12/14/2022] Open
Abstract
Dietary fibre has long been established as a nutritionally important, health-promoting food ingredient. Modern dietary practices have seen a significant reduction in fibre consumption compared with ancestral habits. This is related to the emergence of low-fibre “Western diets” associated with industrialised nations, and is linked to an increased prevalence of gut diseases such as inflammatory bowel disease, obesity, type II diabetes mellitus and metabolic syndrome. The characteristic metabolic parameters of these individuals include insulin resistance, high fasting and postprandial glucose, as well as high plasma cholesterol, low-density lipoprotein (LDL) and high-density lipoprotein (HDL). Gut microbial signatures are also altered significantly in these cohorts, suggesting a causative link between diet, microbes and disease. Dietary fibre consumption has been hypothesised to reverse these changes through microbial fermentation and the subsequent production of short-chain fatty acids (SCFA), which improves glucose and lipid parameters in individuals who harbour diseases associated with dysfunctional metabolism. This review article examines how different types of dietary fibre can differentially alter glucose and lipid metabolism through changes in gut microbiota composition and function.
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Affiliation(s)
- Peter Cronin
- Department of Biological Sciences, University of Limerick, V94 T9PX Limerick, Ireland;
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland; (S.A.J.); (P.W.O.)
| | - Susan A. Joyce
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland; (S.A.J.); (P.W.O.)
- School of Biochemistry and Cell Biology, University College Cork, T12 K8AF Cork, Ireland
| | - Paul W. O’Toole
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland; (S.A.J.); (P.W.O.)
- Department of Microbiology, University College Cork, T12 K8AF Cork, Ireland
| | - Eibhlís M. O’Connor
- Department of Biological Sciences, University of Limerick, V94 T9PX Limerick, Ireland;
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland; (S.A.J.); (P.W.O.)
- Health Research Institute, University of Limerick, V94 T9PX Limerick, Ireland
- Correspondence:
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Björkqvist O, Rangel I, Serrander L, Magnusson C, Halfvarson J, Norén T, Bergman-Jungeström M. Faecalibacterium prausnitzii increases following fecal microbiota transplantation in recurrent Clostridioides difficile infection. PLoS One 2021; 16:e0249861. [PMID: 33836037 PMCID: PMC8034738 DOI: 10.1371/journal.pone.0249861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/26/2021] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE Fecal microbiota transplantation (FMT) is a highly effective treatment for Clostridioides difficile infection (CDI). However, the fecal transplant's causal components translating into clearance of the CDI are yet to be identified. The commensal bacteria Faecalibacterium prausnitzii may be of great interest in this context, since it is one of the most common species of the healthy gut microbiota and produces metabolites with anti-inflammatory properties. Although there is mounting evidence that F. prausnitzii is an important regulator of intestinal homeostasis, data about its role in CDI and FMT are relatively scarce. METHODS Stool samples from patients with recurrent CDI were collected to investigate the relative abundance of F. prausnitzii before and after FMT. Twenty-one patients provided fecal samples before the FMT procedure, at 2 weeks post-FMT, and at 2-4 months post-FMT. The relative abundance of F. prausnitzii was determined using quantitative polymerase chain reaction. RESULTS The abundance of F. prausnitzii was elevated in samples (N = 9) from donors compared to pre-FMT samples (N = 15) from patients (adjusted P<0.001). No significant difference in the abundance of F. prausnitzii between responders (N = 11) and non-responders (N = 4) was found before FMT (P = 0.85). In patients with CDI, the abundance of F. prausnitzii significantly increased in the 2 weeks post-FMT samples (N = 14) compared to the pre-FMT samples (N = 15, adjusted P<0.001). The increase persisted 2-4 months post-FMT (N = 15) compared to pre-FMT samples (N = 15) (adjusted P<0.001). CONCLUSIONS FMT increases the relative abundance of F. prausnitzii in patients with recurrent CDI, and this microbial shift remains several months later. The baseline abundance of F. prausnitzii in donors or recipients was not associated with future treatment response, although a true predictive capacity cannot be excluded because of the limited sample size. Further studies are needed to discern whether F. prausnitzii plays an active role in the resolution of CDI.
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Affiliation(s)
- Olle Björkqvist
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- * E-mail:
| | - Ignacio Rangel
- School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Lena Serrander
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Cecilia Magnusson
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Infectious Diseases, Region Jönköping County, Jönköping, Sweden
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Torbjörn Norén
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides Difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
| | - Malin Bergman-Jungeström
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
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Dissecting Individual Interactions between Pathogenic and Commensal Bacteria within a Multispecies Gut Microbial Community. mSphere 2021; 6:6/2/e00013-21. [PMID: 33762315 PMCID: PMC8546675 DOI: 10.1128/msphere.00013-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Interactions of commensal bacteria within the gut microbiota and with invading pathogens are critical in determining the outcome of an infection. While murine studies have been valuable, we lack in vitro models to monitor community responses to pathogens at a single-species level. We have developed a multispecies community of nine representative gut species cultured together as a mixed biofilm and tracked numbers of individual species over time using a quantitative PCR (qPCR)-based approach. Introduction of the major nosocomial gut pathogen, Clostridioides difficile, to this community resulted in increased adhesion of commensals and inhibition of C. difficile multiplication. Interestingly, we observed an increase in individual Bacteroides species accompanying the inhibition of C. difficile. Furthermore, Bacteroides dorei reduced C. difficile growth within biofilms, suggesting a role for Bacteroides spp. in prevention of C. difficile colonization. We report here an in vitro tool with excellent applications for investigating bacterial interactions within a complex community. IMPORTANCE Studying interactions between bacterial species that reside in the human gut is crucial for gaining a better insight into how they provide protection from pathogen colonization. In vitro models of multispecies bacterial communities wherein behaviors of single species can be accurately tracked are key to such studies. Here, we have developed a synthetic, trackable, gut microbiota community which reduces growth of the human gut pathogen Clostridioides difficile. We report that Bacteroides spp. within this community respond by multiplying in the presence of this pathogen, resulting in reduction of C. difficile growth. Defined in vitro communities that can be tailored to include different species are well suited to functional genomic approaches and are valuable tools for understanding interbacterial interactions.
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Faecal microbiota transplantation for Clostridioides difficile: mechanisms and pharmacology. Nat Rev Gastroenterol Hepatol 2021; 18:67-80. [PMID: 32843743 DOI: 10.1038/s41575-020-0350-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/07/2020] [Indexed: 12/14/2022]
Abstract
Faecal microbiota transplantation (FMT) has emerged as a remarkably successful treatment for recurrent Clostridioides difficile infection that cannot be cured with antibiotics alone. Understanding the complex biology and pathogenesis of C. difficile infection, which we discuss in this Perspective, is essential for understanding the potential mechanisms by which FMT cures this disease. Although FMT has already entered clinical practice, different microbiota-based products are currently in clinical trials and are vying for regulatory approval. However, all these therapeutics belong to an entirely new class of agents that require the development of a new branch of pharmacology. Characterization of microbiota therapeutics uses novel and rapidly evolving technologies and requires incorporation of microbial ecology concepts. Here, we consider FMT within a pharmacological framework, including its essential elements: formulation, pharmacokinetics and pharmacodynamics. From this viewpoint, multiple gaps in knowledge become apparent, identifying areas that require systematic research. This knowledge is needed to help clinical providers use microbiota therapeutics appropriately and to facilitate development of next-generation microbiota products with improved safety and efficacy. The discussion here is limited to FMT as a representative of microbiota therapeutics and recurrent C. difficile as the indication; however, consideration of the intrinsic basic principles is relevant to this entire class of microbiota-based therapeutics.
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D. Goldenberg S, Merrick B. The role of faecal microbiota transplantation: looking beyond Clostridioides difficile infection. Ther Adv Infect Dis 2021; 8:2049936120981526. [PMID: 33614028 PMCID: PMC7841662 DOI: 10.1177/2049936120981526] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022] Open
Abstract
Faecal microbiota transplantation (FMT) is the transfer of screened and minimally processed faecal material from a 'healthy' donor to 'diseased' recipient. It has an established role, and is recommended as a therapeutic strategy, in the management of recurrent Clostridioides difficile infection (CDI). Recognition that gut dysbiosis is associated with, and may contribute to, numerous disease states has led to interest in exploiting FMT to 'correct' this microbial imbalance. Conditions for which it is proposed to be beneficial include inflammatory bowel disease, irritable bowel syndrome, liver disease and hepatic encephalopathy, neuropsychiatric conditions such as depression and anxiety, systemic inflammatory states like sepsis, and even coronavirus disease 2019. To understand what role, if any, FMT may play in the management of these conditions, it is important to consider the potential risks and benefits of the therapy. Regardless, there are several barriers to its more widespread adoption, which include incompletely understood mechanism of action (especially outside of CDI), inability to standardise treatment, disagreement on its active ingredients and how it should be regulated, and lack of long-term outcome and safety data. Whilst the transfer of faecal material from one individual to another to treat ailments or improve health has a history dating back thousands of years, there are fewer than 10 randomised controlled trials supporting its use. Moving forward, it will be imperative to gather as much data from FMT donors and recipients over as long a timeframe as possible, and for trials to be conducted with rigorous methodology, including appropriate control groups, in order to best understand the utility of FMT for indications beyond CDI. This review discusses the history of FMT, its appreciable mechanisms of action with reference to CDI, indications for FMT with an emerging evidence base above and beyond CDI, and future perspectives on the field.
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Affiliation(s)
- Simon D. Goldenberg
- Centre for Clinical Infection & Diagnostics Research, King’s College London and Guy’s & St. Thomas’ NHS Foundation Trust, 5th floor, North Wing, St Thomas’ hospital, Westminster Bridge Road, London, SE1 7EH, UK
| | - Blair Merrick
- Centre for Clinical Infection & Diagnostics Research, King’s College London and Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
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26
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Cold F, Kousgaard SJ, Halkjaer SI, Petersen AM, Nielsen HL, Thorlacius-Ussing O, Hansen LH. Fecal Microbiota Transplantation in the Treatment of Chronic Pouchitis: A Systematic Review. Microorganisms 2020; 8:E1433. [PMID: 32962069 PMCID: PMC7565999 DOI: 10.3390/microorganisms8091433] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
The objective was to evaluate available literature on treatment of chronic pouchitis with fecal microbiota transplantation (FMT) focusing on clinical outcomes, safety, and different approaches to FMT preparation and delivery. A systematic review of electronic databases was conducted using Medline, EMBASE, and the Cochrane Central Register of Controlled Trials Library from inception through April 2020. Human studies of all study types reporting results of FMT to treat chronic pouchitis were included. Nine studies, reporting FMT treatment of 69 patients with chronic pouchitis were found eligible for the review. Most studies were case series and cohort studies rated as having fair to poor quality due to high risk of bias and small sample size. Only one randomized controlled trial was included, finding no beneficial effect of FMT. In total clinical response after FMT was reported in 14 (31.8%) out of 44 evaluated patients at various timepoints after FMT, and clinical remission in ten (22.7%) patients. Only minor self-limiting adverse events were reported. FMT varied greatly regarding preparation, length of treatment, and route of delivery. The effects of FMT on symptoms of chronic pouchitis are not established, though some studies show promising results. Future controlled well-designed studies are warranted.
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Affiliation(s)
- Frederik Cold
- Department of Plant and Environmental Sciences, Section for Microbial Ecology and Biotechnology, Copenhagen University, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark;
- Gastrounit, Medical Division, Copenhagen University Hospital Hvidovre, 2650 Hvidovre, Denmark; (S.I.H.); (A.M.P.)
| | - Sabrina Just Kousgaard
- Department of Gastrointestinal Surgery, Aalborg University Hospital, 9100 Aalborg, Denmark; (S.J.K.); (O.T.-U.)
- Department of Clinical Medicine, Aalborg University, 9100 Aalborg, Denmark;
| | - Sofie Ingdam Halkjaer
- Gastrounit, Medical Division, Copenhagen University Hospital Hvidovre, 2650 Hvidovre, Denmark; (S.I.H.); (A.M.P.)
| | - Andreas Munk Petersen
- Gastrounit, Medical Division, Copenhagen University Hospital Hvidovre, 2650 Hvidovre, Denmark; (S.I.H.); (A.M.P.)
- Department of Clinical Microbiology, Copenhagen University Hospital Hvidovre, 2650 Hvidovre, Denmark
| | - Hans Linde Nielsen
- Department of Clinical Medicine, Aalborg University, 9100 Aalborg, Denmark;
- Department of Clinical Microbiology, Aalborg University Hospital, 9100 Aalborg, Denmark
| | - Ole Thorlacius-Ussing
- Department of Gastrointestinal Surgery, Aalborg University Hospital, 9100 Aalborg, Denmark; (S.J.K.); (O.T.-U.)
- Department of Clinical Medicine, Aalborg University, 9100 Aalborg, Denmark;
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, Section for Microbial Ecology and Biotechnology, Copenhagen University, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark;
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Ren W, Bin P, Yin Y, Wu G. Impacts of Amino Acids on the Intestinal Defensive System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1265:133-151. [PMID: 32761574 DOI: 10.1007/978-3-030-45328-2_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The intestine interacts with a diverse community of antigens and bacteria. To keep its homeostasis, the gut has evolved with a complex defense system, including intestinal microbiota, epithelial layer and lamina propria. Various factors (e.g., nutrients) affect the intestinal defensive system and progression of intestinal diseases. This review highlights the current understanding about the role of amino acids (AAs) in protecting the intestine from harm. Amino acids (e.g., arginine, glutamine and tryptophan) are essential for the function of intestinal microbiota, epithelial cells, tight junction, goblet cells, Paneth cells and immune cells (e.g., macrophages, B cells and T cells). Through the modulation of the intestinal defensive system, AAs maintain the integrity and function of the intestinal mucosa and inhibit the progression of various intestinal diseases (e.g., intestinal infection and intestinal colitis). Thus, adequate intake of functional AAs is crucial for intestinal and whole-body health in humans and other animals.
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Affiliation(s)
- Wenkai Ren
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Institute of Subtropical Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Peng Bin
- Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product, Safety of Ministry of Education of China, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yulong Yin
- Laboratory of Animal Nutrition and Health and Key Laboratory of Agro-Ecology, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, China
| | - Guoyao Wu
- Department of Animal Science, Texas A&M University, College Station, TX, USA.
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Weinberg SE, Villedieu A, Bagdasarian N, Karah N, Teare L, Elamin WF. Control and management of multidrug resistant Acinetobacter baumannii: A review of the evidence and proposal of novel approaches. Infect Prev Pract 2020; 2:100077. [PMID: 34368717 PMCID: PMC8336160 DOI: 10.1016/j.infpip.2020.100077] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
Hospital-acquired infections are on the rise and are a substantial cause of clinical and financial burden for healthcare systems. While infection control plays a major role in curtailing the spread of outbreak organisms, it is not always successful. One organism of particular concern is Acinetobacter baumannii, due to both its persistence in the hospital setting and its ability to acquire antibiotic resistance. A. baumannii has emerged as a nosocomial pathogen that exhibits high levels of resistance to antibiotics, and remains resilient against traditional cleaning measures with resistance to Colistin increasingly reported. Given the magnitude and costs associated with hospital acquired infections, and the increase in multidrug-resistant organisms, it is worth re-evaluating our current approaches and looking for alternatives or adjuncts to traditional antibiotics therapies. The aims of this review are to look at how this organism is spread within the hospital setting, discuss current treatment modalities, and propose alternative methods of outbreak management.
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Key Words
- ABC, A.baumannii complex
- AMP, Antimicrobial peptides
- Acinetobacter baumannii
- Antimicrobial peptide
- Bacteriophage
- CRAB, carbapenem-resistant A.baumannii
- Colistin
- EPIC, Extended Prevalence of Infection in Intensive Care study
- EU/EEA, European Union (EU) and European Economic Area (EEA) countries
- FMT, faecal microbiota transplantation
- HPV, Hydrogen peroxide vapour
- MDR-AB, Multidrug-resistant Acinetobacter baumannii
- MDR-GNB, Multidrug-resistant Gram-negative bacteria
- MIC, minimal inhibitory concentrations
- Microbiome restoration
- Multidrug-resistance
- SOAP, Sepsis in European ICUs study
- UVC, UV-C light
- XDR, Extensively-drug resistant
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Affiliation(s)
- S E Weinberg
- Department of Microbiology, Mid Essex Hospital Services NHS Trust, United Kingdom
| | - A Villedieu
- Department of Microbiology, Mid Essex Hospital Services NHS Trust, United Kingdom
| | | | - N Karah
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, Sweden
| | - L Teare
- Department of Microbiology, Mid Essex Hospital Services NHS Trust, United Kingdom
| | - W F Elamin
- Department of Microbiology, Mid Essex Hospital Services NHS Trust, United Kingdom.,King's College Hospital, Dubai, United Arab Emirates
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Jouhten H, Ronkainen A, Aakko J, Salminen S, Mattila E, Arkkila P, Satokari R. Cultivation and Genomics Prove Long-Term Colonization of Donor's Bifidobacteria in Recurrent Clostridioides difficile Patients Treated With Fecal Microbiota Transplantation. Front Microbiol 2020; 11:1663. [PMID: 32760391 PMCID: PMC7373762 DOI: 10.3389/fmicb.2020.01663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/25/2020] [Indexed: 12/17/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridioides difficile infection (rCDI) and it’s also considered for treating other indications. Metagenomic studies have indicated that commensal donor bacteria may colonize FMT recipients, but cultivation has not been employed to verify strain-level colonization. We combined molecular profiling of Bifidobacterium populations with cultivation, molecular typing, and whole genome sequencing (WGS) to isolate and identify strains that were transferred from donors to recipients. Several Bifidobacterium strains from two donors were recovered from 13 recipients during the 1-year follow-up period after FMT. The strain identities were confirmed by WGS and comparative genomics. Our results show that specific donor-derived bifidobacteria can colonize rCDI patients for at least 1 year, and thus FMT may have long-term consequences for the recipient‘s microbiota and health. Conceptually, we demonstrate that FMT trials combined with microbial profiling can be used as a platform for discovering and isolating commensal strains with proven colonization capacity for potential therapeutic use.
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Affiliation(s)
- Hanne Jouhten
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Aki Ronkainen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Juhani Aakko
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Eero Mattila
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Perttu Arkkila
- Department of Gastroenterology, Helsinki University Hospital, Helsinki, Finland
| | - Reetta Satokari
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Yu S, Shi W, Yang B, Gao G, Chen H, Cao L, Yu Z, Wang J. Effects of repeated oral inoculation of artificially fed lambs with lyophilized rumen fluid on growth performance, rumen fermentation, microbial population and organ development. Anim Feed Sci Technol 2020. [DOI: 10.1016/j.anifeedsci.2020.114465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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31
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Jukes CA, Ijaz UZ, Buckley A, Spencer J, Irvine J, Candlish D, Li JV, Marchesi JR, Douce G. Bile salt metabolism is not the only factor contributing to Clostridioides ( Clostridium) difficile disease severity in the murine model of disease. Gut Microbes 2020; 11:481-496. [PMID: 31793403 PMCID: PMC7524298 DOI: 10.1080/19490976.2019.1678996] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Susceptibility of patients to antibiotic-associated C. difficile disease is intimately associated with specific changes to gut microbiome composition. In particular, loss of microbes that modify bile salt acids (BSA) play a central role; primary bile acids stimulate spore germination whilst secondary bile acids limit C. difficile vegetative growth. To determine the relative contribution of bile salt (BS) metabolism on C. difficile disease severity, we treated mice with three combinations of antibiotics prior to infection. Mice given clindamycin alone became colonized but displayed no tissue pathology while severe disease, exemplified by weight loss and inflammatory tissue damage occurred in animals given a combination of five antibiotics and clindamycin. Animals given only the five antibiotic cocktails showed only transient colonization and no disease. C. difficile colonization was associated with a reduction in bacterial diversity, an inability to amplify bile salt hydrolase (BSH) sequences from fecal DNA and a relative increase in primary bile acids (pBA) in cecal lavages from infected mice. Further, the link between BSA modification and the microbiome was confirmed by the isolation of strains of Lactobacillus murinus that modified primary bile acids in vitro, thus preventing C. difficile germination. Interestingly, BSH activity did not correlate with disease severity which appeared linked to alternations in mucin, which may indirectly lead to increased exposure of the epithelial surface to inflammatory signals. These data confirm the role of microbial metabolic activity in protection of the gut and highlights the need for greater understanding the function of bacterial communities in disease prevention.
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Affiliation(s)
- Caitlin A. Jukes
- Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, Glasgow, UK
| | - Umer Zeeshan Ijaz
- School of Engineering, College of Science and Engineering, University of Glasgow, Glasgow, UK
| | - Anthony Buckley
- Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, Glasgow, UK,Leeds Institute of Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - Janice Spencer
- Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, Glasgow, UK,School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
| | - June Irvine
- Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, Glasgow, UK
| | - Denise Candlish
- Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jia V. Li
- Faculty of Medicine, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Julian R. Marchesi
- Faculty of Medicine, Department of Surgery & Cancer, Imperial College London, London, UK,School of Biosciences, Cardiff University, Cardiff, UK,CONTACT Julian R. Marchesi Faculty of Medicine, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Gillian Douce
- Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, Glasgow, UK,Gillian Douce Institute of Infection, Immunity and Inflammation, College of Veterinary Medical and Life Sciences, University of Glasgow, UK
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Abstract
Advances in the understanding of the pathogenesis of type 2 diabetes mellitus (T2D) have revealed a role for gut microbiota dysbiosis in driving this disease. This suggests the possibility that approaches to restore a healthy host-microbiota relationship might be a means of ameliorating T2D. Indeed, recent studies indicate that many currently used treatments for T2D are reported to impact gut microbiota composition. Such changes in gut microbiota may mediate and/or reflect the efficacy of these interventions. This article outlines the rationale for considering the microbiota as a central determent of development of T2D and, moreover, reviews evidence that impacting microbiota might be germane to amelioration of T2D, both in terms of understanding mechanisms that mediate efficacy of exiting T2D therapies and in developing novel treatments for this disorder.
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Affiliation(s)
- Aneseh Adeshirlarijaney
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA,CONTACT Andrew Gewirtz Institute for Biomedical Sciences, Georgia State University, Atlanta, GA30303, USA
| | - Andrew T. Gewirtz
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
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33
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Antushevich H. Fecal microbiota transplantation in disease therapy. Clin Chim Acta 2020; 503:90-98. [DOI: 10.1016/j.cca.2019.12.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022]
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Mefferd CC, Bhute SS, Phan JR, Villarama JV, Do DM, Alarcia S, Abel-Santos E, Hedlund BP. A High-Fat/High-Protein, Atkins-Type Diet Exacerbates Clostridioides ( Clostridium) difficile Infection in Mice, whereas a High-Carbohydrate Diet Protects. mSystems 2020; 5:e00765-19. [PMID: 32047064 PMCID: PMC7018531 DOI: 10.1128/msystems.00765-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile (formerly Clostridium difficile) infection (CDI) can result from the disruption of the resident gut microbiota. Western diets and popular weight-loss diets drive large changes in the gut microbiome; however, the literature is conflicted with regard to the effect of diet on CDI. Using the hypervirulent strain C. difficile R20291 (RT027) in a mouse model of antibiotic-induced CDI, we assessed disease outcome and microbial community dynamics in mice fed two high-fat diets in comparison with a high-carbohydrate diet and a standard rodent diet. The two high-fat diets exacerbated CDI, with a high-fat/high-protein, Atkins-like diet leading to severe CDI and 100% mortality and a high-fat/low-protein, medium-chain-triglyceride (MCT)-like diet inducing highly variable CDI outcomes. In contrast, mice fed a high-carbohydrate diet were protected from CDI, despite the high levels of refined carbohydrate and low levels of fiber in the diet. A total of 28 members of the Lachnospiraceae and Ruminococcaceae decreased in abundance due to diet and/or antibiotic treatment; these organisms may compete with C. difficile for amino acids and protect healthy animals from CDI in the absence of antibiotics. Together, these data suggest that antibiotic treatment might lead to loss of C. difficile competitors and create a favorable environment for C. difficile proliferation and virulence with effects that are intensified by high-fat/high-protein diets; in contrast, high-carbohydrate diets might be protective regardless of the source of carbohydrate or of antibiotic-driven loss of C. difficile competitors.IMPORTANCE The role of Western and weight-loss diets with extreme macronutrient composition in the risk and progression of CDI is poorly understood. In a longitudinal study, we showed that a high-fat/high-protein, Atkins-type diet greatly exacerbated antibiotic-induced CDI, whereas a high-carbohydrate diet protected, despite the high monosaccharide and starch content. Our study results, therefore, suggest that popular high-fat/high-protein weight-loss diets may enhance CDI risk during antibiotic treatment, possibly due to the synergistic effects of a loss of the microorganisms that normally inhibit C. difficile overgrowth and an abundance of amino acids that promote C. difficile overgrowth. In contrast, a high-carbohydrate diet might be protective, despite reports on the recent evolution of enhanced carbohydrate metabolism in C. difficile.
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Affiliation(s)
| | - Shrikant S Bhute
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Jacqueline R Phan
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Jacob V Villarama
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Dung M Do
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Stephanie Alarcia
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Ernesto Abel-Santos
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
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35
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Yu S, Zhang G, Liu Z, Wu P, Yu Z, Wang J. Repeated inoculation with fresh rumen fluid before or during weaning modulates the microbiota composition and co-occurrence of the rumen and colon of lambs. BMC Microbiol 2020; 20:29. [PMID: 32028889 PMCID: PMC7006167 DOI: 10.1186/s12866-020-1716-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 01/29/2020] [Indexed: 12/31/2022] Open
Abstract
Background Many recent studies have gravitated towards manipulating the gastrointestinal (GI) microbiome of livestock to improve host nutrition and health using dietary interventions. Few studies, however, have evaluated if inoculation with rumen fluid could effectively reprogram the development of GI microbiota. We hypothesized that inoculation with rumen fluid at an early age could modulate the development of GI microbiota because of its low colonization resistance. Results In this study, we tested the above hypothesis using young lambs as a model. Young lambs were orally inoculated repeatedly (four times before or twice during gradual weaning) with the rumen fluid collected from adult sheep. The oral inoculation did not significantly affect starter intake, growth performance, or ruminal fermentation. Based on sequencing analysis of 16S rRNA gene amplicons, however, the inoculation (both before and during weaning) affected the assemblage of the rumen microbiota, increasing or enabling some bacterial taxa to colonize the rumen. These included operational taxonomic units (OTUs) belonging to Moryella, Acetitomaculum, Tyzzerella 4, Succiniclasticum, Prevotella 1, Lachnospiraceae, Christensenellaceae R-7 group, Family XIII AD3011, and Bacteroidales S24–7 corresponding to inoculation before weaning; and OTUs belonging to Succiniclasticum, Prevotellaceae UCG-003, Erysipelotrichaceae UCG-004, Prevotella 1, Bacteroidales S24–7 gut group uncultured bacterium, and candidate Family XIII AD3011 corresponding to inoculation during weaning. Compared to the inoculation during weaning, the inoculation before weaning resulted in more co-occurrences of OTUs that were exclusively predominant in the inoculum. However, inoculation during weaning appeared to have more impacts on the colonic microbiota than the inoculation before weaning. Considerable successions in the microbial colonization of the GI tracts accompanied the transition from liquid feed to solid feed during weaning. Conclusions Repeated rumen fluid inoculation during early life can modulate the establishment of the microbiota in both the rumen and the colon and co-occurrence of some bacteria. Oral inoculation with rumen microbiota may be a useful approach to redirect the development of the microbiota in both the rumen and colon.
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Affiliation(s)
- Shaobo Yu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Guangyu Zhang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zhibo Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Peng Wu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Jiakun Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
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36
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Harris C, Kim PT, Waterhouse D, Feng Z, Niergarth J, Lee CH. Precision medicine and gut dysbiosis. Healthc Manage Forum 2020; 33:107-110. [PMID: 31934800 DOI: 10.1177/0840470419899426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Clostridioides difficile Infection (CDI) is a leading cause of healthcare-associated infections in Canada, affecting the gastrointestinal tract which can lead to fever, abdominal pain, and diarrhea. Effective treatment for patients with Recurrent CDI (rCDI) can be achieved by Fecal Microbiota Transplantation (FMT) by introducing the gut micro-organisms of a healthy person (donor) into the bowel of the affected individual. Research has shown that an increase in the specific bacterial phyla post-FMT may be partly responsible for this gut restoration and elimination of disease. Furthermore, in understanding the key bacteria associated with successful FMT, full treatment plans can be developed for the individual needs of the patient by matching an infected individual with a donor possessing ideal microbiota for the specific patient. This development of precision medicine and more systematic adoption of FMT can be the next step toward more rapid resolution of rCDI.
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Affiliation(s)
| | - Peter T Kim
- University of Guelph, Guelph, Ontario, Canada.,Vancouver Island Health Authority, Victoria, British Columbia, Canada
| | - Dawn Waterhouse
- Vancouver Island Health Authority, Victoria, British Columbia, Canada
| | - Zeny Feng
- University of Guelph, Guelph, Ontario, Canada
| | | | - Christine H Lee
- Vancouver Island Health Authority, Victoria, British Columbia, Canada
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37
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Ortigão R, Pimentel-Nunes P, Dinis-Ribeiro M, Libânio D. Gastrointestinal Microbiome - What We Need to Know in Clinical Practice. GE-PORTUGUESE JOURNAL OF GASTROENTEROLOGY 2020; 27:336-351. [PMID: 32999906 DOI: 10.1159/000505036] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 11/14/2019] [Indexed: 12/12/2022]
Abstract
Human gut microbiota plays an important role in individual health. When the balance between host and gut microbiota is disrupted, changes in microbiota composition and function occur, which is referred as dysbiosis. Environmental factors as diet, proton pump inhibitors, and antibiotics can lead to a permanent dysbiotic disruption. Clarification of these imbalances was made possible by recent advances in genome sequencing methods that supported acknowledgment of the interplay between microbiome and intestinal and extraintestinal disorders. This review focuses on the microbiota impact in inflammatory bowel disease, gastric cancer, colorectal cancer, nonalcoholic fatty liver disease (NAFLD), irritable bowel syndrome (IBS), and Clostridium difficile infection (CDI). Furthermore, novel therapies are summarized. Fecal microbiota transplant (FMT) is a successful and established therapy in recurrent CDI, and its application in other dysbiosis-related diseases is attracting enormous interest. Pre- and probiotics target microbial rebalance and have positive effects mainly in NAFLD, ulcerative colitis, IBS, and CDI patients. Promising anticarcinogenic effects have also been demonstrated in animal models. The literature increasingly describes microbial changes in many dysbiotic disorders and shows what needs to be treated. However, probiotics and FMT application in clinical practice suffers from a shortage of randomized controlled trials with standardized therapy regimens to support their recommendation.
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Affiliation(s)
- Raquel Ortigão
- Department of Gastroenterology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Pedro Pimentel-Nunes
- Department of Gastroenterology, Portuguese Oncology Institute of Porto, Porto, Portugal.,MEDCIDS - Department of Community Medicine, Information and Decision in Health, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Mário Dinis-Ribeiro
- Department of Gastroenterology, Portuguese Oncology Institute of Porto, Porto, Portugal.,MEDCIDS - Department of Community Medicine, Information and Decision in Health, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Diogo Libânio
- Department of Gastroenterology, Portuguese Oncology Institute of Porto, Porto, Portugal.,MEDCIDS - Department of Community Medicine, Information and Decision in Health, Faculty of Medicine, University of Porto, Porto, Portugal
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38
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Ng SC, Kamm MA, Yeoh YK, Chan PKS, Zuo T, Tang W, Sood A, Andoh A, Ohmiya N, Zhou Y, Ooi CJ, Mahachai V, Wu CY, Zhang F, Sugano K, Chan FKL. Scientific frontiers in faecal microbiota transplantation: joint document of Asia-Pacific Association of Gastroenterology (APAGE) and Asia-Pacific Society for Digestive Endoscopy (APSDE). Gut 2020; 69:83-91. [PMID: 31611298 PMCID: PMC6943253 DOI: 10.1136/gutjnl-2019-319407] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/06/2019] [Accepted: 09/24/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE The underlying microbial basis, predictors of therapeutic outcome and active constituent(s) of faecal microbiota transplantation (FMT) mediating benefit remain unknown. An international panel of experts presented key elements that will shape forthcoming FMT research and practice. DESIGN Systematic search was performed, FMT literature was critically appraised and a 1-day round-table discussion was conducted to derive expert consensus on key issues in FMT research. RESULTS 16 experts convened and discussed five questions regarding (1) the role of donor and recipient microbial (bacteria, viruses, fungi) parameters in FMT; (2) methods to assess microbiota alterations; (3) concept of keystone species and microbial predictors of FMT, (4) influence of recipient profile and antibiotics pretreatment on FMT engraftment and maintenance and (5) new developments in FMT formulations and delivery. The panel considered that variable outcomes of FMT relate to compositional and functional differences in recipient's microbiota, and likely donor-associated and recipient-associated physiological and genetic factors. Taxonomic composition of donor intestinal microbiota may influence the efficacy of FMT in recurrent Clostridioides difficile infections and UC. FMT not only alters bacteria composition but also establishes trans-kingdom equilibrium between gut fungi, viruses and bacteria to promote the recovery of microbial homeostasis. FMT is not a one size fits all and studies are required to identify microbial components that have specific effects in patients with different diseases. CONCLUSION FMT requires optimisation before their therapeutic promise can be evaluated for different diseases. This summary will guide future directions and priorities in advancement of the science and practice of FMT.
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Affiliation(s)
- Siew C Ng
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Michael A Kamm
- St Vincent's Hospital and University of Melbourne, Melbourne, Victoria, Australia
| | - Yun Kit Yeoh
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Microbiology and LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Microbiology and LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Tao Zuo
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Whitney Tang
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ajit Sood
- Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - Akira Andoh
- Department of Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Naoki Ohmiya
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Yongjian Zhou
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Choon Jin Ooi
- Gleneagles Medical Centre and Duke-NUS Medical School, Singapore, Singapore
| | - Varocha Mahachai
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- National Gastric Cancer and Gastrointestinal Diseases Research Center, Pathumthani, Thailand
| | - Chun-Ying Wu
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
- Division of Gastroenterology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Faming Zhang
- Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Division of Microbiotherapy, Sir Run Run Shaw Hospital, Nanjing Medical University, Nanjing, China
| | - Kentaro Sugano
- Department of Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Francis K L Chan
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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Freitag TL, Hartikainen A, Jouhten H, Sahl C, Meri S, Anttila VJ, Mattila E, Arkkila P, Jalanka J, Satokari R. Minor Effect of Antibiotic Pre-treatment on the Engraftment of Donor Microbiota in Fecal Transplantation in Mice. Front Microbiol 2019; 10:2685. [PMID: 31824463 PMCID: PMC6881239 DOI: 10.3389/fmicb.2019.02685] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI) and is also considered a potential treatment for a wide range of intestinal and systemic diseases. FMT corrects the microbial dysbiosis associated with rCDI, and the engraftment of donor microbiota is likely to play a key role in treatment efficacy. For disease indications other than rCDI, FMT treatment efficacy has been moderate. This may be partly due to stronger resilience of resident host microbiota in patients who do not suffer from rCDI. In rCDI, patients typically have undergone several antibiotic treatments prior to FMT, depleting the microbiota. In this study, we addressed the effect of broad-spectrum antibiotics (Ab) as a pre-treatment to FMT on the engraftment of donor microbiota in recipients. We conducted a pre-clinical study of FMT between two healthy mouse strains, Balb/c as donors and C57BL/6 as recipients, to perform FMT within the same species and to mimic interindividual FMT between human donors and patients. Microbiota composition was assessed with high-throughput 16S rDNA amplicon sequencing. The microbiota of Balb/c and C57BL/6 mice differed significantly, which allowed for the assessment of microbiota transplantation from the donor strain to the recipient. Our results showed that Ab-treatment depleted microbiota in C57BL/6 recipient mice prior to FMT. The diversity of microbiota did not recover spontaneously to baseline levels during 8 weeks after Ab-treatment, but was restored already at 2 weeks in mice receiving FMT. Interestingly, pre-treatment with antibiotics prior to FMT did not increase the overall similarity of the recipient’s microbiota to that of the donor’s, as compared with mice receiving FMT without Ab-treatment. Pre-treatment with Ab improved the establishment of only a few donor-derived taxa, such as Bifidobacterium, in the recipients, thus having a minor effect on the engraftment of donor microbiota in FMT. In conclusion, pre-treatment with broad-spectrum antibiotics did not improve the overall engraftment of donor microbiota, but did improve the engraftment of specific taxa. These results may inform future therapeutic studies of FMT.
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Affiliation(s)
- Tobias L Freitag
- Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Hartikainen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hanne Jouhten
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Cecilia Sahl
- Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Seppo Meri
- Translational Immunology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Veli-Jukka Anttila
- Department of Infectious Disease, Helsinki University Central Hospital, Helsinki, Finland
| | - Eero Mattila
- Department of Infectious Disease, Helsinki University Central Hospital, Helsinki, Finland
| | - Perttu Arkkila
- Department of Gastroenterology, Helsinki University Central Hospital, Helsinki, Finland
| | - Jonna Jalanka
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Reetta Satokari
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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40
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Mullish BH, McDonald JAK, Pechlivanis A, Allegretti JR, Kao D, Barker GF, Kapila D, Petrof EO, Joyce SA, Gahan CGM, Glegola-Madejska I, Williams HRT, Holmes E, Clarke TB, Thursz MR, Marchesi JR. Microbial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent Clostridioides difficile infection. Gut 2019; 68:1791-1800. [PMID: 30816855 PMCID: PMC6839797 DOI: 10.1136/gutjnl-2018-317842] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/26/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Faecal microbiota transplant (FMT) effectively treats recurrent Clostridioides difficile infection (rCDI), but its mechanisms of action remain poorly defined. Certain bile acids affect C. difficile germination or vegetative growth. We hypothesised that loss of gut microbiota-derived bile salt hydrolases (BSHs) predisposes to CDI by perturbing gut bile metabolism, and that BSH restitution is a key mediator of FMT's efficacy in treating the condition. DESIGN Using stool collected from patients and donors pre-FMT/post-FMT for rCDI, we performed 16S rRNA gene sequencing, ultra performance liquid chromatography mass spectrometry (UPLC-MS) bile acid profiling, BSH activity measurement, and qPCR of bsh/baiCD genes involved in bile metabolism. Human data were validated in C. difficile batch cultures and a C57BL/6 mouse model of rCDI. RESULTS From metataxonomics, pre-FMT stool demonstrated a reduced proportion of BSH-producing bacterial species compared with donors/post-FMT. Pre-FMT stool was enriched in taurocholic acid (TCA, a potent C. difficile germinant); TCA levels negatively correlated with key bacterial genera containing BSH-producing organisms. Post-FMT samples demonstrated recovered BSH activity and bsh/baiCD gene copy number compared with pretreatment (p<0.05). In batch cultures, supernatant from engineered bsh-expressing E. coli and naturally BSH-producing organisms (Bacteroides ovatus, Collinsella aerofaciens, Bacteroides vulgatus and Blautia obeum) reduced TCA-mediated C. difficile germination relative to culture supernatant of wild-type (BSH-negative) E. coli. C. difficile total viable counts were ~70% reduced in an rCDI mouse model after administration of E. coli expressing highly active BSH relative to mice administered BSH-negative E. coli (p<0.05). CONCLUSION Restoration of gut BSH functionality contributes to the efficacy of FMT in treating rCDI.
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Affiliation(s)
- Benjamin H Mullish
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Julie A K McDonald
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Alexandros Pechlivanis
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Jessica R Allegretti
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital, Boston, Massachusetts, USA,Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - Dina Kao
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Grace F Barker
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Diya Kapila
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Elaine O Petrof
- Division of Infectious Diseases/ GI Diseases Research Unit Wing, Department of Medicine, Kingston General Hospital, Queen’s University, Kingston, Ontario, Canada
| | - Susan A Joyce
- APC Microbiome Institute, University College Cork, Cork, Ireland,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Cormac G M Gahan
- APC Microbiome Institute, University College Cork, Cork, Ireland,School of Pharmacy, University College Cork, Cork, Ireland
| | | | - Horace R T Williams
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Elaine Holmes
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Thomas B Clarke
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Mark R Thursz
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Julian R Marchesi
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK,School of Biosciences, Cardiff University, Cardiff, UK
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41
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Zhang Z, Mocanu V, Cai C, Dang J, Slater L, Deehan EC, Walter J, Madsen KL. Impact of Fecal Microbiota Transplantation on Obesity and Metabolic Syndrome-A Systematic Review. Nutrients 2019; 11:nu11102291. [PMID: 31557953 PMCID: PMC6835402 DOI: 10.3390/nu11102291] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/11/2019] [Accepted: 09/23/2019] [Indexed: 02/07/2023] Open
Abstract
Fecal microbiota transplantation (FMT) is a gut microbial-modulation strategy that has been investigated for the treatment of a variety of human diseases, including obesity-associated metabolic disorders. This study appraises current literature and provides an overview of the effectiveness and limitations of FMT as a potential therapeutic strategy for obesity and metabolic syndrome (MS). Five electronic databases and two gray literature sources were searched up to 10 December 2018. All interventional and observational studies that contained information on the relevant population (adult patients with obesity and MS), intervention (receiving allogeneic FMT) and outcomes (metabolic parameters) were eligible. From 1096 unique citations, three randomized placebo-controlled studies (76 patients with obesity and MS, body mass index = 34.8 ± 4.1 kg/m2, fasting plasma glucose = 5.8 ± 0.7 mmol/L) were included for review. Studies reported mixed results with regards to improvement in metabolic parameters. Two studies reported improved peripheral insulin sensitivity (rate of glucose disappearance, RD) at 6 weeks in patients receiving donor FMT versus patients receiving the placebo control. In addition, one study observed lower HbA1c levels in FMT patients at 6 weeks. No differences in fasting plasma glucose, hepatic insulin sensitivity, body mass index (BMI), or cholesterol markers were observed between two groups across all included studies. While promising, the influence of FMT on long-term clinical endpoints needs to be further explored. Future studies are also required to better understand the mechanisms through which changes in gut microbial ecology and engraftment of microbiota affect metabolic outcomes for patients with obesity and MS. In addition, further research is needed to better define the optimal fecal microbial preparation, dosing, and method of delivery.
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Affiliation(s)
- Zhengxiao Zhang
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton T6G 2E1 AB, Canada.
| | - Valentin Mocanu
- Division of General Surgery, University of Alberta, Edmonton T6G 2E1, AB, Canada.
| | - Chenxi Cai
- Program for Pregnancy and Postpartum Health, Women and Children's Health Research Institute, University of Alberta, Edmonton T6G 2E1 AB, Canada.
| | - Jerry Dang
- Division of General Surgery, University of Alberta, Edmonton T6G 2E1, AB, Canada.
| | - Linda Slater
- John W. Scott Health Sciences Library, University of Alberta, Edmonton T6G 2E1, ON, Canada.
| | - Edward C Deehan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton T6G 2E1, AB, Canada.
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton T6G 2E1, AB, Canada.
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E1, AB, Canada.
| | - Karen L Madsen
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton T6G 2E1 AB, Canada.
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Satokari R. Modulation of Gut Microbiota for Health by Current and Next-Generation Probiotics. Nutrients 2019; 11:nu11081921. [PMID: 31443276 PMCID: PMC6723275 DOI: 10.3390/nu11081921] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 01/24/2023] Open
Abstract
The human gut microbiota is a complex ecosystem and has an essential role in maintaining intestinal and systemic health. Microbiota dysbiosis is associated with a number of intestinal and systemic conditions and its modulation for human health is of great interest. Gut microbiota is a source of novel health-promoting bacteria, often termed as next-generation probiotics in order to distinguish them from traditional probiotics. The previous lessons learned with traditional probiotics can help the development of next-generation probiotics that target specific health issues and needs.
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Affiliation(s)
- Reetta Satokari
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland.
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43
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Farowski F, Solbach P, Tsakmaklis A, Brodesser S, Cruz Aguilar MR, Cornely OA, Dettmer K, Higgins PG, Suerbaum S, Jazmati N, Oefner PJ, Vehreschild MJGT. Potential biomarkers to predict outcome of faecal microbiota transfer for recurrent Clostridioides difficile infection. Dig Liver Dis 2019; 51:944-951. [PMID: 30770201 DOI: 10.1016/j.dld.2019.01.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/15/2019] [Accepted: 01/17/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Faecal microbiota transplantation (FMT) has proven high clinical efficacy in the management of recurrent Clostridioides difficile infection (rCDI) with cure rates of over 80% after a single treatment. Nevertheless, the reasons for failure in the remaining 20% remain elusive. The aim of the present study was to investigate different potential predictors of response to FMT. METHODS Faecal specimens of sixteen patients undergoing FMT for rCDI, as well as samples from the respective donors were collected and analyzed by 16S rRNA gene profiling, bile acid-inducible (baiCD) gene specific qPCR, and liquid chromatography tandem-mass spectrometry (LC-MS/MS) to quantify the concentrations of primary and secondary bile acids. RESULTS Using the faecal concentration of the secondary bile acid lithocholic acid (LCA)within the patient specimens, we were able to predict response to FMT (accuracy 95.2%, sensitivity 100%, specificity 90.9%). By combining the faecal LCA concentration with the urinary pCS concentration, an accuracy of 100% was achieved. CONCLUSION LCA appears to be a promising marker candidate for prediction of clinical response to FMT. Other makers, such as urinary concentration of pCS, but not 3-IS, might be used to improve accuracy of prediction. Further studies are warranted to validate these candidate markers.
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Affiliation(s)
- Fedja Farowski
- Department I of Internal Medicine, University Hospital of Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany
| | - Philipp Solbach
- Hannover Medical School, Department of Gastroenterology, Hepatology and Endocrinology, Hannover, Germany; Hannover Medical School, Institute of Medical Microbiology and Hospital Epidemiology, Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Anastasia Tsakmaklis
- Department I of Internal Medicine, University Hospital of Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany
| | - Susanne Brodesser
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
| | | | - Oliver A Cornely
- Department I of Internal Medicine, University Hospital of Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
| | - Katja Dettmer
- Institute of Functional Genomics, University of Regensburg, Germany
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany
| | - Sebastian Suerbaum
- Hannover Medical School, Institute of Medical Microbiology and Hospital Epidemiology, Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany; Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany
| | - Nathalie Jazmati
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany; Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Germany
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Germany
| | - Maria J G T Vehreschild
- Department I of Internal Medicine, University Hospital of Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany.
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Exploring the diversity and dynamic of bacterial community vertically distributed in Tongguling National Nature Reserve in Hainan Island, China. Braz J Microbiol 2019; 50:729-737. [PMID: 31104215 DOI: 10.1007/s42770-019-00078-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/27/2019] [Indexed: 10/26/2022] Open
Abstract
National nature reserves are important for preserving ecological resources and constructing national ecological security barriers. Tongguling National Nature Reserve (TNNR) is known for its unique tropical island ecosystem and abundant biological resources. This study was conducted to characterize and compare its bacterial community diversity and composition in soils from 10, 20, and 30 cm in depth using high-throughput sequencing of 16S rDNA genes. We found that soils from 20 cm had the highest diversity and might serve as a "middle bridge" to the dynamic distribution between the 10- and 30-cm soil samples. The diversity pattern indicated that the main abundant groups varied distinctly and significantly among soils of different depths. Moreover, Chloroflexi was the most dynamic group in TNNR soils, together with another abundant but rarely reported group, Verrucomicrobia, which greatly enhanced the microbial diversity of TNNR soils. Overall, the results of this study emphasize the urgent need for greater understanding of bacterial community variations in response to human activities and climate change.
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Anonye BO, Hassall J, Patient J, Detamornrat U, Aladdad AM, Schüller S, Rose FRAJ, Unnikrishnan M. Probing Clostridium difficile Infection in Complex Human Gut Cellular Models. Front Microbiol 2019; 10:879. [PMID: 31114553 PMCID: PMC6503005 DOI: 10.3389/fmicb.2019.00879] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/05/2019] [Indexed: 12/11/2022] Open
Abstract
Interactions of anaerobic gut bacteria, such as Clostridium difficile, with the intestinal mucosa have been poorly studied due to challenges in culturing anaerobes with the oxygen-requiring gut epithelium. Although gut colonization by C. difficile is a key determinant of disease outcome, precise mechanisms of mucosal attachment and spread remain unclear. Here, using human gut epithelial monolayers co-cultured within dual environment chambers, we demonstrate that C. difficile adhesion to gut epithelial cells is accompanied by a gradual increase in bacterial numbers. Prolonged infection causes redistribution of actin and loss of epithelial integrity, accompanied by production of C. difficile spores, toxins, and bacterial filaments. This system was used to examine C. difficile interactions with the commensal Bacteroides dorei, and interestingly, C. difficile growth is significantly reduced in the presence of B. dorei. Subsequently, we have developed novel models containing a myofibroblast layer, in addition to the epithelium, grown on polycarbonate or three-dimensional (3D) electrospun scaffolds. In these more complex models, C. difficile adheres more efficiently to epithelial cells, as compared to the single epithelial monolayers, leading to a quicker destruction of the epithelium. Our study describes new controlled environment human gut models that enable host-anaerobe and pathogen-commensal interaction studies in vitro.
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Affiliation(s)
- Blessing O. Anonye
- Microbiology and Infection Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Jack Hassall
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jamie Patient
- Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Usanee Detamornrat
- Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Afnan M. Aladdad
- Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Stephanie Schüller
- Norwich Medical School, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, United Kingdom
- Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Felicity R. A. J. Rose
- Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Meera Unnikrishnan
- Microbiology and Infection Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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Hibbard J, Jiang ZD, DuPont H. Fecal calprotectin and fecal indole predict outcome of fecal microbiota transplantation in subjects with recurrent Clostridium difficile infection. Anaerobe 2019; 56:102-105. [DOI: 10.1016/j.anaerobe.2019.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/28/2019] [Accepted: 03/05/2019] [Indexed: 01/10/2023]
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Identification of the microbial diversity after fecal microbiota transplantation therapy for chronic intractable constipation using 16s rRNA amplicon sequencing. PLoS One 2019; 14:e0214085. [PMID: 30889205 PMCID: PMC6424423 DOI: 10.1371/journal.pone.0214085] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/06/2019] [Indexed: 02/06/2023] Open
Abstract
Background Fecal microbiota transplantation (FMT) is an effective therapeutic approach for the treatment of functional gastrointestinal disease by restoring gut microbiota; however, there is a lack of sufficient understanding regarding which microbial populations successfully colonize the recipient gut. This study characterized microbial composition and diversity in patients diagnosed with chronic constipation at 1 month and 1 year after FMT. Methods We explored the microbial diversity of pre- and posttransplant stool specimens from patients using 16S rRNA gene sequencing, followed by functional analysis. Results The results identified 22 species of microorganisms colonized in the recipients from the donors at 1 month after FMT. One-year follow-up of the patient identified the colonization of 18 species of microorganisms, resulting in identification of species in significant abundance, including Bacteroides fragilis and Hungatella hathewayi in the recipient at 1 month after FMT and Dialister succinatiphilus, Coprococcus catus, and Sutterella stercoricanis at 1 year after FMT. The majority of the colonized species belong to the phylum Firmicutes and carry genes related to polysaccharide metabolism and that enhance the energy-harvesting efficiency of the host. Conclusion These results suggest that FMT is effective for the treatment of chronic constipation through the restoration and colonization of donor microbiota in the recipient gut up to 1 year after FMT.
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Abu-Sbeih H, Ali FS, Wang Y. Clinical Review on the Utility of Fecal Microbiota Transplantation in Immunocompromised Patients. Curr Gastroenterol Rep 2019; 21:8. [PMID: 30815766 DOI: 10.1007/s11894-019-0677-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fecal microbiota transplantation (FMT) represents a promising management modality for Clostridium difficile infection (CDI). In immunocompromised patients, FMT is utilized for CDI as well as emerging non-CDI indications such as inflammatory bowel disease and graft versus host disease. PURPOSE OF REVIEW: This review aims to shed light on the safety and efficacy of FMT in immunocompromised patients, including patients suffering for human immunodeficiency virus infection, solid organ and hematopoietic stem cell transplant recipients, cancer patients, and patients on immunosuppressive therapies. RECENT FINDINGS: Though the body of evidence concerning the use of FMT in immunocompromised is growing, no clinical trials exist to date. Present literature weighs in favor of FMT in immunocompromised patients, with an acceptable adverse effect profile and minimal risk of infectious adverse events. Further large scale studies and randomized controlled trials to validate the utility of FMT in immunocompromised individuals will be a welcomed endeavor.
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Affiliation(s)
- Hamzah Abu-Sbeih
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 1466, Houston, TX, 77030, USA
| | - Faisal S Ali
- Department of Internal Medicine, Presence Saint Joseph Hospital, Chicago, IL, USA
| | - Yinghong Wang
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 1466, Houston, TX, 77030, USA.
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Carlucci C, Jones CS, Oliphant K, Yen S, Daigneault M, Carriero C, Robinson A, Petrof EO, Weese JS, Allen-Vercoe E. Effects of defined gut microbial ecosystem components on virulence determinants of Clostridioides difficile. Sci Rep 2019; 9:885. [PMID: 30696914 PMCID: PMC6351598 DOI: 10.1038/s41598-018-37547-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 11/28/2018] [Indexed: 12/19/2022] Open
Abstract
Many cases of Clostridioides difficile infection (CDI) are poorly responsive to standard antibiotic treatment strategies, and often patients suffer from recurrent infections characterized by severe diarrhea. Our group previously reported the successful cure of two patients with recurrent CDI using a standardized stool-derived microbial ecosystem therapeutic (MET-1). Using an in vitro model of the distal gut to support bacterial communities, we characterized the metabolite profiles of two defined microbial ecosystems derived from healthy donor stool (DEC58, and a subset community, MET-1), as well as an ecosystem representative of a dysbiotic state (ciprofloxacin-treated DEC58). The growth and virulence determinants of two C. difficile strains were then assessed in response to components derived from the ecosystems. CD186 (ribotype 027) and CD973 (ribotype 078) growth was decreased upon treatment with DEC58 metabolites compared to ciprofloxacin-treated DEC58 metabolites. Furthermore, CD186 TcdA and TcdB secretion was increased following treatment with ciprofloxacin-treated DEC58 spent medium compared to DEC58 spent medium alone. The net metabolic output of C. difficile was also modulated in response to spent media from defined microbial ecosystems, although several metabolite levels were divergent across the two strains examined. Further investigation of these antagonistic properties will guide the development of microbiota-based therapeutics for CDI.
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Affiliation(s)
- Christian Carlucci
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
| | - Carys S Jones
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Kaitlyn Oliphant
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Sandi Yen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Michelle Daigneault
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Charley Carriero
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Avery Robinson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Elaine O Petrof
- Division of Infectious Diseases/Gastrointestinal Diseases Research Unit, Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - J Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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50
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Abstract
Our understanding of the human gut microbiome continues to evolve at a rapid pace, but practical application of thisknowledge is still in its infancy. This review discusses the type of studies that will be essential for translating microbiome research into targeted modulations with dedicated benefits for the human host.
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Affiliation(s)
- Thomas S B Schmidt
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Jeroen Raes
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, 3000 Leuven, Belgium; VIB, Center for Microbiology, Heerestraat 49, 3000 Leuven, Belgium.
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
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