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Mullish BH, Merrick B, Quraishi MN, Bak A, Green CA, Moore DJ, Porter RJ, Elumogo NT, Segal JP, Sharma N, Marsh B, Kontkowski G, Manzoor SE, Hart AL, Settle C, Keller JJ, Hawkey P, Iqbal TH, Goldenberg SD, Williams HRT. The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridioides difficile infection and other potential indications: second edition of joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines. Gut 2024; 73:1052-1075. [PMID: 38609165 DOI: 10.1136/gutjnl-2023-331550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/03/2024] [Indexed: 04/14/2024]
Abstract
The first British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS)-endorsed faecal microbiota transplant (FMT) guidelines were published in 2018. Over the past 5 years, there has been considerable growth in the evidence base (including publication of outcomes from large national FMT registries), necessitating an updated critical review of the literature and a second edition of the BSG/HIS FMT guidelines. These have been produced in accordance with National Institute for Health and Care Excellence-accredited methodology, thus have particular relevance for UK-based clinicians, but are intended to be of pertinence internationally. This second edition of the guidelines have been divided into recommendations, good practice points and recommendations against certain practices. With respect to FMT for Clostridioides difficile infection (CDI), key focus areas centred around timing of administration, increasing clinical experience of encapsulated FMT preparations and optimising donor screening. The latter topic is of particular relevance given the COVID-19 pandemic, and cases of patient morbidity and mortality resulting from FMT-related pathogen transmission. The guidelines also considered emergent literature on the use of FMT in non-CDI settings (including both gastrointestinal and non-gastrointestinal indications), reviewing relevant randomised controlled trials. Recommendations are provided regarding special areas (including compassionate FMT use), and considerations regarding the evolving landscape of FMT and microbiome therapeutics.
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Affiliation(s)
- Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College London, London, UK
| | - Mohammed Nabil Quraishi
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, London, UK
| | - Aggie Bak
- Healthcare Infection Society, London, UK
| | - Christopher A Green
- Department of Infectious Diseases & Tropical Medicine, University Hospitals NHS Foundation Trust, Birmingham Heartlands Hospital, Birmingham, UK
- School of Chemical Engineering, University of Birmingham, Birmingham, UK
| | - David J Moore
- Institute of Applied Health Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Robert J Porter
- Department of Microbiology, Royal Devon and Exeter Hospitals, Barrack Road, UK
| | - Ngozi T Elumogo
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norfolk and Norwich University Hospital, Norwich, UK
| | - Jonathan P Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Naveen Sharma
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, London, UK
| | - Belinda Marsh
- Lay representative for FMT Working Party, Healthcare Infection Society, London, UK
| | - Graziella Kontkowski
- Lay representative for FMT Working Party, Healthcare Infection Society, London, UK
- C.diff support, London, UK
| | - Susan E Manzoor
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK
| | - Ailsa L Hart
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Department of Gastroenterology and Inflammatory Bowel Disease Unit, St Mark's Hospital and Academic Institute, Middlesex, UK
| | | | - Josbert J Keller
- Department of Gastroenterology, Haaglanden Medisch Centrum, The Hague, The Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Hawkey
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK
- Public Health Laboratory, Faculty of Medicine, University of Birmingham, Birmingham, UK
| | - Tariq H Iqbal
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, London, UK
| | - Simon D Goldenberg
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College London, London, UK
| | - Horace R T Williams
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
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2
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Mullish BH, Merrick B, Quraishi MN, Bak A, Green CA, Moore DJ, Porter RJ, Elumogo NT, Segal JP, Sharma N, Marsh B, Kontkowski G, Manzoor SE, Hart AL, Settle C, Keller JJ, Hawkey P, Iqbal TH, Goldenberg SD, Williams HRT. The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridioides difficile infection and other potential indications: second edition of joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines. J Hosp Infect 2024; 148:189-219. [PMID: 38609760 DOI: 10.1016/j.jhin.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
The first British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS)-endorsed faecal microbiota transplant (FMT) guidelines were published in 2018. Over the past 5 years, there has been considerable growth in the evidence base (including publication of outcomes from large national FMT registries), necessitating an updated critical review of the literature and a second edition of the BSG/HIS FMT guidelines. These have been produced in accordance with National Institute for Health and Care Excellence-accredited methodology, thus have particular relevance for UK-based clinicians, but are intended to be of pertinence internationally. This second edition of the guidelines have been divided into recommendations, good practice points and recommendations against certain practices. With respect to FMT for Clostridioides difficile infection (CDI), key focus areas centred around timing of administration, increasing clinical experience of encapsulated FMT preparations and optimising donor screening. The latter topic is of particular relevance given the COVID-19 pandemic, and cases of patient morbidity and mortality resulting from FMT-related pathogen transmission. The guidelines also considered emergent literature on the use of FMT in non-CDI settings (including both gastrointestinal and non-gastrointestinal indications), reviewing relevant randomised controlled trials. Recommendations are provided regarding special areas (including compassionate FMT use), and considerations regarding the evolving landscape of FMT and microbiome therapeutics.
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Affiliation(s)
- B H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK; Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - B Merrick
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College London, London, UK
| | - M N Quraishi
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK; Institute of Cancer and Genomic Sciences, University of Birmingham, London, UK
| | - A Bak
- Healthcare Infection Society, London, UK
| | - C A Green
- Department of Infectious Diseases & Tropical Medicine, University Hospitals NHS Foundation Trust, Birmingham Heartlands Hospital, Birmingham, UK; School of Chemical Engineering, University of Birmingham, Birmingham, UK
| | - D J Moore
- Institute of Applied Health Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - R J Porter
- Department of Microbiology, Royal Devon and Exeter Hospitals, Barrack Road, UK
| | - N T Elumogo
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK; Norfolk and Norwich University Hospital, Norwich, UK
| | - J P Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Melbourne, Victoria, Australia; Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - N Sharma
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK; Institute of Cancer and Genomic Sciences, University of Birmingham, London, UK
| | - B Marsh
- Lay Representative for FMT Working Party, Healthcare Infection Society, London, UK
| | - G Kontkowski
- Lay Representative for FMT Working Party, Healthcare Infection Society, London, UK; C.diff support, London, UK
| | - S E Manzoor
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK
| | - A L Hart
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK; Department of Gastroenterology and Inflammatory Bowel Disease Unit, St Mark's Hospital and Academic Institute, Middlesex, UK
| | - C Settle
- South Tyneside and Sunderland NHS Foundation Trust, South Shields, UK
| | - J J Keller
- Department of Gastroenterology, Haaglanden Medisch Centrum, The Hague, The Netherlands; Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - P Hawkey
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK; Public Health Laboratory, Faculty of Medicine, University of Birmingham, Birmingham, UK
| | - T H Iqbal
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK; Institute of Cancer and Genomic Sciences, University of Birmingham, London, UK
| | - S D Goldenberg
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College London, London, UK.
| | - H R T Williams
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK; Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK.
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Facchin S, Bertin L, Bonazzi E, Lorenzon G, De Barba C, Barberio B, Zingone F, Maniero D, Scarpa M, Ruffolo C, Angriman I, Savarino EV. Short-Chain Fatty Acids and Human Health: From Metabolic Pathways to Current Therapeutic Implications. Life (Basel) 2024; 14:559. [PMID: 38792581 PMCID: PMC11122327 DOI: 10.3390/life14050559] [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: 03/25/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
The gastrointestinal tract is home to trillions of diverse microorganisms collectively known as the gut microbiota, which play a pivotal role in breaking down undigested foods, such as dietary fibers. Through the fermentation of these food components, short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate are produced, offering numerous health benefits to the host. The production and absorption of these SCFAs occur through various mechanisms within the human intestine, contingent upon the types of dietary fibers reaching the gut and the specific microorganisms engaged in fermentation. Medical literature extensively documents the supplementation of SCFAs, particularly butyrate, in the treatment of gastrointestinal, metabolic, cardiovascular, and gut-brain-related disorders. This review seeks to provide an overview of the dynamics involved in the production and absorption of acetate, propionate, and butyrate within the human gut. Additionally, it will focus on the pivotal roles these SCFAs play in promoting gastrointestinal and metabolic health, as well as their current therapeutic implications.
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Affiliation(s)
- Sonia Facchin
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Luisa Bertin
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Erica Bonazzi
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Greta Lorenzon
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Caterina De Barba
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Brigida Barberio
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Fabiana Zingone
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Daria Maniero
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
| | - Marco Scarpa
- General Surgery Unit, Department of Surgery, Oncology and Gastroenterology, University of Padova, 35138 Padua, Italy (C.R.); (I.A.)
| | - Cesare Ruffolo
- General Surgery Unit, Department of Surgery, Oncology and Gastroenterology, University of Padova, 35138 Padua, Italy (C.R.); (I.A.)
| | - Imerio Angriman
- General Surgery Unit, Department of Surgery, Oncology and Gastroenterology, University of Padova, 35138 Padua, Italy (C.R.); (I.A.)
| | - Edoardo Vincenzo Savarino
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University Hospital of Padua, 35128 Padua, Italy (L.B.); (B.B.)
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Zhang D, Jian YP, Zhang YN, Li Y, Gu LT, Sun HH, Liu MD, Zhou HL, Wang YS, Xu ZX. Short-chain fatty acids in diseases. Cell Commun Signal 2023; 21:212. [PMID: 37596634 PMCID: PMC10436623 DOI: 10.1186/s12964-023-01219-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/09/2023] [Indexed: 08/20/2023] Open
Abstract
Short-chain fatty acids (SCFAs) are the main metabolites produced by bacterial fermentation of dietary fibre in the gastrointestinal tract. The absorption of SCFAs is mediated by substrate transporters, such as monocarboxylate transporter 1 and sodium-coupled monocarboxylate transporter 1, which promote cellular metabolism. An increasing number of studies have implicated metabolites produced by microorganisms as crucial executors of diet-based microbial influence on the host. SCFAs are important fuels for intestinal epithelial cells (IECs) and represent a major carbon flux from the diet, that is decomposed by the gut microbiota. SCFAs play a vital role in multiple molecular biological processes, such as promoting the secretion of glucagon-like peptide-1 by IECs to inhibit the elevation of blood glucose, increasing the expression of G protein-coupled receptors such as GPR41 and GPR43, and inhibiting histone deacetylases, which participate in the regulation of the proliferation, differentiation, and function of IECs. SCFAs affect intestinal motility, barrier function, and host metabolism. Furthermore, SCFAs play important regulatory roles in local, intermediate, and peripheral metabolisms. Acetate, propionate, and butyrate are the major SCFAs, they are involved in the regulation of immunity, apoptosis, inflammation, and lipid metabolism. Herein, we review the diverse functional roles of this major class of bacterial metabolites and reflect on their ability to affect intestine, metabolic, and other diseases. Video Abstract.
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Affiliation(s)
- Dan Zhang
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, 130021, China
| | - Yong-Ping Jian
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, 130021, China
- School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Yu-Ning Zhang
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, 130021, China
| | - Yao Li
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, 130021, China
| | - Li-Ting Gu
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, 130021, China
| | - Hui-Hui Sun
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, 130021, China
| | - Ming-Di Liu
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, 130021, China
| | - Hong-Lan Zhou
- Department of Urology, The First Hospital of Jilin University, Changchun, 130021, China.
| | - Yi-Shu Wang
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, 130021, China.
| | - Zhi-Xiang Xu
- Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, 130021, China.
- School of Life Sciences, Henan University, Kaifeng, 475004, China.
- Department of Urology, The First Hospital of Jilin University, Changchun, 130021, China.
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Liu F, Lu H, Dong B, Huang X, Cheng H, Qu R, Hu Y, Zhong L, Guo Z, You Y, Xu ZZ. Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/– Bacteria. mSystems 2023; 8:e0073822. [PMID: 36971593 PMCID: PMC10134872 DOI: 10.1128/msystems.00738-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing technologies and downstream bioinformatic analyses, we gained an insight into the high-resolution microbial community composition of human saliva and feces, yet we know very little about whether such community DNA sequences represent viable microbes.
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Caley LR, White H, de Goffau MC, Floto RA, Parkhill J, Marsland B, Peckham DG. Cystic Fibrosis-Related Gut Dysbiosis: A Systematic Review. Dig Dis Sci 2023; 68:1797-1814. [PMID: 36600119 DOI: 10.1007/s10620-022-07812-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023]
Abstract
BACKGROUND AND AIMS Cystic Fibrosis (CF) is associated with gut dysbiosis, local and systemic inflammation, and impaired immune function. Gut microbiota dysbiosis results from changes in the complex gut milieu in response to CF transmembrane conductance regulator (CFTR) dysfunction, pancreatic malabsorption, diet, medications, and environmental influences. In several diseases, alteration of the gut microbiota influences local and systemic inflammation and disease outcomes. We conducted a systematic review of the gut microbiota in CF and explored factors influencing dysbiosis. METHODS An electronic search of three databases was conducted in January 2019, and re-run in June 2021. Human, animal, and in vitro studies were included. The primary outcome was differences in the gut microbiota between people with CF (pwCF) and healthy controls. Secondary outcomes included the relationship between the gut microbiota and other factors, including diet, medication, inflammation, and pulmonary function in pwCF. RESULTS Thirty-eight studies were identified. The literature confirmed the presence of CF-related gut dysbiosis, characterized by reduced diversity and several taxonomic changes. There was a relative increase of bacteria associated with a pro-inflammatory response coupled with a reduction of those considered anti-inflammatory. However, studies linking gut dysbiosis to systemic and lung inflammation were limited. Causes of gut dysbiosis were multifactorial, and findings were variable. Data on the impact of CFTR modulators on the gut microbiota were limited. CONCLUSIONS CF-related gut dysbiosis is evident in pwCF. Whether this influences local and systemic disease and is amenable to interventions with diet and drugs, such as CFTR modulators, requires further investigation.
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Affiliation(s)
- L R Caley
- Leeds Institute of Medical Research, St James's University Hospital, Clinical Sciences Building, Leeds, LS9 7TF, UK
| | - H White
- Nutrition, Health & Environment, Leeds Beckett University, Leeds, UK
| | - M C de Goffau
- Wellcome Sanger Institute, Cambridge, UK.,Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - R A Floto
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
| | - J Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - B Marsland
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Australia
| | - D G Peckham
- Leeds Institute of Medical Research, St James's University Hospital, Clinical Sciences Building, Leeds, LS9 7TF, UK. .,Department of Respiratory Medicine, Leeds Teaching Hospitals NHS Trust, Leeds, UK.
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Lazarevic V, Gaïa N, Girard M, Mauffrey F, Ruppé E, Schrenzel J. Effect of bacterial DNA enrichment on detection and quantification of bacteria in an infected tissue model by metagenomic next-generation sequencing. ISME COMMUNICATIONS 2022; 2:122. [PMID: 37938717 PMCID: PMC9792467 DOI: 10.1038/s43705-022-00208-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 10/28/2023]
Abstract
Before implementing metagenomic next-generation sequencing (mNGS) in the routine diagnostic laboratory, several challenges need to be resolved. To address strengths and limitations of mNGS in bacterial detection and quantification in samples with overwhelming host DNA abundance, we used the pig muscle tissue spiked with a home-made bacterial mock community, consisting of four species from different phyla. From the spiked tissue, we extracted DNA using: (i) a procedure based on mechanical/chemical lysis (no bacterial DNA enrichment); (ii) the Ultra-Deep Microbiome Prep (Molzym) kit for bacterial DNA enrichment; and (iii) the same enrichment kit but replacing the original proteinase K treatment for tissue solubilization by a collagenases/thermolysin digestion and cell filtration. Following mNGS, we determined bacterial: 'host' read ratios and taxonomic abundance profiles. We calculated the load of each mock-community member by combining its read counts with read counts and microscopically-determined cell counts of other co-spiked bacteria. In unenriched samples, bacterial quantification and taxonomic profiling were fairly accurate but at the expense of the sensitivity of detection. The removal of 'host' DNA by the modified enrichment protocol substantially improved bacterial detection in comparison to the other two extraction procedures and generated less distorted taxonomic profiles as compared to the original enrichment protocol.
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Affiliation(s)
- Vladimir Lazarevic
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland.
| | - Nadia Gaïa
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Myriam Girard
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Florian Mauffrey
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Etienne Ruppé
- Université Sorbonne Paris Nord and INSERM UMR1137 IAME, Université de Paris Cité, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
| | - Jacques Schrenzel
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
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8
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Impact of Freeze Storage on the Estimation of Phenotypic Antimicrobial Resistance Prevalence in Escherichia coli Collected from Faecal Samples from Healthy Humans and Chickens. Antibiotics (Basel) 2022; 11:antibiotics11111643. [DOI: 10.3390/antibiotics11111643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Many studies on phenotypic antimicrobial resistance (AMR) of bacteria from healthy populations are conducted on freeze-stored samples. However, the impact of this practice on phenotypic AMR is not known. We investigated the prevalence of phenotypic AMR in Escherichia coli from chicken (n = 10) and human (n = 11) faecal samples collected from healthy subjects, subject to freeze storage (−20 °C and −80 °C) for 1, 2, 3, and 6 months. We compared counts of E. coli and prevalence of phenotypic resistance against five antimicrobials commonly used in chicken farming (ciprofloxacin, enrofloxacin, doxycycline, gentamicin, and florfenicol) with samples processed within 24 h of collection. Prevalence of phenotypic AMR was estimated by performing differential counts on agar media with and without antimicrobials. At −20 °C, there was a considerable reduction in E. coli counts over time, and this reduction was greater for human samples (−0.630 log10 units per 100 days) compared with chicken samples (−0.178 log10 units per 100 days). For most antimicrobials, AMR prevalence estimates decreased in freeze-stored samples both in humans and chickens over time. Based on these results, we conclude that results on the prevalence of phenotypic AMR on samples from freeze-stored samples are unreliable, and only fresh samples should be used in such studies.
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Alcazar CGM, Paes VM, Shao Y, Oesser C, Miltz A, Lawley TD, Brocklehurst P, Rodger A, Field N. The association between early-life gut microbiota and childhood respiratory diseases: a systematic review. THE LANCET. MICROBE 2022; 3:e867-e880. [PMID: 35988549 PMCID: PMC10499762 DOI: 10.1016/s2666-5247(22)00184-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/29/2022] [Accepted: 06/08/2022] [Indexed: 01/14/2023]
Abstract
Data from animal models suggest a role of early-life gut microbiota in lung immune development, and in establishing susceptibility to respiratory infections and asthma in humans. This systematic review summarises the association between infant (ages 0-12 months) gut microbiota composition measured by genomic sequencing, and childhood (ages 0-18 years) respiratory diseases (ie, respiratory infections, wheezing, or asthma). Overall, there was evidence that low α-diversity and relative abundance of particular gut-commensal bacteria genera (Bifidobacterium, Faecalibacterium, Ruminococcus, and Roseburia) are associated with childhood respiratory diseases. However, results were inconsistent and studies had important limitations, including insufficient characterisation of bacterial taxa to species level, heterogeneous outcome definitions, residual confounding, and small sample sizes. Large longitudinal studies with stool sampling during the first month of life and shotgun metagenomic approaches to improve bacterial and fungal taxa resolution are needed. Standardising follow-up times and respiratory disease definitions and optimising causal statistical approaches might identify targets for primary prevention of childhood respiratory diseases.
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Affiliation(s)
| | - Veena Mazarello Paes
- Institute for Child Health, University College London, London, UK; John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Clarissa Oesser
- Institute for Global Health, University College London, London, UK
| | - Ada Miltz
- Institute for Global Health, University College London, London, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Peter Brocklehurst
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Alison Rodger
- Institute for Global Health, University College London, London, UK; Royal Free Hospital, Royal Free London NHS Foundation Trust, London, UK
| | - Nigel Field
- Institute for Global Health, University College London, London, UK
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10
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Cerquetella M, Marchegiani A, Rossi G, Trabalza-Marinucci M, Passamonti F, Isidori M, Rueca F. Case Report: Oral Fecal Microbiota Transplantation in a Dog Suffering From Relapsing Chronic Diarrhea-Clinical Outcome and Follow-Up. Front Vet Sci 2022; 9:893342. [PMID: 35859811 PMCID: PMC9289623 DOI: 10.3389/fvets.2022.893342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/06/2022] [Indexed: 12/01/2022] Open
Abstract
The present case report describes the effects of orally administered fecal microbiota transplantation (FMT) (frozen capsules) in a dog suffering from relapsing chronic diarrhea, needing a continuous low prednisolone dose to maintain the condition under acceptable control. Through FMT, we aimed at evaluating the possibility of improving the clinical score and/or reducing/suspending steroid administration. During a first period of strict monitoring (21 days), the canine inflammatory bowel disease activity index (CIBDAI) score passed from mild to clinically insignificant disease. Furthermore, two additional gastrointestinal signs that had been reported, bloating and episodes of painful defecation, rapidly improved (bloating) or even resolved (painful defecation). The patient was then followed for 18 months (to the authors' knowledge, the longest follow-up time ever reported in a dog), during which no serious relapses occurred and no increase in prednisolone dose was necessary. No adverse clinical effects were ever reported during monitoring. The present description provides a further experience increasing those already present in the veterinary literature, in which an agreement on how to use FMT has not yet been achieved although strongly needed and recommended.
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Affiliation(s)
- Matteo Cerquetella
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Andrea Marchegiani
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Giacomo Rossi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | | | | | - Marco Isidori
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - Fabrizio Rueca
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
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11
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Secombe KR, Al-Qadami GH, Subramaniam CB, Bowen JM, Scott J, Van Sebille YZ, Snelson M, Cowan C, Clarke G, Gheorghe CE, Cryan JF, Wardill HR. Guidelines for reporting on animal fecal transplantation (GRAFT) studies: recommendations from a systematic review of murine transplantation protocols. Gut Microbes 2022; 13:1979878. [PMID: 34586011 PMCID: PMC8489962 DOI: 10.1080/19490976.2021.1979878] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Fecal microbiota transplant (FMT) is a powerful tool used to connect changes in gut microbial composition with a variety of disease states and pathologies. While FMT enables potential causal relationships to be identified, the experimental details reported in preclinical FMT protocols are highly inconsistent and/or incomplete. This limitation reflects a current lack of authoritative guidance on reporting standards that would facilitate replication efforts and ultimately reproducible science. We therefore systematically reviewed all FMT protocols used in mouse models with the goal of formulating recommendations on the reporting of preclinical FMT protocols. Search strategies were applied across three databases (PubMed, EMBASE, and Ovid Medline) until June 30, 2020. Data related to donor attributes, stool collection, processing/storage, recipient preparation, administration, and quality control were extracted. A total of 1753 papers were identified, with 241 identified for data extraction and analysis. Of the papers included, 92.5% reported a positive outcome with FMT intervention. However, the vast majority of studies failed to address core methodological aspects including the use of anaerobic conditions (91.7% of papers lacked information), storage (49.4%), homogenization (33.6%), concentration (31.5%), volume (19.9%) and administration route (5.3%). To address these reporting limitations, we developed theGuidelines for Reporting Animal Fecal Transplant (GRAFT) that guide reporting standards for preclinical FMT. The GRAFT recommendations will enable robust reporting of preclinical FMT design, and facilitate high-quality peer review, improving the rigor and translation of knowledge gained through preclinical FMT studies.
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Affiliation(s)
- Kate R. Secombe
- School of Biomedicine, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia,CONTACT Kate R. Secombe The University of Queensland, Australia
| | - Ghanyah H. Al-Qadami
- School of Biomedicine, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Courtney B. Subramaniam
- School of Biomedicine, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Joanne M. Bowen
- School of Biomedicine, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Jacqui Scott
- School of Biomedicine, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia,Precision Medicine Theme (Cancer), South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | | | - Matthew Snelson
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Caitlin Cowan
- School of Psychology and Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, Department of Anatomy and Neuroscience, and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Cassandra E. Gheorghe
- Department of Psychiatry and Neurobehavioural Science and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - John F. Cryan
- Department of Anatomy and Neuroscience and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Hannah R. Wardill
- School of Biomedicine, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia,Precision Medicine Theme (Cancer), South Australian Health and Medical Research Institute, Adelaide, SA, Australia
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12
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Harder CB, Persson S, Christensen J, Ljubic A, Nielsen EM, Hoorfar J. Molecular diagnostics of Salmonella and Campylobacter in human/animal fecal samples remain feasible after long-term sample storage without specific requirements. AIMS Microbiol 2022; 7:399-414. [PMID: 35071939 PMCID: PMC8712530 DOI: 10.3934/microbiol.2021024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/05/2021] [Indexed: 11/27/2022] Open
Abstract
Rapid advances in the development of sequencing technologies, numbers of commercial providers and diminishing costs have made DNA-based identification and diagnostics increasingly accessible to doctors and laboratories, eliminating the need for local investments in expensive technology and training or hiring of skilled technicians. However, reliable and comparable molecular analyses of bacteria in stool samples are dependent on storage and workflow conditions that do not introduce post-sampling bias, the most important factor being the need to keep the DNA at a stable detectable level. For that reason, there may remain other prohibitively costly requirements for cooling or freezing equipment or special chemical additives. This study investigates the diagnostic detectability of Salmonella and Campylobacter DNA in human, pig and chicken stool samples, stored at different temperatures and with different preservation methods. Stool samples were spiked with 106 CFU/mL of both Salmonella and Campylobacter strains stored at −20 °C, 5 °C and 20 °C (Room temperature, RT) and treated with either RNAlater, EDTA or Silica/ethanol. DNA was extracted at 9 different time points within 30 days and quantified by Qubit (total DNA) and qPCR (Salmonella and Campylobacter DNA). We found no statistically significant differences among the different preservation methods, and DNA from both species was easily detected at all time points and at all temperatures, both with and without preservation. This suggests that infections by these bacteria can be diagnosed and possibly also analysed in further detail simply by taking a stool sample in any suitable sealed container that can be transported to laboratory analysis without special storage or preservation requirements. We briefly discuss how this finding can benefit infection control in both developed and developing countries.
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Affiliation(s)
- C B Harder
- Statens Serum institut, Dept. Bacteriology, Parasitology and Fungi, Artillerivej 5, 2300 Copenhagen, Denmark.,Molecular Ecology, Microbial Ecology and Evolutionary Genetics, Lund University, Sölvegatan 37, 223 62 Lund
| | - S Persson
- Statens Serum institut, Dept. Bacteriology, Parasitology and Fungi, Artillerivej 5, 2300 Copenhagen, Denmark
| | - J Christensen
- Danish Veterinary and Food Administration, Microbiological department, Søndervang 4, 4100 Ringsted
| | - A Ljubic
- AGC Biologics, Process Transfer, Vandtårnsvej 83, 2860 Søborg, Denmark
| | - E M Nielsen
- Statens Serum institut, Dept. Bacteriology, Parasitology and Fungi, Artillerivej 5, 2300 Copenhagen, Denmark
| | - J Hoorfar
- Technical University of Denmark, National Food Institute, 2800 Kgs. Lyngby, Denmark
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13
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Bhattacharjee A, Dubey S, Sharma S. Storage of soil microbiome for application in sustainable agriculture: prospects and challenges. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3171-3183. [PMID: 34718953 DOI: 10.1007/s11356-021-17164-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Soil microbiome is a dynamic micro-ecosystem driving and fine-tuning several biological processes in the global macro-ecosystems. Its tremendous potential towards mediating sustainability in the ecosystem necessitates the urgent need to store it optimally and efficiently as "next-generation biologicals" for future applications via soil transplantation. The challenge, therefore, is to devise a strategy for the storage of soil microbiome such that its "functionality" is preserved for later application. This review discusses the current endeavours made towards storage of the soil microbiome. The methods for assessing the integrity of soil microbiome by targeting the structural diversity and functional potential of the preserved microbiomes have also been discussed. Further, the success stories related to the storage of fecal microbiome for application in transplants have also been highlighted. This is done primarily with the objective of learning lessons, and parallel application of the knowledge gained, in bringing about improvement in the research domain of soil microbiome storage. Subsequently, the limitations of current techniques of preservation have also been delineated. Further, the open questions in the area have been critically discussed. In conclusion, possible alternatives for storage, comprehensive analyses of the composition of the stored microbiome and their potential have been presented.
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Affiliation(s)
- Annapurna Bhattacharjee
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shubham Dubey
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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14
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Agarwal A, Maheshwari A, Verma S, Arrup D, Phillips L, Vinayek R, Nair P, Hagan M, Dutta S. Superiority of Higher-Volume Fresh Feces Compared to Lower-Volume Frozen Feces in Fecal Microbiota Transplantation for Recurrent Clostridioides Difficile Colitis. Dig Dis Sci 2021; 66:2000-2004. [PMID: 32656604 DOI: 10.1007/s10620-020-06459-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/28/2020] [Indexed: 01/26/2023]
Abstract
GOALS To compare the clinical outcomes of different protocols for fecal microbiota transplantation (FMT) in two community hospitals with similar patient demographics. BACKGROUND FMT is commonly performed for recurrent or refractory Clostridioides difficile infection (rCDI). The clinical efficacy of FMT for this indication has been well established. However, there has been no standardization or optimization of the amount of fecal material, method of feces preparation, or route of delivery for FMT. STUDY In this retrospective study, patients with rCDI received FMT using commercially available frozen fecal preparation (22.7 g) at Center A and locally prepared fresh fecal filtrate (30-50 g) at Center B. The primary outcome was defined as complete resolution of clinical symptoms related to rCDI after at least 8 weeks of follow-up. RESULTS Fifty patients from each center were included in the study. Clinical success after initial FMT with lower-volume frozen fecal preparation at Center A was 32/50 (64.0%) compared to 49/50 (98.0%) with higher-volume fresh fecal filtrate at Center B (p < 0.0001). Seventeen patients in Center A and 1 patient in Center B underwent at least one repeat FMT. Overall clinical success was achieved in 43/50 (86%) of patients in Center A and 50/50 (100%) in Center B (p = 0.012). CONCLUSIONS Our results suggest superior clinical efficacy of a larger amount of fresh fecal filtrate over a smaller amount of commercially available frozen fecal preparation. Further studies are needed to examine the effect of varying amounts of feces and the optimal protocol for FMT in patients with rCDI.
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Affiliation(s)
- Amol Agarwal
- Mercy Medical Center, 301 St Paul Pl, Physician's Office Building, 7th Floor, Baltimore, MD, 21202, USA
| | - Anurag Maheshwari
- Mercy Medical Center, 301 St Paul Pl, Physician's Office Building, 7th Floor, Baltimore, MD, 21202, USA.
| | | | | | | | | | | | - Matilda Hagan
- Mercy Medical Center, 301 St Paul Pl, Physician's Office Building, 7th Floor, Baltimore, MD, 21202, USA
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15
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Kazantseva J, Malv E, Kaleda A, Kallastu A, Meikas A. Optimisation of sample storage and DNA extraction for human gut microbiota studies. BMC Microbiol 2021; 21:158. [PMID: 34051731 PMCID: PMC8164492 DOI: 10.1186/s12866-021-02233-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023] Open
Abstract
Background New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important. Results Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution. Conclusions Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02233-y.
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Affiliation(s)
- Jekaterina Kazantseva
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia.
| | - Esther Malv
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
| | - Aleksei Kaleda
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
| | - Aili Kallastu
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
| | - Anne Meikas
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
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16
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Comparison of the Gut Microbiota of Jeju and Thoroughbred Horses in Korea. Vet Sci 2021; 8:vetsci8050081. [PMID: 34064714 PMCID: PMC8151153 DOI: 10.3390/vetsci8050081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/27/2022] Open
Abstract
(1) Background: The large intestine of horses is an anaerobic fermentative chamber filled with fibrolytic bacteria that play essential roles in digesting and absorbing nutrients for energy production. Although Jeju horses are a prominent local breed in Korea, few studies have investigated the gut microbiota of Jeju horses; (2) Methods: This study performed sequencing of V3 and V4 hypervariable regions of the partial 16S rRNA genes obtained from horse fecal samples and compared the gut microbiota between Jeju and Thoroughbred horses. Thirty and 24 fecal samples were obtained from Jeju and Thoroughbred horses, respectively; (3) Results: The gut microbiota belonged to 23 phyla and 159 families. Firmicutes and Bacteroidetes were the most abundant and predominant phyla, followed by Verrucomicrobia, Euryachaeota, and Spirochaete. The ratio of Firmicutes to Bacteroidetes (F/B), which is known as a relevant marker of gut dysbiosis, was 1.84 for Jeju horses, whereas it was 1.76 for Thoroughbred horses. Moreover, at the genus level, 21 genera were significantly different between the Jeju and Thoroughbred horses (p < 0.05); (4) Conclusions: The Thoroughbred horse's gut microbiotas had significantly higher diversity than the Jeju horses (p < 0.05). In addition, beneficial commensal bacteria that produce short-chain fatty acids thus providing a significant source of energy are also more abundant in Thoroughbred horses. These results provide novel information on the horse gut microbiota and insights for further studies related to the horse gut microbiota.
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17
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Pribyl AL, Parks DH, Angel NZ, Boyd JA, Hasson AG, Fang L, MacDonald SL, Wills BA, Wood DLA, Krause L, Tyson GW, Hugenholtz P. Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME COMMUNICATIONS 2021; 1:14. [PMID: 37938632 PMCID: PMC9645250 DOI: 10.1038/s43705-021-00014-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/14/2021] [Accepted: 04/06/2021] [Indexed: 05/04/2023]
Abstract
The ability to preserve microbial communities in faecal samples is essential as increasing numbers of studies seek to use the gut microbiome to identify biomarkers of disease. Here we use shotgun metagenomics to rigorously evaluate the technical and compositional reproducibility of five room temperature (RT) microbial stabilisation methods compared to the best practice of flash-freezing. These methods included RNALater, OMNIGene-GUT, a dry BBL swab, LifeGuard, and a novel method for preserving faecal samples, a Copan FLOQSwab in an active drying tube (FLOQSwab-ADT). Each method was assessed using six replicate faecal samples from five participants, totalling 180 samples. The FLOQSwab-ADT performed best for both technical and compositional reproducibility, followed by RNAlater and OMNIgene-GUT. LifeGuard and the BBL swab had unpredictable outgrowth of Escherichia species in at least one replicate from each participant. We further evaluated the FLOQSwab-ADT in an additional 239 samples across 10 individuals after storage at -20 °C, RT, and 50 °C for four weeks compared to fresh controls. The FLOQSwab-ADT maintained its performance across all temperatures, indicating this method is an excellent alternative to existing RT stabilisation methods.
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Affiliation(s)
| | | | | | - Joel A Boyd
- Microba Life Sciences, Brisbane, QLD, Australia
| | | | - Liang Fang
- Microba Life Sciences, Brisbane, QLD, Australia
| | | | | | | | - Lutz Krause
- Microba Life Sciences, Brisbane, QLD, Australia
| | - Gene W Tyson
- Microba Life Sciences, Brisbane, QLD, Australia
- Centre for Microbiome Research, School of Biomedical Science, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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18
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Miguela-Villoldo P, Moreno MA, Hernández M, Rodríguez-Lázaro D, Gallardo A, Borge C, Quesada A, Domínguez L, Ugarte-Ruiz M. Complementarity of Selective Culture and qPCR for Colistin Resistance Screening in Fresh and Frozen Pig Cecum Samples. Front Microbiol 2020; 11:572712. [PMID: 33240230 PMCID: PMC7680854 DOI: 10.3389/fmicb.2020.572712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/15/2020] [Indexed: 02/05/2023] Open
Abstract
Retrospective studies involving the screening of frozen stored collections of samples are commonplace when a new threat emerges, but it has been demonstrated that the freeze-thaw process can affect bacterial viability. The study of colistin-resistant bacteria in human and animal samples is an example of this issue. In this study, we compared culture-based and PCR-based methods for analyzing relative occurrence and diversity of colistin-resistant bacteria in caecal samples to determine the most appropriate method for frozen samples. Thus, 272 samples from the caecal contents of healthy pigs were tested before and after a 6-month freezing period. A selective medium was used when traditional isolation of colistin-resistant bacteria was tested, while a real-time SYBR® Green I PCR assay was applied for mcr-1 quantification. The number of samples with colistin-resistant isolates was higher in fresh samples (247/272) than in frozen ones (67/272) and showed a higher diversity of colistin-resistant genera. PCR identification of mcr colistin resistance genes evidenced that mcr-1 was the most prevalent mcr gene and mcr-2 was detected for the first time in pigs from Spanish animal production. The number of samples with mcr-1-carrying bacteria after a freezing period decreased, while real-time quantitation of the mcr-1 gene showed similar values in frozen and fresh samples. Therefore, when frozen cecal samples need to be analyzed, molecular detection of DNA could be the best option to provide a highly representative frame of the initial population present in the sample, and culture-based methods might be a useful complement to study colistin resistance levels.
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Affiliation(s)
- Pedro Miguela-Villoldo
- VISAVET Health Surveillance Centre, Universidad Complutense, Madrid, Spain.,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Miguel A Moreno
- VISAVET Health Surveillance Centre, Universidad Complutense, Madrid, Spain.,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Marta Hernández
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain
| | - David Rodríguez-Lázaro
- Área de Microbiología, Departamento de Biotecnología y Ciencia de los Alimentos, Facultad de Ciencias, Universidad de Burgos, Burgos, Spain
| | - Alejandro Gallardo
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Carmen Borge
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Alberto Quesada
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain.,INBIO G+C, Universidad de Extremadura, Cáceres, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Universidad Complutense, Madrid, Spain.,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Universidad Complutense, Madrid, Spain
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19
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Lai D, Hedlund BP, Xie W, Liu J, Phelps TJ, Zhang C, Wang P. Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments. Front Microbiol 2020; 11:572017. [PMID: 33224115 PMCID: PMC7674655 DOI: 10.3389/fmicb.2020.572017] [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: 06/12/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Archaea are widespread in marine sediments and play important roles in the cycling of sedimentary organic carbon. However, factors controlling the distribution of archaea in marine sediments are not well understood. Here we investigated benthic archaeal communities over glacial-interglacial cycles in the northern South China Sea and evaluated their responses to sediment organic matter sources and inter-species interactions. Archaea in sediments deposited during the interglacial period Marine Isotope Stage (MIS) 1 (Holocene) were significantly different from those in sediments deposited in MIS 2 and MIS 3 of the Last Glacial Period when terrestrial input to the South China Sea was enhanced based on analysis of the long-chain n-alkane C31. The absolute archaeal 16S rRNA gene abundance in subsurface sediments was highest in MIS 2, coincident with high sedimentation rates and high concentrations of total organic carbon. Soil Crenarchaeotic Group (SCG; Nitrososphaerales) species, the most abundant ammonia-oxidizing archaea in soils, increased dramatically during MIS 2, likely reflecting transport of terrestrial archaea during glacial periods with high sedimentation rates. Co-occurrence network analyses indicated significant association of SCG archaea with benthic deep-sea microbes such as Bathyarchaeota and Thermoprofundales in MIS 2 and MIS 3, suggesting potential interactions among these archaeal groups. Meanwhile, Thermoprofundales abundance was positively correlated with total organic carbon (TOC), along with n-alkane C31 and sedimentation rate, indicating that Thermoprofundales may be particularly important in processing of organic carbon in deep-sea sediments. Collectively, these results demonstrate that the composition of heterotrophic benthic archaea in the South China Sea may be influenced by terrestrial organic input in tune with glacial-interglacial cycles, suggesting a plausible link between global climate change and microbial population dynamics in deep-sea marine sediments.
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Affiliation(s)
- Dengxun Lai
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China.,School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jingjing Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Tommy J Phelps
- Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Peng Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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20
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Santiago-Rodriguez TM, Hollister EB. Potential Applications of Human Viral Metagenomics and Reference Materials: Considerations for Current and Future Viruses. Appl Environ Microbiol 2020; 86:e01794-20. [PMID: 32917759 PMCID: PMC7642086 DOI: 10.1128/aem.01794-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Viruses are ubiquitous particles comprising genetic material that can infect bacteria, archaea, and fungi, as well as human and other animal cells. Given that determining virus composition and function in association with states of human health and disease is of increasing interest, we anticipate that the field of viral metagenomics will continue to expand and be applied in a variety of areas ranging from surveillance to discovery and will rely heavily upon the continued development of reference materials and databases. Information regarding viral composition and function readily translates into biological and clinical applications, including the rapid sequence identification of pathogenic viruses in various sample types. However, viral metagenomic approaches often lack appropriate standards and reference materials to enable cross-study comparisons and assess potential biases which can be introduced at the various stages of collection, storage, processing, and sequence analysis. In addition, implementation of appropriate viral reference materials can aid in the benchmarking of current and development of novel assays for virus identification, discovery, and surveillance. As the field of viral metagenomics expands and standardizes, results will continue to translate into diverse applications.
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Deschamps C, Fournier E, Uriot O, Lajoie F, Verdier C, Comtet-Marre S, Thomas M, Kapel N, Cherbuy C, Alric M, Almeida M, Etienne-Mesmin L, Blanquet-Diot S. Comparative methods for fecal sample storage to preserve gut microbial structure and function in an in vitro model of the human colon. Appl Microbiol Biotechnol 2020; 104:10233-10247. [PMID: 33085024 DOI: 10.1007/s00253-020-10959-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/28/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022]
Abstract
In vitro gut models, such as the mucosal artificial colon (M-ARCOL), provide timely and cost-efficient alternatives to in vivo assays allowing mechanistic studies to better understand the role of human microbiome in health and disease. Using such models inoculated with human fecal samples may require a critical step of stool storage. The effects of preservation methods on microbial structure and function in in vitro gut models have been poorly investigated. This study aimed to assess the impact of three commonly used preserving methods, compared with fresh fecal samples used as a control, on the kinetics of lumen and mucus-associated microbiota colonization in the M-ARCOL model. Feces from two healthy donors were frozen 48 h at - 80 °C with or without cryoprotectant (10% glycerol) or lyophilized with maltodextrin and trehalose prior to inoculation of four parallel bioreactors (e.g., fresh stool, raw stool stored at - 80 °C, stool stored at - 80 °C with glycerol and lyophilized stool). Microbiota composition and diversity (qPCR and 16S metabarcoding) as well as metabolic activity (gases and short chain fatty acids) were monitored throughout the fermentation process (9 days). All the preservative treatments allowed the maintaining inside the M-ARCOL of a complex and functional microbiota, but considering stabilization time of microbial profiles and activities (and not technical constraints associated with the supply of frozen material), our results highlighted 48 h freezing at - 80 °C without cryoprotectant as the most efficient method. These results will help scientists to determine the most accurate method for fecal storage prior to inoculation of in vitro gut microbiome models. KEY POINTS: • In vitro ARCOL model reproduces luminal and mucosal human microbiome. • Short-term storage of fecal sample influences microbial stabilization and activity. • 48 h freezing at - 80°C: most efficient method to preserve microbial ecosystem. • Scientific and technical requirements: influencers of preservation method.
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Affiliation(s)
- Charlotte Deschamps
- Université Clermont Auvergne, INRAe, UMR 454 MEDIS, 28 place Henri Dunant, F-63000, Clermont-Ferrand, France
| | - Elora Fournier
- Université Clermont Auvergne, INRAe, UMR 454 MEDIS, 28 place Henri Dunant, F-63000, Clermont-Ferrand, France
| | - Ophélie Uriot
- Université Clermont Auvergne, INRAe, UMR 454 MEDIS, 28 place Henri Dunant, F-63000, Clermont-Ferrand, France
| | - Frédérique Lajoie
- Département de Pharmacologie et Physiologie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Cécile Verdier
- Université Clermont Auvergne, INRAe, UMR 454 MEDIS, 28 place Henri Dunant, F-63000, Clermont-Ferrand, France
| | - Sophie Comtet-Marre
- Université Clermont Auvergne, INRAe, UMR 454 MEDIS, 28 place Henri Dunant, F-63000, Clermont-Ferrand, France
| | - Muriel Thomas
- Micalis Institute, INRAe, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Nathalie Kapel
- Laboratoire de Coprologie Fonctionnelle, Hôpital Pitié-Salpêtrière, 75013, Paris, France.,INSERM UMR-S1139, Université de Paris, 75006, Paris, France
| | - Claire Cherbuy
- Micalis Institute, INRAe, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Monique Alric
- Université Clermont Auvergne, INRAe, UMR 454 MEDIS, 28 place Henri Dunant, F-63000, Clermont-Ferrand, France
| | - Mathieu Almeida
- MetaGénoPolis, INRAe, Université Paris-Saclay, Jouy-en-Josas, France
| | - Lucie Etienne-Mesmin
- Université Clermont Auvergne, INRAe, UMR 454 MEDIS, 28 place Henri Dunant, F-63000, Clermont-Ferrand, France
| | - Stéphanie Blanquet-Diot
- Université Clermont Auvergne, INRAe, UMR 454 MEDIS, 28 place Henri Dunant, F-63000, Clermont-Ferrand, France.
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