1
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Kiu R, Shaw AG, Sim K, Acuna-Gonzalez A, Price CA, Bedwell H, Dreger SA, Fowler WJ, Cornwell E, Pickard D, Belteki G, Malsom J, Phillips S, Young GR, Schofield Z, Alcon-Giner C, Berrington JE, Stewart CJ, Dougan G, Clarke P, Douce G, Robinson SD, Kroll JS, Hall LJ. Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains. Nat Microbiol 2023; 8:1160-1175. [PMID: 37231089 PMCID: PMC10234813 DOI: 10.1038/s41564-023-01385-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/17/2023] [Indexed: 05/27/2023]
Abstract
Clostridium perfringens is an anaerobic toxin-producing bacterium associated with intestinal diseases, particularly in neonatal humans and animals. Infant gut microbiome studies have recently indicated a link between C. perfringens and the preterm infant disease necrotizing enterocolitis (NEC), with specific NEC cases associated with overabundant C. perfringens termed C. perfringens-associated NEC (CPA-NEC). In the present study, we carried out whole-genome sequencing of 272 C. perfringens isolates from 70 infants across 5 hospitals in the United Kingdom. In this retrospective analysis, we performed in-depth genomic analyses (virulence profiling, strain tracking and plasmid analysis) and experimentally characterized pathogenic traits of 31 strains, including 4 from CPA-NEC patients. We found that the gene encoding toxin perfringolysin O, pfoA, was largely deficient in a human-derived hypovirulent lineage, as well as certain colonization factors, in contrast to typical pfoA-encoding virulent lineages. We determined that infant-associated pfoA+ strains caused significantly more cellular damage than pfoA- strains in vitro, and further confirmed this virulence trait in vivo using an oral-challenge C57BL/6 murine model. These findings suggest both the importance of pfoA+ C. perfringens as a gut pathogen in preterm infants and areas for further investigation, including potential intervention and therapeutic strategies.
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Affiliation(s)
- Raymond Kiu
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | | | - Kathleen Sim
- Faculty of Medicine, Imperial College London, London, UK
| | | | | | - Harley Bedwell
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Sally A Dreger
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Wesley J Fowler
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Emma Cornwell
- Faculty of Medicine, Imperial College London, London, UK
| | - Derek Pickard
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gusztav Belteki
- Neonatal Intensive Care Unit, The Rosie Hospital, Cambridge, UK
| | - Jennifer Malsom
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Sarah Phillips
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Gregory R Young
- Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne, UK
| | - Zoe Schofield
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | | | - Janet E Berrington
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Neonatal Services, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Neonatal Services, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Paul Clarke
- Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Gillian Douce
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Stephen D Robinson
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - J Simon Kroll
- Faculty of Medicine, Imperial College London, London, UK
| | - Lindsay J Hall
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK.
- Norwich Medical School, University of East Anglia, Norwich, UK.
- Intestinal Microbiome, School of Life Sciences, ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany.
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2
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McKee AM, Kirkup BM, Madgwick M, Fowler WJ, Price CA, Dreger SA, Ansorge R, Makin KA, Caim S, Le Gall G, Paveley J, Leclaire C, Dalby M, Alcon-Giner C, Andrusaite A, Feng TY, Di Modica M, Triulzi T, Tagliabue E, Milling SW, Weilbaecher KN, Rutkowski MR, Korcsmáros T, Hall LJ, Robinson SD. Antibiotic-induced disturbances of the gut microbiota result in accelerated breast tumor growth. iScience 2021; 24:103012. [PMID: 34522855 PMCID: PMC8426205 DOI: 10.1016/j.isci.2021.103012] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 04/29/2021] [Accepted: 08/17/2021] [Indexed: 02/08/2023] Open
Abstract
The gut microbiota's function in regulating health has seen it linked to disease progression in several cancers. However, there is limited research detailing its influence in breast cancer (BrCa). This study found that antibiotic-induced perturbation of the gut microbiota significantly increases tumor progression in multiple BrCa mouse models. Metagenomics highlights the common loss of several bacterial species following antibiotic administration. One such bacteria, Faecalibaculum rodentium, rescued this increased tumor growth. Single-cell transcriptomics identified an increased number of cells with a stromal signature in tumors, and subsequent histology revealed an increased abundance of mast cells in the tumor stromal regions. We show that administration of a mast cell stabilizer, cromolyn, rescues increased tumor growth in antibiotic treated animals but has no influence on tumors from control cohorts. These findings highlight that BrCa-microbiota interactions are different from other cancers studied to date and suggest new research avenues for therapy development.
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Affiliation(s)
- Alastair M. McKee
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
| | - Benjamin M. Kirkup
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
| | - Matthew Madgwick
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Wesley J. Fowler
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
| | - Christopher A. Price
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
| | - Sally A. Dreger
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
| | - Rebecca Ansorge
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
| | - Kate A. Makin
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Shabhonam Caim
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
| | - Gwenaelle Le Gall
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Jack Paveley
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
| | - Charlotte Leclaire
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
| | - Matthew Dalby
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
| | - Cristina Alcon-Giner
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
| | - Anna Andrusaite
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Tzu-Yu Feng
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Martina Di Modica
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Instituto Nazionale di Tumori, Milan, 20133, Italy
| | - Tiziana Triulzi
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Instituto Nazionale di Tumori, Milan, 20133, Italy
| | - Elda Tagliabue
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Instituto Nazionale di Tumori, Milan, 20133, Italy
| | - Simon W.F. Milling
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Katherine N. Weilbaecher
- Department of Internal Medicine, Division of Molecular Oncology, Washington University in St Louis, St. Louis, MO, 63110, USA
| | - Melanie R. Rutkowski
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Tamás Korcsmáros
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Lindsay J. Hall
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
- Chair of Intestinal Microbiome, School of Life Sciences, ZIEL – Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Stephen D. Robinson
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7AU, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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3
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Alcon-Giner C, Dalby MJ, Caim S, Ketskemety J, Shaw A, Sim K, Lawson MA, Kiu R, Leclaire C, Chalklen L, Kujawska M, Mitra S, Fardus-Reid F, Belteki G, McColl K, Swann JR, Kroll JS, Clarke P, Hall LJ. Microbiota Supplementation with Bifidobacterium and Lactobacillus Modifies the Preterm Infant Gut Microbiota and Metabolome: An Observational Study. Cell Rep Med 2020; 1:100077. [PMID: 32904427 PMCID: PMC7453906 DOI: 10.1016/j.xcrm.2020.100077] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 04/28/2020] [Accepted: 07/31/2020] [Indexed: 12/11/2022]
Abstract
Supplementation with members of the early-life microbiota as “probiotics” is increasingly used in attempts to beneficially manipulate the preterm infant gut microbiota. We performed a large observational longitudinal study comprising two preterm groups: 101 infants orally supplemented with Bifidobacterium and Lactobacillus (Bif/Lacto) and 133 infants non-supplemented (control) matched by age, sex, and delivery method. 16S rRNA gene profiling on fecal samples (n = 592) showed a predominance of Bifidobacterium and a lower abundance of pathobionts in the Bif/Lacto group. Metabolomic analysis showed higher fecal acetate and lactate and a lower fecal pH in the Bif/Lacto group compared to the control group. Fecal acetate positively correlated with relative abundance of Bifidobacterium, consistent with the ability of the supplemented Bifidobacterium strain to metabolize human milk oligosaccharides into acetate. This study demonstrates that microbiota supplementation is associated with a Bifidobacterium-dominated preterm microbiota and gastrointestinal environment more closely resembling that of full-term infants. Bifidobacterium dominates the gut microbiota in supplemented preterm infants Supplemented preterm infants have lower abundance of potential pathobionts Metabolomic analysis show higher fecal acetate and lower pH in supplemented infants In vitro and genomic analysis confirm HMO metabolism in Bifidobacterium supplement
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Affiliation(s)
- Cristina Alcon-Giner
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Matthew J. Dalby
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Shabhonam Caim
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Jennifer Ketskemety
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Alex Shaw
- Department of Medicine, Section of Pediatrics, Imperial College London, London, UK
| | - Kathleen Sim
- Department of Medicine, Section of Pediatrics, Imperial College London, London, UK
| | - Melissa A.E. Lawson
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Raymond Kiu
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Charlotte Leclaire
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Lisa Chalklen
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Magdalena Kujawska
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Suparna Mitra
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Fahmina Fardus-Reid
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Gustav Belteki
- Neonatal Intensive Care Unit, The Rosie Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Katherine McColl
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospital, Norwich, UK
| | - Jonathan R. Swann
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - J. Simon Kroll
- Department of Medicine, Section of Pediatrics, Imperial College London, London, UK
| | - Paul Clarke
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Lindsay J. Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Chair of Intestinal Microbiome, School of Life Sciences, Technical University of Munich, Freising, Germany
- ZIEL – Institute for Food & Health, Technical University of Munich, Freising, Germany
- Corresponding author
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4
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Chen Y, Brook TC, Soe CZ, O'Neill I, Alcon-Giner C, Leelastwattanagul O, Phillips S, Caim S, Clarke P, Hall LJ, Hoyles L. Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors. Microb Genom 2020; 6:e000377. [PMID: 32436839 PMCID: PMC7371107 DOI: 10.1099/mgen.0.000377] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/26/2020] [Indexed: 01/08/2023] Open
Abstract
Klebsiella spp. are frequently enriched in the gut microbiota of preterm neonates, and overgrowth is associated with necrotizing enterocolitis (NEC), nosocomial infections and late-onset sepsis. Little is known about the genomic and phenotypic characteristics of preterm-associated Klebsiella, as previous studies have focused on the recovery of antimicrobial-resistant isolates or culture-independent molecular analyses. The aim of this study was to better characterize preterm-associated Klebsiella populations using phenotypic and genotypic approaches. Faecal samples from a UK cohort of healthy and sick preterm neonates (n=109) were screened on MacConkey agar to isolate lactose-positive Enterobacteriaceae. Whole-genome sequences were generated for Klebsiella spp., and virulence and antimicrobial resistance genes identified. Antibiotic susceptibility profiling and in vitro macrophage and iron assays were undertaken for the Klebsiella strains. Metapangenome analyses with a manually curated genome dataset were undertaken to examine the diversity of Klebsiella oxytoca and related bacteria in a publicly available shotgun metagenome dataset. Approximately one-tenth of faecal samples harboured Klebsiella spp. (Klebsiella pneumoniae, 7.3 %; Klebsiella quasipneumoniae, 0.9 %; Klebsiella grimontii, 2.8 %; Klebsiella michiganensis, 1.8 %). Isolates recovered from NEC- and sepsis-affected infants and those showing no signs of clinical infection (i.e. 'healthy') encoded multiple β-lactamases. No difference was observed between isolates recovered from healthy and sick infants with respect to in vitro siderophore production (all encoded enterobactin in their genomes). All K. pneumoniae, K. quasipneumoniae, K. grimontii and K. michiganensis faecal isolates tested were able to reside and persist in macrophages, indicating their immune evasion abilities. Metapangenome analyses of published metagenomic data confirmed our findings regarding the presence of K. michiganensis in the preterm gut. There is little difference in the phenotypic and genomic characteristics of Klebsiella isolates recovered from healthy and sick infants. Identification of β-lactamases in all isolates may prove problematic when defining treatment regimens for NEC or sepsis, and suggests that healthy preterm infants contribute to the resistome. Refined analyses with curated sequence databases are required when studying closely related species present in metagenomic data.
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Affiliation(s)
- Yuhao Chen
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Thomas C. Brook
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Cho Zin Soe
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Ian O'Neill
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Cristina Alcon-Giner
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Onnicha Leelastwattanagul
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian Campus), Bangkok, Thailand
| | - Sarah Phillips
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Shabhonam Caim
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Paul Clarke
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Lindsay J. Hall
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Lesley Hoyles
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
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5
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Hughes KR, Schofield Z, Dalby MJ, Caim S, Chalklen L, Bernuzzi F, Alcon-Giner C, Le Gall G, Watson AJM, Hall LJ. The early life microbiota protects neonatal mice from pathological small intestinal epithelial cell shedding. FASEB J 2020; 34:7075-7088. [PMID: 32253791 PMCID: PMC7610993 DOI: 10.1096/fj.202000042r] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/16/2022]
Abstract
The early life gut microbiota plays a crucial role in regulating and maintaining the intestinal barrier, with disturbances in these communities linked to dysregulated renewal and replenishment of intestinal epithelial cells. Here we sought to determine pathological cell shedding outcomes throughout the postnatal developmental period, and which host and microbial factors mediate these responses. Surprisingly, neonatal mice (Day 14 and 21) were highly refractory to induction of cell shedding after intraperitoneal administration of liposaccharide (LPS), with Day 29 mice showing strong pathological responses, more similar to those observed in adult mice. These differential responses were not linked to defects in the cellular mechanisms and pathways known to regulate cell shedding responses. When we profiled microbiota and metabolites, we observed significant alterations. Neonatal mice had high relative abundances of Streptococcus, Escherichia, and Enterococcus and increased primary bile acids. In contrast, older mice were dominated by Candidatus Arthromitus, Alistipes, and Lachnoclostridium, and had increased concentrations of SCFAs and methyamines. Antibiotic treatment of neonates restored LPS-induced small intestinal cell shedding, whereas adult fecal microbiota transplant alone had no effect. Our findings further support the importance of the early life window for microbiota-epithelial interactions in the presence of inflammatory stimuli and highlights areas for further investigation.
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Affiliation(s)
- Kevin R Hughes
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich, UK.,Norwich Medical School, University of East Anglia, Norwich, UK
| | - Zoe Schofield
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich, UK
| | - Matthew J Dalby
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich, UK
| | - Shabhonam Caim
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich, UK
| | - Lisa Chalklen
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich, UK
| | | | | | - Gwénaëlle Le Gall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich, UK.,Norwich Medical School, University of East Anglia, Norwich, UK
| | | | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich, UK.,Norwich Medical School, University of East Anglia, Norwich, UK
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6
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Leggett RM, Alcon-Giner C, Heavens D, Caim S, Brook TC, Kujawska M, Martin S, Peel N, Acford-Palmer H, Hoyles L, Clarke P, Hall LJ, Clark MD. Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens. Nat Microbiol 2020; 5:430-442. [PMID: 31844297 PMCID: PMC7044117 DOI: 10.1038/s41564-019-0626-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/01/2019] [Indexed: 12/29/2022]
Abstract
The MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used the MinION platform coupled to the NanoOK RT software package to perform shotgun metagenomic sequencing and profile mock communities and faecal samples from healthy and ill preterm infants. Using Nanopore data, we reliably classified a 20-species mock community and captured the diversity of the immature gut microbiota over time and in response to interventions such as probiotic supplementation, antibiotic treatment or episodes of suspected sepsis. We also performed rapid real-time runs to assess gut-associated microbial communities in critically ill and healthy infants, facilitated by NanoOK RT software package, which analysed sequences as they were generated. Our pipeline reliably identified pathogenic bacteria (that is, Klebsiella pneumoniae and Enterobacter cloacae) and their corresponding antimicrobial resistance gene profiles within as little as 1 h of sequencing. Results were confirmed using pathogen isolation, whole-genome sequencing and antibiotic susceptibility testing, as well as mock communities and clinical samples with known antimicrobial resistance genes. Our results demonstrate that MinION (including cost-effective Flongle flow cells) with NanoOK RT can process metagenomic samples to a rich dataset in < 5 h, which creates a platform for future studies aimed at developing these tools and approaches in clinical settings with a focus on providing tailored patient antimicrobial treatment options.
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Affiliation(s)
| | | | | | - Shabhonam Caim
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | | | - Samuel Martin
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Ned Peel
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | | | - Paul Clarke
- Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Lindsay J Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
| | - Matthew D Clark
- Earlham Institute, Norwich Research Park, Norwich, UK.
- Natural History Museum, London, UK.
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7
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Scott NA, Andrusaite A, Andersen P, Lawson M, Alcon-Giner C, Leclaire C, Caim S, Le Gall G, Shaw T, Connolly JPR, Roe AJ, Wessel H, Bravo-Blas A, Thomson CA, Kästele V, Wang P, Peterson DA, Bancroft A, Li X, Grencis R, Mowat AM, Hall LJ, Travis MA, Milling SWF, Mann ER. Antibiotics induce sustained dysregulation of intestinal T cell immunity by perturbing macrophage homeostasis. Sci Transl Med 2019; 10:10/464/eaao4755. [PMID: 30355800 DOI: 10.1126/scitranslmed.aao4755] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 06/19/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022]
Abstract
Macrophages in the healthy intestine are highly specialized and usually respond to the gut microbiota without provoking an inflammatory response. A breakdown in this tolerance leads to inflammatory bowel disease (IBD), but the mechanisms by which intestinal macrophages normally become conditioned to promote microbial tolerance are unclear. Strong epidemiological evidence linking disruption of the gut microbiota by antibiotic use early in life to IBD indicates an important role for the gut microbiota in modulating intestinal immunity. Here, we show that antibiotic use causes intestinal macrophages to become hyperresponsive to bacterial stimulation, producing excess inflammatory cytokines. Re-exposure of antibiotic-treated mice to conventional microbiota induced a long-term, macrophage-dependent increase in inflammatory T helper 1 (TH1) responses in the colon and sustained dysbiosis. The consequences of this dysregulated macrophage activity for T cell function were demonstrated by increased susceptibility to infections requiring TH17 and TH2 responses for clearance (bacterial Citrobacter rodentium and helminth Trichuris muris infections), corresponding with increased inflammation. Short-chain fatty acids (SCFAs) were depleted during antibiotic administration; supplementation of antibiotics with the SCFA butyrate restored the characteristic hyporesponsiveness of intestinal macrophages and prevented T cell dysfunction. Butyrate altered the metabolic behavior of macrophages to increase oxidative phosphorylation and also promoted alternative macrophage activation. In summary, the gut microbiota is essential to maintain macrophage-dependent intestinal immune homeostasis, mediated by SCFA-dependent pathways. Oral antibiotics disrupt this process to promote sustained T cell-mediated dysfunction and increased susceptibility to infections, highlighting important implications of repeated broad-spectrum antibiotic use.
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Affiliation(s)
- Nicholas A Scott
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PT, UK.,Manchester Collaborative Centre for Inflammation Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Anna Andrusaite
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Peter Andersen
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Melissa Lawson
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UA, UK
| | | | - Charlotte Leclaire
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UA, UK
| | - Shabhonam Caim
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UA, UK
| | - Gwenaelle Le Gall
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UA, UK
| | - Tovah Shaw
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PT, UK.,Manchester Collaborative Centre for Inflammation Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - James P R Connolly
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Andrew J Roe
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Hannah Wessel
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Alberto Bravo-Blas
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Carolyn A Thomson
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Verena Kästele
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Ping Wang
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PT, UK
| | - Daniel A Peterson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Eli Lilly and Company, Indianapolis, 46285 IN, USA
| | - Allison Bancroft
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PT, UK.,Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Xuhang Li
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Richard Grencis
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PT, UK.,Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Allan McI Mowat
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Lindsay J Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UA, UK
| | - Mark A Travis
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PT, UK.,Manchester Collaborative Centre for Inflammation Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK.,Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, UK
| | - Simon W F Milling
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Elizabeth R Mann
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester M13 9PT, UK. .,Manchester Collaborative Centre for Inflammation Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK.,Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
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8
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Chen Y, Brook TC, Alcon-Giner C, Clarke P, Hall LJ, Hoyles L. Draft Genome Sequences of Citrobacter freundii and Citrobacter murliniae Strains Isolated from the Feces of Preterm Infants. Microbiol Resour Announc 2019; 8:e00494-19. [PMID: 31416863 PMCID: PMC6696638 DOI: 10.1128/mra.00494-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/22/2019] [Indexed: 01/08/2023] Open
Abstract
Here, we describe the draft genome sequences of three strains of Citrobacter isolated from feces of preterm neonates with suspected sepsis. Strains P106E PI and P079F I were Citrobacter freundii Strain P080C CL represents the first draft genome sequence of Citrobacter murliniae.
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Affiliation(s)
- Yuhao Chen
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Thomas C Brook
- Department of Biomedical Sciences, University of Westminster, London, United Kingdom
| | - Cristina Alcon-Giner
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Paul Clarke
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospital, Norwich, United Kingdom
| | - Lindsay J Hall
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom
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9
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Rowe WPM, Carrieri AP, Alcon-Giner C, Caim S, Shaw A, Sim K, Kroll JS, Hall LJ, Pyzer-Knapp EO, Winn MD. Streaming histogram sketching for rapid microbiome analytics. Microbiome 2019; 7:40. [PMID: 30878035 PMCID: PMC6420756 DOI: 10.1186/s40168-019-0653-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/01/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research, allowing for the design of new studies, augmentation of novel datasets and reanalysis of published works. This vast amount of microbiome data, as well as the widespread proliferation of microbiome research and the looming era of clinical metagenomics, means there is an urgent need to develop analytics that can process huge amounts of data in a short amount of time. To address this need, we propose a new method for tyrhe compact representation of microbiome sequencing data using similarity-preserving sketches of streaming k-mer spectra. These sketches allow for dissimilarity estimation, rapid microbiome catalogue searching and classification of microbiome samples in near real time. RESULTS We apply streaming histogram sketching to microbiome samples as a form of dimensionality reduction, creating a compressed 'histosketch' that can efficiently represent microbiome k-mer spectra. Using public microbiome datasets, we show that histosketches can be clustered by sample type using the pairwise Jaccard similarity estimation, consequently allowing for rapid microbiome similarity searches via a locality sensitive hashing indexing scheme. Furthermore, we use a 'real life' example to show that histosketches can train machine learning classifiers to accurately label microbiome samples. Specifically, using a collection of 108 novel microbiome samples from a cohort of premature neonates, we trained and tested a random forest classifier that could accurately predict whether the neonate had received antibiotic treatment (97% accuracy, 96% precision) and could subsequently be used to classify microbiome data streams in less than 3 s. CONCLUSIONS Our method offers a new approach to rapidly process microbiome data streams, allowing samples to be rapidly clustered, indexed and classified. We also provide our implementation, Histosketching Using Little K-mers (HULK), which can histosketch a typical 2 GB microbiome in 50 s on a standard laptop using four cores, with the sketch occupying 3000 bytes of disk space. ( https://github.com/will-rowe/hulk ).
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Affiliation(s)
- Will PM Rowe
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington, UK
| | | | | | - Shabhonam Caim
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Alex Shaw
- Department of Medicine, Section of Paediatrics, Imperial College London, London, UK
| | - Kathleen Sim
- Department of Medicine, Section of Paediatrics, Imperial College London, London, UK
| | - J. Simon Kroll
- Department of Medicine, Section of Paediatrics, Imperial College London, London, UK
| | - Lindsay J. Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Martyn D. Winn
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington, UK
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10
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Kiu R, Caim S, Alcon-Giner C, Belteki G, Clarke P, Pickard D, Dougan G, Hall LJ. Preterm Infant-Associated Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum Strains: Genomic and Evolutionary Insights. Genome Biol Evol 2018; 9:2707-2714. [PMID: 29044436 PMCID: PMC5647805 DOI: 10.1093/gbe/evx210] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2017] [Indexed: 01/14/2023] Open
Abstract
Clostridium species (particularly Clostridium difficile, Clostridium botulinum, Clostridium tetani and Clostridium perfringens) are associated with a range of human and animal diseases. Several other species including Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum have also been linked with sporadic human infections, however there is very limited, or in some cases, no genomic information publicly available. Thus, we isolated one C. tertium strain, one C. cadaveris strain and three C. paraputrificum strains from preterm infants residing within neonatal intensive care units and performed Whole Genome Sequencing (WGS) using Illumina HiSeq. In this report, we announce the open availability of the draft genomes: C. tertium LH009, C. cadaveris LH052, C. paraputrificum LH025, C. paraputrificum LH058, and C. paraputrificum LH141. These genomes were checked for contamination in silico to ensure purity, and we confirmed species identity and phylogeny using both 16S rRNA gene sequences (from PCR and in silico) and WGS-based approaches. Average Nucleotide Identity (ANI) was used to differentiate genomes from their closest relatives to further confirm speciation boundaries. We also analysed the genomes for virulence-related factors and antimicrobial resistance genes, and detected presence of tetracycline and methicillin resistance, and potentially harmful enzymes, including multiple phospholipases and toxins. The availability of genomic data in open databases, in tandem with our initial insights into the genomic content and virulence traits of these pathogenic Clostridium species, should enable the scientific community to further investigate the disease-causing mechanisms of these bacteria with a view to enhancing clinical diagnosis and treatment.
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Affiliation(s)
- Raymond Kiu
- The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom.,Norwich Medical School, Norwich Research Park, University of East Anglia, Norwich, United Kingdom
| | - Shabhonam Caim
- The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Cristina Alcon-Giner
- The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Gusztav Belteki
- Neonatal Intensive Care Unit, The Rosie Hospital, Cambridge University Hospitals NHS Foundation Trust, United Kingdom
| | - Paul Clarke
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, United Kingdom
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Lindsay J Hall
- The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
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11
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Hughes KR, Harnisch LC, Alcon-Giner C, Mitra S, Wright CJ, Ketskemety J, van Sinderen D, Watson AJM, Hall LJ. Bifidobacterium breve reduces apoptotic epithelial cell shedding in an exopolysaccharide and MyD88-dependent manner. Open Biol 2017; 7:rsob.160155. [PMID: 28123052 PMCID: PMC5303268 DOI: 10.1098/rsob.160155] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 12/15/2016] [Indexed: 12/14/2022] Open
Abstract
Certain members of the microbiota genus Bifidobacterium are known to positively influence host well-being. Importantly, reduced bifidobacterial levels are associated with inflammatory bowel disease (IBD) patients, who also have impaired epithelial barrier function, including elevated rates of apoptotic extrusion of small intestinal epithelial cells (IECs) from villi—a process termed ‘cell shedding’. Using a mouse model of pathological cell shedding, we show that mice receiving Bifidobacterium breve UCC2003 exhibit significantly reduced rates of small IEC shedding. Bifidobacterial-induced protection appears to be mediated by a specific bifidobacterial surface exopolysaccharide and interactions with host MyD88 resulting in downregulation of intrinsic and extrinsic apoptotic responses to protect epithelial cells under highly inflammatory conditions. Our results reveal an important and previously undescribed role for B. breve, in positively modulating epithelial cell shedding outcomes via bacterial- and host-dependent factors, supporting the notion that manipulation of the microbiota affects intestinal disease outcomes.
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Affiliation(s)
- K R Hughes
- The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK .,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7UQ, UK
| | - L C Harnisch
- The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7UQ, UK
| | - C Alcon-Giner
- The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - S Mitra
- The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - C J Wright
- The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7UQ, UK
| | - J Ketskemety
- The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - D van Sinderen
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - A J M Watson
- The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK .,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7UQ, UK
| | - L J Hall
- The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
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12
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Alcon-Giner C, Caim S, Mitra S, Ketskemety J, Wegmann U, Wain J, Belteki G, Clarke P, Hall LJ. Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants. BMC Genomics 2017; 18:841. [PMID: 29096601 PMCID: PMC5668952 DOI: 10.1186/s12864-017-4229-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/20/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Infants born prematurely, particularly extremely low birth weight infants (ELBW) have altered gut microbial communities. Factors such as maternal health, gut immaturity, delivery mode, and antibiotic treatments are associated with microbiota disturbances, and are linked to an increased risk of certain diseases such as necrotising enterocolitis. Therefore, there is a requirement to optimally characterise microbial profiles in this at-risk cohort, via standardisation of methods, particularly for studying the influence of microbiota therapies (e.g. probiotic supplementation) on community profiles and health outcomes. Profiling of faecal samples using the 16S rRNA gene is a cost-efficient method for large-scale clinical studies to gain insights into the gut microbiota and additionally allows characterisation of cohorts were sample quantities are compromised (e.g. ELBW infants). However, DNA extraction method, and the 16S rRNA region targeted can significantly change bacterial community profiles obtained, and so confound comparisons between studies. Thus, we sought to optimise a 16S rRNA profiling protocol to allow standardisation for studying ELBW infant faecal samples, with or without probiotic supplementation. METHODS Using ELBW faecal samples, we compared three different DNA extraction methods, and subsequently PCR amplified and sequenced three hypervariable regions of the 16S rRNA gene (V1 + V2 + V3), (V4 + V5) and (V6 + V7 + V8), and compared two bioinformatics approaches to analyse results (OTU and paired end). Paired shotgun metagenomics was used as a 'gold-standard'. RESULTS Results indicated a longer bead-beating step was required for optimal bacterial DNA extraction and that sequencing regions (V1 + V2 + V3) and (V6 + V7 + V8) provided the most representative taxonomic profiles, which was confirmed via shotgun analysis. Samples sequenced using the (V4 + V5) region were found to be underrepresented in specific taxa including Bifidobacterium, and had altered diversity profiles. Both bioinformatics 16S rRNA pipelines used in this study (OTU and paired end) presented similar taxonomic profiles at genus level. CONCLUSIONS We determined that DNA extraction from ELBW faecal samples, particularly those infants receiving probiotic supplementation, should include a prolonged beat-beating step. Furthermore, use of the 16S rRNA (V1 + V2 + V3) and (V6 + V7 + V8) regions provides reliable representation of ELBW microbiota profiles, while inclusion of the (V4 + V5) region may not be appropriate for studies where Bifidobacterium constitutes a resident microbiota member.
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Affiliation(s)
- Cristina Alcon-Giner
- The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, UK
| | - Shabhonam Caim
- The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, UK
| | - Suparna Mitra
- The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, UK.,Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Jennifer Ketskemety
- The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, UK
| | - Udo Wegmann
- The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, UK
| | - John Wain
- Norwich Medical School, University of East Anglia, Norwich Research Park, Colney, Norwich, UK
| | - Gusztav Belteki
- Neonatal Intensive Care Unit, The Rosie Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Paul Clarke
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Lindsay J Hall
- The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, UK.
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