1
|
Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P. Towards standards for human fecal sample processing in metagenomic studies. Nat Biotechnol 2017; 35:1069-1076. [PMID: 28967887 DOI: 10.1038/nbt.3960] [Citation(s) in RCA: 455] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/11/2017] [Indexed: 12/30/2022]
Abstract
Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.
Collapse
Affiliation(s)
- Paul I Costea
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Eric Pelletier
- CEA - Institut François Jacob - Genoscope, Evry, France.,CNRS UMR-8030, Evry, France.,Université Evry Val d'Essonne, Evry, France
| | | | - Florence Levenez
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Melanie Tramontano
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marja Driessen
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rajna Hercog
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ferris-Elias Jung
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens Roat Kultima
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthew R Hayward
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, Ontario, Canada
| | | | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Jillian R M Brown
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | | | - Michelle Daigneault
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.,Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Francisco Guarner
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hans Heilig
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Ruth Ann Luna
- Texas Children's Hospital, Feigin Center, Houston, Texas, USA
| | | | - Jana Junick
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Philippe Langella
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Chaysavanh Manichanh
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Jennifer C Martin
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | | | - Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Céline Orvain
- CEA - Institut François Jacob - Genoscope, Evry, France
| | - Kiran Raosaheb Patil
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - John Penders
- School of Nutrition and Translational Research in Metabolism (NUTRIM) and Care and Public Health Research Institute (Caphri), Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Søren Persson
- Unit of Foodborne Infections, Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Nicolas Pons
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Anne Salonen
- Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Delphine Saulnier
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Karen P Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Bhagirath Singh
- Centre for Human Immunology, Department of Microbiology & Immunology and Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Kathleen Slezak
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | | | | | - Liping Zhao
- Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - S Dusko Ehrlich
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London, UK
| | - Joel Dore
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany.,Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| |
Collapse
|
2
|
Hill CJ, Brown JRM, Lynch DB, Jeffery IB, Ryan CA, Ross RP, Stanton C, O'Toole PW. Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants. Microbiome 2016; 4:19. [PMID: 27160322 PMCID: PMC4862223 DOI: 10.1186/s40168-016-0164-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 03/07/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND Alterations in intestinal microbiota have been correlated with a growing number of diseases. Investigating the faecal microbiota is widely used as a non-invasive and ethically simple proxy for intestinal biopsies. There is an urgent need for collection and transport media that would allow faecal sampling at distance from the processing laboratory, obviating the need for same-day DNA extraction recommended by previous studies of freezing and processing methods for stool. We compared the faecal bacterial DNA quality and apparent phylogenetic composition derived using a commercial kit for stool storage and transport (DNA Genotek OMNIgene GUT) with that of freshly extracted samples, 22 from infants and 20 from older adults. RESULTS Use of the storage vials increased the quality of extracted bacterial DNA by reduction of DNA shearing. When infant and elderly datasets were examined separately, no differences in microbiota composition were observed due to storage. When the two datasets were combined, there was a difference according to a Wilcoxon test in the relative proportions of Faecalibacterium, Sporobacter, Clostridium XVIII, and Clostridium XlVa after 1 week's storage compared to immediately extracted samples. After 2 weeks' storage, Bacteroides abundance was also significantly different, showing an apparent increase from week 1 to week 2. The microbiota composition of infant samples was more affected than that of elderly samples by storage, with significantly higher Spearman distances between paired freshly extracted and stored samples (p < 0.001). When the microbiota profiles were analysed at the operational taxonomic unit (OTU) level, three infant datasets in the study did not cluster together, while only one elderly dataset did not. The lower microbiota diversity of the infant gut microbiota compared to the elderly gut microbiota (p < 0.001) means that any alteration in the infant datasets has a proportionally larger effect. CONCLUSIONS The commercial storage vials appear to be suitable for high diversity microbiota samples, but may be less appropriate for lower diversity samples. Differences between fresh and stored samples mean that where storage is unavoidable, a consistent storage regime should be used. We would recommend extraction ideally within the first week of storage.
Collapse
Affiliation(s)
- Cian J Hill
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Jillian R M Brown
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Denise B Lynch
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Ian B Jeffery
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - C Anthony Ryan
- Department of Neonatology, Cork University Maternity Hospital, Wilton, Cork, Ireland
| | - R Paul Ross
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Catherine Stanton
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Cork, Ireland.
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
| |
Collapse
|