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Fernández-Pato A, Sinha T, Gacesa R, Andreu-Sánchez S, Gois MFB, Gelderloos-Arends J, Jansen DBH, Kruk M, Jaeger M, Joosten LAB, Netea MG, Weersma RK, Wijmenga C, Harmsen HJM, Fu J, Zhernakova A, Kurilshikov A. Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses. Sci Rep 2024; 14:3911. [PMID: 38366085 PMCID: PMC10873414 DOI: 10.1038/s41598-024-54353-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/29/2023] [Accepted: 02/12/2024] [Indexed: 02/18/2024] Open
Abstract
The lack of standardization in the methods of DNA extraction from fecal samples represents the major source of experimental variation in the microbiome research field. In this study, we aimed to compare the metagenomic profiles and microbiome-phenotype associations obtained by applying two commercially available DNA extraction kits: the AllPrep DNA/RNA Mini Kit (APK) and the QIAamp Fast DNA Stool Mini Kit (FSK). Using metagenomic sequencing data available from 745 paired fecal samples from two independent population cohorts, Lifelines-DEEP (LLD, n = 292) and the 500 Functional Genomics project (500FG, n = 453), we confirmed significant differences in DNA yield and the recovered microbial communities between protocols, with the APK method resulting in a higher DNA concentration and microbial diversity. Further, we observed a massive difference in bacterial relative abundances at species-level between the APK and the FSK protocols, with > 75% of species differentially abundant between protocols in both cohorts. Specifically, comparison with a standard mock community revealed that the APK method provided higher accuracy in the recovery of microbial relative abundances, with the absence of a bead-beating step in the FSK protocol causing an underrepresentation of gram-positive bacteria. This heterogeneity in the recovered microbial composition led to remarkable differences in the association with anthropometric and lifestyle phenotypes. The results of this study further reinforce that the choice of DNA extraction method impacts the metagenomic profile of human gut microbiota and highlight the importance of harmonizing protocols in microbiome studies.
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Affiliation(s)
- Asier Fernández-Pato
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Milla F Brandao Gois
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Jody Gelderloos-Arends
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Dianne B H Jansen
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Marloes Kruk
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Hermie J M Harmsen
- Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands.
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