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Alili R, Belda E, Le P, Wirth T, Zucker JD, Prifti E, Clément K. Exploring Semi-Quantitative Metagenomic Studies Using Oxford Nanopore Sequencing: A Computational and Experimental Protocol. Genes (Basel) 2021; 12:1496. [PMID: 34680891 PMCID: PMC8536095 DOI: 10.3390/genes12101496] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022] Open
Abstract
The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed for characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenge. To facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. Here, we propose a computational and experimental protocol for whole-genome semi-quantitative metagenomic studies of human gut microbiome with Oxford Nanopore sequencing technology (ONT) that could be applied to other microbial ecosystems. We developed a bioinformatics protocol to analyze ONT sequences taxonomically and functionally and optimized preanalytic protocols, including stool collection and DNA extraction methods to maximize read length. This is a critical parameter for the sequence alignment and classification. Our protocol was evaluated using simulations of metagenomic communities, which reflect naturally occurring compositional variations. Next, we validated both protocols using stool samples from a bariatric surgery cohort, sequenced with ONT, Illumina, and SOLiD technologies. Results revealed similar diversity and microbial composition profiles. This protocol can be implemented in a clinical or research setting, bringing rapid personalized whole-genome profiling of target microbiome species.
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Affiliation(s)
- Rohia Alili
- École Pratique des Hautes Études, PSL University, Les Patios Saint-Jacques, 4-14 Rue Ferrus, 75014 Paris, France; (R.A.); (T.W.); (K.C.)
- Nutrition Department, CRNH, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, 75013 Paris, France
- Nutrition and Obesity, Systemic Approaches (NutriOmics), INSERM, Sorbonne Université, 75013 Paris, France; (P.L.); (J.-D.Z.); (E.P.)
| | - Eugeni Belda
- Unit of Insect Vector Genetics and Genomics, Integrative Phenomics, 8 Rue des Pirogues de Bercy, 75012 Paris, France
| | - Phuong Le
- Nutrition and Obesity, Systemic Approaches (NutriOmics), INSERM, Sorbonne Université, 75013 Paris, France; (P.L.); (J.-D.Z.); (E.P.)
| | - Thierry Wirth
- École Pratique des Hautes Études, PSL University, Les Patios Saint-Jacques, 4-14 Rue Ferrus, 75014 Paris, France; (R.A.); (T.W.); (K.C.)
- Département Systématique et Evolution 16 Rue Buffon, ISYEB, UMR-CNRS, 75231 Paris, France
| | - Jean-Daniel Zucker
- Nutrition and Obesity, Systemic Approaches (NutriOmics), INSERM, Sorbonne Université, 75013 Paris, France; (P.L.); (J.-D.Z.); (E.P.)
- Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, Institute of Research for Development(IRD), Sorbonne Université, 93143 Bondy, France
| | - Edi Prifti
- Nutrition and Obesity, Systemic Approaches (NutriOmics), INSERM, Sorbonne Université, 75013 Paris, France; (P.L.); (J.-D.Z.); (E.P.)
- Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, Institute of Research for Development(IRD), Sorbonne Université, 93143 Bondy, France
| | - Karine Clément
- École Pratique des Hautes Études, PSL University, Les Patios Saint-Jacques, 4-14 Rue Ferrus, 75014 Paris, France; (R.A.); (T.W.); (K.C.)
- Nutrition and Obesity, Systemic Approaches (NutriOmics), INSERM, Sorbonne Université, 75013 Paris, France; (P.L.); (J.-D.Z.); (E.P.)
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