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Angell IL, Nilsen M, Carlsen KCL, Carlsen KH, Hedlin G, Jonassen CM, Marsland B, Nordlund B, Rehbinder EM, Saunders C, Skjerven HO, Staff AC, Söderhäll C, Vettukattil R, Rudi K. De novo species identification using 16S rRNA gene nanopore sequencing. PeerJ 2020; 8:e10029. [PMID: 33150059 PMCID: PMC7585375 DOI: 10.7717/peerj.10029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 03/13/2020] [Accepted: 09/03/2020] [Indexed: 01/05/2023] Open
Abstract
Nanopore sequencing is rapidly becoming more popular for use in various microbiota-based applications. Major limitations of current approaches are that they do not enable de novo species identification and that they cannot be used to verify species assignments. This severely limits applicability of the nanopore sequencing technology in taxonomic applications. Here, we demonstrate the possibility of de novo species identification and verification using hexamer frequencies in combination with k-means clustering for nanopore sequencing data. The approach was tested on the human infant gut microbiota of 3-month-old infants. Using the hexamer k-means approach we identified two new low abundant species associated with vaginal delivery. In addition, we confirmed both the vaginal delivery association for two previously identified species and the overall high levels of bifidobacteria. Taxonomic assignments were further verified by mock community analyses. Therefore, we believe our de novo species identification approach will have widespread application in analyzing microbial communities in the future.
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Affiliation(s)
- Inga Leena Angell
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Morten Nilsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Karin C Lødrup Carlsen
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kai-Håkon Carlsen
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Gunilla Hedlin
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Christine M Jonassen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Genetic Unit, Centre for Laboratory Medicine, Østfold Hospital Trust, Kalnes, Norway
| | - Benjamin Marsland
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Björn Nordlund
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Eva Maria Rehbinder
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Dermatology, Oslo University Hospital, Oslo, Norway
| | - Carina Saunders
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Håvard Ove Skjerven
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anne Cathrine Staff
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division of Obstetrics and Gynaecology, Oslo University Hospital, Oslo, Norway
| | - Cilla Söderhäll
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Riyas Vettukattil
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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