METASEED: a novel approach to full-length 16S rRNA gene reconstruction from short read data

• Published in: BMC bioinformatics Vol. 25; no. 1; pp. 237 - 16
• Main Authors: Philip, Melcy, Rudi, Knut, Ormaasen, Ida, Angell, Inga Leena, Pettersen, Ragnhild, Keeley, Nigel B, Snipen, Lars-Gustav
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 12-07-2024; BioMed Central; BMC
• Subjects: 16S rRNA; Analysis; Data analysis; Data mining; Databases, Genetic; DNA; Error analysis; Evaluation; Gene sequencing; Genes; Genetic aspects; Genomes; Metagenome - genetics; Metagenomics; Microorganisms; Onsite; Reconstruction; RNA sequencing; RNA, Ribosomal, 16S - genetics; rRNA 16S; Seafloor sediment; Sediments; Seeds; Sequence Analysis, DNA - methods; Taxonomic profile; Norway; 16S rRNA; Metagenomics; Seafloor sediment; Taxonomic profile
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-024-05837-z

With the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error level and structure, the analysis of such data demands some database of reference sequences. However, many taxa from complex and diverse environments, have poor representation in publicly available databases. In this paper, we propose the METASEED pipeline for the reconstruction of full-length 16S sequences from such environments, in order to improve the reference for the subsequent use of on-site sequencing.
We show that combining high-precision short-read sequencing of both 16S and full metagenome from the same samples allow us to reconstruct high-quality 16S sequences from the more abundant taxa. A significant novelty is the carefully designed collection of metagenome reads that matches the 16S amplicons, based on a combination of uniqueness and abundance. Compared to alternative approaches this produces superior results.
Our pipeline will facilitate numerous studies associated with various unknown microorganisms, thus allowing the comprehension of the diverse environments. The pipeline is a potential tool in generating a full length 16S rRNA gene database for any environment.