SinoXivA pipeline for improved 16S rRNA gene-based phylogeny and diversity analyses of Bacteria and Archaea
Abstract
The LTP database compiling 16S rRNA gene sequences of all type strains of Bacteria and Archaea has served taxonomists for two decades. Here we report the LTPlus, a manually curated and aligned database expanding LTP with high quality sequences covering most of the phylogenetic diversity hitherto detected. To this purpose, the sequences were selected from the SILVA non-redundant and the GTDB databases, together with the highest quality 16S rRNA gene sequences deposited at the NCBI in the timeframe from 2019 to 2025. The LTPlus was kept compact by just integrating non-redundant sequences, applying a 98.7% identity threshold. The LTPlus was used to reconstruct a phylogenetic tree, which we believe is currently offering the most robust topology of prokaryotic lineages based on 16S rRNA gene sequences. Using the LTPlus as reference enables more accurate identification of new sequences and improved phylogenetic inferences. LTPlus, together with the newly developed OPUcheck tool, serves as a pipeline for fast diversity analysis of environmental microbiomes based on amplicon and 16S rRNA metagenome reads.
Citation Information
@article{ramonrossellomora2026,
title={A pipeline for improved 16S rRNA gene-based phylogeny and diversity analyses of Bacteria and Archaea},
author={Ramon Rossello-Mora and Tomeu Viver and Pere Palmer-Rodríguez and Ralf Westram and Esteban Bustos-Caparros and Joan Francisco Gago and Jaime Gonzalez-Mendez and Mercè Llabrés and Wolfgang Ludwig and Rudolf Amann},
journal={Nature Portfolio},
year={2026},
doi={https://doi.org/10.21203/rs.3.rs-9370187/v1}
}
