Biology subjects

Davies, C. S.

Publications and source records attributed to Davies, C. S..

3 recordsLinked to original sources

bioRxiv2026

Contamination of widely used databases compromises rRNA based taxonomic assignment of metagenomes and metatranscriptomes

Taxonomic annotation of metagenomic and metatranscriptomic datasets frequently relies on aligning small subunit (SSU) rRNA reads to annotated reference databases. However, widely used SSU databases, including SILVA, GTDB, Eukaryome, and those distributed with SortMeRNA, are contaminated with large subunit (LSU) rRNA sequences. Low levels of LSU contamination can lead to large numbers of LSU reads being incorrectly identified as SSU and have serious consequences for downstream taxonomic assignments. The problem can be avoided by rigorously removing LSU sequences from databases used for taxonomic annotation, which we have done for KSGP 4.0. Alternatively, initial SSU read selection can be carried out with a carefully curated small SSU database that is free of LSU contamination. We illustrate these two approaches in combination using a metatranscriptomic dataset from an estuarine sediment. Without database cleaning, LSU-derived reads can make up half of supposed SSU sequences and are assigned to a small number of apparently dominant but artefactual taxa. Database cleaning removes this problem and we provide a script, total_rnaseq, to annotate total RNASeq or metagenomic data using this approach. The KSGP 4.0 database provides substantially improved annotation of Archaea compared to the SILVA database and moderate and small improvements for eukaryotes and bacteria respectively.

bioinformatics↗

bioRxiv2023

Improved taxonomic annotation of Archaea communities using LotuS2, the Genome Taxonomy Database and RNAseq data

Metabarcoding is increasingly used to uncover diversity and characterise communities of Archaea In various habitats, but taxonomic annotation of their sequences remains more challenging than for bacteria. Fewer reference sequences are available; widely used databases do not reflect recent revisions of higher level archaeal taxonomy and a substantial fraction of their phylogenetic diversity remains to be fully characterised. We address these gaps with a systematic and tractable approach based around the Genome Taxonomy Database (GTDB). GTDB provides a standardized taxonomy with normalized ranks based on protein coding genes, allowing us to identify and remove incongruent SSU sequences. We then use this in combination with the eukaryote PR2 database to annotate a collection of near full length rRNA sequences and the Archaea SSU sequences in SILVA, creating a new reference database, KSGP (Karst, Silva, GTDB and PR2). GTDB SSUs alone provides a small improvement in annotation of an example marine Archaea OTU data set over standardized SSU databases such as SILVA and Greengenes2, while KSGP increases Class and Order assignments by 145% and 280% respectively and is likely to provide some improvement in annotation of bacterial sequences too. We make the KSGP database and a cleaned and deduplicated subset of GTDB SSU sequences available at ksgp.earlham.ac.uk; integrate them into a metabarcoding pipeline, LotuS2 and outline rapid and robust strategies to generate a set of annotated Archaea OTUs and to determine the proportion of Archaea sequences in metatranscriptomic data. We also demonstrate simple tools to visualise the completeness of database coverage and outline strategies to further understand poorly characterised components of the archaeal community which will be equally applicable to bacteria.

microbiology↗

bioRxiv2021

A heritable androgenic mechanism of female intrasexual competition in cooperatively breeding meerkats

Female intrasexual competition can be intense in cooperatively breeding species, with the dominant breeder or matriarch limiting reproduction in subordinates via aggression, eviction or infanticide. In males, these tendencies bidirectionally link to testosterone, but in females, there has been no systematic investigation of androgen-mediated behaviour within and across generations. In 22 wild meerkat (Suricata suricatta) clans, we show that matriarchs 1) express peak androgen concentrations during late gestation, 2) when displaying peak feeding competition, dominance, and evictions, and 3) relative to subordinates, produce offspring that are more aggressive in early development. Late-gestation, antiandrogen treatment of matriarchs 4) reduced their dominance behaviour, was associated with infrequent evictions, decreased social centrality within the clan, 5) increased aggression in cohabiting subordinate dams, and 6) reduced their offsprings aggression. These effects implicate androgen-mediated aggression in the operation of female sexual selection, and intergenerational transmission of masculinised phenotypes in the evolution of meerkat cooperative breeding.

animal behavior and cognition↗