Leighton Pritchard

genomeRxiv: a genome-based identification web server that bridges the gap between taxonomy and strain typing

The paper introduces genomeRxiv, a web server that enables precise strain-level identification of prokaryotes using ANI-based LINs, overcoming limitations of traditional taxonomic classification.

A bacterial Rhesus transporter retunes a structurally conserved ammonium pore into a reversible nitrogen valve

This study shows how a bacterial Rhesus transporter modifies a conserved ammonium pore to function as a reversible nitrogen valve through specific residue changes.

Lipid-associated architecture and divergent ammonium transport distinguish a bacterial Rhesus protein

This study determines the structure and function of NeRh50, a Rh-family protein in Nitrosomonas europaea, revealing lipid associations and divergent ammonium transport properties compared to canonical Amt proteins.

Carbohydrate active enzymes in Pectobacteriaceae: coevolving enzyme sets and host adaptation

The paper catalogs and analyzes CAZyme complements in Pectobacterium and Dickeya genomes, finding coevolution of CAZymes linked to host adaptation and tissue preference.

16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces

This study shows that 16S rRNA phylogeny and clustering are unreliable for classifying Streptomyces species, as they often conflict with whole-genome-based taxonomy.

Characterisation of prophages in Clostridium clostridioforme: an understudied component of the intestinal microbiome

This study characterizes prophages in Clostridium clostridioforme LM41, identifying 15 prophages and their potential roles in host fitness and genetic diversity.

THAPBI PICT - a fast, cautious, and accurate metabarcoding analysis pipeline

THAPBI PICT is a metabarcoding pipeline that processes Illumina paired-end reads, reduces noise, and classifies sequences using a curated database, providing interpretable outputs for non-specialists.

cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets

cazy_webscraper compiles and integrates CAZyme data from CAZy and other sources, enabling large-scale bioinformatic analysis and candidate screening for biotechnological applications.

Mining underutilized whole-genome sequencing projects to improve 16S rRNA databases

The paper improves 16S rRNA databases by reassembling whole-genome sequencing data to generate high-quality sequences, enhancing taxonomic classification accuracy.

Easily phylotyping E. coli via the EzClermont web app and command-line tool.

The paper implements an in silico Clermont PCR method for E. coli phylotyping as a web app and command-line tool.

riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions

riboSeed improves bacterial genome assembly by leveraging conserved ribosomal operon flanking regions to bridge contigs and aid genome closure.