D. H. Parks

Diverse Arctic lake sediment microbiota shape methane emission temperature sensitivity

This study shows that spatial variations in sediment microbiota influence methane emission temperature sensitivity in Arctic lakes.

Reclassification of Shigella species as later heterotypic synonyms of Escherichia coli in the Genome Taxonomy Database

The paper reclassifies Shigella species as synonyms of Escherichia coli based on genomic data and resolves classification conflicts in the GTDB.

A rank-normalized archaeal taxonomy based on genome phylogeny resolves widespread incomplete and uneven classifications

This paper introduces a rank-normalized archaeal taxonomy based on genome phylogeny, resolving classification issues in 93.3% of archaeal genomes.

Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales

This study shows that Thermoplasmata archaea lack methanogenesis genes, suggesting methanogenesis was laterally acquired by Methanomassiliicoccales, and identifies new Thermoplasmata lineages with diverse metabolic capabilities.

Lateral gene transfer drives metabolic flexibility in the anaerobic methane oxidising archaeal family Methanoperedenaceae

This study identifies novel respiratory strategies in Methanoperedenaceae archaea acquired through lateral gene transfer, expanding their metabolic flexibility in anaerobic methane oxidation.

Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy

The paper introduces 24,706 species clusters for bacterial and archaeal genomes to create a complete genome-based taxonomy using ANI criteria and placeholder names for uncultivated species.

A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome

The paper presents a comprehensive genomic resource of over 280,000 human gut microbiome genomes and their protein sequences, highlighting gaps in functional annotations and genomic diversity.

A proposal for a standardized bacterial taxonomy based on genome phylogeny

The paper proposes a standardized bacterial taxonomy based on genome phylogeny, identifying 99 phyla and making significant taxonomic changes across 73% of taxa.