P. Hugenholtz

Fecal microbial transfer and complex carbohydrates mediate protection against COPD

This study shows that fecal microbial transfer and complex carbohydrates can reduce COPD symptoms in mice and humans, linking gut microbiota to disease progression.

An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event

This paper uses machine learning and phylogenetic reconciliation to estimate the evolutionary timeline of Bacteria, linking transitions to aerobic lifestyles to the Great Oxidation Event.

Anaerobic gut fungal communities in marsupial hosts

This study characterizes anaerobic gut fungal communities in marsupials, finding low abundance and lack of host-specific selection compared to placental herbivores.

The power and limitations of species tree-aware phylogenetics

This paper reviews species tree-aware phylogenetic methods, evaluates their reliability, and discusses their applications and limitations in inferring gene and species trees.

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.

Metabolic flexibility allows generalist bacteria to become dominant in a frequently disturbed ecosystem

This study shows that metabolically flexible bacteria dominate in disturbed ecosystems, outcompeting specialists during habitat disturbance.

Recoding enhances the metabolic capabilities of two novel methylotrophic Asgardarchaeota lineages

This study identifies two new Asgardarchaeota lineages with methylotrophic metabolism enhanced by genetic code expansions, including selenocysteine and pyrrolysine recoding.

A rooted phylogeny resolves early bacterial evolution

The paper infers a rooted bacterial phylogeny using gene duplication, transfer, and loss events, revealing a basal split between Terrabacteria and Gracilicutes and rejecting a root between CPR and other Bacteria.

Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diverse and widespread in the environment.

The paper identifies a broad phylogenetic diversity of B3 MBLs in environmental microbes and shows that a variant (B3-RQK) is sensitive to clavulanic acid due to a lysine residue in its active site.

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.

American Gut: an Open Platform for Citizen-Science Microbiome Research

The paper uses citizen-science data to analyze human stool microbiomes, revealing new insights into microbial diversity, metabolome composition, and associations with diet and health.

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.