Philip Hugenholtz

The paper expands plasmid diversity by analyzing long-read metagenomes, identifying novel plasmid lineages and providing tools for plasmid discovery.

This paper develops lyophilized faecal inoculation capsules for koala rehabilitation, showing they retain microbial composition and survive for a year, but face challenges in clinical administration.

This paper develops a microbial-abiotic sulfur relay to remediate bauxite residue by generating acidity and dealkalizing it, enabling plant colonization.

The paper examines how marine reserves affect seawater microbial communities in the Great Barrier Reef, finding distinct microbiomes between protected and fished areas.

The paper presents a microbial genomes database for the Great Barrier Reef, highlighting underrepresented prokaryotic and viral genomes and their utility in predicting reef management impacts.

The paper constructs a global genome catalog of 53,501 long-read MAGs from activated sludge, representing 12,047 prokaryotic species and enabling analysis of functional traits and ecological roles in wastewater treatment systems.

This paper shows that adding noise to gene content data improves machine learning predictions of bacterial phenotypes across evolutionary time, concluding the last bacterial common ancestor was anaerobic, double-membraned, and moderately thermophilic.

gTranslate predicts prokaryotic translation tables with high accuracy using machine learning, outperforming existing methods and identifying new genetic code variations.

The paper identifies stop codon reassignment of UGA to tryptophan in the Actinomycetota phylum, expanding known bacterial lineages with this genetic code plasticity.

This paper presents a comprehensive analysis of the faecal microbiomes of 23 marsupial species, revealing novel microbial genomes and highlighting the influence of host phylogeny on microbiome composition.

Structome-AlignViewer evaluates structure-aware alignments by mapping alignment columns to protein structures and providing confidence scores to identify reliable regions.

This study analyzes marsupial gut microbiomes to identify genetic factors contributing to their low methane emissions compared to ruminants.

This study uses long-read sequencing and optimized bioinformatics to recover high-quality microbial genomes from soil and sediment samples, revealing over 15,000 novel prokaryotic species and expanding microbial community characterization.

This paper proposes a new genus and species, Patescibacterium danicum, to provide nomenclatural stability for the phylum Ca. Patescibacteria.

This paper identifies microbiome-derived therapeutics for IBD using a metagenome-guided approach, showing improved disease markers and safety in preclinical models.

Greengenes2 aligns 16S rRNA and shotgun metagenomic data using a whole-genome phylogeny, showing agreement in principal coordinates, taxonomy, and phenotype effect size.

GTDB-Tk v2 improves memory efficiency for taxonomic classification by using a two-step approach with reduced memory usage while maintaining accuracy.

The paper identifies new methane-metabolizing archaea in Bathyarchaeota and Verstraetearchaeota, expanding known methane metabolism beyond Euryarchaeota.