Torben N Nielsen

The paper presents 229 new Omnitrophota genomes, revealing their phylogenetic diversity, long proteins, and metabolic profile, and releases them as a community resource.

The paper introduces a cohort-HMM marker recruitment pipeline to improve phylogenomic supermatrix construction by addressing biases in orthogroup recovery and paralog filtering across different taxonomic scales.

The paper analyzes a deep-groundwater metagenome, identifying Omnitrophota as dominant in cross-replicon lateral gene transfer, with unique mobile elements and gene transfer patterns.

The paper presents 208 complete Nanobdellota genomes and identifies recurrent Form III RuBisCO transfer between archaea and Patescibacteriota.

The paper uses high-resolution metagenomic sequencing to reveal contrasting population structures in a microbial community, showing distinct evolutionary strategies coexisting within a single sample.

This paper presents 135 complete Pelagibacter genomes, identifies 52 species, and reveals genomic diversity mechanisms and functional auxotrophies within the genus.

This paper presents 84 complete genomes of Actinomarina, a marine bacterial order, revealing novel species, a hypervariable region, selenocysteine usage, and extensive auxotrophies.

The paper introduces a β-VAE-based embedding for long-read metagenomic sequences using multi-scale k-mer frequencies, achieving high clustering purity and revealing eukaryotic contigs overlooked by prokaryotic tools.

The paper identifies lactuchelins, novel lipopeptide siderophores from Pseudomonas lactucae, which inhibit Xanthomonas campestris pv. campestris 8004 through iron chelation.

This study identifies pathway partitioning as a mechanism for complete denitrification in microbial communities and shows how imbalances in substrate utilization can disrupt cooperativity and lead to nitrous oxide emissions.

This study investigates how genomic and environmental factors influence the distribution of Castellaniella species in a contaminated subsurface, identifying genetic mechanisms underlying their adaptation to stress.

The paper analyzes MGEs from heavy metal contaminated and unimpacted subsurface regions, finding enriched HMRGs in contaminated areas associated with specific bacterial hosts.

This paper introduces a method to assemble complete microbial genomes from metagenomics data, resulting in 34 circular CPR genomes and other circular genomes from public datasets.