Thomas Schmidt

The paper surveys global prokaryotic carbon fixation pathways, revealing an oxygen-tolerant rTCA cycle in surface ocean Campylobacterota lineages.

The paper catalogs diazotroph genomes and analyzes their distribution across environments, identifying freshwater and sedimentary ecosystems as key nitrogen-fixation reservoirs.

The paper introduces microntology, a controlled vocabulary for microbial habitats, and provides annotations for over 300,000 metagenomic samples.

MicrobeAtlas unifies over two million microbiome samples to enable cross-technology insights into microbial ecosystems and their global patterns.

Metalog manually curates and harmonises contextual metadata for 110,733 metagenomic samples from humans, animals, ocean water and other environments, linked to taxonomic profiles and SPIRE genomes.

The paper presents a structure-based classification framework for Caudoviricetes using whole-proteome structural clustering to resolve distant viral relationships.

The paper quantifies discoverable bacterial and archaeal diversity in metagenomes, finding many novel phyla and genera hidden in current data.

This study shows that fecal microbial load, not disease, is the main driver of gut microbiome changes and identifies it as a major confounder in microbiome studies.

The paper constructs a global microbial small ORFs catalogue and identifies a tool for annotating small proteins in microbial genomes.

The paper refines enterotypes in global fecal metagenomes using fuzzy clustering and introduces an Enterotype Dysbiosis Score to assess disease associations.

GUNC detects and quantifies chimerism in prokaryotic genomes by analyzing contig lineage homogeneity, improving genome quality.

treeclimbR identifies optimal hierarchical resolutions for detecting entities associated with phenotypes in multi-resolution data.

The paper analyzes pan-genomes of 155 prokaryotic species to assess how environmental and phylogenetic factors influence strain diversity and pan-genome features.

MAPseq improves speed and accuracy of rRNA metagenomic analysis by providing faster and more consistent taxonomy classifications and OTU mappings.