Andrey Nikolaevich Shkoporov

Prevalent Gut Phages Encode Modular Adhesins Mediating Epithelial Binding and Endoplasmic Reticulum Trafficking

The paper identifies gut phages with adhesin proteins that bind epithelial cells and traffic to the endoplasmic reticulum, revealing potential interactions with the human virome.

Eggerthella lenta evades bacteriophage through reversible megabase-scale inversions of capsular polysaccharide gene clusters

This study identifies a phage-resistant sub-population of Eggerthella lenta in mice, linked to reversible genomic inversions and altered capsule production.

Ratatoskr: A tool for automated retrieval of taxonomic type strain sequences and metadata

Ratatoskr automates retrieval of bacterial taxonomic type strain sequences and metadata, resolving nomenclature inconsistencies across databases.

Large scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome

The paper uses nanopore sequencing to analyze capsid-packaged DNA in gut microbiomes, finding bacterial DNA encapsidation is widespread and associated with specific bacterial families.

A novel approach to Caudoviricetes taxonomy utilising whole proteome structure-structure comparison

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

Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages

This study identifies phase variation of capsular polysaccharides and other resistance mechanisms as key strategies enabling stable coexistence between gut Bacteroidales and their lytic bacteriophages.

The human oral phageome is highly diverse and rich in jumbo phages

The paper profiles and compares the phageome of oral and gut sites across individuals, finding distinct phage compositions and high diversity in oral sites, particularly on the tongue.

VIGA: a sensitive, precise and automatic de novo VIral Genome Annotator.

VIGA is a de novo viral genome annotator that accurately identifies coding sequences and reduces non-informative annotations in viral (meta)genomics data.