Biology subjects

Shkoporov, A. N.

Publications and source records attributed to Shkoporov, A. N..

8 recordsLinked to original sources

bioRxiv2026

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

Bacteriophages are a promising tool for microbiome editing, yet their development has been constrained by limited insights into bacteriophage-host interactions within their shared mammalian body habitat. We isolated a lytic phage {Phi}KL11 that efficiently targets a disease-associated member of the human gut microbiota, Eggerthella lenta, during in vitro growth. However, {Phi}KL11 selects for a pre-existing and reversible bacteriophage-resistant sub-population in mice. Long-read sequencing revealed a massive genomic inversion event, representing >50% of the E. lenta genome, enriched in response to bacteriophage infection. Transcriptomics linked this inversion to the altered expression of three capsular polysaccharide synthesis (CPS) gene clusters and transmission electron microscopy confirmed differential capsule production. Finally, we show that {Phi}KL11 has a broad host range attributable to CPS and other strain-variable genes. These findings suggest a previously unrecognized strategy for phage evasion in the gut, involving megabase-scale genomic inversions and reversible capsule variation driving phage resistance.

microbiology↗

bioRxiv2026

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

Bacteriophages are crucial components of the human microbiome and hold promise as therapeutic agents. Yet, their physical interactions with mammalian cells remain poorly understood. Here, we developed a high-throughput platform to identify phages that adhere to epithelial layers and the proteins that mediate this interaction. The identified phages encode immunoglobulin (Ig)-like domain-containing proteins that, when displayed on a non-adherent phage, confer epithelial binding and internalization in vitro, and increased phage retention in the mouse gut in vivo. Phages encoding these adhesins are among the most abundant and prevalent human gut phages, including crAss-like phages and a distinct cluster of uncharacterized myophages. Domain sequence variation alters epithelial interaction profiles, and internalized phages traffic to the endoplasmic reticulum through the Golgi apparatus, suggesting access to non-degradative internalization pathways. These findings reveal widespread phage-human interactions in the human virome, with potential impacts on health and implications for next-generation phage therapeutics.

microbiology↗

bioRxiv2026

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

Bacterial taxonomic type strains anchor species names to physical and genomic reference material, making them essential for reproducible and comparable prokaryotic research. While reference strains are often well-characterised through curated metadata, nomenclature histories, and sequence records, no single database holds up-to-date information on all these aspects, resulting in fragmented information. Gathering the complete set of information for a type strain is further complicated by inconsistencies in nomenclature between sources due to the often-numerous synonyms that can describe a single strain. As a result, collecting type strain data for taxonomic proposals and emendations can be an onerous task requiring extensive manual curation. To address this issue, we introduce Ratatoskr, a Python-based tool that automates the retrieval of sequences and metadata for bacterial taxonomic type strains. Ratatoskr facilitates this by collecting the latest type strain information of the List of Prokaryotic names with Standing in Nomenclature (LPSN) and using this information to query the BacDive and NCBI databases. By applying known taxonomic synonym information Ratatoskr is able to resolve cross-database inconsistencies and streamline the retrieval process. We show that through its use, Ratatoskr can obtain metadata and sequence data for type strains of bacteria within minutes to seconds, depending on the number of members within the requested taxon. By automating this retrieval, Ratatoskr provides fast, accurate, and readily shareable starting points for studies involving the use of taxonomic type strains and data, such as new taxonomic proposals or emendations. Data summaryRatatoskr was developed using Python 3 and is freely available at https://github.com/Fabian-Bastiaanssen/Ratatoskr under a GPL-3.0 licence.

bioinformatics↗

bioRxiv2025

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

Viral proteins often evolve so rapidly that sequence similarity is lost even among conserved functional genes, complicating phylogenetic analysis and classification. This challenge is acute for Caudoviricetes, a highly diverse class of dsDNA tailed bacteriophages recently redefined by the International Committee on Taxonomy of Viruses (ICTV). To address the limitations of sequence-based taxonomy, we present a structure-based classification framework using whole-proteome structural clustering. From 4,082 exemplar genomes, we predicted 445,098 protein structures with ESMFold and clustered them using Foldseek. Genomes were encoded as binary profiles of structural fold presence, and phylogenetic distances were inferred and normalized using Relative Evolutionary Divergence (RED). This yielded a revised structural taxonomy comprising 159 orders, 267 families, 502 subfamilies, and 1,189 genera. We also introduce PhagePleats, a Python tool for classifying novel phage genomes based on structural similarity. Our approach highlights the utility of protein structure for resolving distant viral relationships.

microbiology↗

bioRxiv2024

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

BackgroundBacteriophages (phages) and bacteria within the gut microbiome persist in long-term stable coexistence. These interactions are driven by eco-evolutionary dynamics, where bacteria employ a variety of mechanisms to evade phage infection, while phages rely on counterstrategies to overcome these defences. Among the most abundant phages in the gut are the crAss-like phages that infect members of the Bacteroidales, in particular Bacteroides. In this study, we explored some of the mechanisms enabling the co-existence of four phage-Bacteroidales host pairs in vitro using a multi-omics approach (transcriptomics, proteomics and metabolomics). These included three Bacteroides species paired with three crAss-like phages (Bacteroides intestinalis and {phi}crAss001, Bacteroides xylanisolvens and {phi}crAss002, and an acapsular mutant of Bacteroides thetaiotaomicron with DAC15), and Parabacteroides distasonis paired with the siphovirus {phi}PDS1. ResultsWe show that phase variation of individual capsular polysaccharides (CPSs) is the primary mechanism promoting phage co-existence in Bacteroidales, but this is not the only strategy. Alternative resistance mechanisms, while potentially less efficient than CPS phase variation, can be activated to support bacterial survival by regulating gene expression and resulting in metabolic adaptations, particularly in amino acid degradation pathways. These mechanisms, also likely regulated by phase variation, enable bacterial populations to persist in the presence of phages, and vice versa. An acapsular variant of B. thetaiotaomicron demonstrated broader transcriptomic, proteomic, and metabolomic changes, supporting the involvement of additional resistance mechanisms beyond CPS variation. ConclusionsThis study advances our understanding of long-term phage-host interaction, offering insights into the long-term persistence of crAss-like phages and extending these observations to other phages, such as {phi}PDS1. Knowledge of the complexities of phage-bacteria interactions is essential for designing effective phage therapies and improving human health through targeted microbiome interventions.

microbiology↗

bioRxiv2024

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

Transducing bacteriophages and gene transfer agents (GTA) are constrained by their capsids structural properties in the length of host DNA they can package. Nanopore sequencing of intact capsid-packaged DNA molecules with full-sized reads can be used to establish the precise lengths and identity of individual packaged DNA molecules and their association with specific bacterial hosts. This approach was validated using a few well-characterised transducing systems, and then applied to study bacterial DNA encapsidation in the faecal microbiomes from three healthy human donors. Bacterial DNA encapsidation appears to be widespread in the microbiome with up to 5.4% of capsid-packaged DNA in the gut virome being of bacterial (non-prophage) origin. Generalised transduction and GTA activity are especially prevalent in the families Oscillospiraceae and Ruminococcaceae, whereas an example of lateral transduction was observed in genus Bacteroides. In addition to that, induction of prophages in a variety of highly prevalent gut bacteria was observed.

microbiology↗

bioRxiv2020

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis

The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of classical lysogeny, these viruses demonstrate unexplained long-term persistence in the human gut microbiome, dominating the virome in some individuals. Here we demonstrate that rapid phase variation of alternate capsular polysaccharides plays an important role in dynamic equilibrium between phage sensitivity and resistance in B. intestinalis cultures, allowing phage and bacteria to multiply in parallel. The data also suggests the role of concomitant phage persistence mechanisms associated with delayed lysis of infected cells, such as carrier state infection. From an ecological and evolutionary standpoint this type of phage-host interaction is consistent with the Piggyback-the-Winner model, which suggests a preference towards lysogenic or other "benign" forms of phage infection when the host is stably present at high abundance. TeaserCrAss-like phage persistence in Bacteroides is associated with capsule phase-variation and additional unexplored mechanisms.

microbiology↗

bioRxiv2018

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

Viral (meta)genomics is a rapidly growing field of study that is hampered by an inability to annotate the majority of viral sequences; therefore, the development of new bioinformatic approaches is very important. Here, we present a new automatic de novo genome annotation pipeline, called VIGA, to annotate prokaryotic and eukaryotic viral sequences from (meta)genomic studies. VIGA was benchmarked on a database of known viral genomes and a viral metagenomics case study. VIGA generated the most accurate outputs according to the number of coding sequences and their coordinates, outputs also had a lower number of non-informative annotations compared to other programs.

bioinformatics↗