Biology subjects

Avershina, E.

Publications and source records attributed to Avershina, E..

4 recordsLinked to original sources

bioRxiv2026

CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut

Bacteria in the human gut influence host physiology and disease risk, but their ecology is strongly shaped by mobile genetic elements (MGEs) such as phages and plasmids. Past interactions between bacteria and MGEs can be inferred from CRISPR-Cas cassettes, which contain short DNA fragments derived from invading elements. To lay the groundwork for research on the impact of such interactions on the human host, we examined bacteria, MGEs, and CRISPR-Cas in the gut microbiome. Using fecal shotgun metagenomes from 1034 Norwegians, we constructed an extended microbiome resource comprising 1.7K prokaryotic mOTUs, 19.5K viral vOTUs and 24.2K plasmid PTUs. We also recovered 74.2K unique CRISPR-Cas cassettes to map past bacteria-MGE interactions and assessed their associations with human diet and lifestyle factors. CRISPR-Cas spacers, and which viruses and plasmids they targeted, varied substantially within bacterial species, but were predominantly directed towards cohort-specific MGEs. Moreover, bacteria were more likely to target MGEs present in the same sample, consistent with local exposure. Bacteria also shared more targets within taxonomic families than across families, where mobilizable plasmids were more frequent among the targets. We did not find evidence that CRISPR-Cas spacers were related to characteristics of the human host, beyond the host-bacteria associations. Together, this research provides a large-scale resource and a structured analysis of bacteria-MGE interactions in the gut microbiome, and their contribution to microbial ecosystem dynamics.

molecular biology↗

bioRxiv2025

VirMake: a flexible and user-friendly pipeline for viral taxonomic and functional characterisation from shotgun metagenomic sequencing data

BackgroundBacteriophages (phages) are recognized as key regulators of microbial communities, and it is pivotal to understand viral ecology, diversity, and evolution. However, identification and characterization of phages from shotgun metagenome sequencing pose unique bioinformatic challenges owing to the inherent complexity and scale of the data. ResultsHere, we introduce VirMake, a comprehensive, flexible, and scalable pipeline developed for viral taxonomic and functional analysis of shotgun metagenome data. It enables high-throughput end-to-end processing, assembly, and annotation of metagenomic data, including viral sequence identification, taxonomic and functional annotation, and using a modular framework, allows users to integrate viral analysis at different stages of metagenome data analysis. VirMake can be installed on Linux operating systems that support Conda and is freely available at https://github.com/Rounge-lab/VirMake. Here, we showcase VirMake capabilities using three metagenome datasets of varying sizes (up to 2.9 Tbp), generated from various environments (human gut and water) and using different sample preparation protocols (VLP enrichment and bulk DNA extraction). ConclusionsVirMake enabled robust processing of all datasets, showing viral genome richness, taxonomy and integration status to vary according to sampling environments and laboratory protocols.

bioinformatics↗

bioRxiv2022

Multi-excitation Raman Spectroscopy Complements Whole Genome Sequencing for Rapid Detection of Bacterial Infection and Resistance in WHO Priority Pathogens

Current methods for diagnosing acute and complex infections mostly rely on culture-based methods and, for biofilms, fluorescence in-situ hybridization. These techniques are labor-intensive and can take 2-4 days to return a test result, especially considering an extra culturing step required for the antibiotic susceptibility testing (AST). This places a significant burden on healthcare providers, delaying treatment and leading to adverse patient outcomes. Here, we report the complementary use of our newly developed multi-excitation Raman spectroscopy (ME-RS) method with whole-genome sequencing (WGS). Four WHO priority pathogens are AST phenotyped and their antimicrobial resistance (AMR) profile determined by WGS. On application of ME-RS method we find high correlation with the WGS characterization. Highly accurate classification based on the species (98.93%), wild-type/non-wild type (99.45%), and presence or absence of thick peptidoglycan layers in cell walls (100%), as well as at the individual strain level (99.29%). These results clearly demonstrate the potential of ME-RS as a rapid and first-stage tool for species, resistance and strain-level classification which can be followed up by WGS for confirmation. Such a workflow can facilitate efficient antimicrobial stewardship to handle and prevent the spread of AMR.

microbiology↗

bioRxiv2017

Genetic diversity and mother-child overlap of the gut associated microbiota determined by reduced genome sequencing

The genetic diversity and sharing of the mother-child associated microbiota remain largely unexplored. This severely limits our functional understanding of gut microbiota transmission patterns. The aim of our work was therefore to use a novel reduced metagenome sequencing in combination with shotgun and 16S rRNA gene sequencing to determine both the metagenome genetic diversity and the mother-to-child sharing of the microbiota. For a cohort of 17 mother-child pairs we found an increase of the collective metagenome size from about 100 Mbp for 4-day-old children to about 500 Mbp for mothers. The 4-day-old children shared 7% of the metagenome sequences with the mothers, while the metagenome sequence sharing was more than 30% among the mothers. We found 15 genomes shared across more than 50% of the mothers, of which 10 belonged to Clostridia. Only Bacteroides showed a direct mother-child association, with B. vulgatus being abundant in both 4-day-old children and mothers. In conclusion, our results support a common pool of gut bacteria that are transmitted from adults to infants, with most of the bacteria being transmitted at a stage after delivery.

microbiology↗