Biology subjects

Bochkareva, O.

Publications and source records attributed to Bochkareva, O..

3 recordsLinked to original sources

bioRxiv2025

Nutrient landscape shapes the genetic diversification of the human gut commensal Bacteroides thetaiotaomicron

Bacteroides thetaiotaomicron is a prominent member of the human gut microbiome that has evolved a suite of polysaccharide utilization loci (PUL) to break down a range of diet- and host-derived glycans. To gain insight into the evolution of this bacterium on ecologically meaningful time scales, we carried out an in vitro evolution study in which B. thetaiotaomicron was cultivated on media of different carbohydrate complexity for three months. Shotgun sequencing of the evolved populations revealed an increased number of single nucleotide polymorphisms with increased medium complexity, suggesting that genetic diversification is driven in part by the nutrient landscape. We also observed high-frequency reversible DNA inversions mediated by site-specific DNA integrases, which may be important to production and maintenance of phenotypic heterogeneity in the population. Competition experiments against the ancestor revealed adaption to the experimental conditions, with a fitness gain of the evolved populations and lineages thereof. This fitness advantage was accompanied by an increase in cell size, faster glucose depletion rates, and increased amylopectin degradation in the presence of glucose. In conclusion, rapid adaptive genetic diversification in B. thetaiotaomicron is induced and maintained in part by a complex nutritional environment.

microbiology↗

bioRxiv2021

PaReBrick: PArallel REarrangements and BReakpoints identification toolkit

MotivationHigh plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions, and duplications may independently occur in different strains, providing parallel adaptation. Specifically, such rearrangements might be responsible for multi-virulence, antibiotic resistance, and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. ResultsHere we define the term "parallel rearrangements" as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial population, as a tool PaReBrick. The tool takes synteny blocks and a phylogenetic tree as input and outputs rearrangement events. The tool tests each rearrangement for consistency with a tree, and sorts the events by their parallelism score and provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We proved PaReBricks efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. AvailabilityPaReBrick is written in Python and is available on GitHub

bioinformatics↗

bioRxiv2018

Comparative analysis of Streptococcus genomes

BackgroundGenome sequencing of multiple strains demonstrated high variability in gene content even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome, that is, the complete set of genes observed in a given species or a higher level taxon. Here we analysed the pan-genome structure and the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.\n\nResultsFractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.\n\nAbout 7% of single-copy periphery genes have been found in different syntenic regions. More than a half of these genes are rare in all Streptococcus species; others are rare in at least one species. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are candidates for horizontal transfer between species.\n\nAn inversion of length 15 kB found in four independent branches of S. pneumoniae has breakpoints formed by genes encoding a surface antigen protein (PhtD). The observed parallelism may indicate the action of an antigen variation mechanism.\n\nConclusionsMembers of the genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, understanding of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.

genomics↗