Dmitry Alexeev

ITMO University | SPbNRU ITMO · Department of Information Technologies

Probiotics and vitamins can impact immune responses and modulate gut microbiome. We evaluated the effects of consuming a yogurt fortified with vitamins and probiotic Lacticaseibacillus casei and rhamnosus on upper respiratory tract infections frequency and gut microbiome during a 3-month intervention. The study included 2 case groups (consuming dif...

Benchmark of cost-efficient and accurate methods for quantifying probiotics in dairy products represents great interest to the food industry. The advantages of cultivation-independent techniques over the traditionally used cultivation-based ones are to be investigated in this context. We evaluated the levels of Lacticaseibacillus casei and rhamnosu...

Background Viliuisk encephalomyelitis (VE) is a rare endemic neurodegenerative disease occurring in the Yakut population of Northeastern Siberia. The main clinical features of VE are spasticity, dysarthria, dementia, central paresis and paralysis, and cortical atrophy observed via MRI. Many hypotheses have been proposed regarding its etiology, incl...

Genome-wide association studies have led to a significant progress in identification of genomic loci affecting coronary artery disease (CAD) risk. However, revealing the causal genes responsible for the observed associations is challenging. In the present study, we aimed to prioritize CAD-relevant genes based on cumulative evidence from the publish...

Nowadays the advent of innovative high-throughput sequencing allows obtaining high-quality microbiome profiling. However, PCR-based tests are still considered the “golden standard” for many clinical applications. Here, we designed a qPCR-based platform with fluorescent-labeled oligonucleotide probes for assessing human gut microbiome composition. T...

Microbial ecosystems of the built environments have become key mediators of health as people worldwide tend to spend large amount of time indoors. Underexposure to microbes at an early age is linked to increased risks of allergic and autoimmune diseases. Transportation systems are of particular interest, as they are globally the largest space for i...

Gut microbiota is an up-to date theme that is widely studied. Now it is obvious that microbiota could be considered as one of the factors affecting aging process. Some reports suggested the potential mechanisms by which gut microbes may influence human health span. Aging-related conditions are accompanied by decline in immune system functioning and...

Accumulated data suggests that the gut microbiome can rapidly respond to changes in diet. Consumption of fermented dairy products (FDP) fortified with probiotic microbes may be associated with positive impact on human health. However, the extent and details of the possible impact of FDP consumption on gut community structure tends to vary across in...

Background Crohn’s disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated. Methods We performed a metagenomic study investigati...

Background Metagenomic surveys of human microbiota are becoming increasingly widespread in academic research as well as in food and pharmaceutical industries and clinical context. Intuitive tools for investigating experimental data are of high interest to researchers. Results Knomics-Biota is a web-based resource for exploratory analysis of human...

The aim of this paper was to study gut microbiota composition in patients with different metabolic statuses. Methods: 92 participants aged 25⁻76 years (26 of whom were men), with confirmed absence of cardiovascular and other chronic diseases (but with the possible presence of cardiovascular risk factors) were included. Carotid ultrasound examinat...

GWAS have identified >200 risk loci for Inflammatory Bowel Disease (IBD). The majority of disease associations are known to be driven by regulatory variants. To identify the putative causative genes that are perturbed by these variants, we generate a large transcriptome data set (nine disease-relevant cell types) and identify 23,650 cis-eQTL. We sh...

We aimed to replicate, in a specific athletic event cohort (only track and field) and in two different ethnicities (Japanese and East European, i.e. Russian and Polish), original findings showing the association of the angiotensin-II receptor type-2 gene (AGTR2) rs11091046 A>C polymorphism with athlete status. We compared genotypic frequencies of t...

Personalized nutrition is of increasing interest to individuals actively monitoring their health. The relations between the duration of diet intervention and the effects on gut microbiota have yet to be elucidated. Here we examined the associations of short-term dietary changes, long-term dietary habits and lifestyle with gut microbiota. Stool samp...

Metagenomic surveys of human microbiota are becoming increasingly widespread in academic research as well as in food and pharmaceutical industries and clinical context. Intuitive tools for exploration of experimental data are of high interest to researchers. Knomics-Biota is a Web-based resource for exploratory analysis of human gut metagenomes. Us...

Long Interspersed Nuclear Element-1 (LINE-1, L1) is a mobile genetic element active in human genomes. L1-encoded ORF1 and ORF2 proteins bind L1 RNAs, forming ribonucleoproteins (RNPs). These RNPs interact with diverse host proteins, some repressive and others required for the L1 lifecycle. Using differential affinity purifications, quantitative mas...

Background: Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut...

Background Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn’s disease (CD). The phylogeny of E. coli isolated from Crohn’s disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. Results We perfor...

Surveys of environmental microbial communities using metagenomic approach produce vast volumes of multidimensional data regarding the phylogenetic and functional composition of the microbiota. Faced with such complex data, a metagenomic researcher needs to select the means for data analysis properly. Data visualization became an indispensable part...

Metagenomics, the application of high-throughput DNA sequencing for surveys of environmental samples, has revolutionized our view on the taxonomic and genetic composition of complex microbial communities. An enormous richness of microbiota keeps unfolding in the context of various fields ranging from biomedicine and food industry to geology. Primar...

Aim. To investigate on the relation of microbiota content and cardiovascular risk factors among persons with no clinical signs of cardiovascular diseases. Material and methods. In the study, 92 Moscow and Moscow Region inhabitants included, men and women at age 25-76 y. o., with no clinical signs of chronic non-infectious diseases, not taking any m...

1. Summary Long Interspersed Nuclear Element-1 (LINE-1, L1) is a mobile genetic element active in human genomes. L1-encoded ORF1 and ORF2 proteins bind L1 RNAs, forming ribonucleoproteins (RNPs). These RNPs interact with diverse host proteins, some repressive and others required for the L1 lifecycle. Using differential affinity purifications and q...

Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metabolically versatile thermophilic bacterium, inhabiting subsurface biosphere of the West-Siberian megabasin and capable of growing on various substrates and electron acceptors. Genomic analysis followed by inhibitor studies and membrane potential measurement...

The aim of this research was to study the association between the gut microbiota composition and arterial wall properties. The study included 92 participants, men and women aged 25–76 years old without clinical manifestation of chronic diseases but with the possible presence of cardiovascular risk factors. Carbohydrate metabolism examination, duple...

Introduction: Mechanisms of interaction between the gut microbiota composition and cardiovascular diseases are actively investigated. The aim of the study was to assess the relationship between the gut microbiota composition, inflammatory markers and level of blood pressure (BP) in apparently healthy individuals living in Moscow and Moscow region....

Spearman and Pearson correlations of abundance vectors between three methods: Catalogue-based method, direct mapping method and “ground truth”. (XLSX)

Discrepancy ratio distribution for 5 gene groups. Each dot represents a value of discrepancy ratio for a gene group in a single metagenome. Samples with zero or infinite discrepancy ratios are not shown. (TIFF)

Total relative abundance of phage terminases in healthy gut metagenomes. The abundance distribution in groups is shown with boxplots in logarithmic scale. A) Distribution of all phage terminases; B) Distribution of Caudovirales phages terminases only. (TIFF)

Group-wise average abundance of RiPPs biosynthesis clusters in healthy and obese individuals from Denmark. Cluster names along the X axis are indicated as in the original article [7]. For each cluster there are 2 colored bars for 2 sample groups, indicating mean abundance of RiPPs biosynthesis cluster in group. (TIFF)

Total relative abundance of antibiotic resistance genes in gut metagenomes. The cohorts are sorted in the increasing order of medians. (TIFF)

Group-wise average abundance of RiPPs biosynthesis clusters in healthy individuals, patients with Crohn’s disease and with ulcerative colitis from Spain. Cluster names along the X axis are indicated as in the original article [7]. For each cluster there are 3 colored bars for 3 sample groups, indicating mean abundance of RiPPs biosynthesis cluster...

Group-wise median abundance of starch degradation genes (EC numbers). For each EC number, there are 5 bars for 5 sample groups indicating mean sum abundance of all genes with corresponding EC number in group. (TIFF)