Dilyara R. Khusnutdinova

Inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), are associated with gut microbiota alterations. While lactobacilli are traditionally considered beneficial probiotics, recent studies report their increased abundance in IBD, suggesting a more complex role. This study aimed to assess the species diversity and representation of lactobacilli in CD and UC patients compared to healthy volunteers. Fecal samples from 40 CD patients, 40 UC patients, and 42 healthy controls were analyzed using 16S rRNA sequencing, shotgun metagenomic sequencing, and qPCR. Both sequencing methods revealed significantly higher Lactobacillaceae family relative proportions in IBD patients versus healthy controls. qPCR confirmed the overall relative enrichment of lactobacilli, while species-level differences were identified by both 16S rRNA and shotgun metagenomic sequencing. Over 28% of IBD patients harbored six or more lactobacilli species versus only 2% of controls. Species-level analysis identified Ligilactobacillus salivarius, Lactobacillus gasseri, and Limosilactobacillus mucosae as having significantly higher relative abundances in IBD patients. The increased occurrence of specific species with known virulence potential challenges the traditional view of lactobacilli as universally beneficial, indicating that certain lactobacilli may be associated with dysbiosis in IBD.

The long-term impact of eradication therapy for Helicobacter pylori on the gut microbiota is a subject of significant interest. To evaluate the influence of the bismuth-based quadruple H. pylori eradication therapy supplemented with butyrate and inulin on functional alterations within the gut microbial community, metagenomic and metabolomic profiling were performed. Fecal samples were collected from 15 patients (aged 19–64 years) prior to the treatment, immediately after the treatment, and one month after the therapy. A significant decrease in the relative abundance of Actinobacteria, such as Bifidobacterium and Collinsella, was observed after the therapeutic intervention. In contrast, the levels of Faecalibacterium prausnitzii remained consistent, while Roseburia faecis levels exhibited a substantial decline, suggesting a disruption in key butyrate-producing bacteria. A moderate increase in the relative abundance of opportunistic Proteobacteria, Firmicutes, and Bacteroides was observed. A comprehensive analysis of short-chain fatty acids (SCFAs) levels in the feces of the patients revealed a decline in the butyric acid concentration in response to the therapy, followed by a return to baseline levels. However, the level of valeric acid declined, and there was no tendency for it to increase after a month-long course of therapy. It is important to note that these shifts persisted for a period of four weeks. Consequently, the H. pylori eradication therapy intervention promotes a persistent microbial reorganization, and the observed recovery is unlikely to be spontaneous and probably reflects the protective effect of butyrate and inulin supplementation. To confirm the conclusions, a larger sample size and longer-duration studies are required.

Background/Objectives: Autism spectrum disorder (ASD) is often associated with gastrointestinal dysfunction and gut microbiota alterations. This study aimed to characterize the gut microbiota in children with ASD in relation to nutritional factors and to evaluate the effects of dietary interventions combined with probiotics. Methods: The study included 96 children with ASD and 39 neurotypical controls. Follow-up data after intervention were available for 60 children with ASD. Gut microbiota composition was assessed by 16S rRNA sequencing, and fecal calprotectin and zonulin were measured before and after intervention. Most children with ASD (n = 91) received a rotational or elimination diet for six months, and all participants with ASD received probiotics for 1.5 months. Results: Children with ASD showed significant microbiota changes compared with controls, including increased Prevotella, Sarcina, NK4A214 group, and RF39 taxon, along with reduced butyrate-producing bacteria, such as Roseburia, Eubacterium xylanophilum group, and Eubacterium ventriosum group. Formula feeding was associated with increased Odoribacter, whereas food selectivity was linked to higher Prevotella, Sarcina, Methanobrevibacter, and RF39. A rotational diet increased Erysipelotrichaceae UCG-003 and Streptococcus, while an elimination diet increased Butyricicoccus and reduced fecal calprotectin (p = 0.023). Fecal zonulin decreased significantly after intervention in the follow-up ASD subgroup (p = 0.018). Conclusions: The obtained data suggest that children with ASD may exhibit certain microbiota features associated with nutritional patterns. Dietary interventions combined with probiotics appear to be associated with microbiota modulation and a tendency toward improvement in markers of intestinal inflammation and barrier function.

Introduction. The problem of male infertility remains a pressing issue in the field of reproductive medicine, as male infertility progresses year after year. The male reproductive microbiome is a complex community of microorganisms that inhabit various parts of the male body, including the urethra, prostate, and seminal vesicles. Research shows that the microbiome plays an important role in maintaining reproductive health and may influence fertility. Objective. To identify differences in the composition of the testicular and urethral microbiota between groups of patients with positive and negative results of assisted reproductive technologies (ART). Materials and methods. A comparative analysis of the taxonomic structure of the testicular and urethral microbiota was conducted in 24 infertile men with obstructive azoospermia (OA) who underwent ART procedures. Pregnancy occurred in 13 cases (ART+ group), while pregnancy was not achieved in 11 cases (ARTgroup). To analyze the bacterial composition of the urogenital tract, biological material was collected from the urethra of all study participants, as well as a testicular biopsy. Analysis of bacterial 16S rRNA gene amplicons was performed using high-throughput next-generation sequencing (NGS). The obtained data were processed using QIIME software (version 1.9.1), which allowed for taxonomic analysis and assessment of microbiota diversity. Results. Our study revealed significant differences in the microbiota composition between testicular and urethral tissue in infertile men with OA, as well as between groups of patients with positive and negative ART results. In testicular tissue, the main microbiota families were Enterobacteriaceae and Burkholderiaceae, while in the urethra, the dominant families were Mycobacteriaceae, Staphylococcaceae, Lactobacillaceae, and Peptoniphilaceae. Despite differences in microbiota composition, no significant differences in alpha diversity indices of testicular and urethral microbiota were found between the ARTand ART+ groups. However, in the ARTgroup, a significantly increased relative representation of 19 bacterial families was observed in the testicular microbiota compared to patients in the ART+ group, including increased representation of two families: Mycobacteriales and Legionellaceae. This may indicate a possible link between microbiota composition and ART success. Correlation analysis revealed a positive association between inhibin levels and testicular microbiota composition. This suggests that testicular microbiota may influence inhibin levels, which are an important marker of testicular function and may play a role in fertility. Conclusions. The results demonstrate that OA-associated disorders lead to changes in the relative representation of individual families of the urethral and testicular microbiota, which has a significant impact on ART outcomes. The practical significance of these data is that microbiota correction may be a potential strategy for improving ART outcomes in patients with OA, opening up new approaches to treatment and enhancing fertility, and suggests the theory of «testicular fertility microbiota» and may subsequently play an important role in pre-conception cryopreservation in ART programs and the creation of new tests for sperm selection in artificial insemination programs.

While the gut microbiome has been intensively investigated for more than twenty years already, its role in various disorders remains to be unraveled. At the same time, questions about what changes in the gut microbiota can be considered as normal or pathological and whether communities are able to recover after exposure to negative factors (diseases, medications, environmental factors) are still unclear. Here, we describe changes in the gut microbiota composition and the content of short-chain fatty acids in adult healthy volunteers (n = 15) over a 24 month-period. Intraindividual variability in gut microbial composition was 40%, whereas the short chain fatty acids profile remained relatively stable (2-year variability 20%, inter-individual 26%). The changes tend to accumulate over time. Nevertheless, both short-term and long-term changes in the gut microbiome composition were significantly smaller within individuals than interindividual differences (two-year interindividual variability was 75%). Seasonal changes in gut microbiota were found more often in autumn and spring involving the content of minor representatives (less than 1.5% of the community in average) in the phyla Actinobacteriota, Firmicutes and Proteobacteria.

Introduction. The study of the human microbiome has become of increasing scientific interest. A balanced and diverse microbiota of the male re- productive system is essential for optimal reproductive health. Today, there are no diagnostic tests to determine the effect of specific microorganisms on the quality of seminal fluid, however, the use of next-generation sequencing (NGS), using the 16S rRNA gene sequence as a molecular marker, provides us with the opportunity to understand the complexity of the relationship between the microbiome and its host. The aim of the study. To conduct a comparative analysis of the taxonomic structure of the microbiota between patients with obstructive and nonobstructive azoospermia and the fertility group (patients with a history of having children). Materials and methods. The study included (n=57) patients (infertile patients with obstructive azoospermia (OA), non-obstructive azoospermia (NOA) and a control group (FERT). All patients underwent percutaneous aspiration of sperm from the testicle (testicular sperm aspiration, MESA), with subsequent in vitro fertilization using ICSI technology, or cryopreservation of biological material. The amplicons of the bacterial 16S rRNA gene were analyzed using high-performance next-generation sequencing (NGS). For this research of bacterial composition of the urogenital tract and control the purity of the method, samples has been taken from the urethra of each patient who underwent testicular biopsy. The data was processed using the QUICKTIME program (version 1.9.1). Results. No significant differences were found in the comparison groups during the study of the urethral bacterial composition. The species diversity, as well as the total number of detected taxonomic units (OTE) in the NOA and OA groups are significantly lower than in the FERT group. The presentation of the phylum like Proteobacteria, Firmicutes, Bacteroidetes, Bifidobacterium adolescentis in the studied groups is different. Three microorganisms were identified with the same frequency in the urethra and testicular tissue (the exact Fisher criterion was used, adjusted for multiple comparison by the Benjamin-Hochberg method). The representation of the phylum Prevotella, Comamonadaceae, Veillonella dispa, Comamonadaceae in the studied groups differs. Conclusion. Testicular tissue is not sterile and has its own unique microbial landscape for each comparison group. Bacterial communities of testicular tissue in patients with azoospermia are characterized by a reduced diversity and a specific composition that differs from the urethral microbiota. These results may be useful in further to study the role of microbiota in the pathology of spermatogenesis and developing new approaches to the treatment and diagnosis of male infertility.

H. pylori eradication therapy leads to significant changes in the gut microbiome, including influence on the gut microbiome’s functional potential. Probiotics are one of the most studied potential methods for reducing the microbiota-related consequences of antibiotics. However, the beneficial effects of probiotics are still under discussion. In addition, there are some concerns about the safety of probiotics, emphasizing the need for research of other therapeutic interventions. The aim of our study was to evaluate the influence of butyric acid+inulin supplements on gut microbiota changes (the gut microbiota composition, abundance of metabolic pathways, and gut resistome) caused by H. pylori eradication therapy. Materials and methods. Twenty two H. pylori-positive patients, aged 19 to 64 years, were enrolled in the study and randomized into two treatment groups, as follows: (1) ECAB-14 (n = 11), with esomeprazole 20 mg, clarithromycin 500 mg, amoxicillin 1000 mg, and bismuthate tripotassium dicitrate 240 mg, twice daily, per os, for 14 days, and (2), ECAB-Z-14 (n = 11), with esomeprazole 20 mg, clarithromycin 500 mg, amoxicillin 1000 mg, and bismuthate tripotassium dicitrate 240 mg, twice daily, along with butyric acid+inulin (Zacofalk), two tablets daily, each containing 250 mg of butyric acid, and 250 mg of inulin, per os, for 14 days. Fecal samples were collected from each subject prior to eradication therapy (time point I), after the end of eradication therapy (time point II), and a month after the end of eradication therapy (time point III). The total DNA from the fecal samples was isolated for whole genome sequencing using the Illumina NextSeq 500 platform. Qualitative and quantitative changes in gut microbiota were assessed, including alpha and beta diversity, functional potential and antibiotic resistance gene profiling. Results. Gut microbiota alpha diversity significantly decreased compared with the baseline immediately after eradication therapy in both treatment groups (ECAB-14 and ECAB-Z-14). This diversity reached its baseline in the ECAB-Z-14 treatment group a month after the end of eradication therapy. However, in the ECAB-14 treatment arm, a reduction in the Shannon index was observed up to a month after the end of H. pylori eradication therapy. Fewer alterations in the gut microbiota functional potential were observed in the ECAB-Z-14 treatment group. The abundance of genes responsible for the metabolic pathway associated with butyrate production decreased only in the ECAB-14 treatment group. The prevalence of antibiotic-resistant genes in the gut microbiota increased significantly in both treatment groups by the end of treatment. However, more severe alterations were noted in the ECAB-14 treatment group. Conclusions. H. pylori eradication therapy leads to taxonomic changes, a reduction in the alpha diversity index, and alterations in the functional potential of the gut microbiota and gut resistome. Taking butyric acid+inulin supplements during H. pylori eradication therapy could help maintain the gut microbiota in its initial state and facilitate its recovery after H. pylori eradication.

The Volga River is one of the largest rivers in Russia, which plays an important role in the life of many plants, animals and humans. Annual research of the river microbiota is an integral part of the work to preserve the river ecosystem and ensure its sustainable development. The work analysed the composition of the microbiota using high-throughput sequencing methods, as well as physicochemical indicators over a three-year period from 2017 to 2019. A stable microbiota community and changes in chemical oxygen consumption and microbial diversity of the Volga River community were revealed.

Introduction. Everywhere, about 15% of couples of reproductive age have the problem of infertility, with the male factor being the main cause in 50% of cases. The lack of effective treatment for male