Recent studies have suggested that periodontal disease and alterations in the oral microbiome may be associated with cognitive decline and Alzheimer’s disease (AD) development. Here, we report a case-control study of oral microbiota diversity in AD patients compared to healthy seniors from Central Asia. We have characterized the bacterial taxonomic composition of the oral microbiome from AD patients (n = 64) compared to the healthy group (n = 71) using 16S ribosomal RNA sequencing. According to our results, the oral microbiome of AD has a higher microbial diversity, with an increase in Firmicutes and a decrease in Bacteroidetes in the AD group. LEfSe analysis showed specific differences at the genus level in both study groups. A region-based analysis of the oral microbiome compartment in AD was also performed, and specific differences were identified, along with the absence of differences in bacterial richness and on the functional side. Noteworthy findings demonstrated the decrease in periodontitis-associated bacteria in the AD group. Distinct differences were revealed in the distribution of metabolic pathways between the two study groups. Our study confirms that the oral microbiome is altered in AD. However, a comprehensive picture of the complete composition of the oral microbiome in patients with AD requires further investigation.

Background: Ulcerative colitis (UC) is an idiopathic and heterogeneous large intestine disease, characterized by chronic mucosa and submucosa inflammation. Alteration of the intestinal microbiome in UC may be responsible for modifications in metabolite production. Aim: To investigate the microbiota status and trimethylamine-N-oxide (TMAO) metabolite levels in patients with UC according to clinical and endoscopic activity. Methods: As part of a grant project AP14871959 from September 2022 to October 2023, 31 patients with UC and 15 healthy volunteers over 18 years at the Clinic of NCJSC “KMU” were assessed for blood TMAO level and metagenomic sequencing of fecal microbiome. Results: A significant depletion of the main representatives of Bacteroides, Parabacteroides, Prevotella; and an increase in the relative abundance of the genera Actinomyces, Klebsiella, Limosilactobacillus, Streptococcus, Escherichia-Shigella were detected in patients with UC. The number of p_Actinobacteria (g_Collinsella) and p_Eubacterium (g_Xylanophilum) representatives with genes encoding TMA-trimethylamine conversion is significantly reduced in UC patients. TMAO levels were significantly lower in UC patients than in healthy individuals (0.233 µmol/L, p = 0.004). TMAO decreased with disease severity and significantly differed between patients with different activities (p = 0.034). Conclusions: The composition of the intestinal microbiome changes and the level of TMAO decreases in patients with UC at different activities.

Background: The impact of maternal obesity on offspring health remains a major and pressing issue. We investigated its impact on the development of the infant gut microbiome during the first six months of life, examining the taxonomic composition, metabolic pathways, and antibiotic resistance genes. Methods: Twenty-four mother–infant pairs were divided into maternally obese (OB, BMI > 36) and normal weight (BM) groups. Shotgun metagenomic sequencing was performed on stool samples collected at birth and at 1, 3, and 6 months. A total of 12 maternal samples and 23 infant samples (n = 35) in the obese group and 12 maternal samples and 30 infant samples (n = 42) in the control group were sequenced. The analysis included taxonomic profiling (MetaPhlAn 4), metabolic pathway analysis (HUMAnN 3), and antibiotic resistance gene screening (CARD/ABRicate). Results: The OB group showed reduced alpha diversity in the first month (p ≤ 0.01) and an increased Firmicutes/Bacteroidetes ratio, peaking at 3 months (p ≤ 0.001). The metabolic profiling revealed enhanced carbohydrate breakdown (p ≤ 0.001) in the BM group and lipid biosynthesis (p ≤ 0.0001) in the OB group pathways. Strong correlations emerged between Lactobacillales and fatty acid biosynthesis (r = 0.7, p ≤ 0.0001) and between Firmicutes and lincosamide (r = 0.8, p ≤ 0.0001). Conclusions: The infants of obese mothers had significantly altered development of the infant gut microbiome, affecting both composition and metabolic potential. These changes may have long-term health consequences and suggest potential therapeutic targets for intervention.

Roux-en-Y gastric bypass (RYGB) surgery induces profound gut microbiota alterations that may impact metabolic outcomes. This study investigated site-specific effects of a multicomponent bovine colostrum-honey-serviceberry (CHJ) complex on post-RYGB microbiome changes in obese rats. Twenty-nine Wistar rats underwent RYGB surgery with CHJ supplementation, followed by mucosal-associated microbiota analysis from five gastrointestinal segments using 16S rRNA sequencing and serum metabolite profiling. RYGB caused regional-specific changes: decreased alpha diversity, systematic Proteobacteria increases (31.2 ± 5.1% in duodenum), and reductions in SCFA-producing bacteria (Romboutsia, Roseburia). CHJ supplementation exhibited dual effects on the microbiome: restoration of beneficial bacteria (Lactobacillus, Bifidobacterium) in distal segments while concurrently promoting Enterobacteriaceae growth in proximal regions. CHJ also maintained alpha diversity levels of the mucosa-associated microbiota comparable to those observed in the control group. Disconnects emerged between predicted microbial functions and systemic metabolites: thiamine pathway activation accompanied 78.5% serum vitamin B1 reduction, indicating severe absorption deficits. Three distinct patterns emerged: pro-inflammatory (proximal), decolonization (widespread Helicobacteraceae loss), and restorative (selective CHJ-mediated recovery). Results demonstrate that post-RYGB dysbiosis exhibits profound regional heterogeneity requiring segment-specific interventions and highlight complex interactions between nutritional supplementation and surgically altered gut ecology in determining metabolic outcomes.

Crohn’s disease (CD) is a multifactorial inflammatory bowel disease whose pathogenetic mechanisms are a field of ongoing study. Changes in the intestinal microbiome in CD may influence metabolite production and reflect the disease’s severity. We investigate the relationship between trimethylamine N-oxide (TMAO) and lipopolysaccharide-binding protein (LPS) levels and changes in the gut microbiome in patients with CD of various degrees of activity. Methods: In total, 29 CD patients and 15 healthy individuals were investigated for their levels of TMAO by HPLC-MS, and LPS protein by ELISA and metagenomic 16 s-sequencing of feces was performed. Results: We found significant differences in TMAO levels in patients in the remission/mild and moderate/severe groups compared to the control group (p = 0.02 and p = 0.014), changes in alpha diversity with the Shannon index (p = 0. 0151 and p = 0.0018) and in beta diversity (ANOSIM p = 0.009 and PERMANOVA p = 0.005) in both groups compared to controls. Strongly positive correlations in TMAO levels and mixed correlations of LPS with alpha diversity metrics were found, as well as significant correlations with microbiota species. Conclusions: Changes in the level of metabolites may reflect specific disturbances in the composition of the intestinal microbiome at different degrees of severity of CD.

Radioactive compounds, including silicon dioxide ( ³¹ SiO ₂ ), may enter the environment and affect biological systems, yet their impact on the gut microbiota remains poorly studied. This study aimed to evaluate the effects of radioactive ³¹ SiO ₂ , compared to non-radioactive SiO ₂ and gamma irradiation, on the composition and functionality of the gut microbiota in laboratory Wistar rats (n = 28). Gut microbiota analysis of the large intestine, small intestine, and Peyer’s patches was conducted at 90 min and 72 h post-exposure using 16S rRNA sequencing. Alpha-diversity results showed increased species richness in Peyer’s patches at 90 min after exposure to radioactive ³¹ SiO ₂ , with elevated Bacilli and Gammaproteobacteria, a trend persisting at 72 h. In the small intestine, radioactive ³¹ SiO ₂ increased Bacilli and Clostridia at 3 days, while Gammaproteobacteria considerably decreased; by 72 h, Bacilli and Clostridia maintained growth, with Gammaproteobacteria recovering. These findings demonstrate that radioactive ³¹ SiO ₂ dynamically alters gut microbiota composition and diversity, highlighting its unique influence on microbial communities.