Soil health is a critical determinant of agricultural productivity and environmental sustainability. Traditional assessment methods often fail to provide a comprehensive understanding of soil microbial communities and their functions. This study addresses this challenge by employing metagenomic techniques to assess the functionality of soil microbiomes in Russian black soil, renowned for its high fertility. We utilized shotgun metagenomic sequencing to analyze soil samples from Western Siberia subjected to different degrees of agro-soil disturbance. We identified functional genes involved in carbon (accA, argG, acsA, mphE, miaB), phosphorus (phoB, ppa, pstB, pnp, phnJ), and nitrogen (queC, amiF, pyrG, guaA, guaB, napA) metabolic pathways and associated with changes in microbial diversity, in general, and higher representation of certain bacterial species—Bradyrhizobium spp. The results demonstrated significant differences in microbial composition and functional potential between tillage treatments. No-Till technology and conventional tillage practices promoted beneficial microbial communities and enhanced soil health compared to long-term fallow soil. This work underscores the potential of metagenomic analysis in providing a comprehensive understanding of soil health, marking a significant advancement in the field.

Soil health is a critical determinant of agricultural productivity and environmental sustainability. Traditional assessment methods often fail to provide a comprehensive understanding of soil microbial communities and their functions. This study addresses this challenge by employing metagenomic techniques to assess the functionality of soil microbiomes in Russian black soil, renowned for its high fertility. We utilized shotgun metagenomic sequencing to analyze soil samples from Western Siberia subjected to different degrees of agro-soil disturbance. We identified functional genes involved in carbon (accA, argG, acsA, mphE, miaB), phosphorus (phoB, ppa, pstB, pnp, phnJ), and nitrogen (queC, amiF, pyrG, guaA, guaB, napA) metabolic pathways and associated with changes in microbial diversity in general and higher representation of certain bacterial species - Bradyrhizobium spp. Results demonstrated significant differences in microbial composition and functional potential between tillage treatments. No-Till technology and conventional tillage practices promoted beneficial microbial communities and enhanced soil health compared to long-term fallow soil. This work underscores the potential of metagenomic analysis in providing a comprehensive understanding of soil health, marking a significant advancement in the field.

Agricultural and industrial activities are increasing pollution of water bodies with low doses of xenobiotics that have detrimental effects on aquaculture. The aim of this work was to determine the possibility of using Levilactobacillus brevis 47f culture in fish aquaculture under the influence of low doses of xenobiotics as an adaptogen. An increase in the survival of Danio rerio individuals exposed to the xenobiotic bisphenol A solution and fed with the L. brevis 47f was shown compared to control groups and, at the same time, the cytokine profile in the intestinal tissues of Danio rerio was also investigated. Analysis of differential gene expression of the L. brevis 47f grown under the action of high concentrations of bisphenol A showed changes in mRNA levels of a number of genes, including genes of various transport proteins, genes involved in fatty acid synthesis, genes of transcriptional regulators, genes of the arabinose operon, and the oppA gene. The identification of L. brevis 47f proteins from polyacrylamide gel by mass spectrometry revealed L-arabinose isomerase, Clp chaperone subunit, ATP synthase subunits, pentose phosphate pathway and glycolysis enzyme proteins, which are likely part of the L. brevis 47f strain’s anti-stress response, but probably do not affect its adaptogenic activity toward Danio rerio.

In 2022, the World Health Organization reported that tuberculosis (TB) was the second leading cause of death globally from a single infectious agent, following COVID-19. The development of new antitubercular agents with novel mechanisms of action for use in complex TB therapy is considered a key approach to combating TB. In this study, we examined the gene expression profile of M. smegmatis when exposed to a promising antituberculosis agent, quinoxaline 1,4-dioxide (QdNO) 7-chloro-2-(ethoxycarbonyl)-3-methyl-6-(piperazin-1-yl)quinoxaline-1,4-dioxide-1 (LCTA-3368). We investigated how the bacterial response changed with different doses (1/4 × MIC, 1/2 × MIC, and 1 × MIC) and durations (30 minutes and 90 minutes) of treatment with the drug. Our analysis revealed significant upregulation of genes involved in DNA repair and replication processes, as well as changes in the expression of 95 genes encoding proteins with oxidoreductase activity. These findings support the proposed mechanism of antibacterial action of QdNOs, which is associated with the formation of free radicals leading to DNA damage.

Faecalibacterium prausnitzii is a dominant commensal bacterium in the human gut, widely known for its anti-inflammatory and immunomodulatory properties and currently considered a potential pharmabiotic for the treatment of various human diseases. In this study, ten new strains of F. prausnitzii were isolated from stool samples of Russian children and characterized using hybrid genome sequencing and metabolomic analyses. Comparative genomics revealed an open pangenome structure and significant strain-specific variability, reflecting the high adaptive potential of strains in humans and confirming the heterogeneity of this species previously described in the literature. Several isolates (fp1, fp5, fp7, fp9) showed increased butyrate production, while fp1 showed increased formate synthesis. In silico analysis confirmed the presence of genes associated with anti-inflammatory, antioxidant, and neuromodulatory metabolites, as well as the absence of antibiotic resistance genes. These results expand on previously described findings on the genetic diversity of F. prausnitzii and identify promising, safe strains with high pharmabiotics potential for future human therapy.

Faecalibacterium prausnitzii is a dominant commensal bacterium in the human gut, widely known for its production of bioactive metabolites and currently considered a potential pharmabiotic for the treatment of various human diseases. In this study, ten novel strains of Faecalibacterium prausnitzii were isolated from stool samples of Russian infants and characterized using whole genome sequencing and metabolomic analyses. Comparative genomic analysis revealed an open pangenome structure and significant strain-specific variability, reflecting the strains’ high adaptive potential within the human host and confirming the heterogeneity of this species. Four isolates (MSK-01, MSK-05, MSK-07, MSK-09) exhibited elevated butyrate production, and MSK-01 additionally displayed enhanced formate synthesis. The previously developed catalog of genes with anti-inflammatory, immune, and neuromodulatory activity was used for in silico analysis and targeted annotation of sequenced genomes. In silico analysis confirmed the presence of genes associated with anti-inflammatory, antioxidant, and neuromodulatory metabolites. Strains MSK-07 and MSK-09 were selected as the top candidates for development as infant pharmabiotics. These results expand on previously described findings on the genetic diversity of Faecalibacterium prausnitzii and identify promising strains with high pharmabiotic potential for future human therapy. These findings allow us to proceed to the next stages of selection and development of pharmabiotics for microbiome correction.