Natalia Danilova

BACKGROUND: Several studies have highlighted the role of host-microbiome interactions in the pathogenesis of inflammatory bowel disease (IBD), resulting in an increasing amount of data mainly focusing on Western patients. Because of the increasing prevalence of IBD in newly industrialized countries such as those in Asia, the Middle East, and South America, there is mounting interest in elucidating the gut microbiota of these populations. We present a comprehensive analysis of several IBD-related biomarkers and gut microbiota profiles and functions of a unique population of patients with IBD and healthy patients from Kazan (Republic of Tatarstan, Russia). METHODS: Blood and fecal IBD biomarkers, serum cytokines, and fecal short-chain fatty acid (SCFA) content were profiled. Finally, fecal microbiota composition was analyzed by 16S and whole-genome shotgun sequencing. RESULTS: Fecal microbiota whole-genome sequencing confirmed the presence of classic IBD dysbiotic features at the phylum level, with increased abundance of Proteobacteria, Actinobacteria, and Fusobacteria and decreased abundance of Firmicutes, Bacteroidetes, and Verrucomicrobia. At the genus level, the abundance of both fermentative (SCFA-producing and hydrogen (H2)-releasing) and hydrogenotrophic (H2-consuming) microbes was affected in patients with IBD. This imbalance was confirmed by the decreased abundance of SCFA species in the feces of patients with IBD and the change in anaerobic index, which mirrors the redox status of the intestine. CONCLUSIONS: Our analyses highlighted how IBD-related dysbiotic microbiota-which are generally mainly linked to SCFA imbalance-may affect other important metabolic pathways, such as H2 metabolism, that are critical for host physiology and disease development.

AIM: The aim of the study was to study the taxonomic and functional composition of the gut microbiota in ulcerative colitis (UC) and Crohn's disease (CD) patients to identify key markers of dysbiosis in IBD. MATERIALS AND METHODS: Fecal samples obtained from 95 IBD patients (78 UC and 17 CD) as well as 96 healthy volunteers were used for whole-genome sequencing carried out on the SOLiD 5500 W platform. Taxonomic profiling was performed by aligning the reeds, not maped on hg19, on MetaPhlAn2 reference database. Reeds were mapped using the HUNAnN2 algorithm to the ChocoPhlAn database to assess the representation of microbial metabolic pathways. Short-chain fatty acids (SCFA) level were measured in fecal samples by gas-liquid chromatographic analysis. RESULTS: Changes in IBD patients gut microbiota were characterized by an increase in the representation of Proteobacteria and Bacteroidetes phyla bacteria and decrease in the number of Firmicutes phylum bacteria and Euryarchaeota phylum archaea; a decrease in the alpha-diversity index, relative representation of butyrate-producing, hydrogen-utilizing bacteria, and Methanobrevibacter smithii; increase in the relative representation of Ruminococcus gnavus in UC and CD patients and Akkermansia muciniphila in CD patients. Reduction of Butyryl-CoA: acetate CoA transferase gene relative representation in CD patients, decrease of absolute content of SCFA total number as well as particular SCFAs and main SCFAs ratio in IBD patients may indicate inhibition of functional activity and number of anaerobic microflora and/or an change in SCFA utilization by colonocytes. CONCLUSION: the revealed changes can be considered as typical signs of dysbiosis in IBD patients and can be used as potential targets for IBD patients personalized treatment development.

Abstract Background Antibiotics are widely used to treat animals from infections. After fertilizing, antibacterials can remain in the soil while adversely affecting the soil microorganisms. The concentration of oxytetracycline (OTC) in the soil and its effect on the soil microbial community was assessed. To assess the impact of OTC on the soil microbial community, it was added to the soil at concentrations of 50, 150, and 300 mg kg –1 and incubated for 35 days. Results The concentration of OTC added to the soil decreased from 150 to 7.6 mg kg –1 during 30 days of incubation, as revealed by LC-MS. The deviations from the control values in the level of substrate-induced respiration on the 5th day of the experiment were, on average, 26, 68, and 90%, with OTC concentrations at 50, 150, and 300 mg kg –1 , respectively. In samples with 150 and 300 mg kg –1 of OTC, the number of bacteria from the 3rd to 14th day was 2–3 orders of magnitude lower than in the control. The addition of OTC did not affect the fungal counts in samples except on the 7th and 14th days for the 150 and 300 mg kg –1 contaminated samples. Genes tet (M) and tet (X) were found in samples containing 50, 150, and 300 mg kg –1 OTC, with no significant differences in the number of copies of tet (M) and tet (X) genes from the OTC concentration. Conclusions Our results showed that even after a decrease in antibiotic availability, its influence on the soil microbial community remains.

Crystalline Ni2B, Ni3B, and Ni4B3 are synthesized by a single-step method using autogenous pressure from the reaction of NaBH4 and Ni precursors. The effect of reaction temperature, pressure, time, and starting materials on the composition of synthesized products, particle morphologies, and magnetic properties is demonstrated. High yields of Ni2B (>98%) are achieved at 2.3–3.4 MPa and ~670 °C over five hours. Crystalline Ni3B or Ni4B3 form in conjunction with Ni2B at higher temperature or higher autogenous pressure in proportions influenced by the ratios of initial reactants. For the same starting ratios of reactants, a longer reaction time or higher pressure shifts equilibria to lower yields of Ni2B. Using this approach, yields of ~88% Ni4B3 (single phase orthorhombic) and ~72% Ni3B are obtained for conditions 1.9 MPa < Pmax < 4.9 MPa and 670 °C < Tmax < 725 °C. Gas-solid reaction is the dominant transformation mechanism that results in formation of Ni2B at lower temperatures than conventional solid-state methods.

Antibiotics enter the soil with compost prepared from livestock manures and other sources. There is concern that they may influence plant growth and cause antibiotic resistance in soil and plant endospheric microbiomes. In the present work, lettuce plants were cultivated in soil and hydroponics spiked with oxytetracycline (0, 15, and 300 mg × kg−1 and 0, 15, and 50 mg × L–1, respectively) during a 28-day greenhouse experiment. It was revealed that the antibiotic reduced the chlorophyll content, the biomass, and the length of the roots and stems by 1.4–4.7, 1.8–39, 2.5–3.2, and 1.8–6.3 times in soil and in hydroponics. The copy numbers of the tet(A) and tet(X) genes were revealed to be 4.51 × 103–1.58 × 105 and 8.36 × 106–1.07 × 108 copies × g–1, respectively, suggesting the potential migration of these genes from soil/hydroponics to plant roots and leaves. According to a non-metric multidimensional scaling (NMDS) analysis of the 16S rRNA amplicon sequencing data, endospheric bacterial communities were similar in leaves and roots independent of the growing substrate and antibiotic concentration. While soil bacterial communities were unaffected by the presence of antibiotics, hydroponic communities exhibited dependency, likely attributable to the absence of the mitigating effect of soil particle absorption.