Almagul Kushugulova

Subspecies in the global human gut microbiome

Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large‐scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture‐independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single‐nucleotide variation clearly indicates the existence of sub‐populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies‐specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro‐inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.

Gut microbiome and aging: Physiological and mechanistic insights

The development of human gut microbiota begins as soon as the neonate leaves the protective environment of the uterus (or maybe in-utero) and is exposed to innumerable microorganisms from the mother as well as the surrounding environment. Concurrently, the host responses to these microbes during early life manifest during the development of an otherwise hitherto immature immune system. The human gut microbiome, which comprises an extremely diverse and complex community of microorganisms inhabiting the intestinal tract, keeps on fluctuating during different stages of life. While these deviations are largely natural, inevitable and benign, recent studies show that unsolicited perturbations in gut microbiota configuration could have strong impact on several features of host health and disease. Our microbiota undergoes the most prominent deviations during infancy and old age and, interestingly, our immune health is also in its weakest and most unstable state during these two critical stages of life, indicating that our microbiota and health develop and age hand-in-hand. However, the mechanisms underlying these interactions are only now beginning to be revealed. The present review summarizes the evidences related to the age-associated changes in intestinal microbiota and vice-versa, mechanisms involved in this bi-directional relationship, and the prospective for development of microbiota-based interventions such as probiotics for healthy aging.

Expanding the Metchnikoff Postulate: Oral Health Is Crucial in a Successful Global Aging Management Strategy

The mouth offers a unique opportunity for the physician and dental hygienist to evaluate and monitor a number of early nutritional-related diseases and vitamin deficiencies in still-healthy people. Increasing evidence suggests that periodontal disease might be associated with several systemic diseases (diabetes, immunosuppression, obesity, hormonal changes). Conversely, oral/periodontal disease might be the perpetuating factor or possibly the trigger of chronic illnesses via the activation of pro-inflammatory cytokines from monocytes and polymorphonuclear leukocytes in the sub-gingival biofilm and oral microbiome unbalance. Office-based microbiological and susceptibility genomic testing in the oral cavity (e.g., BACTOdent-DENTYgen, 4P-Genomics, Luxembourg) are expected to be widespread tools in a global approach for an age-management strategy connecting oral health and personalized solutions.

Antioxidant activity of the probiotic consortium in vitro

Introduction Available evidence suggests that probiotics have different biological functions that depend on several mechanisms, such as antioxidant and DNA-protective activities. The probiotic consortium includes bacterial cultures such as Streptococcus thermophilus, Lactococcus lactis, Lactobacillus plantarum, and other bacterial cultures isolated from traditional Kazakh dairy products (ayran, kumys, shubat, and healthy clinical material). The aim of this study was to investigate the total antioxidant activity of the consortium of probiotic bacteria and to determine the activity of superoxide dismutase, glutathione reductase, and DNA-protective action. Material and methods In vitro comet assay was used to determine the antigenotoxicity of the probiotic consortium. Total antioxidant activity was determined using a method of analysis with Trolox as the equivalent. The analysis method of superoxide dismutase activity assesses the inhibition rate of the nitroblue tetrazolium reduction to formazan by superoxide dismutase. Determination of glutathione reductase activity is based on the measurement of the NADPH oxidation speed. Results A significantly high level of the total antioxidant activity of the probiotic consortium intact cells (15.3 mM/ml) was observed whereas the activity index of lysate was 11.1 mM/ml. The superoxide dismutase activity of probiotic consortium lysate was evaluated, with values that peaked at 0.24 U/mg protein. The superoxide dismutase activity of the consortium was lower in comparison to L.fernentum E-3 and L.fernentum E-18 cultures with values of 0.85 U/mg and 0.76 U/mg protein, respectively. SOD activity of probiotic consortium whole cells was not observed, which is typical for lactic acid bacteria. Glutathione reductase plays an important role in the optimal protection from oxidative stress. Glutathione reductase activity of the studied probiotic consortium was low; moreover, the activity of the lysate was two times higher than the activity of the cells reaching 0.01 units/ml. Investigations by Dr. Li have shown that the intracellular glutathione may give a significant protection of Lactococcus from the damaging action of H2O2, even at very low concentrations. The data from our study suggests that the co-incubation of the epithelial cells with probiotic bacteria reduces the percentage of damaged cells (damage index–0.60). Conclusion The studied probiotic consortium has antigenotoxic and antioxidant activities. Preparations and products of this probiotic consortium may serve as a protective component in the intestinal microbial ecosystem.

Metagenomic analysis of gut microbial communities from a Central Asian population

Objective Changes in the gut microbiota are increasingly recognised to be involved in many diseases. This ecosystem is known to be shaped by many factors, including climate, geography, host nutrition, lifestyle and medication. Thus, knowledge of varying populations with different habits is important for a better understanding of the microbiome. Design We therefore conducted a metagenomic analysis of intestinal microbiota from Kazakh donors, recruiting 84 subjects, including male and female healthy subjects and metabolic syndrome (MetS) patients aged 25–75 years, from the Kazakh administrative centre, Astana. We characterise and describe these microbiomes, the first deep-sequencing cohort from Central Asia, in comparison with a global dataset (832 individuals from five countries on three continents), and explore correlations between microbiota, clinical and laboratory parameters as well as with nutritional data from Food Frequency Questionnaires. Results We observe that Kazakh microbiomes are relatively different from both European and East Asian counterparts, though similar to other Central Asian microbiomes, with the most striking difference being significantly more samples falling within the Prevotella-rich enterotype, potentially reflecting regional diet and lifestyle. We show that this enterotype designation remains stable within an individual over time in 82% of cases. We further observe gut microbiome features that distinguish MetS patients from controls (eg, significantly reduced Firmicutes to Bacteroidetes ratio, Bifidobacteria and Subdoligranulum, alongside increased Prevotella), though these overlap little with previously published reports and thus may reflect idiosyncrasies of the present cohort. Conclusion Taken together, this exploratory study describes gut microbiome data from an understudied population, providing a starting point for further comparative work on biogeography and research on widespread diseases. Trial registration number ISRCTN37346212; Post-results.

Analysis of genetic aspects of therapy with Rosuvastatin

Statins widely used in clinical practice in decreasing the level of lipids in blood plasma. Difference of response for therapy may be associated with structural changes in genes of metabolism of drugs. Main polymorphisms of genes of metabolism which impact on effectiveness and security of rosuvastatin are studied in review.

Draft Genome Sequence of Lactobacillus rhamnosus CLS17

ABSTRACT We announce the draft genome sequence of the type strain Lactobacillus rhamnosus CLS17 (2,889,314 nt, with a GC content of 46.8%), which is one of the most prevalent lactic acid bacteria present during the manufacturing process of dairy products; the genome consists of 71 large contigs (>100 bp in size). It contains 2,643 protein-coding sequences, single predicted copies of the 5S, 16S, and 23S rRNA genes, and 51 predicted tRNAs.

Gut-targeted immunonutrition boosting natural killer cell activity using saccharomyces boulardii lysates in immuno-compromised healthy elderly subjects

The aim of this study was to assess the immunomodulatory effect of KC-1317 (a symbiotic mixture containing Saccharomyces boulardii lysate in a cranberry, colostrum-derived lactoferrin, fragaria, and lactose mixture) supplementation in immune-compromised but otherwise healthy elderly subjects. A liquid formulation of KC-1317 was administered in a randomized controlled trial (RCT) fashion to healthy volunteers (65-79 years) previously selected for low natural killer (NK) cell activity, and this parameter was checked at the completion of the study. A significant improvement in NK cell activity of KC-1317 consumers was observed as compared to placebo at the end of 2 months. Although preliminary, these beneficial immune-modulatory effects of KC-1317 in aged individuals might indicate its employment within a wider age-management strategy.

Influence of Probiotic Consortium on TH1 and TH2 Immune Response

Introduction The main role of probiotics is to maintain homeostasis in the intestines and improve bowel protective function. The aim of the present study is to investigate immuno-modulatory effects of a probiotic consortium. Methods Observations were carried out in vitro. The presence of IL-2, IL-4, IL-6, IL-8, IL-10, TNF-α, IFN-γ, IgA, IgM, and IgE was studied using a solid-phase enzyme immunosorbent assay on the VECTOR-BEST sets (Russia). Results Immunomodulatory properties of the probiotic consortium were studied, which consisted of the following strains: Streptococcus thermophilus, Lactococcus lactis, Lactobacillus plantarum, Lactobacillus fermentum, Lactobacillus acidophilus, Bifidobacterium longum, and Bifidobacterium bifidum. Elevated concentrations of INFγ in control samples decreased 3.9 times (p < 0.05) after a saturation of blood with the probiotic consortium. Significant reduction of cytokine levels after the probiotic effects of the consortium was observed in IL-10 by 2.1 times (p < 0.05) and IgA by 1.87 times (p < 0.0005). There was a significant increase in the levels of IL-4, IgE, IL-6, and IL-8 by 1.3 (p < 0.005), 1.1 (p < 0.5), 18.0 (p < 0.005), and 6 (p < 0.05) times, respectively, in comparison with the control samples. IL-4 and INFγ have different effects on the synthesis of IgE. Soluble low affinity receptors FcɛRII (CD23) in association with IL-4 facilitate a differentiation of the B-lymphocytes in IgE-synthesizing cells, while γ-INF inhibits this process. It is known that the intracellular expression of γ-INF and IL-4 is the most reliable marker for Th1 and Th2 immune responses, respectively. The conducted studies determined that the ratio of INF-γ/IL-4 was 0.9 (control 4.8, P < 0.005) after the saturation of the blood cells with probiotic consortium. NF-γ/IL4 ratio decreased by 5.3 times compared with a control value, which indicates a reduction in the functional activity of Th1 type lymphocytes in comparison with the function of Th2 cells. Conclusion The application of the probiotic consortium results in the maintenance of homeostasis by the stimulation of immune function through the activation of humoral immunity. Moreover, the probiotic application changes the orientation of the immunological memory causing the cancellation of the recruitment of Th1 cells in the response.

Health benefits of new symbiotic “NAR”

Introduction The immune-modulatory effects of synbiotics and their ability to reduce free radical levels may be useful for functional food that is able to be active throughout whole period of colonization of the gastrointestinal tract. The aim of the present study was to investigate the immune-modulatory and antioxidant effects of the synbiotic product “NАR,” a probiotic beverage. Methods The presence of IL-2, IL-4, IL-6, IL-8, IL-10, αTNF, γIFN, Ig A, Ig M, and Ig E was studied in vitro using a solid immunosorbent analysis. The total antioxidant activities of superoxide dismutase and glutathione reductase were determined by a spectrophotometry using the Sigma-Aldrich sets. Results Studies of the immune-modulatory properties of the synbiotic product NAR showed 1.7 fold increase of γINF levels (p<0.01) in blood after consumption of the synbiotic product “NAR” in comparison to control values, whereas the concentrations of IL-4 and Ig E decreased 2.0 times (treatment: 9.3; control: 18.7; p<0.01) and 1.3 times (p<0.1), respectively. The consumption of the synbiotic product “NAR” caused an increase in the proportion of γINF/IL 4 (treatment: 15.4; control: 4.4; p<0.01), which indicates a reduction in functional activity of Th2-type lymphocytes in comparison with the function of Th1 cells. Our study showed a high level of the total antioxidant activity of the synbiotic product (67.4 mmol/ml). The antioxidant activity of the intact cells of consortium (15.3 mM/ml), which was the basis for the preparation of the symbiotic product, is several times lower than the activity observed in the symbiotic samples. Expression of SOD is one of the mechanisms of antioxidant stress radicals inactivation by bacteria. The analysis identified a superoxide dismutase activity of synbiotic product (1.42 U/mg protein). A glutathione reductase activity of the synbiotic product was elevated (0.06 U/ml). Conclusion The majority of the inflammatory mediators found in the blood after the consumption of symbiotic product NAR were inflammatory mediators that activate a cellular component of the resistance. Moreover, the symbiotic product has a high antioxidant activity.