Development of a novel prostate Cancer-Stroma Sphere (CSS) model for In Vitro tumor microenvironment studies.

Tumor employs non-cancerous cells to gain beneficial features that promote growth and survival of cancer cells. Despite intensive research in the area of tumor microenvironment, there is still a lack of reliable and reproducible in vitro model for tumor and tumor-microenvironment cell interaction studies. Herein we report the successful development of a heterogeneous cancer-stroma sphere (CSS) model composed of prostate adenocarcinoma PC3 cells and immortalized mesenchymal stem cells (MSC). The CSS model demonstrated a structured spatial layout of the cells, with stromal cells concentrated at the center of the spheres and tumor cells located on the periphery. Significant increase in the levels of VEGFA, IL-10, and IL1a has been detected in the conditioned media of CSS as compared to PC3 spheres. Single cell RNA sequencing data revealed that VEGFA was secreted by MSC cells within heterogeneous spheroids. Enhanced expression of extracellular membrane (ECM) proteins was also shown for CSS-derived MSCs. Furthermore, we demonstrated that the multicellular architecture altered cancer cell response to chemotherapeutic agents: the inhibition of sphere formation by topotecan was 74.92 ± 4.56 % for PC3 spheres and 45.95 ± 7.84 % for CSS spheres (p < 0.01), docetaxel showed 37,51± 20,88 % and 15,67± 14,08 % inhibition, respectively (p < 0.05). Thus, CSS present an effective in vitro model for examining the extracellular matrix composition and cell-to-cell interactions within the tumor, as well as for evaluating the antitumor activity of drugs.

Genome-Wide Association Study of Exercise-Induced Fat Loss Efficiency.

There is a wide range of individual variability in the change of body weight in response to exercise, and this variability partly depends on genetic factors. The study aimed to determine DNA polymorphisms associated with fat loss efficiency in untrained women with normal weight in response to a 12-week aerobic training program using the GWAS approach, followed by a cross-sectional study in athletes. The study involved 126 untrained young Polish women (age 21.4 ± 1.7 years; body mass index (BMI): 21.7 (2.4) kg/m2) and 550 Russian athletes (229 women, age 23.0 ± 4.1; 321 men, age 23.9 ± 4.7). We identified one genome-wide significant polymorphism (rs116143768) located in the ACSL1 gene (acyl-CoA synthetase long-chain family member 1, implicated in fatty acid oxidation), with a rare T allele associated with higher fat loss efficiency in Polish women (fat mass decrease: CC genotype (n = 122) -3.8%; CT genotype (n = 4) -31.4%; p = 1.18 × 10-9). Furthermore, male athletes with the T allele (n = 7) had significantly lower BMI (22.1 (3.1) vs. 25.3 (4.2) kg/m2, p = 0.046) than subjects with the CC genotype (n = 314). In conclusion, we have shown that the rs116143768 T allele of the ACSL1 gene is associated with higher fat loss efficiency in response to aerobic training in untrained women and lower BMI in physically active men.

Anti-Citrullinated Peptide Antibodies Control Oral Porphyromonas and Aggregatibacter species in Patients with Rheumatoid Arthritis.

Oral microbiome changes take place at the initiation of rheumatoid arthritis (RA); however, questions remain regarding the oral microbiome at pre-RA stages in individuals with clinically suspect arthralgia (CSA). Two cross-sectional cohorts were selected including 84 Tatarstan women (15 early-RA as compared to individuals with CSA ranging from CSA = 0 [n = 22], CSA = 1 [n = 19], CSA = 2 [n = 11], and CSA ≥ 3 [n = 17]) and 42 women with established RA (median: 5 years from diagnosis [IQ: 2-11]). Amplicon sequence variants (ASVs) obtained from oral samples (16S rRNA) were analyzed for alpha and beta diversity along with the abundance at the genus level. A decrease in oral Porphyromonas sp. is observed in ACPA-positive individuals, and this predominates in early-RA patients as compared to non-RA individuals irrespective of their CSA score. In the RA-established cohort, Porphyromonas sp. and Aggregatibacter sp. reductions were associated with elevated ACPA levels. In contrast, no associations were reported when considering individual, genetic and clinical RA-associated factors. Oral microbiome changes related to the genera implicated in post-translational citrullination (Porphyromonas sp. and Aggregatibacter sp.) characterized RA patients with elevated ACPA levels, which supports that the role of ACPA in controlling the oral microbiome needs further evaluation.

Diversity and Adaptations of Escherichia coli Strains: Exploring the Intestinal Community in Crohn's Disease Patients and Healthy Individuals.

Crohn's disease (CD) is characterized by a chronic, progressive inflammation across the gastrointestinal tract with a series of exacerbations and remissions. A significant factor in the CD pathogenesis is an imbalance in gut microbiota composition, particularly the prevalence of Escherichia coli. In the present study, the genomes of sixty-three E. coli strains from the gut of patients with CD and healthy subjects were sequenced. In addition, eighteen E. coli-like metagenome-assembled genomes (MAGs) were reconstructed from the shotgun-metagenome sequencing data of fecal samples. The comparative analysis revealed the similarity of E. coli genomes regardless of the origin of the strain. The strains exhibited similar genetic patterns of virulence, antibiotic resistance, and bacteriocin-producing systems. The study showed antagonistic activity of E. coli strains and the metabolic features needed for their successful competition in the human gut environment. These observations suggest complex bacterial interactions within the gut which may affect the host and cause intestinal damage.

Inflammatory Bowel Disease-Associated Changes in the Gut: Focus on Kazan Patients.

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.

Whole genome sequencing of elite athletes.

Whole genome sequencing (WGS) has great potential to explore all possible DNA variants associated with physical performance, psychological traits and health conditions of athletes. Here we present, for the first time, annotation of genomic variants of elite athletes, based on the WGS of 20 Tatar male wrestlers. The maximum number of high-quality variants per sample was over 3.8 M for single nucleotide polymorphisms (SNPs) and about 0.64 M for indels. The maximum number of nonsense mutations was 148 single nucleotide variants (SNVs) per individual. Athletes' genomes on average contained 18.9 nonsense SNPs in a homozygous state per sample, while non-athletes' exomes (Tatar controls, n = 19) contained 18 nonsense SNPs. Finally, we applied genomic data for the association analysis and used reaction time (RT) as an example. Out of 1884 known genome-wide significant SNPs related to RT, we identified four SNPs (KIF27 rs10125715, APC rs518013, TMEM229A rs7783359, LRRN3 rs80054135) associated with RT in wrestlers. The cumulative number of favourable alleles (KIF27 A, APC A, TMEM229A T, LRRN3 T) was significantly correlated with RT both in wrestlers (P = 0.0003) and an independent cohort (n = 43) of physically active subjects (P = 0.029). Furthermore, we found that the frequencies of the APC A (53.3 vs 44.0%, P = 0.033) and LRRN3 T (7.5 vs 2.8%, P = 0.009) alleles were significantly higher in elite athletes (n = 107) involved in sports with RT as an essential component of performance (combat sports, table tennis and volleyball) compared to less successful (n = 176) athletes. The LRRN3 T allele was also over-represented in elite athletes (7.5%) in comparison with 189 controls (2.9%, P = 0.009). In conclusion, we present the first WGS study of athletes showing that WGS can be applied in sport and exercise science.

The association of HFE gene H63D polymorphism with endurance athlete status and aerobic capacity: novel findings and a meta-analysis.

PURPOSE: Iron is an important component of the oxygen-binding proteins and may be critical to optimal athletic performance. Previous studies have suggested that the G allele of C/G rare variant (rs1799945), which causes H63D amino acid replacement, in the HFE is associated with elevated iron indexes and may give some advantage in endurance-oriented sports. The aim of the present study was to investigate the association between the HFE H63D polymorphism and elite endurance athlete status in Japanese and Russian populations, aerobic capacity and to perform a meta-analysis using current findings and three previous studies. METHODS: The study involved 315 international-level endurance athletes (255 Russian and 60 Japanese) and 809 healthy controls (405 Russian and 404 Japanese). Genotyping was performed using micro-array analysis or by PCR. VO2max in 46 male Russian endurance athletes was determined using gas analysis system. RESULTS: The frequency of the iron-increasing CG/GG genotypes was significantly higher in Russian (38.0 vs 24.9%; OR 1.85, P = 0.0003) and Japanese (13.3 vs 5.0%; OR 2.95, P = 0.011) endurance athletes compared to ethnically matched controls. The meta-analysis using five cohorts (two French, Japanese, Spanish, and Russian; 586 athletes and 1416 controls) showed significant prevalence of the CG/GG genotypes in endurance athletes compared to controls (OR 1.96, 95% CI 1.58-2.45; P = 1.7 × 10-9). Furthermore, the HFE G allele was associated with high V̇O2max in male athletes [CC: 61.8 (6.1), CG/GG: 66.3 (7.8) ml/min/kg; P = 0.036]. CONCLUSIONS: We have shown that the HFE H63D polymorphism is strongly associated with elite endurance athlete status, regardless ethnicities and aerobic capacity in Russian athletes.

Shifts in the Human Gut Microbiota Structure Caused by Quadruple Helicobacter pylori Eradication Therapy.

The human gut microbiome plays an important role both in health and disease. Use of antibiotics can alter gut microbiota composition, which can lead to various deleterious events. Here we report a whole genome sequencing metagenomic/genomic study of the intestinal microbiota changes caused by Helicobacter pylori (HP) eradication therapy. Using approaches for metagenomic data analysis we revealed a statistically significant decrease in alpha-diversity and relative abundance of Bifidobacterium adolescentis due to HP eradication therapy, while the relative abundance of Enterococcus faecium increased. We have detected changes in general metagenome resistome profiles as well: after HP eradication therapy, the ermB, CFX group, and tetQ genes were overrepresented, while tetO and tetW genes were underrepresented. We have confirmed these results with genome-resolved metagenomic approaches. MAG (metagenome-assembled genomes) abundance profiles have changed dramatically after HP eradication therapy. Focusing on ermB gene conferring resistance to macrolides, which were included in the HP eradication therapy scheme, we have shown a connection between antibiotic resistance genes (ARGs) and some overrepresented MAGs. Moreover, some E. faecium strains isolated from stool samples obtained after HP eradication have manifested greater antibiotic resistance in vitro in comparison to other isolates, as well as the higher number of ARGs conferring resistance to macrolides and tetracyclines.

A Genome-Wide Association Study of Sprint Performance in Elite Youth Football Players.

Pickering, C, Suraci, B, Semenova, EA, Boulygina, EA, Kostryukova, ES, Kulemin, NA, Borisov, OV, Khabibova, SA, Larin, AK, Pavlenko, AV, Lyubaeva, EV, Popov, DV, Lysenko, EA, Vepkhvadze, TF, Lednev, EM, Leonska-Duniec, A, Pajak, B, Chycki, J, Moska, W, Lulinska-Kuklik, E, Dornowski, M, Maszczyk, A, Bradley, B, Kana-ah, A, Cieszczyk, P, Generozov, EV, and Ahmetov, II. A genome-wide association study of sprint performance in elite youth football players. J Strength Cond Res 33(9): 2344-2351, 2019-Sprint speed is an important component of football performance, with teams often placing a high value on sprint and acceleration ability. The aim of this study was to undertake the first genome-wide association study to identify genetic variants associated with sprint test performance in elite youth football players and to further validate the obtained results in additional studies. Using micro-array data (600 K-1.14 M single nucleotide polymorphisms [SNPs]) of 1,206 subjects, we identified 12 SNPs with suggestive significance after passing replication criteria. The polymorphism rs55743914 located in the PTPRK gene was found as the most significant for 5-m sprint test (p = 7.7 × 10). Seven of the discovered SNPs were also associated with sprint test performance in a cohort of 126 Polish women, and 4 were associated with power athlete status in a cohort of 399 elite Russian athletes. Six SNPs were associated with muscle fiber type in a cohort of 96 Russian subjects. We also examined genotype distributions and possible associations for 16 SNPs previously linked with sprint performance. Four SNPs (AGT rs699, HSD17B14 rs7247312, IGF2 rs680, and IL6 rs1800795) were associated with sprint test performance in this cohort. In addition, the G alleles of 2 SNPs in ADRB2 (rs1042713 & rs1042714) were significantly over-represented in these players compared with British and European controls. These results suggest that there is a genetic influence on sprint test performance in footballers, and identifies some of the genetic variants that help explain this influence.

Draft Genome Sequence of a Medium- and Long-Chain n-Alkane-Degrading Bacterium, Tsukamurella tyrosinosolvens Strain PS2, with Two Genetic Systems for Alkane Degradation.

Here, we report the genome sequence of Tsukamurella tyrosinosolvens strain PS2, which was isolated from hydrocarbon sludge of an organic synthesis factory. This strain was able to utilize a wide range of n-alkanes, from C16 to C35, as sole carbon sources. Knowledge of the genome will provide insights into long-chain n-alkane biodegradation mechanisms.

Skin Microbiota in Contact Sports Athletes and Selection of Antiseptics for Professional Hygiene.

BACKGROUND: The aim of this study was to assess changes in skin microbiota of wrestlers during training sessions and to determine the sensitivity of hemolytic bacterial isolates to antiseptics. METHODS: The main skin bacterial isolates obtained from the skin of 15 wrestlers were identified by cultivation method, with the following MALDI Biotyper and 16S rRNA gene sequencing methods. The sensitivity of hemolytic isolates to antiseptics (Veltosept-2, Cutasept F, Chlorhexidine, Miramistin, and Hydrogen Peroxide) was evaluated by measuring the size of bacterial growth inhibition zone on agar plates. RESULTS: Opportunistic bacteria of the species Bacillus cereus, Staphylococcus aureus, S. epidermidis, and S. saprophyticus were the most commonly found species in skin microbiota of wrestlers before and after training sessions. Representatives of all these species mostly had a hemolytic activity. An alcohol-containing antiseptic Veltosept-2 showed the strongest inhibitory effect on the bacterial isolates of athletes' skin microbiota most frequently detected in this study. CONCLUSIONS: The general increase in the bacterial colonization of wrestlers' skin, as well as the presence of hemolytic forms of opportunistic bacteria in cutaneous microbiota, indicates dysbiotic changes and a decrease in the protective features of the host organism. Veltosept-2 application can reduce the incidence of skin infections in contact sports athletes with the highest efficiency.

Genome Sequences of Acholeplasma laidlawii Strains with Increased Resistance to Tetracycline and Melittin.

Acholeplasma laidlawii is a well-suited model for studying the molecular basis for adapting mollicutes to environmental conditions. Here, we present the whole-genome sequences of two strains of A. laidlawii with increased resistance to tetracycline and melittin.

Genome Sequences of Acholeplasma laidlawii Strains Differing in Sensitivity to Ciprofloxacin.

Acholeplasma laidlawii is a well-suited model for study of the molecular basis of the adaptation of mollicutes to environmental conditions. Here we present the whole-genome sequences of four strains of A. laidlawii with differential sensitivity to ciprofloxacin.

Shotgun metagenomic data on the human stool samples to characterize shifts of the gut microbial profile after the Helicobacter pylori eradication therapy.

The shotgun sequencing data presented in this report are related to the research article named "Gut microbiome shotgun sequencing in assessment of microbial community changes associated with H. pylori eradication therapy" (Khusnutdinova et al., 2016) [1]. Typically, the H. pylori eradication protocol includes a prolonged two-week use of the broad-spectrum antibiotics. The presented data on the whole-genome sequencing of the total DNA from stool samples of patients before the start of the eradication, immediately after eradication and several weeks after the end of treatment could help to profile the gut microbiota both taxonomically and functionally. The presented data together with those described in Glushchenko et al. (2017) [2] allow researchers to characterize the metagenomic profiles in which the use of antibiotics could result in dramatic changes in the intestinal microbiota composition. We perform 15 gut metagenomes from 5 patients with H. pylori infection, obtained through the shotgun sequencing on the SOLiD 5500 W platform. Raw reads are deposited in the ENA under project ID PRJEB21338.

High-quality draft genome sequence of a new phytase-producing microorganism Pantoea sp. 3.5.1.

Strain 3.5.1 was isolated from soils of the Republic of Tatarstan, Russia, on the basis of presence of a high phytate-degrading activity. Strains with such activities attract special interest because of its potential use as feed additives and natural manures. Strain 3.5.1 harbors a 99 % 16S rRNA nucleotide sequence similarity to different Pantoea species (P. vagans, P. ananatis, P. agglomerans, P. anthophila and Pantoea sp.) and exhibits unique biochemical properties that do not allow strain identification up to species. Moreover, the strain 3.5.1 shows a low ANI and MALDI-TOF Mass Spectrometry scores. Thus, it is likely that the strain 3.5.1 represents a new Pantoea species. Here, we present the genome sequence of Pantoea sp. strain 3.5.1. The 4,964,649 bp draft genome consists of 23 contigs with 4,556 protein-coding and 143 RNA genes. Genome sequencing and annotation revealed two phytase genes and putative regulatory genes controlling its activity.

Draft Genome Sequence of Bacillus ginsengihumi Strain M2.11 with Phytase Activity.

This paper announces the genome sequence of Bacillus ginsengihumi strain M2.11, which has been characterized as a strain which produces the enzyme with the ability to degrade phytase. The genome of the strain M2.11 is 3.7 Mb and harbors 3,082 coding sequences.

Effect of the Organic Loading Rate Increase and the Presence of Zeolite on Microbial Community Composition and Process Stability During Anaerobic Digestion of Chicken Wastes.

This study investigates the effect of the organic loading rate (OLR) increase from 1.0 to 3.5 g VS L(-1) day(-1) at constant hydraulic retention time (HRT) of 35 days on anaerobic reactors' performance and microbial diversity during mesophilic anaerobic digestion of ammonium-rich chicken wastes in the absence/presence of zeolite. The effects of anaerobic process parameters on microbial community structure and dynamics were evaluated using a 16S ribosomal RNA gene-based pyrosequencing approach. Maximum 12 % of the total ammonia nitrogen (TAN) was efficiently removed by zeolite in the fixed zeolite reactor (day 87). In addition, volatile fatty acids (VFA) in the fixed zeolite reactor accumulated in lower concentrations at high OLR of 3.2-3.5 g VS L(-1) day(-1). Microbial communities in the fixed zeolite reactor and reactor without zeolite were dominated by various members of Bacteroidales and Methanobacterium sp. at moderate TAN and VFA levels. The increase of the OLR accompanied by TAN and VFA accumulation and increase in pH led to the predominance of representatives of the family Erysipelotrichaceae and genera Clostridium and Methanosarcina. Methanosarcina sp. reached relative abundances of 94 and 57 % in the fixed zeolite reactor and reactor without zeolite at the end of the experimental period, respectively. In addition, the diminution of Synergistaceae and Crenarchaeota and increase in the abundance of Acholeplasmataceae in parallel with the increase of TAN, VFA, and pH values were observed.

Impact of the substrate loading regime and phosphoric acid supplementation on performance of biogas reactors and microbial community dynamics during anaerobic digestion of chicken wastes.

This study evaluates the effects of increasing organic loading rate (OLR) and decreasing hydraulic retention time (HRT) as well as phosphoric acid addition on mesophilic reactors' performance and biogas production from chicken wastes. Furthermore, microbial community composition in reactors was characterized by a 16S rRNA gene-based pyrosequencing analysis. Each step of increasing OLR impacted on the activity of microorganisms what caused a temporary decrease in biogas production. The addition of phosphoric acid resulted in the increased biogas production with values between 361 and 447 mL g(VS)(-1) from day 61 to day 74 compared to control reactor (309-350 mL g(VS)(-1)). With reactors' operation, Bacteroidetes phylotypes were noticeably replaced with Firmicutes representatives, and significant increase of Clostridium sp. was identified. Within Euryarchaeota, Methanosarcina sp. dominated in all analyzed samples, in which high ammonium levels were detected (3.4-4.9 NH4(+)-N g L(-1)). These results can help in better understanding the anaerobic digestion process of simultaneously ammonium/phosphate-rich substrates.