bioRxiv (Cold Spring Harbor Laboratory), Apr 11, 2023
The previously underestimated effects of commensal gut microbiota on the human body are increasin... more The previously underestimated effects of commensal gut microbiota on the human body are increasingly being investigated using omics. The discovery of active molecules of interaction between the microbiota and the host may be an important step towards elucidating the mechanisms of symbiosis. Here, we show that in the bloodstream of healthy people, there are over 900 peptides that are fragments of proteins from microorganisms which naturally inhabit human biotopes, including the intestinal microbiota. Absolute quantitation by multiple reaction monitoring has confirmed the presence of bacterial peptides in the blood plasma and serum in the range of approximately 0.1 nM to 1 μM. The abundance of microbiota peptides reaches its maximum about 5h after a meal. Most of the peptides correlate with the bacterial composition of the small intestine and are likely obtained by hydrolysis of membrane proteins with trypsin, chymotrypsin and pepsin -the main proteases of the gastrointestinal tract. The peptides have physicochemical properties allowing them selectively pass the intestinal mucosal barrier and resist fibrinolysis. Proposed approach to the identification of microbiota peptides in the blood may be useful for determining the microbiota composition of hardto-reach intestinal areas and for monitoring the permeability of the intestinal mucosal barrier. Blood plasma and serum / healthy donors / immunomodulatory peptide properties / microbiota of the small intestine / selective permeability of mucus barriers. . .
Proceedings of Universities. Applied Chemistry and Biotechnology, 2021
Microorganisms are known for their ability to adapt easily to any environment, forming specific e... more Microorganisms are known for their ability to adapt easily to any environment, forming specific ecosystems capable of surviving in harsh media. White phosphorus is one of the most dangerous and toxic pollutants, whose widespread use for various industrial and military purposes creates conditions for environmental pollution. It has previously been shown that some microbial cultures can adapt to the presence of white phosphorus in the environment, oxidizing it to a phosphate and then using it as a source of biogenic macronutrients. In prior studies, we have demonstrated the possibility of white phosphorus biodegradation by the fungal strains of Aspergillus niger. However, it is important to study the resistance of this species to such a toxic substance as white phosphorus. There may be several probable mechanisms, including the following: the cell wall of the fungus is a barrier to the penetration of white phosphorus into the cell, in which case an increase in the thickness of the cel...
Molecular Genetics Microbiology and Virology (Russian version), 2016
The facultative aerobic bacteria isolated from the mucosa of rectum in patients with colorectal c... more The facultative aerobic bacteria isolated from the mucosa of rectum in patients with colorectal cancer in the zone of malignant tumor and neighboring normal mucosa was studied using molecular-genetic methods. The species attribution of bacteria was implemented using the cultural-morphological analysis and sequencing of the 16S rRNA locus. The microorganisms with the intraepithelial invasion to rectal mucosa isolated were identified as representatives of the adherent-invasive (AIEC) subgroup of Escherichia coli and species Klebsiella pneumonia. The molecular analysis by genetic determinants controlling adhesive, hemolytic, and toxigenic activity revealed that some bacterial isolates were able to produce toxins with potential cancerogenic activity (e.g., colibactin and cytotoxic necrotic factor I). Certain bacterial species isolated from malignant and normal rectum epithelium of the same patient demonstrated no difference between analyzed factors of toxigenicity.
Background In recent years, there was a growing interest in the modulation and manipulation of th... more Background In recent years, there was a growing interest in the modulation and manipulation of the intestinal flora to treat patients through fecal microbiota transplantation (FMT). Unfortunately, 2 cases of bacteremia via FMT in 2019 occurred in patients due to extended-spectrum beta–lactamase–producing E. coli from the same stool donor. However, one of the recipients did not get an active infection. So, the association between health status and bacterial ability to resist chemicals requires further investigations. Methods Totally, 63 E. coli strains from 32 fecal samples (14 CD patients and 18 controls) were whole-genome sequenced on the Miseq platform (project #0671-2020-0058). The strains were tested against 15 antibiotics by a disc-diffusion assay according to EUCAST guidelines. E. coli ATCC 25922 was used as a control. Antibiotic resistance genes were predicted by the Resistance Gene Identifier and CARD database. Results All strains tested were susceptible only to meropenem (F...
Experimental studies suggest anti-TNF failure depends on dysbiosis. The aim of this study was to ... more Experimental studies suggest anti-TNF failure depends on dysbiosis. The aim of this study was to evaluate the effect of combining FOS and adalimumab on dysbiosis in faecal samples from Crohn's disease patients. Methods: CD patients who required treatment with an anti-TNF agent by standard clinical practice and who chose adalimumab, were proposed to participate in the study to receive co-treatment with FOS. All patients received FOS (Actilight® Beghin Meiji, Paris, France) 6 g p.o. once daily, starting two weeks before Adalimumab and in combination for the next 12 weeks. Adalimumab was administered according to standard schedule. Total bacteria, F. prausnitzii, and Bifidobacteria counts were assessed by qPCR in fecal samples at time points −2, 0, 2, 6 and 14 weeks. Crohn's disease activity index (CDAI), CRP and fecal calprotectin were assessed at each time-point. Results: Thirty-four patients were included, median age of 41 years, 68% female and 18% current smokers. Fifty-three percent had disease located in terminal ileum, 59% a non-stricturing, non-penetrating behaviour, 29% perianal disease and 18% had extraintestinal manifestations. At baseline, 24 patients had F. prausnitzii levels below 109 CFU/g (median 1.76 × 10 7). Lower F. prausnitzii levels were associated with stricturing disease and a previous intestinal resection (p < 0.05). FOS did not significantly increase F. prausnitzii levels, but it had an effect on Bifidobacteria counts (median baseline 4.78 × 10 7 vs. Week 6 1.54 × 10 9 , p < 0.01). Adalimumab treatment significantly lowered CDAI scores (median delta 23) and calprotectin levels (median delta 99) regardless of F. prausnitzii levels at baseline. Two patients with previous depletion of F. prausnitzii restored levels to above 109 CFU/g, both achieving disease remission at the end of the study. Conclusions: Adalimumab improved clinical scores and inflammatory markers. Combination with FOS did not increase F. prausnitzii levels but Bifidobacteria were significantly incremented. Most patients presented abnormally low F. prausnitzii levels at baseline. Depletion of F. prausnitzii was related to a past severe disease course, but it did not affect response to Adalimumab. Restoring F. prausnitzii to normal levels was linked to good clinical outcome.
Conclusions: Sb shows an anti-inflammatory effect on experimental colitis and has a protective ef... more Conclusions: Sb shows an anti-inflammatory effect on experimental colitis and has a protective effect of intestinal mucosal mechanical barrier, which is as effective as mesalazine. Combined Sb with mesalazine does not show a better effect. Dysbacteriosis exist in DSS induced colitis, which are expressed in decreased Firmicutes and increased Proteobacteria. Sb can upregulate the abundance of family S24-7 specifically, which may be a mechanism of its functioning.
Contact sports athletes often suffer from various skin disorders (inflammatory diseases of bacter... more Contact sports athletes often suffer from various skin disorders (inflammatory diseases of bacterial and fungal origin, atopic dermatitis, psoriasis, etc.) resulting in long breaks in training which ruin athletic performance. Wrestling implies intense skin-to-skin contact that creates perfect conditions for transmission of the infectious agents. Following the standard rules of hygiene (showering and handwashing directly after each competition and training) does not exclude the possibility to get an infection from sparring partner. To characterize the skin microbial composition of wrestlers who do not have current manifestation of any skin disorders, the metagenomic analysis was performed. Absolute predominance of Bacillus genus in metagenomic profiles of wrestlers' skin was observed in contrast with the existing literature data. Classic microbiological approaches allowed to detect hemolytic forms of microorganisms. Wrestlers' skin appeared to be colonized with hemolytic bacilli, whereas the non-wrestler athletes did not have such bacteria on their skin. Such dysbiotic shifts in the microbial community may cause the emergence of skin diseases. Revealed properties could help to design highly effective antiseptics for the contact sports hygiene.
In contrast with the traditional methods applied to assessment of population diversity, high-thro... more In contrast with the traditional methods applied to assessment of population diversity, high-throughput sequencing technologies have a wider application in clinical practice with greater potential to find novel diseasecausing variants for multifactorial disorders. Widely used test panels may not meet their goal to diagnose the patient's condition with a full reliability since this method often does not take into account the population frequencies of analyzed genetic markers. Here, we analyzed 57 male individuals of five ethnic groups from Russia and Tajikistan using the whole exome sequencing technique (Ion AmpliSeq Exome), which resulted in detecting more than 299,000 single nucleotide polymorphisms. Samples formed clusters on the PCA plot according to the geographical location of the corresponding populations. Thereby, the methodology of whole-exome sequencing, in general, and the Ion AmpliSeq Exome panel, in particular, could be positively applied for the purposes of population genetics and for detection of the novel clinically relevant variants. Keywords Whole exome sequencing . Diagnostic panel . Ion AmpliSeq Exome . SNP . North Eurasian populations * Eugenia A. Boulygina
Abstract:The presence of nitrogen-fixing bacteria in petrochemicalsludges was established first b... more Abstract:The presence of nitrogen-fixing bacteria in petrochemicalsludges was established first by using of asepticallyrecovered cores drilled from about 0,3 m-deep layer of industrial sludge repositories, which are the resultof permanent discharges of petrochemicalsolid wastes. Bacteria isolated on nitrogen-freemedium,were examinedfor the presence of nitrogenase gene (nifH) and the ability to biological fixation of atmospheric N , 2 which corresponds to acetylene
The results of recent studies indicate a significant role of gut microbiota in the pathogenesis o... more The results of recent studies indicate a significant role of gut microbiota in the pathogenesis of inflammatory bowel diseases (IBD). 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 and discussion. Changes in IBD patients gut microbiota were characterized by an increase in the r...
P053 Overabundance of Lactobacillus species in gut microbiota of IBD patients
Journal of Crohn's and Colitis
Background Changes in the composition of gut microbiota, and their metabolic pathways, are import... more Background Changes in the composition of gut microbiota, and their metabolic pathways, are important factors in the pathogenesis of inflammatory bowel disease (IBD). Many clinical trials have shown that taking probiotics based on Lactobacillus has a positive effect on patients with IBD. However, Lactobacillus should be used more carefully during the active phase of IBD, since some strains can negatively affect the pathogenesis of the disease1,2. The aim of this study was to assess the diversity of Lactobacillus species in the gut microbiome of IBD patients and healthy volunteers. Methods In the study, 62 stool samples from healthy people, 31 from patients with Crohn’s disease (CD), and 34 - ulcerative colitis (UC) in active phase were analyzed. DNA was isolated using the QIAamp Fast DNA Stool Mini Kit (Qiagen, USA) following with shotgun metagenomic sequencing the NextSeq 500 (project #0671-2020-0058). Bioinformatic analysis was performed with the MetaPhlAn2 package. Results An incr...
PAHs distribution and cultivable PAHs degraders’ biodiversity in soils and surface sediments of the impact zone of the Novocherkassk thermal electric power plant (Russia)
Poster presentations cal remission (n=32). Taxa analysis showed reduced relative abundance (RA) o... more Poster presentations cal remission (n=32). Taxa analysis showed reduced relative abundance (RA) of Gammaproteobacteria, Coriobacteria and Fusobacteria (0.01<q<0.04) in asymptomatic relative to clinically active patients. Increasing RA of Actinobacteria micrococcaceae correlated with increasing CDAI and partial Mayo scores (p=0.001, coeffi-cient=0.34). In contrast, microbiome composition in quiescent IBD was compared in patients with (n=12) and without clinical activity (n=65) and to HC (n=48). HC had greater Chao1 alpha diversity (q=0.003) when compared to IBD. Among IBD patients, Fusobacteriaceae RA was increased patients reporting symptoms despite endoscopic remission (q=0.02). Symptomatic patients have greater RA of Bacteroidaceae (q=0.004), Fusobacteria (q=0.004) and Actinobacteria (q=0.01) relative to clinical remission. Conclusions: In IBD patients with and without mucosal healing, increasing clinical symptoms correlated with greater abundance of bacteria including Actinobacteria and Fusobacteria. The relationship between inflammation and intestinal dysbiosis remains unclear. These data suggest an association between specific taxa and clinical symptoms in active and quiescent IBD and may help to further explain why there may be poor correlation between clinical and endoscopic activity.
Here we present a draft genome of Pseudomonas stutzeri strain KOS6. This strain was isolated from... more Here we present a draft genome of Pseudomonas stutzeri strain KOS6. This strain was isolated from industrial hydrocarbon sludge as a diazotrophic microorganism. It represents one of the major parts of the culturable community of the waste and has potential importance for phytoremediation technology.
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Papers by T. Grigoryeva