Bulletin of Russian State Medical University

The symbiotic relationship with the microbial flora inhabiting our bodies plays an immense role in maintaining our vitality. The microbiota protects us from pathogens, hardwires our immunity, and engages in the production of essential micronutrient components. The human microbiota encompasses several thousands of fungi, eubacteria, archaea and viruses, with eubacterial cells alone totaling over 10 trillion and outnumbering our body cells 100 to 1. Next generation sequencing has allowed researchers to comprehensively assess the diversity of microbial species in the human microbiota and to estimate their proportions with stunning accuracy. This has led to a breakthrough in our understanding of associations between human health and the microbiota. This review focuses on the current state of research on key microbial communities inhabiting the human body: those of the gastrointestinal and genitourinary systems. Less studied microbial communities colonizing the nose, nasopharynx, auditory canal, eye, and skin, as well as some others, are not included in the review.

Antibiotic resistance is one of the biggest threats to modern medicine. Response to antimicrobial treatment is seriously disrupted by aminoglycoside phosphotransferases (Aph) - enzymes produced by bacteria. The genes were annotated in many bacterial species, including commensals of the gut microbiota that can transfer these genes to clinically important strains. For this study we prepared a catalog of 21 genes. The analysis of 11 intestinal microbiomes of healthy Russians revealed the presence of 3 cataloged genes in 7 microbiota samples, namely , and . The most frequent was the gene detected in 6 metagenomes. Of note, this gene was first discovered in , but in this study we observed it in sequences typical for commensal and opportunistic , , and . Similarly, originally present in was detected in a sequence typical for . Our findings are consistent with the reports on the strong association between the geographical origin of the individual and frequency of genes. We suggest that clinical examination should include antibiotic sensitivity tests run not only on the causative agent, but also on the gut microbiota, for a better treatment outcome.

Serine/threonine protein kinases (STPKs) of bacteria are involved in signal transduction, cell growth and division, biofilm formation and virulence regulation. They are found in both pathogenic microbes and symbiotic residents of the human microbiota. Previously we proposed a classification scheme for STPKs of gram-positive bacteria based on the signature sequence of 9 amino acid residues in the ATP-binding pocket. Accordingly, protein kinases and bacterial species that contained those kinases were divided into 20 groups. We hypothesized that STPKs with identical signatures would interact with the same low-molecular-weight compounds that could be used as selective inhibitors of STPK to suppress growth and virulence of certain residents of the human gut microbiota (GM). GM represented by over 400 bacterial species is critical in maintaining homeostasis in the human body. In healthy individuals GT composition is balanced in terms of genera/species abundance. Shifts in the GT composition are thought to trigger pathology. In this connection various approaches are being developed to regulating the composition of the human microbiota. This article proposes the use of bacterial STPK inhibitors as “gentle” therapeutic agents for correcting taxonomic imbalances of GM triggered by non-infectious diseases and reducing virulence of pathogenic microbes with minimal impact on human protein kinases.

Metagenomic sequencing is widely used in both scientific research and clinical practice for characterization of taxonomic profiles including estimation of relative abundance of prokaryotes in microbial communities in various media. Metagenomic sequencing of single marker genes is an excellent tool for studying the human microbiome. Unlike whole-genome sequencing, it targets those genome regions that can be instrumental in identification of microorganism species and genus. The 16S ribosomal RNA (16S rRNA) gene sequence is highly conserved but at the same time there are regions containing species-specific sequences that can discriminate between different bacteria and archaea. These regions can be amplified using universal primers, which makes the whole procedure more cost-effective and less time-consuming. Good primers and protocol design for PCR at the step of library preparation is crucial for achieving high data accuracy. Below we describe how to choose the optimal PCR protocol and universal primers to amplify V3 and V4 regions of the 16S rRNA gene for further sample sequencing using lllumnia platform.

Many sexually transmitted diseases are caused by bacteria. While we fairly well understand the role of some microorganisms in the development of genitourinary tract infections, there is still a vast majority of those whose contribution is unclear. It is believed that sexual partners share their genitourinary microbiota, meaning that treatment regimens should be the same for both of them. This article reports results of the study of seminal and cervical microbial communities conducted in 50 married couples who did not use barrier birth control and did not take any antibiotics at least 3 months before the study. All couples presented with complaints of primary or secondary infertility, recurrent miscarriages or sought preconceptional counseling. The mean age of male and female participants was 34.8 ± 7.8 and 30.4 ± 6.2 years, respectively. Samples of the seminal fluid and vaginal secretions were studied by real-time polymerase chain reaction (real-time PCR) with Androflor and Femoflor reagent kits. The following bacteria were more frequent in the vaginal microbiota than in the seminal fluid: (p < 0.005), (p = 0.002), (p = 0.002), (p = 0.004). was 3 times more frequent in women, was 4 times more frequent in men; however, this difference was not significant. In 4 (8 %) couples both partners had normal microbiota; 23 (46 %) couples shared at least one microbiota resident. Also, microbial communities were totally different in 23 couples. The obtained data indicate that both sexual partners should be examined to decide on the most effective treatment for each of them. Qualitative and quantitative real-time PCR assays Androflor and Femoflor provide comprehensive data essential for adequate treatment planning.

Criteria of normality for the vaginal microbiota of healthy women are still a subject of discussion. A decision to assign a study participant to a group of healthy individuals is quite subjective if based on the absence of complaints and physical examination only, which renders study results ambiguous. Below we compare occurrence of the normal vaginal flora and vaginal dysbiosis in women divided into 3 groups according to the examination type (patient’s subjective evaluation of her condition, physical examination, and laboratory tests). We examined 234 women of reproductive age from Yekaterinburg (mean age was 30.3 ± 6.6 years). Microbiota composition and lactobacillus diversity (, , , , , ) were evaluated by real-time polymerase chain reaction using the Femoflor assay and reagent kits by DNA-Technology, Russia. One in 5 women of reproductive age who had no health complaints was found to have dysbiosis. The normal microbiota of those women was dominated mostly by , while dominant were observed in every third participant. Prevailing were also found in the normal microbiota of 46.2 % of women who were considered healthy based on the doctor’s examination and laboratory tests. Thus, clinical evaluation of the female lower reproductive tract can be compromised by doctor’s subjectivity if not supported by laboratory tests and may overlook vaginal dysbiosis in the patient.

Moderate vaginal dysbiosis is a shift in normal vaginal microbiota composition characterized by increased levels of opportunistic microbes and an ordinary high proportion of lactobacilli that make up 20 to 80 % of the total microbial population of the vagina. Some women with vaginal dysbiosis do not show any symptoms of the infectious inflammatory condition (IIC), which raises the question of whether their dysbiosis should be corrected. We studied the association between some parameters of the microbiota and clinical symptoms of IIC in female patients with moderate vaginal dysbiosis. Participants were distributed into two groups: group 1 included patients with clinical symptoms of IIC (n = 91), group 2 was comprised of asymptomatic patients (n = 44). Mean age was 26.9 ± 6.9 years. Vaginal microbial communities were studied using real-time polymerase chain reaction assays. Levels of six Lactobacillus species were measured in the vaginal discharge: , , , , , and . We found that dominated the microbiota of 45 (49.5 %) symptomatic patients and only 9 (20.5 %) asymptomatic individuals (p = 0.002), unlike that significantly prevailed in the samples of asymptomatic patients: 23 (52.3 %) women vs 21 (23.1 %) in the group of patients with clinical signs of IIC (p = 0.001).

Interferon-based regimens for chronic hepatitis C (HCV) are quite common, just like interferon-free treatments, and are extensively used in Russia because interferon is widely available to most patients. In 2013 the original Russian drug cepeginterferon alpha-2b (cepegIFN alpha-2b marketed as Algeron by Biocad, Russia) was introduced into clinical practice. The aim of this study was to assess effectiveness and safety of cepegIFN alpha-2b as part of the combination therapy with ribavirin in patients with chronic HCV infection. The study was conducted over the period from 2014 to 2016 and recruited 37 patients with chronic genotype 1 HCV infection: 22 men and 15 women (mean age of 42.0 ±5.2 years). All of them received the following combination antiviral therapy (AT): 1.5 pg/kg cepegIFN alpha-2b once a week and 15 pg/kg ribavirin daily over the period of 48 weeks. Effectiveness of AT was assessed by the rate of sustained virological response (SVR), i. e. aviremia achieved 24 weeks after the onset of treatment. In our SVR was observed in 26 patients (70.3 %). Adverse effects seen in the course of AT were typical of interferon-based drugs and ribavirin. CepegIFN alpha-2b dosage was corrected in two patients who developed neutropenia; ribavirin dosage was corrected in 3 patients who developed anemia. Based on the obtained results, we recommend including cepegIFN alpha-2b into the combination antiviral therapy in patients with chronic HCV infection.

Premacular hemorrhage occurs in various disorders and causes sudden unilateral or bilateral visual impairment. One of the well-established techniques to treat this condition is Ng:YAG laser hyaloidotomy. Below we report a case of premacular hemorrhage in the right and left eyes of a 23-year old patient with acute myeloblastic leukemia. Ng:YAG laser hyaloidotomy was successfully performed on both patient’s eyes at different puncture sites.

An extensive collection of plants gathered in the European part of Russia was screened for a substrate of fungal luciferase. This work was inspired by the recently discovered mechanism of bioluminescence in higher fungi and the structural similarity of fungal luciferin with some plant metabolites. Of all studied leaf extracts obtained from 200 different plants, bioluminescent activity was discovered in 10 species. Each of these species contained a plurality of active compounds. All the luminescent substrates were not identical to fungal luciferin (3-hydroxyhispidin) and were chemically unstable, rendering the attempt to isolate individual compounds for further structural characterization yet unsuccessful. This study is the first step towards engineering a self-luminescent plant based on a fungal enzyme-substrate bioluminescent system.