Gut Microbiota Patterns in Patients with Non-Alcoholic Fatty Liver Disease: A Comprehensive Assessment Using Three Analysis Methods

Non-alcoholic fatty liver disease (NAFLD) is considered the most common chronic liver disease worldwide, affecting nearly 25% of the global adult population. Increasing evidence suggests that functional and compositional changes in the gut microbiota may contribute to the development and promote the progression of NAFLD. 16S rRNA gene next-generation sequencing is widely used to determine specific features of the NAFLD microbiome, but a complex system such as the gut microbiota requires a comprehensive approach. We used three different approaches: MALDI-TOF-MS of bacterial cultures, qPCR, and 16S NGS sequencing, as well as a wide variety of statistical methods to assess the differences in gut microbiota composition between NAFLD patients without significant fibrosis and the control group. The listed methods showed enrichment in Collinsella sp. and Oscillospiraceae for the control samples and enrichment in Lachnospiraceae (and in particular Dorea sp.) and Veillonellaceae in NAFLD. The families, Bifidobacteriaceae, Lactobacillaceae, and Enterococcaceae (particularly Enterococcus faecium and Enterococcus faecalis), were also found to be important taxa for NAFLD microbiome evaluation. Considering individual method observations, an increase in Candida krusei and a decrease in Bacteroides uniformis for NAFLD patients were detected using MALDI-TOF-MS. An increase in Gracilibacteraceae, Chitinophagaceae, Pirellulaceae, Erysipelatoclostridiaceae, Muribaculaceae, and Comamonadaceae, and a decrease in Acidaminococcaceae in NAFLD were observed with 16S NGS, and enrichment in Fusobacterium nucleatum was shown using qPCR analysis. These findings confirm that NAFLD is associated with changes in gut microbiota composition. Further investigations are required to determine the cause-and-effect relationships and the impact of microbiota-derived compounds on the development and progression of NAFLD.

Diversities in the Gut Microbial Patterns in Patients with Atherosclerotic Cardiovascular Diseases and Certain Heart Failure Phenotypes

To continue progress in the treatment of cardiovascular disease, there is a need to improve the overall understanding of the processes that contribute to the pathogenesis of cardiovascular disease (CVD). Exploring the role of gut microbiota in various heart diseases is a topic of great interest since it is not so easy to find such reliable connections despite the fact that microbiota undoubtedly affect all body systems. The present study was conducted to investigate the composition of gut microbiota in patients with atherosclerotic cardiovascular disease (ASCVD) and heart failure syndromes with reduced ejection fraction (HFrEF) and HF with preserved EF (HFpEF), and to compare these results with the microbiota of individuals without those diseases (control group). Fecal microbiota were evaluated by three methods: living organisms were determined using bacterial cultures, total DNA taxonomic composition was estimated by next generation sequencing (NGS) of 16S rRNA gene (V3-V4) and quantitative assessment of several taxa was performed using qPCR (quantitative polymerase chain reaction). Regarding the bacterial culture method, all disease groups demonstrated a decrease in abundance of Enterococcus faecium and Enterococcus faecalis in comparison to the control group. The HFrEF group was characterized by an increased abundance of Streptococcus sanguinus and Streptococcus parasanguinis. NGS analysis was conducted at the family level. No significant differences between patient's groups were observed in alpha-diversity indices (Shannon, Faith, Pielou, Chao1, Simpson, and Strong) with the exception of the Faith index for the HFrEF and control groups. Erysipelotrichaceae were significantly increased in all three groups; Streptococcaceae and Lactobacillaceae were significantly increased in ASCVD and HFrEF groups. These observations were indirectly confirmed with the culture method: two species of Streptococcus were significantly increased in the HFrEF group and Lactobacillus plantarum was significantly increased in the ASCVD group. The latter observation was also confirmed with qPCR of Lactobacillus sp. Acidaminococcaceae and Odoribacteraceae were significantly decreased in the ASCVD and HFrEF groups. Participants from the HFpEF group showed the least difference compared to the control group in all three study methods. The patterns found expand the knowledge base on possible correlations of gut microbiota with cardiovascular diseases. The similarities and differences in conclusions obtained by the three methods of this study demonstrate the need for a comprehensive approach to the analysis of microbiota.

ISO 20387 biobanking standard. Analysis of requirements and experience of implementation

Currently one of the most important problems facing biobanking specialists is the standardization of biobanks operation. Close attention is paid to this issue by international biobanking organizations, such as ISBER and BBMRI-ERIC, which develop regulatory documentation in this area. The article provides examples of standardization tools - implementation of the ISO 9001 quality standard and ISBER Best Practices. General information about the development, scope, and structure of the ISO 20387 standard is provided. The standard does not provide ready-made solutions and does not contain specific requirements for storage temperature or biosamples processing in biobanks, allowing each biobank to adapt its own management system to existing conditions and needs. The standard contains requirements for both the organization of the biobanking and the supporting processes - personnel competence; requirements for biological safety; infrastructure management, including equipment used by the biobank, environmental parameters that affect the storage of biomaterial. The standard contains requirements for the quality management system of biobank, as a necessary element of the organization of any biorepository. At the initiative of the Russian National Association of biobanks and biobanking specialists (NASBIO), development of the Russian standard GOST R ISO 20387 «Biotechnology. Collection and storage of biological samples in biobanks. General requirements» is included in the plan of the National Standardization Program for 2020 by order of Rosstandart No. 2612 of 11/01/2019. Implementing quality standards is a long and painstaking process that requires the involvement of all employees and certain resources. However, the effectiveness of strict compliance exceeds the cost of developing, implementing and maintaining management systems, as it significantly increases the confidence of researchers in the work of biobanks, guarantees high quality of biospecimens and associated data, and creates opportunities for cooperation, both at the national and international level, based on the application of common quality standards in the work.

Actual approaches to the transportation of biological samples at low temperatures

Taking into account the impact of shipment method of biosamples is necessary for obtaining high-quality biological samples in biobanking and laboratory research. The impact of liquid nitrogen, dry ice and cold accumulators on the quality of biological markers was considered, as well as recommendations to reduce the impact of these methods of shipment. The liquid nitrogen provides the best preservation of samples, however, dry ice is used much more often during their transportation. When transporting certain types of cells using dry ice, there is the way to use CryoStor CS1 and Cell Banker 1 cryoprotectors. The dry ice has a significant effect on both the pH of liquid biological samples and the coagulological parameters of plasma samples. The penetration of CO2 into the sample leads to changes in the parameters of PTT and APPT, as well as to decrease the protein C and fibrinogen level under certain conditions. Serum and plasma samples exposed to dry ice for more than 16 hours should be thawed open at room temperature, or instead of it should be kept at -80 °C for 24 hours to avoid changes in coagulation parameters, The use of cold accumulators is unacceptable for long-term shipment of serum and plasma containing unstable biomarkers because of insufficiently low temperature (increase over time to -25 °C and above). Besides, metal pellets can be used as cold storage batteries at low temperatures (up to -80 ° C), but they are not as effective as dry ice, since it is able to hold the required temperature for much longer.

[Current best practices and biobanking recomedations.]

The biobank is a structure established with the goal of long-term responsible storage of biological samples and the associated data for their further use in scientific and clinical research. The objectives of biobanking are the creation of unified recommendations on: the planning of premises and the selection of equipment for storage; development of management methods and staff training; standardization of methods for the collection, shipping, processing and storage of biomaterial of various origins, as well as methods for quality control and validation of the applied methods; creation and use of databases of information accompanying biospecimens. The lack of common standards for conducting the preanalytical phase has been the cause of low accuracy and poor reproducibility of research results. To date, a large number of guidelines and best practices have been published that provide an answer to a wide range of problems in organizing the biobanking process. The article provides an overview of the most famous biobanking guidelines that can be used to solve various research problems. Biobanking in Russia is actively developing. Since 1996 there is a work on the legislative regulation of biobanking activities, as a result of which a number of regulatory documents have been issued. An important stage in the development of biobanking in Russia was the establishment of the "National Association of Biobanks and Biobanking Specialists" (NASBio) in 2018, which included representatives of medical and research institutions, commercial firms, and qualified specialists in the field of biobanking. One of the key tasks of NASBio is the adaptation and implementation of the best biobanking practices in Russian research institutes and centers. The use of modern guidelines and best practices on biobanking will lead to an increase in the quality of research and publications.

P3351The new organizational scheme for research on rare and interesting clinical cases in cardiology

Introduction

There is a challenge to study rare and unusual diseases in cardiology. Patients with such cases often concentrate in large scientific medical centers, where implementation of new organizational research approaches may be useful to overcome this challenge.

Purpose

To develop and approbate new organizational scheme to study of rare and interesting clinical cases in cardiology.

Methods

The new organizational scheme for research on rare and interesting clinical cases in cardiology is based on three main interconnected teams: clinical cardiologists, scientific researchers, and biobanking specialists. In 2016 the joint team of experts in these areas developed: 1) criteria for selection of patients with rare and interesting clinical cases, 2) requirements for collection of biomaterial and data, 3) ethical rules, 4) logistics of all processes, 5) organization of teamwork of all participants from different departments, 6) promotion of the project and involvement of all clinicians of the medical scientific center.

Results

The teamwork of cardiologists, scientific researchers and biobanking specialists was organized. Cardiologists are responsible for selection of patients; scientific researchers - for formation and analysis of database; biobanking specialists - for standardization of biospecimens' collection, preparation and safe responsible storage, partly - for database formation. Special training for all participants of the project was conducted. It included issues of selection of patients; the procedure of informed consent signing and information encoding; logistics of interaction of clinical, scientific, and biobank's personnel; proper documentation etc. As a result since the start of the project from June 2016 to January 2019, biomaterial and depersonalized data were collected from 753 patients, including: early (<45 y.o. in men, <50 y.o. in women) development of coronary artery disease – 167, early (<50 y.o.) development of atrial fibrillation – 197, morbid obesity (BMI>40 kg/m2) - 71, primary electric heart diseases - 42, cardiomyopathies - 272, other rare diseases – 96 patients. The project is currently ongoing. This approach allows collecting and preserving valuable biomaterial and data for research in present and future. To date these materials have been already used for several research initiatives such as investigation of hypertrophic and non-compact cardiomyopathies, familial hypercholesterolemia; identification of novel genetic markers of type 2 diabetes and obesity; reports and publications about rare clinical cases.

Conclusion

The integrated teamwork of clinical cardiologists, scientific researchers and biobanking specialists in large scientific medical center gives qualitatively new opportunities: increase of the dynamicity, efficiency, standardization, and as a result, quality of present and future research on rare and interesting clinical cases in cardiology.

219Serum Trimethylamine N-Oxide levels and 16S rRNA gut microbiota profiling in patients with heart failure and preserved ejection fraction and healthy individuals

Introduction

Recent evidence suggests the role of gut microbiota dysregulation in the pathophysiology of chronic heart failure (HF). Elevated levels of Trimethylamine N-Oxide (TMAO) have shown to increase the risk of cardiovascular events and HF. Among patients with HF and preserved ejection fraction (HF-pEF) the link between TMAO levels and ventricular fibrosis was observed in studies, however, the data regarding 16S rRNA microbiome profiling in this particular group of HF are lacking.

Purpose

The research was aimed at investigating the gut microbiome diversity and composition as well as the serum TMAO levels among two groups of patients: healthy controls (HC) and HF-pEF.

Methods

44 patients with HF-pEF and 45 HC with body mass index <35 kg/m2, no history of acute coronary syndrome, myocardial infarction or diabetes were enrolled in the study. All patients underwent transthoracic echocardiography with Doppler study to exclude diastolic dysfunction (E/e' <8 cm/s) or to prove HF-pEF (according to the recent ESC guidelines based on E/e' ratio, N-terminal pro-B type natriuretic peptide >125 pg/ml and symptoms of HF). The intestinal microbiome was investigated using high-throughput sequencing of bacterial 16S rRNA gene. TMAO levels were determined by liquid chromatography tandem mass spectrometry.

Results

The age in HC was 57,5 [48; 63] (28% men), age in HF-pEF group was 67 [64; 74] years (52% men). The serum concentration of TMAO in HC was 3.72 uM, in HF-pEF was 5.24 uM. The group of HF-pEF had significantly higher levels of the marker, p=0,003. Bacterial communities of both groups were dominated by the Firmicutes and Bacteroidetes phyla. The most abundant genus in both groups were Bacteroides. The Shannon index, the Chao 1 estimator, and the Simpson index assessing α diversity were not significantly different between groups. However, Bacteroides, Alistipes, Pseudomonas, and Fusobacterium were enriched in the common core microbiota of HF-pEF patients, while Lachnospira, Roseburia, Eubacterium, Methanobrevibacter and Faecalibacterium were depleted. To note, Lactobacillus and Bifidobacterium were depleted in HF-pEF patients too.

TMAO levels in HC and HF-pEF groups

Conclusions

We have shown significant structural alterations of the intestinal microbiome and increased TMAO levels in HF-pEF patients' serum compared to HC. These findings may enable deeper understanding of the complex multifactorial pathogenesis of HF-pEF for the future development of personalized microbiome-based diagnostics and therapies for individuals at risk.

[Quality management in biobank. World tendencies and experience of biobank of FSI «NMRC for preventive medicine» of the Ministry of healthcare of Russia.]

This paper provides several definitions of the term "biobank"; a list of standards developed by the International Organization for Standardization (ISO) applicable to the activities of biobanks; analyzes the legal and ethical requirements; the Russian legal framework in the field of biobanking, the best international practices and recommendations; describes the experience of the development and implementation of quality management systems according to ISO 9001 in Biobanks established in different countries, and the experience of the Bank of Biological Material of the National Medical Research Center for Preventive Medicine of the Ministry of Healthcare of Russia. The ISO 20387 Biobanking Standard, released in August 2018, combined the knowledge and experience of specialists from around the world and defined the general requirements that must be fulfilled by biobanks and repositories wishing to guarantee their customers the high quality of the preanalytical stage of scientific research, biological samples and associated data. In 2019, the Russian version of this standard is expected. Documents of the quality management system provide the reproducibility of activities on the main storage processes and facilitates the process of incorporating a new employee; conducting internal and external audits; Biobank knowledge management - continuous staff education. The introduction of an effective quality management system into biobank activity warrants the high quality of biological samples, the standardized pre-analytical stage, reliable, regulated long-term storage of biomaterial and related information for use in research purposes today and in future.

Growth Hormone, Insulin-Like Growth Factor-1, Insulin Resistance, and Leukocyte Telomere Length as Determinants of Arterial Aging in Subjects Free of Cardiovascular Diseases

Background: Increased arterial stiffness (AS), intima-media thickness (IMT), and the presence of atherosclerotic plaques (PP) have been considered as important aspects of vascular aging. It is well documented that the cardiovascular system is an important target organ for growth hormone (GH) and insulin-like growth factor (IGF)-1 in humans, and GH /IGF-1 deficiency significantly increases the risk for cardiovascular diseases (CVD). The telomere length of peripheral blood leukocytes (LTL) is a biomarker of cellular senescence and that has been proposed as an independent predictor of (CVD). The aim of this study is to determine the role of GH/IGF-1, LTL and their interaction cardiovascular risk factors (CVRF) in the vascular aging. Methods: The study group included 303 ambulatory participants free of known CVD (104 males and 199 females) with a mean age of 51.8 ± 13.3 years. All subjects had one or more CVRF [age, smoking, arterial hypertension, obesity, dyslipidemia, fasting hyperglycemia, insulin resistance-HOMA (homeostatic model assessment) >2.5, or high glycated hemoglobin]. The study sample was divided into the two groups according to age as "younger" (m ≤ 45 years, f ≤ 55 years) and "older" (m > 45 years, f > 55 years). IMT and PP were determined by ultrasonography, AS was determined by measuring the carotid-femoral pulse wave velocity (c-f PWV) using the SphygmoCor system (AtCor Medical). LTL was determined by PCR. Serum IGF-1 and GH concentrations we measured by immunochemiluminescence analysis. Results: Multiple linear regression analysis with adjustment for CVRF indicated that HOMA, GH, IGF-1, and LTL had an independent relationship with all the arterial wall parameters investigated in the younger group. In the model with c-f PWV as a dependent variable, p < 0.001 for HOMA, p = 0.03 for GH, and p = 0.004 for LTL. In the model with IMT as a dependent variable, p = 0.0001 for HOMA, p = 0.044 for GH, and p = 0.004 for IGF-1. In the model with the number of plaques as a dependent variable, p = 0.0001 for HOMA, and p = 0.045 for IGF-1. In the older group, there were no independent significant associations between GH/IGF-1, LTL, HOMA, and arterial wall characteristics. Conclusions: GH/IGF-1, IR, HOMA, and LTL were the important parameters of arterial aging in younger healthy participants.

Expression of the plague plasminogen activator in Yersinia pseudotuberculosis and Escherichia coli

Enteropathogenic yersiniae (Yersinia pseudotuberculosis and Yersinia enterocolitica) typically cause chronic disease as opposed to the closely related Yersinia pestis, the causative agent of bubonic plague. It is established that this difference reflects, in part, carriage by Y. pestis of a unique 9.6-kb pesticin or Pst plasmid (pPCP) encoding plasminogen activator (Pla) rather than distinctions between shared approximately 70-kb low-calcium-response, or Lcr, plasmids (pCD in Y. pestis and pYV in enteropathogenic yersiniae) encoding cytotoxic Yops and anti-inflammatory V antigen. Pla is known to exist as a combination of 32.6-kDa (alpha-Pla) and slightly smaller (beta-Pla) outer membrane proteins, of which at least one promotes bacterial dissemination in vivo and degradation of Yops in vitro. We show here that only alpha-Pla accumulates in Escherichia coli LE392/pPCP1 cultivated in enriched medium and that either autolysis or extraction of this isolate with 1.0 M NaCl results in release of soluble alpha and beta forms possessing biological activity. This process also converted cell-bound alpha-Pla to beta-Pla and smaller forms in Y. pestis KIM/pPCP1 and Y. pseudotuberculosis PB1/+/pPCP1 but did not promote solubilization. Pla-mediated posttranslational hydrolysis of pulse-labeled Yops in Y. pseudotuberculosis PB1/+/pPCP1 occurred more slowly than that in Y. pestis but was otherwise similar except for accumulation of stable degradation products of YadA, a pYV-mediated fibrillar adhesin not encoded in frame by pCD. Carriage of pPCP by Y. pseudotuberculosis did not significantly influence virulence in mice.

The difference in the lcrV sequences between Y. pestis and Y. pseudotuberculosis and its application for characterization of Y. pseudotuberculosis strains

We have sequenced the lcrGVH operon from Y. pseudotuberculosis plasmid pYV995 and compared its sequence with that of Y. pestis. The sequences were highly homological, however, six base pair substitutions were found in one short 14 bp region termed variable sequence. Two oligonucleotides corresponding to variable sequence of Y. pestis (pes-V) or Y. pseudotuberculosis (ptb-V) were synthesized and were used as molecular probes in hybridization experiments with sets of Y. pestis and Y. pseudotuberculosis strains. All 17 Y. pestis strains tested were positive only with the pes-V probe, 18 of 21 Y. pseudotuberculosis strains were positive with the ptb-V probe, while three Y. pseudotuberculosis strains reacted with the pes-V probe but not the ptb-V probe. The 200 bp fragment including variable sequence was sequenced in seven Y. pseudotuberculosis strains. The Y. pseudotuberculosis strains which were positive with the pes-V probe possessed the 200 bp fragment sequence almost identical with that from Y. pestis. No correlation between the Y. pestis-like lcrV sequence and virulence was found for these strains. Moreover, the Y. pseudotuberculosis strains with Y. pestis-like sequences in contrast to Y. pestis possessed unaltered yadA gene. However, we have found the yadA frameshift mutation characteristic for Y. pestis in one Y. pseudotuberculosis strain 312.