Clinical studies of the human microbiome. Strategies for applying methods and translating results into clinical practice: A review

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Abstract

Current omics methods, which are essential for scientific research, are overviewed. These methods enable studies of the mechanisms of clinical manifestations by analyzing the relationship between the microbiota characteristics and clinical parameters. To represent the complex interactions between the microbiome and host metabolism, metagenomics and metabolomics techniques that contribute to the search for new therapeutic approaches are most relevant. Based on the metagenomic data, the associated taxa are searched, and the metabolic profile indicates the result of the activity of the microbial community. The characteristics of technologies for studying metagenomes using the amplicon sequencing method are considered, and the depth of identification of microorganisms, the level of sequencing errors and the preference in terms of cost are evaluated. Studying the evolution of pathogens and metabolic processes, expressed genes, and determinants of antibiotic resistance contributes to the development of rational strategies for disease therapy and control of the spread of infectious diseases. In recent years, the number of scientific projects in the field of microbiota research has been steadily increasing, which necessitates the need to raise physicians' awareness of modern methods and research approaches in order to apply relevant data in practical work.

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About the authors

Stanislav I. Koshechkin

Nobias Technologies LLC

Author for correspondence.
Email: St.Koshechkin@gmail.com
ORCID iD: 0000-0002-7389-0476

Cand. Sci. (Med.)

 

Russian Federation, Moscow

Vera E. Odintsova

Nobias Technologies LLC

Email: St.Koshechkin@gmail.com
ORCID iD: 0000-0003-1897-4033

Сhief bioinformatician

Russian Federation, Moscow

Alexander V. Karasev

Laboratory "ABT"

Email: St.Koshechkin@gmail.com
ORCID iD: 0000-0001-7484-4992

Chief Executive Officer

Russian Federation, Moscow

Irina N. Zakharova

Russian Medical Academy of Continuous Professional Education

Email: St.Koshechkin@gmail.com
ORCID iD: 0000-0003-4200-4598

Sci. (Med.), Prof.

 

Russian Federation, Moscow

Irina V. Berezhnaya

Russian Medical Academy of Continuous Professional Education

Email: St.Koshechkin@gmail.com
ORCID iD: 0000-0002-2847-6268

Cand. Sci. (Med.)

Russian Federation, Moscow

Olesya V. Pervishko

Kuban State Medical University

Email: ole-pervishko@yandex.ru
ORCID iD: 0000-0003-1083-2807

Cand. Sci. (Med.), Assoc. Prof.

Russian Federation, Krasnodar

Anastasiya E. Kuchina

Russian Medical Academy of Continuous Professional Education

Email: St.Koshechkin@gmail.com
ORCID iD: 0000-0002-8998-264X

pediatrician

 

Russian Federation, Moscow

Anastasiya E. Yudina

Bauman City Clinical Hospital №29

Email: St.Koshechkin@gmail.com
ORCID iD: 0000-0002-6920-8024

Department Head

Russian Federation, Moscow

Irina S. Kuznetsova

Russian Medical Academy of Continuous Professional Education

Email: St.Koshechkin@gmail.com
ORCID iD: 0000-0001-5164-682X

Assistant

Russian Federation, Moscow

Diana K. Dmitrieva

Russian Medical Academy of Continuous Professional Education

Email: St.Koshechkin@gmail.com
ORCID iD: 0000-0002-1593-0732

Graduate Student

Russian Federation, Moscow

Yana V. Orobinskaya

Russian Medical Academy of Continuous Professional Education

Email: St.Koshechkin@gmail.com
ORCID iD: 0009-0005-2121-4010

Graduate Student

Russian Federation, Moscow

Liudmila S. Serikova

National Medical Research Center for High Medical Technologies – Vishnevsky Central Military Clinical Hospital

Email: St.Koshechkin@gmail.com

pediatrician

Russian Federation, Moscow

Anastasia V. Makhaeva

Russian Medical Academy of Continuous Professional Education; Children's City Polyclinic №140

Email: St.Koshechkin@gmail.com
ORCID iD: 0000-0002-0006-5889

Graduate Student, Russian Medical Academy of Continuous Professional Education, pediatrician, Department Head, Children's City Polyclinic №140

Russian Federation, Moscow; Moscow

Vladimir A. Romanov

Nobias Technologies LLC

Email: St.Koshechkin@gmail.com
ORCID iD: 0000-0002-7540-5884

clinical research manager

Russian Federation, Moscow

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Supplementary files

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1. JATS XML
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2. Fig. 1. Schematic diagram of the sequencing by synthesis technology.

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3. Fig. 2. Schematic diagram of the nanopore sequencing technology.

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4. Fig. 3. The main characteristics of the microbiome, methods for their visualization and statistical analysis.

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5. Fig. 4. Component-by-component and compositional comparison vs the comparison of the proportions of microbes on a contrived example of the antibiotic effect on a microbiota consisting of 3 microorganisms

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