2019 / 04

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DOI: 10.24075/brsmu.2019.048

ORIGINAL RESEARCH

Application of culture-based, mass spectrometry and molecular methods to the study of gut microbiota in children

Efimov BA, Chaplin AV, Sokolova SR, Chernaia ZA, Pikina AP, Savilova AM, Kafarskaya LI
About authors

Pirogov Russian National Research Medical University, Moscow, Russia

Correspondence should be addressed: Boris A. Efimov
Ostrovityanova St. 1, Moscow, 117997; ur.liam@ab_vomife

About paper

Funding: the study was supported by Russian Science Foundation (research grant № 17-15-01488).

Author contribution: Efimov BA — research planning, literature analysis, screening children, specimen collection, microbiological research, mass spectrometry research, analysis and interpretation of data, preparing a draft manuscript; Chaplin AV — research planning, literature analysis, isolation of bacterial DNA, carrying out PCR, amplicons purification for sequencing, data analysis and interpretation, preparing a draft manuscript; Sokolova SR — research planning, literature analysis, specimen collection, microbiological research, isolation of bacterial DNA, carrying out PCR, amplicons purification for sequencing, data analysis and interpretation preparing a draft manuscript; Chernaia ZA — research planning, literature analysis, microbiological research, mass spectrometry research, data analysis and interpretation, preparing a draft manuscript; Pikina AP — research planning, literature analysis, microbiological research, mass spectrometry research, data analysis and interpretation, preparing a draft manuscript; Savilova AM — literature analysis, microbiological research, preparing a draft manuscript; Kafarskaya LI — research planning, literature analysis, screening children, microbiological research, analysis and interpretation of data, preparing a draft manuscript

Received: 2019-06-27 Accepted: 2019-07-12 Published online: 2019-08-09
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Table 1. Species identity of the Actinobacteria phylum cultured bacteria of the gastrointestinal tract microflora isolated from healthy children (n = 20)
Note (used in this table and tables 2–5): a Frequency of occurrence (absolute number of subjects/percentage of subjects); b Mean ± standard deviation log10 of the number of viable microorganisms in 1 g of feces (CFU/g — colony forming units in 1 g of feces); c */* — A group of phylogenetically related microorganisms, identity was established using the MALDI TOF MS method on the Vitek MS Plus unit with the Saramis Premium V. 4.10 software; d Smaller and larger value of the log10 index of the number of viable microorganisms, if they were found only in two examined children in the group; e Names of the growth media used for isolation and registration of the relevant microorganisms types. SAA — Schaedler Anaerobe Agar; ABA — Anaerobe Basal Agar; CA — Columbia Agar; BA — Bifidobacterium Agar; PAB — Perfringens Agar Base; MRS — Lactobacillus MRS Agar; EA — Endo Agar; SSA — Salmonella–Shigella-Agar; GMSA — Gelatin Mannitol Salt Agar (Stаphylococcus Agar # 110); mEA — mEnterococcus Agar; CAa — Columbia Agar, plates with which were incubated aerobically; SC2A — Sabouraud Chloramphenicol 2 Agar.
Table 2. Species identity of the Firmicutes phylum cultured bacteria of the gastrointestinal tract microflora isolated from healthy children (n = 20)
Table 3. Species identity of the Bacteroidetes phylum cultured bacteria of the gastrointestinal tract microflora isolated from healthy children (n = 20)
Table 4. Species identity of the Proteobacteria phylum cultured bacteria of the gastrointestinal tract microflora isolated from healthy children (n = 20)
Table 5. Species identity of the Saccharomycetales order fungi isolated from healthy children (n = 20)
Table 6. New gastrointestinal tract bacteria phylotypes isolated from healthy children and the values of the nucleotide sequences of their 16S rDNA levels of homology with the same sequences of typical strains of the most closely related validated species in accordance with the International Code of Nomenclature of Bacteria (Bacteriological Code)