Features of the oropharyngeal microbiota of healthy children and those with acute respiratory infections. A prospective single-center randomized study
Authors: Kuznetsova Irina S. , Berezhnaya Irina V. , Koshechkin Stanislav I. , Romanov Vladimir A. , Cherednikova Tatyana A. , Zakharova Irina N. 
Published: October 2024

Background. The oropharyngeal microbiota is involved in the development of colonization resistance, affecting viral adhesion and metabolism. Any deviations in the stability of the environmental microbial niches of the oropharynx alter the local immune response and can trigger severe chronic somatic disorders.
Aim. To compare the composition of the microbiota of children during an episode of respiratory infection and healthy volunteers examined in different periods of convalescence. The obtained data can be used to predict the course of the disease, analyze the risk of complications, and assess the frequency of the diseases in the future.
Materials and methods. From 20.01.2022 to 23.12.2022, an open-label prospective single-center randomized comparative study was conducted, which included 120 children aged 5-10 who presented with symptoms of acute respiratory infection. The control group consisted of 15 asymptomatic children examined at different periods of convalescence. The study compared changes in the oral microbiota composition of patients and healthy children. The evaluation was performed using complete 16S rRNA gene sequencing on the Oxford Nanopore platform. Taxonometric analysis at the species and genera level was performed using the Knomics-Biota platform. The R programming language was used for statistical processing. In addition, the parameters of α- and β-diversity of the microbiota were assessed. The Chao1 and Shannon indices were calculated to assess α-diversity (diversity within one community). The Chao1 index is based on the number of species found in the sample and also rare species that are found only 1 or 2 times, thus preventing underestimation of diversity. The Shannon index includes both the number of species and their uniformity in the community. A change in the index indicates the dominance of one or more species. The following indicators were used to assess the β-diversity describing the differences between two microbiota samples at the species and genera level: Bray–Curtis dissimilarity (characterizing the ratios of common and different microorganisms between the samples) and the Aitchison distance (reflecting the differences in the proportions of microorganisms). In addition, the balance between the two groups of microorganisms was evaluated using the NearesBalance method, which characterizes the differences between the microbiota of the main and control groups.
Results. The results of our study show that during respiratory infection, the state of the oropharyngeal microbiota is characterized by an increase in α-diversity, which is associated with an increase in the proportion of species of Streptococcus salivarius, Streptococcus pneumoniae, Streptococcus pseudopneumoniae, Streptococcus pyogenes, Streptococcus thermophilus and A12 versus the proportion of Streptococcus mitis, Streptococcus oralis, Streptococcus gwangjuense, Streptococcus sanguinis, Streptococcus gordonii and FDAARGOS_192. In the control group, the oropharyngeal microbiota was divided into two clusters. The dominance of streptococci was observed in the first group (control), while the second group had a more uniform representation. Analysis of the changes in microbial communities in the main and control groups can show the stages of oral microbiota recovery after an acute respiratory infection episode.
Conclusion. More research is needed in the field of the oropharyngeal microbiome on a larger sample of healthy children, to standardize the communities of the oropharyngeal microbiota, to study the interaction within communities and with the body as a whole. Analysis of the impact of the microbiota on the frequency and course of respiratory infections and the rate of complications opens up new prospects in treating, rehabilitating, and preventing diseases. These research areas can contribute to improving children's health and quality of life and introducing new approaches into clinical practice.