@article {Babenko2021.09.20.461025, author = {V. Babenko and R. Bakhtyev and V. Baklaushev and L. Balykova and P. Bashkirov and J. Bespyatykh and A. Blagonravova and D. Boldyreva and D. Fedorov and I. Gafurov and R. Gaifullina and Y. Galeeva and E. Galova and A. Gospodaryk and E. Ilina and K. Ivanov and D. Kharlampieva and P. Khromova and K. Klimina and K. Kolontarev and N. Kolyshkina and A. Koritsky and V. Kuropatkin and V. Lazarev and A. Manolov and V. Manuvera and D. Matyushkina and M. Morozov and E. Moskaleva and V. Musarova and O. Ogarkov and E. Orlova and A. Pavlenko and A. Petrova and N. Pozhenko and D. Pushkar and A. Rumyantsev and S. Rumyantsev and V. Rumyantsev and L. Rychkova and A. Samoilov and I. Shirokova and V. Sinkov and S. Solovieva and P. Tikhonova and G. Trifonova and A. Troitsky and A. Tulichev and Y. Udalov and A. Varizhuk and A. Vasiliev and V. Veselovsky and A. Volnukhin and G. Yusubalieva and V. Govorun}, title = {Analysis of the upper respiratory tract microbiota in mild and severe COVID-19 patients}, elocation-id = {2021.09.20.461025}, year = {2021}, doi = {10.1101/2021.09.20.461025}, publisher = {Cold Spring Harbor Laboratory}, abstract = {The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, like the intestinal microbiota, it is involved in modulating the immune response to infectious agents in the host organism. A causal relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be hypothesized. We analyze biomaterial from nasopharyngeal smears from 336 patients with a confirmed diagnosis of COVID-19, selected during the first and second waves of the epidemic in Russia. Sequences from a similar study conducted in Spain were also included in the analysis. We investigated associations between disease severity and microbiota at the level of microbial community (community types) and individual microbes (differentially represented species). To search for associations, we performed multivariate analysis, taking into account comorbidities, type of community and lineage of the virus. We found that two out of six community types are associated with a more severe course of the disease, and one of the community types is characterized by high stability (very similar microbiota profiles in different patients) and low level of lung damage. Differential abundance analysis with respect to comorbidities and community type suggested association of Rothia and Streptococcus genera representatives with more severe lung damage, and Leptotrichia, unclassified Lachnospiraceae and Prevotella with milder forms of the disease.Competing Interest StatementThe authors have declared no competing interest.}, URL = {https://www.biorxiv.org/content/early/2021/09/20/2021.09.20.461025}, eprint = {https://www.biorxiv.org/content/early/2021/09/20/2021.09.20.461025.full.pdf}, journal = {bioRxiv} }