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Characteristics of the Airway Microbiome of Cystic Fibrosis Patients

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Abstract

Microbiota as an integral component of human body is actively investigated, including by massively parallel sequencing. However, microbiomes of lungs and sinuses have become the object of scientific attention only in the last decade. For patients with cystic fibrosis, monitoring the state of respiratory tract microorganisms is essential for maintaining lung function. Here, we studied the role of sinuses and polyps in the formation of respiratory tract microbiome. We identified Proteobacteria in the sinuses and samples from the lower respiratory tract (even in childhood). In some cases, they were accompanied by potentially dangerous basidiomycetes. The presence of polyps did not affect formation of the sinus microbiome. Proteobacteria are decisive in reducing the biodiversity of lung and sinus microbiomes, which correlated with the worsening of the lung function indicators. Soft mutations in the CFTR gene contribute to the formation of safer microbiome even in heterozygotes with class I. mutations.

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Abbreviations

CF:

cystic fibrosis

CFTR:

cystic fibrosis transmembrane regulator

FDR:

false discovery rate

FEV1:

forced expiratory volume in one second

ITS:

internal transcribed spacer

MLST:

multilocus sequence typing

OTU:

operational taxonomic unit

PCoA:

principal coordinate analysis

PERMANOVA:

permutational multivariate analysis of variance

SRA:

sequence read archive

ST:

sequence type related to MLST

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Funding

Funding. The study was conducted within the framework of the 2018 State Assignment no. 056-00108-18-00 and 2019–2020 Planning Period and the 2019 State Assignment no. 056-00078-19-00 and 2020–2021 Planning Period for the Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation.

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Authors and Affiliations

  1. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, 123098, Moscow, Russia

    O. L. Voronina, N. N. Ryzhova, M. S. Kunda, E. V. Loseva, E. I. Aksenova & A. L. Gintsburg

  2. Pulmonology Research Institute, Federal Medical-Biological Agency, 115682, Moscow, Russia

    E. L. Amelina & G. L. Shumkova

  3. National Medical Research Center for Children’s Health, Ministry of Health of Russia, 119296, Moscow, Russia

    O. I. Simonova

Authors
  1. O. L. Voronina
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  2. N. N. Ryzhova
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  3. M. S. Kunda
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  4. E. V. Loseva
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  5. E. I. Aksenova
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  6. E. L. Amelina
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  7. G. L. Shumkova
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  8. O. I. Simonova
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  9. A. L. Gintsburg
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Corresponding author

Correspondence to O. L. Voronina.

Additional information

This study is dedicated to the 80th anniversary of the Department of Biochemistry, Lomonosov Moscow State University (see vol. 84, no. 11, 2019).

Conflict of interest. The authors declare no conflict of interest.

Compliance with ethical standards. An informed consent was obtained from adult and CF patients over 15 years old; parental or guardian consent was obtained for pediatric patients under 15 years old. All procedures used to examine biological samples from the patients with CF and congenital lung malformation were approved by the Biomedical Ethics Committee at the Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation (Protocol no. 1, 17.05.2012).

Russian Text © The Author(s), 2020, published in Biokhimiya, 2020, Vol. 85, No. 1, pp. 3–14.

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Voronina, O.L., Ryzhova, N.N., Kunda, M.S. et al. Characteristics of the Airway Microbiome of Cystic Fibrosis Patients. Biochemistry Moscow 85, 1–10 (2020). https://doi.org/10.1134/S0006297920010010

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