The human respiratory tract microbial community structures in healthy and cystic fibrosis infants

• Main Authors: Marie-Madlen Pust, Lutz Wiehlmann, Colin Davenport, Isa Rudolf, Anna-Maria Dittrich, Burkhard Tümmler
• Format: Article
• Language: English
• Published: Nature Publishing Group 2020-12-01
• Series: npj Biofilms and Microbiomes
• Online Access: https://doi.org/10.1038/s41522-020-00171-7

Abstract The metagenome development of the human respiratory tract was investigated by shotgun metagenome metagenomic sequencing of cough swabs from healthy children and children with cystic fibrosis (CF) between 3 weeks and 6 years of age. A healthy microbial community signature was associated with increased absolute abundances in terms of bacterial–human cell ratios of core and rare species across all age groups, with a higher diversity of rare species and a tightly interconnected species co-occurrence network, in which individual members were found in close proximity to each other and negative correlations were absent. Even without typical CF pathogens, the CF infant co-occurrence network was found to be less stable and prone to fragmentation due to fewer connections between species, a higher number of bridging species and the presence of negative species correlations. Detection of low-abundant DNA of the CF hallmark pathogen Pseudomonas aeruginosa was neither disease- nor age-associated in our cohort. Healthy and CF children come into contact with P. aeruginosa on a regular basis and from early on.