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The human respiratory tract microbial community structures in healthy and cystic fibrosis infants
Marie-Madlen Pust1,2, Lutz Wiehlmann3, Colin Davenport3
1Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, Hannover, Germany.
Insights
Healthy respiratory microbiomes in children feature diverse, interconnected species. Cystic fibrosis (CF) microbiomes show instability and fragmentation, even without typical pathogens like Pseudomonas aeruginosa, which is common in both groups from early life.
Area of Science:
- Microbiology
- Human Microbiome
- Pediatric Health
Background:
- The human respiratory tract harbors a complex microbial community that plays a crucial role in health and disease.
- Cystic fibrosis (CF) is a genetic disorder that affects the lungs, leading to chronic infections and inflammation, often associated with specific microbial shifts.
Purpose of the Study:
- To investigate the metagenome development of the human respiratory tract in healthy children and those with cystic fibrosis (CF).
- To characterize the differences in microbial community structure and co-occurrence networks between healthy and CF pediatric populations.
Main Methods:
- Shotgun metagenomic sequencing was performed on cough swab samples from healthy children and children with CF, aged 3 weeks to 6 years.
- Analysis focused on bacterial-human cell ratios, species diversity, and co-occurrence network properties.
Main Results:
- Healthy respiratory microbiomes exhibited higher absolute abundances of core and rare species, greater rare species diversity, and a stable, interconnected co-occurrence network with no negative correlations.
- CF microbiomes displayed less stability and fragmentation, characterized by fewer species connections, more bridging species, and the presence of negative species correlations, even in the absence of typical CF pathogens.
- Pseudomonas aeruginosa DNA was detected in both healthy and CF children from an early age, indicating frequent exposure unrelated to disease status or age in this cohort.
Conclusions:
- A healthy respiratory microbiome is defined by high diversity and stable inter-species interactions.
- Instability and fragmentation of the microbial community in CF patients are evident early in life and are not solely dependent on the presence of established CF pathogens.
- Early and frequent exposure to Pseudomonas aeruginosa occurs in both healthy and CF children, suggesting colonization resistance may differ between these groups.
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.
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