Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life

Abstract

Graphical abstract

Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome

“…The classification performance was validated with the out-of-bag (OOB) estimate of error rate, class errors and the Boruta algorithm ( 77 ). The Boruta algorithm generates shadow attributes by randomly shuffling the original input variables and iteratively comparing random with the corresponding original variables, so that nonrandom features of importance for the classification were distinguishable from random feature assignments ( 42 ). Random forest and Boruta wrapper application runs were repeated 100 times with different seeds set for the classification and for the feature selection procedure to avoid a selection-based bias ( 42 ).…”

“…The focus of past CF microbial airway metagenome studies has been on small cohorts of CF adolescents and adults who naturally expectorate comparably large volumes of respiratory secretions ( 29 – 39 ). We have optimized our wet-lab and in silico protocols so that the taxonomic and functional identification of core and rare species from shotgun metagenome sequencing data has become feasible with samples retrieved from all age groups ( 40 – 42 ).…”

Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach

“…To date, despite growing knowledge in microbiome studies, it remains challenging to define the microbial features that universally characterize a healthy human microbiome. Based on research carried out, it is believed that the pooling of faecal samples from different individuals to prepare standardized inoculum is a valuable measure in population-level association research studies [48][49][50] . The combined faecal inocula are assumed to have a more heterogeneous population and are, therefore, more representative microbiota for the whole population 30 .…”

The Cystic Fibrosis Upper and Lower Airway Metagenome

“…In the case of the human airway, however, completely sequenced reference genomes are already available for almost all bacterial taxa that reside in this habitat. The functional potential of the microbiome can thus be more reliably explored from annotated reference genomes than from metagenome sequence data sets, which, because of their insufficient coverage, will preclude genome assembling, at least from the rare species in the community ( 65 ). Instead, as described in this report, untargeted airway metagenome sequencing has value in the determination of the abundance of microbes ( 3 ) and the sensitive and specific identification of poorly cultivatable, rare, and closely related species ( 65 , 66 ).…”