BACKGROUND: High-throughput sequencing (HTS) analysis of microbial communities from the respiratory airways has heavily relied on the 16S rRNA gene. Given the intrinsic limitations of this approach, airway microbiome research has focused on assessing bacterial composition during health and disease, and its variation in relation to clinical and environmental factors, or other microbiomes. Consequently, very little effort has been dedicated to describing the functional characteristics of the airway microbiota and even less to explore the microbe-host interactions. Here we present a simultaneous assessment of microbiome and host functional diversity and host-microbe interactions from the same RNA-seq experiment, while accounting for variation in clinical metadata. METHODS: Transcriptomic (host) and metatranscriptomic (microbiota) sequences from the nasal epithelium of 8 @entity748 and 6 healthy controls were separated in silico and mapped to available @entity1 and NCBI-NR protein reference databases. @entity1 genes differentially expressed in @entity748 and controls were then used to infer upstream regulators involved in immune and inflammatory responses. Concomitantly, microbial genes were mapped to metabolic databases (COG, SEED, and KEGG) to infer microbial functions differentially expressed in @entity748 and controls. Finally, multivariate analysis was applied to find associations between microbiome characteristics and host upstream regulators while accounting for clinical variation. RESULTS AND DISCUSSION: Our study showed significant differences in the metabolism of microbiomes from asthmatic and non-asthmatic @entity1 for up to 25% of the functional properties tested. Enrichment analysis of 499 differentially expressed host genes for inflammatory and immune responses revealed 43 upstream regulators differentially activated in @entity565 . Microbial adhesion (virulence) and Proteobacteria abundance were significantly associated with variation in the expression of the upstream regulator @entity1192 ; suggesting that microbiome characteristics modulate host inflammatory and immune systems during @entity565 .

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in XXXX .

@entity748 :: ('MESH:D013224', 'Disease') :: ['asthmatics'] @entity1 :: ('9606', 'Species') :: ['children', 'human', 'Human'] @entity1192 :: ('3552', 'Gene') :: ['IL1A'] @entity565 :: ('MESH:D001249', 'Disease') :: ['asthma']
@entity565 :: (MESH:D001249,Disease) :: ['Pediatric Asthma']
