title: Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma.
abstract: 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 asthmatics and 6 healthy controls were separated in silico and mapped to available human and NCBI-NR protein reference databases. Human genes differentially expressed in asthmatics 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 asthmatics and controls. Finally, multivariate analysis was applied to find associations between microbiome characteristics and host upstream regulators while accounting for clinical variation.
  
  
  CONCLUSIONS
  Our study showed significant differences in the metabolism of microbiomes from asthmatic and non-asthmatic children 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 asthma. Microbial adhesion (virulence) and Proteobacteria abundance were significantly associated with variation in the expression of the upstream regulator IL1A; suggesting that microbiome characteristics modulate host inflammatory and immune systems during asthma.
authors.affiliation: Computational Biology Institute, George Washington University, Ashburn, Virginia, United States of America; Division of Emergency Medicine, Children's National Medical Center, Washington, DC, United States of America; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal.
authors.forename: Marcos
authors.initials: M
authors.lastname: Pérez-Losada
authors.affiliation: Computational Biology Institute, George Washington University, Ashburn, Virginia, United States of America; Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago, Chile.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Castro-Nallar
authors.affiliation: Computational Biology Institute, George Washington University, Ashburn, Virginia, United States of America.
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Bendall
authors.affiliation: Division of Emergency Medicine, Children's National Medical Center, Washington, DC, United States of America.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Freishtat
authors.affiliation: Computational Biology Institute, George Washington University, Ashburn, Virginia, United States of America.
authors.forename: Keith A
authors.initials: KA
authors.lastname: Crandall
mesh_terms: D000293:Adolescent; D000328:Adult; D001249:Asthma / Q000235:genetics* / Q000276:immunology / Q000382:microbiology*; D001422:Bacterial Adhesion / Q000276:immunology; D001483:Base Sequence; D044822:Biodiversity; D002648:Child; D005260:Female; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D006801:Humans; D053582:Interleukin-1alpha / Q000096:biosynthesis; D008297:Male; D064307:Microbiota / Q000235:genetics*; D001936:Moraxella catarrhalis / Q000235:genetics / Q000302:isolation & purification; D009297:Nasal Mucosa / Q000382:microbiology*; D025341:Principal Component Analysis; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D055815:Young Adult
chemical_list: C508584:IL1A protein, human; D053582:Interleukin-1alpha; D012336:RNA, Ribosomal, 16S