title: The microbiome of the human lower airways: a next generation sequencing perspective.
abstract: For a long time, the human lower airways were considered a sterile environment where the presence of microorganisms, typically revealed by culturing, was interpreted as an abnormal health state. More recently, high-throughput sequencing-based studies have led to a shift in this perception towards the notion that even in healthy conditions the lower airways show either transient presence or even permanent colonization by microorganisms. However, challenges related to low biomass and contamination in samples still remain, and the composition, structure and dynamics of such putative microbial communities are unclear. Here, we review the evidence for the presence of microbial communities in the human lower airways, in healthy subjects and within the context of medical conditions of interest. We also provide an overview of the methodology pertinent to high-throughput sequencing studies, specifically those based on amplicon sequencing, including a discussion of good practices and common pitfalls.
authors.affiliation: DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 4), 00014 Helsinki, Finland.
authors.forename: Velma T E
authors.initials: VTE
authors.lastname: Aho
authors.affiliation: DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 4), 00014 Helsinki, Finland.
authors.forename: Pedro A B
authors.initials: PAB
authors.lastname: Pereira
authors.affiliation: Skin and Allergy Hospital, Helsinki University Hospital, Helsinki, Finland.
authors.forename: Tari
authors.initials: T
authors.lastname: Haahtela
authors.affiliation: Division of Allergy, Department of Pediatrics, Nippon Medical School, Tokyo, Japan.
authors.forename: Ruby
authors.initials: R
authors.lastname: Pawankar
authors.affiliation: DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 4), 00014 Helsinki, Finland.
authors.forename: Petri
authors.initials: P
authors.lastname: Auvinen
authors.affiliation: DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 4), 00014 Helsinki, Finland.|Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
authors.forename: Kaisa
authors.initials: K
authors.lastname: Koskinen