Culture and Molecular Profiling of the Respiratory Tract Microbiota

Methods Mol Biol. 2018;1849:49-61. doi: 10.1007/978-1-4939-8728-3_4.


Microbiome research of host-associated communities has been advanced recently through improvements in sequencing technologies and bioinformatic methods. Traditional microbiological culture, when combined with molecular techniques, can provide a sensitive platform to comprehensively study the airway microbiota. Here we describe the culture methods necessary to capture a large proportion of the airway microbiota and molecular methods for profiling bacterial communities through the 16S rRNA gene, which, when combined, offer a more complete picture of the diversity of airway microbial communities than either method alone.

Keywords: 16S rRNA gene; Culture enrichment; Human microbiota; Microbiome; Respiratory tract microbiota.

MeSH terms

  • Bacteria / classification*
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Cell Culture Techniques
  • DNA, Bacterial / genetics*
  • Gene Expression Profiling / methods*
  • Humans
  • Microbiota*
  • RNA, Ribosomal, 16S / genetics*
  • Respiratory System / microbiology*
  • Sequence Analysis, DNA / methods*


  • DNA, Bacterial
  • RNA, Ribosomal, 16S