Ventilator-associated pneumonia: when is a pathogen not a pathogen?

The context of respiratory microbiology is changing. 16S rRNA gene sequencing is a workhorse method in the field of environmental microbiology, established for over 30 years.1 Rather than requiring growth of organisms on agar plates it targets the DNA of all the microorganisms present, revealing bacteria irrespective of their particular growth requirements. Together with metagenomics, the untargeted shotgun sequencing of DNA extracted from a sample, these techniques have been applied to the respiratory tract. These approaches have revealed a characteristic respiratory community of microorganisms, a respiratory microbiota that varies in different diseases.2–6 The most prevalent organisms in the healthy respiratory tract are Streptococcus spp., Veillonella spp. and Prevotella spp.; the latter two genera being anaerobic bacteria, intolerant of oxygen and not commonly isolated by classic microbiology approaches.

At times studies that use these techniques might seem to be...