• Bacterial Infection
• Opportunist lung infections
• Pneumonia
• Respiratory Infection
• Assisted Ventilation

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 just describing long lists of bacterial names, but sampling over time reveals dynamic interactions between organisms and with their environment and the word ‘community’ is therefore used deliberately. Not all of these changes in the presence and abundance of these organisms are immediately explicable; they might relate to any one of an enormous number of variables not measured by clinical studies. Forced expiratory volume has very little direct impact on a microorganism in the respiratory tract, whereas the presence of a particular microbial nutrient will.

Molecular methods, such as 16S rRNA gene sequencing, have a different resolution to clinical culture. They are capable of sensitively detecting bacteria without the narrow selection of the limited range of culture conditions commonly used. Conversely, they are not always capable of providing identification beyond the level of genus. Where microbiota analyses really excel is in providing a …