ABCs of the lung microbiome

Abstract

The lungs of healthy humans have traditionally been considered to be sterile when examined by culture-based techniques. However, molecular identification techniques are now being used to explore the lung microbiome in ways that mirror study of other body sites and organ systems. Familiarity with population definitions and indices of diversity will lead to better understanding of the literature now coming to publication. Differences in methodology and sampling may contribute significantly to experimental variability, and the field has not coalesced around standard ways to present data or to perform statistical comparisons. This emerging and exciting field of investigation is leading to new ways of thinking about the lung and about lung disease.

Figure 1.

Secondary structure model of the 16S rDNA. V1 through V9 indicate major hypervariable regions, which are sequenced to identify organizational taxonomic units; V4 and V6 are unlabeled. Reprinted by permission from Reference .

Figure 2.

Neutral model analysis. In this example, the relative abundance of organizational taxonomic units (OTUs) in oral washes is plotted against the detection frequency of OTUs in the lung. A line of identity can be constructed, with confidence intervals indicated by the shaded areas. OTUs falling outside the confidence intervals are deemed significantly enriched in lung or mouth. Adapted by permission from Reference .