Table 1 Comparison of sampling methods for murine lung microbiome studies
Whole lung tissue | Bronchoalveolar lavage fluid | ||
|---|---|---|---|
Sample description | Sample content | All lung lobes homogenized in sterile water | Dislodged airway and alveolar contents (microbes, leukocytes, epithelial cells) in sterile saline |
Biological site sampled | Airway and intra-alveolar space, interstitium, and blood (if not perfused) | Airway and intra-alveolar space only | |
Bacterial biomass | Low | Low | |
Host-to-microbe DNA ratio | High | Low | |
Summary of findings (relative to each other) | Total DNA content | High | Low |
Bacterial DNA content | High | Low | |
Variation among biological replicates | Low | High | |
Similarity to contaminating source “communities” (negative controls) | Low | High | |
Similarity to biological source community (oral microbiome) | High | Low |