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Table 1 Comparison of sampling methods for murine lung microbiome studies

From: Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota

   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