Fig. 9

The neutral theory of community ecology demonstrates that the bronchial and lung tissue microbiota are very closely related. Neutral model comparing the source microbiota with the lung tissue microbiota. Each figure contains a solid line that represents the expected proportion of an OTU in the lung at a given source abundance. The dotted lines represent the 95% confidence interval of the line. The x-axis is presented in log scale for clarity and ease of presentation. Taxa found in the lung but not in the source site are included on the far left of each figure, and a truncated x-axis break is used to indicate that these data points are displayed despite the use of the log scale. (a) When the oral microbiota was used as the source community for the lung tissue microbiota, OTUs corresponding to common oral taxa (labeled 1–15; e.g., Streptococcus, Prevotella, Veillonella, Actinomyces) follow the neutral theory. Many OTUs not found in the oral site (labeled A) and low abundance oral OTUs (labeled B) were more common in the lung tissue than would be predicted by the neutral theory. One common oral OTU (Porphyromonas, labeled G) was less common in the lung tissue than was predicted by the neutral theory. The immigration probability for oral taxa was 0.62. (b) When the nasal microbiota was used as the source community for the lung tissue microbiota, OTUs corresponding to common nasal taxa (labeled 1–5; e.g., Corynebacterium, Staphylococcus, Neisseria) follow the neutral theory. Many OTUs not found in the nasal site (labeled A) and low abundance nasal OTUs (labeled B) were more common in the lung tissue than would be predicted by the neutral theory. Notably, many of these low nasal abundance OTUs are common oral taxa (e.g., Fusobacterium, Actinomyces, Prevotella, Veillonella). Two common nasal abundance OTUs (labeled C and D, including the common COPD pathogen Moraxella) were less common in the lung tissue than was predicted by the neutral theory. The immigration probability for nasal taxa was 0.74. (c) When the bronchial microbiota was used as the source community for the lung tissue microbiota, OTUs corresponding to common bronchial taxa (labeled 1–14, including both common oral and nasal taxa such as Streptococcus, Corynebacterium, Prevotella, and Veillonella) follow the neutral theory. Several low abundance bronchial OTUs (labeled A–F) were more common in the lung tissue than was predicted by the neutral theory. In contrast to the oral and nasal source figures, only one OTU (labeled A, Bacteroides) was not found in the bronchus but was more common in the lung tissue than would be predicted by the neutral theory. Three moderate bronchial abundance OTUs (labeled G–K) were less common in lung tissue than was predicted by the neutral theory. The bronchial microbiota immigration probability was 0.69