The lung microbiome of Ugandan HIV-infected pneumonia patients is compositionally and functionally distinct from that of San Franciscan patients.

TNF-alpha expression was positively correlated with airway bacterial burden (r = 0.41, p<0.01, q<0.05) and negatively correlated with phylogenetic diversity (r = −0.29, p<0.05, q<0.05), though the relationship with community richness did not quite reach significance (r = −0.19, p = 0.18, q = 0.09; Figure 2 ).

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