Table 1.
Study demographics*.
Fig 1.
Principal coordinates analysis (PCoA) of (A-F) bacteriome and (G-L) mycobiome data at different taxa in the three groups. Confidence ellipses are shown for each group, at 0.95% confidence.
Fig 2.
Boxplots showing richness estimates (observed, chao1 and ACE) of (A) bacteriome and (B) mycobiome at phylum, genus, and species levels.
Fig 3.
Venn diagrams showing frequency distribution of (A-C) core bacterial and (D-F) core fungal taxa (detected at abundance > 1%) in the three study groups. Frequency distribution in the core microbiota are shown for (A,D) Phylum, (B,E) Genus and (C,F) Species levels. HIV-SM: HIV-infected smokers, HIV-nSM: HIV-infected non-smokers, nHIV-SM: uninfected smokers.
Fig 4.
Stacked bar charts showing distribution of (A-C) bacterial and (D-F) fungal phyla across the tested samples in the three groups. Phyla present at an abundance of at least 1% relative to the total abundance in each sample were included in the analyses.
Fig 5.
Abundance profile of bacterial and fungal phyla in study groups.
(A) Boxplots showing relative abundance of bacterial and fungal phyla, (B) abundance ratio of Fusobacteria:Proteobacteria (ratio F:P) and Bacteriodetes:Proteobacteria (ratio B:P).
Table 2.
Bacterial genera with significantly different abundance between the three groups.
Table 3.
Fungal genera with significantly different abundance between the three groups.
Table 4.
Abundance of Candida species in the tested samples.
Fig 6.
Intra-kingdom correlations within the bacteriome and mycobiome for (A,D) HIV-infected non-smokers, (B,E) HIV-infected smokers, and (C,F) uninfected smokers. Spearman’s correlation for each comparison was determined for the three groups. Blue circles indicate positive correlations; red circles indicate negative correlation; diameter of circles represent the absolute value of correlation for each pair of the microbe-microbe matrix.
Fig 7.
Inter-kingdom correlations between the bacteriome and mycobiome for (A) HIV-infected non-smokers, (B) HIV-infected smokers, and (C) uninfected smokers. Spearman’s correlation for each comparison was determined for the three groups. Blue tiles indicate positive correlation; red tiles indicate negative correlations; tile sizes represent the absolute value of correlation for each pair of the microbe-microbe matrix.