Table 1.
A: Human subject characteristics. B: Clinical details of TB patients.
Fig 1.
Differences in the abundance of microbiota in active-TB patients and healthy individuals, at the level of phyla.
(A) Taxonomic distributions of bacteria from fecal 16S rDNA sequencing data from healthy (n = 40) and tuberculosis cohorts (n = 42). (B) Relative abundances of Firmicutes, Actinobacteria, Fusobacteria, Tenericutes and Bacteroidetes from fecal 16S rDNA sequencing data from healthy (n = 40) and tuberculosis cohorts (n = 42). p value statistically significant based on Man-Whitney t-test, *p< 0.05; **p< 0.01 and ***p< 0.001.
Table 2.
Log2 Fold change at the phyla level in TB patients and healthy controls.
Fig 2.
Gut microbiota diversity in tuberculosis patients.
(A) Principal coordinates analysis of unweighted UniFrac distance based on 16S rDNA profiling of the gut microbiome from healthy (n = 40) and tuberculosis cohorts (n = 42), p value statistically significant based on Bonferroni-corrected parametric t-test, ****p< 0.001. Gut microbiome in active-TB patients (red) and healthy individuals (blue) display separation in the two groups. Each data point represents the entire microbial signature in individual samples. (B) Shannon diversity index of fecal 16S rDNA sequencing data from healthy (n = 40) and tuberculosis cohorts (n = 42). p value statistically significant based on Man-Whitney t-test, **p< 0.01. (C) Microbiome profiles (84 genera and families where unknown genus contributed to significant difference in comparison with healthy controls) of microbiota shown in a heat map. Unique clusters of genera in active-TB patients are outlined by a yellow box and those in age-matched healthy individuals by the green boxes. Each small square in the heat map represents a genus. Clusters of bacterial genera in TB patients are well separated from those in healthy individuals.
Fig 3.
Linear discriminant analysis effect size (LEfSe) of the top 25 significant families and/or genera in active-TB patients and healthy individuals.
The linear discriminant analysis scores (LDA) predicate and identify enriched microbes. Bacterial genera or families (unknown genus contributing to significant difference) enriched in active-TB patient group (green bars), in comparison to those in healthy control group (red bars).
Fig 4.
The dominating pathways in TB patient group and healthy control group, are based on the dominant microbiota shown in Fig 3.
Fig 5.
Correlations (Spearman) of anti-M. tb. antibodies in active-TB patients to gut microbiota.
Plasma antibodies against 11 M. tb. antigens in plasma samples from active TB patients are shown on X-axis. Microbiota, at the genus, are shown on Y-axis. The Spearman’s ranked correlation test with false discovery rate (FDR) adjustment was used to test the microbiome-antibody correlation. Antibodies against M. tb. Antigens that showed positive correlation with the enriched bacterial genera are shown is red and those that displayed negative correlations with the genera are shown in blue. Statistical analysis was not performed for Fig 5 since it shows a general comparison of microbiota profiling between TB patients and healthy individuals. Microbiota most common in TB patients contain antibodies agaist antigens Rv0934, Rv1926c, Rv1860, Rv3841, and Rv1886c in addition to the whole membrane extract from H37Rv bacteria. The clusters that were boxed and specifically highlighted were identified visually based on the differences between healthy individuals and TB patients. Green box shows the microbiota profiles common in TB patients when the antibodies agaist 6 M.tb. antigens mentioned above are detected. Red box represents the microbiota profiling of healthy individuals who did not have antibodies against these antigens.
Fig 6.
Copy number of bcoA gene in active-TB patients (red) and healthy individuals (blue), per ng of DNA.
Data shown as a box and whisker plot. The line within the box represents the median value, the box represents the interquartile range (IQR), and bars represent the data spread. Copy number of bcoA gene was significantly (p-value: 0.004) lower in active-TB patients (Median: 111.8; IQR: 69.6–203.8) than in the healthy control group (Median: 515.05; IQR: 337.3–684.15); a five-fold reduction in gene copy number among the gut microbiota in TB patients.