Table 1 The distribution of some genera that were uniquely found in the sputum of

pulmonary tuberculosis patients Genera α β Phenylobacterium 13/31 2.15% Stenotrophomonas 12/31 2.15% Cupriavidus 16/31 1.60% Caulobacter 5/31 1.56% Pseudomonas 15/31 1.27% Thermus 14/31 0.71% Sphingomonas 16/31 0.66% Brevundimonas 17/31 0.49% this website Pelomonas 15/31 0.47% Acidovorax 13/31 0.47% Brevibacillus 16/31 0.36% Methylobacterium 13/31 0.34% Diaphorobacter 17/31 0.31% Comamonas 14/31 0.26% Mobilicoccus 20/31 0.24% Fervidicoccus 13/31 0.21% Serpens 5/31 0.19% Lactobacillus 12/31 0.18% Thermobacillus 12/31 0.16% Auritidibacter 13/31 0.14% Deinococcus 9/31 0.13% Lapillicoccus 13/31 0.11% Devriesea 13/31 0.11% “α”: the number of pulmonary tuberculosis patients in whom sequences from the corresponding buy SHP099 genera were found. “β”: the percentage of sequences GDC-0449 nmr of the corresponding genera of all sequences found in pulmonary tuberculosis patients. Discussion This study provides the first report on the microbial composition of the lower respiratory tract of pulmonary tuberculosis patients through the amplification of 16S rRNA V3 hyper-variable regions using bar-coded primers and pyro-sequencing by Roche 454 FLX. The results revealed that the

microbial composition of the lower respiratory tract in pulmonary tuberculosis patients was more diverse (p<0.05) than in healthy participants. Charlson et al reported that the microbial composition of saliva or pharynx secretions can reflect the microbial communities in the lower respiratory tract, and their results showed that there is a topographical continuity of bacterial populations in the healthy human respiratory tract

[17]. Therefore, we chose to use sputum and respiratory secretions in this study. However, the best samples to use would be lung lavage fluid, which perfectly reflects the lower microbial composition of the respiratory tract. However, obtaining lung next lavage fluid is challenging, especially from healthy volunteers, because lung lavage is painful and may even be harmful. This may raise some ethical issues. In contrast, sputum and respiratory secretions are easily obtained through non-invasive, patients-friendly collection methods. Therefore, we chose to analyse sputum and respiratory tract secretions in our study. A previous study showed that fewer than 1% of commensal organisms are able to grow under laboratory conditions [18]; therefore, traditional cultivation-based strategies for analysing the complexity and genetic diversity of microbial communities are strongly biased. However, modern methods, based on barcoded primers and 454 pyro-sequencing allow for a thorough profiling of the microbiota of each enrolled person [19, 20]. Published studies have also proved that the 16S rRNA V3 region sequence ideally suited for distinguishing all bacterial species to the genus level, except for closely related Enterobacteriaceae[21].