Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing

Man Kit Cheung, Wai Yip Lam, Wendy Yin Wan Fung, Patrick Tik Wan Law, Chun Hang Au, Wenyan Nong, Kai Man Kam, Hoi Shan Kwan, Stephen Kwok Wing Tsui, Man Kit Cheung, Wai Yip Lam, Wendy Yin Wan Fung, Patrick Tik Wan Law, Chun Hang Au, Wenyan Nong, Kai Man Kam, Hoi Shan Kwan, Stephen Kwok Wing Tsui

Abstract

Background: Tuberculosis (TB) remains a global threat in the 21st century. Traditional studies of the disease are focused on the single pathogen Mycobacterium tuberculosis. Recent studies have revealed associations of some diseases with an imbalance in the microbial community. Characterization of the TB microbiota could allow a better understanding of the disease.

Methodology/principal findings: Here, the sputum microbiota in TB infection was examined by using 16S rRNA pyrosequencing. A total of 829,873 high-quality sequencing reads were generated from 22 TB and 14 control sputum samples. Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were the five major bacterial phyla recovered, which together composed over 98% of the microbial community. Proteobacteria and Bacteroidetes were more represented in the TB samples and Firmicutes was more predominant in the controls. Sixteen major bacterial genera were recovered. Streptococcus, Neisseria and Prevotella were the most predominant genera, which were dominated by several operational taxonomic units grouped at a 97% similarity level. Actinomyces, Fusobacterium, Leptotrichia, Prevotella, Streptococcus, and Veillonella were found in all TB samples, possibly representing the core genera in TB sputum microbiota. The less represented genera Mogibacterium, Moryella and Oribacterium were enriched statistically in the TB samples, while a genus belonging to the unclassified Lactobacillales was enriched in the controls. The diversity of microbiota was similar in the TB and control samples.

Conclusions/significance: The composition and diversity of sputum microbiota in TB infection was characterized for the first time by using high-throughput pyrosequencing. It lays the framework for examination of potential roles played by the diverse microbiota in TB pathogenesis and progression, and could ultimately facilitate advances in TB treatment.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1. Relative abundance of dominant bacterial…
Figure 1. Relative abundance of dominant bacterial phyla in TB and control samples.
Only phyla >1% in either group were included.
Figure 2. Relative abundance of dominant bacterial…
Figure 2. Relative abundance of dominant bacterial phyla in all individuals under study.
Only phyla >1% in either group were included. The 22 samples on the left were from the TB patients, and the 14 samples on the right were from the control group.
Figure 3. PCoA plots of TB and…
Figure 3. PCoA plots of TB and control samples.
The plots were based on a) weighted and b) unweighted UniFrac distances. The two principal coordinates combined explained 66.44% and 24.31% of the variations in the weighted and unweighted cases, respectively. Red dots represent TB samples; blue dots represent control samples.
Figure 4. Relative abundance of dominant bacterial…
Figure 4. Relative abundance of dominant bacterial genera in TB and control samples.
Only genera >1% in either group were included.
Figure 5. Prevalence of dominant bacterial genera…
Figure 5. Prevalence of dominant bacterial genera in TB (n = 22) and control (n = 14) samples.
Only genera >1% in either group were included.
Figure 6. Relative abundance of dominant bacterial…
Figure 6. Relative abundance of dominant bacterial genera in all individuals under study.
Only genera >1% in either group were included. The 22 samples on the left were from the TB patients, and the 14 samples on the right were from the control group.

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