Sputum microbiota in tuberculosis as revealed by 16S rRNA pyrosequencing

PLoS One. 2013;8(1):e54574. doi: 10.1371/journal.pone.0054574. Epub 2013 Jan 24.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Bacteria / classification
  • Bacteria / genetics*
  • Bacteria / isolation & purification
  • Biodiversity
  • Case-Control Studies
  • Female
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Male
  • Metagenome / genetics*
  • Middle Aged
  • Phylogeny
  • RNA, Ribosomal, 16S / classification
  • RNA, Ribosomal, 16S / genetics*
  • Sequence Analysis, DNA
  • Sputum / microbiology*
  • Tuberculosis, Pulmonary / microbiology*


  • RNA, Ribosomal, 16S

Grant support

This work was supported by the Research Fund for the Control of Infectious Diseases (RFCID) from the Health, Welfare and Food Bureau of the Hong Kong SAR Government (Ref. No. 09080442). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.