Sputum Microbiota in Tuberculosis as Revealed by 16S rRNA Pyrosequencing

Abstract

BackgroundTuberculosis (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 FindingsHere, 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/SignificanceThe 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.

Actinomyces and Related Organisms in Human Infections

“…For example, Actinomyces was found to be a core component of the microbiota in sputum samples from 22 tuberculotic patients and 14 controls examined by 16S rRNA gene pyrosequencing (49). This is consistent with a report that Actinomyces was among the most prevalent genera in the sputum of cystic fibrosis patients (50 (51).…”

Leptotrichia species in human infections II

“…oral taxon, Capnocytophaga spp., C. sputigena , Treponema spp., Treponema sp. oral taxon, T. denticola , Fusobacterium spp., F. nucleatum , F. periodonticum , qPCR 110M/F 22–24 Leptotrichia spp.HealthySaliva Streptococcus , Lachnospiraceae, Peptostreptococcus , Flavobacteriaceae, Aggregatibacter , Porphyromonas, Corynebacterium , Granulicatella, Rothia , Eubacterium, Veillonella , Fusobacterium, Oribacterium , Neisseria, Gemella , Pasteurella, Prevotella , Actinomyces, Haemophilus , Moraxella , SR1, HTS[38]M/F 3–6 Leptotrichia spp.HealthySaliva Streptococcus, Lachnospiraceae, Granulicatella , Fusobacterium, Neisseria , Aggregatibacter, Actinomyces , Haemophilus, Porphyromonas , Pasteurella, Rothia , Veillonella, Oribacterium , Gemella, Prevotella , HTS 1121–60 days Leptotrichia spp.Fermenting Lees liquorLiquor Corynebacterium , Staphylococcus, Microbacterium , Lactobacillus, Bacillus , Clostridium, Streptococcus , Burkholderia, Actobacter , Serratia, Rhodoccous , Pelobacter, Arthrobacter , Curtobacterium, Methanoculleus , Saccharomyces, Aspergillus , Eurotium, Zygosaccharomyces , Saccharomycopsis, Fomitopsis , Pichia, Talaromyces , Trichosporon , 16S rRNA- and 18S rRNA gene sequencing[39]113UK Leptotrichia spp., L. hofstadii Tumor tissueTumor tissues Campylobacter , Fusobacterium spp., F. nucleatum , C. showae , Ralstonia, Selenomonas , S. sputigena , Bacteroides , HTS, PCA[40]UK Unaffected tissueSurgical samples Ruminococcus , Pseudoflavonifractor, Ruminococcaceae , Parabacteroides, Bacteroides , Holdemania, Ralstonia , HTS, PCA 115M/F 20–66 Leptotrichia spp.TBSputumUnclassified Enterobacteriaceae , Veillonella, P. melaninogenica , Neisseria, Fusobacterium , Streptococcus , S. anginosus , S. mitis clone, Mogibacterium, Moryella , P. micra , Oribacterium, Prevotella , Pseudomonas, Lactococcus , L. crispatus , Actinomyces , HTS, PCA[41]M/F 22–82 TB-freeSputum Strep...…”

“…Leptotrichia species were equally isolated from the blood and gastric fluid of patients with coronary artery disease (CAD), candidal esophagitis, chronic kidney disease, diabetic, duodenal ulcer, erythematous gastropathy, gastroesophageal reflux disease, gastric ulcer, hiatal hernia, reflux esophagitis, upper gastrointestinal bleeding, renal transplant, and sarcoidosis (Table 2) [16]. Also, Leptotrichia species were isolated from tumor tissues and sputum of patients with tuberculosis, acute exacerbation of chronic obstructive pulmonary disease, and feces of piglets with porcine epidemic diarrhea virus [40,41,43,50,51]. They were also detected in patient material from tongue plaque with malodor [42], biofilms of caries, oral epithelial cells [48,49], vaginal swabs with high-risk human papillomavirus, and from HIV-positive and -negative subjects [55].…”

Management of lower respiratory tract infections (LRTI's): clinical microbiologists' perspective

“…5 Microbiologist's role becomes crucial in deciding the culture methods to be employed to isolate the suspected causative microorganism and identification of the probable pathogen among mixed growth of the isolated bacteria/fungi. [6][7][8] A previous communication has opined that broncho-alveolar lavage (BAL) and induced sputum must be specimen of choice to reduce the negative results from the regular sputum sample. 9 Report of a recent study also has indicated that an education package for staff on when and how to collect appropriate sputum samples has improved the reliability of culture results and reduced the workload and cost.…”