The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study

Abstract

Each day, approximately 27,000 people become ill with tuberculosis (TB), and 4,000 die from this disease. Pulmonary TB is the main clinical form of TB, and affects the lungs with a considerably heterogeneous manifestation among patients. Immunomodulation by an interplay of host-, environment-, and pathogen-associated factors partially explains such heterogeneity. Microbial communities residing in the host's airways have immunomodulatory effects, but it is unclear if the inter-individual variability of these microbial communities is associated with the heterogeneity of pulmonary TB. Here, we investigated this possibility by characterizing the microbial composition in the sputum of 334 TB patients from Tanzania, and by assessing its association with three aspects of disease manifestations: sputum mycobacterial load, severe clinical findings, and chest x-ray (CXR) findings. Compositional data analysis of taxonomic profiles based on 16S-rRNA gene amplicon sequencing and on whole metagenome shotgun sequencing, and graph-based inference of microbial associations revealed that the airway microbiome of TB patients was shaped by inverse relationships between Streptococcus and two anaerobes: Selenomonas and Fusobacterium. Specifically, the strength of these microbial associations was negatively correlated with Faith's phylogenetic diversity (PD) and with the accumulation of transient genera. Furthermore, low body mass index (BMI) determined the association between abnormal CXRs and community diversity and composition. These associations were mediated by increased abundance of Selenomonas and Fusobacterium, relative to the abundance of Streptococcus, in underweight patients with lung parenchymal infiltrates and in comparison to those with normal chest x-rays. And last, the detection of herpesviruses and anelloviruses in sputum microbial assemblage was linked to co-infection with HIV. Given the anaerobic metabolism of Selenomonas and Fusobacterium, and the hypoxic environment of lung infiltrates, our results suggest that in underweight TB patients, lung tissue remodeling toward anaerobic conditions favors the growth of Selenomonas and Fusobacterium at the expense of Streptococcus. These new insights into the interplay among particular members of the airway microbiome, BMI, and lung parenchymal lesions in TB patients, add a new dimension to the long-known association between low BMI and pulmonary TB. Our results also drive attention to the airways virome in the context of HIV-TB coinfection.

Bacteriomes in lesions of pulmonary tuberculosis and its association with status of Mycobacterium tuberculosis excretion

“…Dominant phyla, with relative abundance from high to low, observed in the TB lesions were successively Proteobacteria , Actinobacteria , Firmicutes , Bacteroidetes , and Cyanobacteria . Ticlla and her colleagues have reported Firmicutes , Proteobacteria , Bacteroidetes , Actinobacteria and Fusobacteria as the major phyla order in sputum samples [ 12 ]. This difference is reasonable because microbes from the upper respiratory tract and the oral cavity can contaminate sputum samples inevitably during the expectoration process, which will bias the microbial profile in sputum.…”

“…We observed a strong correlation of bacterial profiles in TB lesions with the status of MTB excretion among pulmonary TB patients. Interestingly, sputum microbial composition and diversity were also reported to be associated with local lung environment indicated by abnormal chest x-ray findings [ 12 ]. Specific OTUs and indicator genera detected both suggested different micro-ecological environments of TB lesions.…”

“…Besides the physiological and biochemical impacts of TB lesions on MTB colonization [ 4 ], lung bacteria may be another important factor that can affect the growth behavior of MTB. Many studies have investigated the lung bacteria of pulmonary TB patients, but they were carried out using sputum [ 10 – 12 ] or bronchoalveolar lavage fluid (BLF) samples [ 13 , 14 ]. However, microbiota in sputum and BLF samples cannot exactly represent the entire inhabitants in lung, specifically in TB lesions.…”

More than Mycobacterium tuberculosis: specific site-of-disease microbial communities, functional capacities, and their distinct clinical profiles in tuberculous lymphadenitis

“…We identified three lymphotypes within dTBLs termed “ Prevotella-Corynebacterium”, “Prevotella-Streptococcus” , and “ Mycobacterium” , distinguished by different relative abundances of these taxa ( Prevotella co-occurred in the first two lymphotypes). These individual taxa are enriched in respiratory secretions from pulmonary TB cases 29 30 . Furthermore, within dTBLs, Streptococcus is associated with low BMI and extent of lung damage 30 .…”

“…These individual taxa are enriched in respiratory secretions from pulmonary TB cases 29 30 . Furthermore, within dTBLs, Streptococcus is associated with low BMI and extent of lung damage 30 . Prevotella in bronchoalveolar lavage fluid also positively correlates with SCFA concentrations and independently predicts incident TB in people without co-prevalent TB 31 .…”