Respiratory tract clinical sample selection for microbiota analysis in patients with pulmonary tuberculosis

Abstract

BackgroundChanges in respiratory tract microbiota have been associated with diseases such as tuberculosis, a global public health problem that affects millions of people each year. This pilot study was carried out using sputum, oropharynx, and nasal respiratory tract samples collected from patients with pulmonary tuberculosis and healthy control individuals, in order to compare sample types and their usefulness in assessing changes in bacterial and fungal communities.FindingsMost V1-V2 16S rRNA gene sequences belonged to the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria, with differences in relative abundances and in specific taxa associated with each sample type. Most fungal ITS1 sequences were classified as Ascomycota and Basidiomycota, but abundances differed for the different samples. Bacterial and fungal community structures in oropharynx and sputum samples were similar to one another, as indicated by several beta diversity analyses, and both differed from nasal samples. The only difference between patient and control microbiota was found in oropharynx samples for both bacteria and fungi. Bacterial diversity was greater in sputum samples, while fungal diversity was greater in nasal samples.ConclusionsRespiratory tract microbial communities were similar in terms of the major phyla identified, yet they varied in terms of relative abundances and diversity indexes. Oropharynx communities varied with respect to health status and resembled those in sputum samples, which are collected from tuberculosis patients only due to the difficulty in obtaining sputum from healthy individuals, suggesting that oropharynx samples can be used to analyze community structure alterations associated with tuberculosis.

The microbiome at the pulmonary alveolar niche and its role in Mycobacterium tuberculosis infection

“…This study also demonstrated that “nasal” clusters separate from “Sputum” and “Oropharynx”, a finding that has been confirmed very recently by another group (Bassis CM, 2015). This group additionally reported on the presence of fungi in the TB lung, with members of the phylum Ascomycota dominating (Botero, et al, 2014). When comparing the sputum to the oropharynx, this group did not note a difference, a finding likely due to contamination during sputum expectoration.…”

“…However, they also reported finding Fusobacteria and determined that Proteobacteria and Bacteroidetes were the dominant organisms in TB, with Firmicutes predominantly in control lungs (Cheung et al, 2013). A study published last year which unfortunately did not compare TB sputum to healthy sputum nonetheless noted that Bacteroidetes, Fusobacteria, and Actinobacteria were dominant in TB (Botero et al, 2014). This study also demonstrated that “nasal” clusters separate from “Sputum” and “Oropharynx”, a finding that has been confirmed very recently by another group (Bassis CM, 2015).…”

“…Taken together, the four studies of the lung microbiome in TB through early 2015 include only 134 TB patients and 64 controls, with all but one site located within China (Botero, et al, 2014; Cheung, et al, 2013; Cui, et al, 2012; Wu, et al, 2013). Early attempts to determine the composition of the gut microbiome were hampered by a lack of sample diversity, and further study, including sampling of sites in other regions of the world where Mtb is endemic (e.g.…”

<b>ReFDash - </b>A <strong>Re</strong>pository of <strong>F</strong>unctional <strong>Dash</strong>boards providing comprehensive functional insights inferred from 16S microbiome data sets

“…16S rRNA gene-based profiling techniques are widely used for deciphering the structure of bacterial communities residing in varied ecological niches (Gill et al, 2006;Huse et al, 2012;Yatsunenko et al, 2012). In the context of clinical studies, a (cross-sectional/ longitudinal) comparison of community structures between the two or more states of health/ disease can help in preliminary identification of specific bacterial taxa (or groups of taxa) that demonstrate statistically significant association(s) between their presence (or abundance) and the state of health/ disease severity (Alekseyenko et al, 2013;Botero et al, 2014;Cui et al, 2012;Ganju et al, 2016;Griffen et al, 2012; Kirst et al, 2015;Tandon et al, 2018). In some cases, differences in community structure (quantified using alpha or beta diversity measures) of the studied microbial communities have also served as important cues to understand dynamics of specific clinical conditions (Haque et al, 2017;Tandon et al, 2019).…”

The Human Microbiome in the Fight Against Tuberculosis

“…12,13 TB AND THE MICROBIOME In this review, eight studies examined the association between pulmonary TB infection and disease and the microbiome, including an animal study, 30 a case report, 31 and 6 case-control studies (Table 1). 21,[32][33][34][35][36] Key study findings are highlighted in the following two sections (regarding TB and the gut or lung microbiome, respectively), and study methodology is compared in the third section.…”