Sputum microbiota profiles of treatment-naïve TB patients in Uganda before and during first-line therapy

Abstract

Information on microbiota dynamics in pulmonary tuberculosis (TB) in Africa is scarce. Here, we sequenced sputa from 120 treatment-naïve TB patients in Uganda, and investigated changes in microbiota of 30 patients with treatment-response follow-up samples. Overall, HIV-status and anti-TB treatment were associated with microbial structural and abundance changes. The predominant phyla were Bacteroidetes, Firmicutes, Proteobacteria, Fusobacteria and Actinobacteria, accounting for nearly 95% of the sputum microbiota composition; the predominant genera across time were Prevotella, Streptococcus, Veillonella, Haemophilus, Neisseria, Alloprevotella, Porphyromonas, Fusobacterium, Gemella, and Rothia. Treatment-response follow-up at month 2 was characterized by a reduction in abundance of Mycobacterium and Fretibacterium, and an increase in Ruminococcus and Peptococcus; month 5 was characterized by a reduction in Tannerella and Fusobacterium, and an increase in members of the family Neisseriaceae. The microbiota core comprised of 44 genera that were stable during treatment. Hierarchical clustering of this core’s abundance distinctly separated baseline (month 0) samples from treatment follow-up samples (months 2/5). We also observed a reduction in microbial diversity with 9.1% (CI 6–14%) of the structural variation attributed to HIV-status and anti-TB treatment. Our findings show discernible microbiota signals associated with treatment with potential to inform anti-TB treatment response monitoring.

Subtracting the background: Reducing cell-free DNA’s confounding effects onMycobacterium tuberculosisquantitation and the sputum microbiome

“…PEMAX improved detection of microbiome changes in sputum before and after chemotherapy by detecting more discriminatory taxa. It is worth considering if previously documented treatment-related sputum microbiome changes 46,47 overlooked any taxonomic changes that could have been detected using a viability dye.…”

Features of the lung microbiota in tuberculosis infection

“…Только одно из проанализированных исследований не подтвердило влияние противотуберкулезных препаратов на микробиоту легкого [50]. Другие работы действительно показали значительное уменьшение микробного разнообразия в процессе лечения противотуберкулезными препаратами [43,51]. G. Xiao и соавт.…”

The microbiome and the gut-lung axis in tuberculosis: interplay in the course of disease and treatment

“…Alterations of gut and lung microbiota in the course of anti-TB treatment according to selected references using research words "TB treatment," "microbiome," "tuberculosis" "microbiota" in PubMed database NCBI. Arrows indicate genera enrichment or decreased, IC (inconclusive) denotes controversial or non-significant results within references and unknown (UK) and blank spaces for missing data in the references reviewed (Botero et al, 2014;Khan et al, 2016;Krishna et al, 2016;Namasivayam et al, 2017;Wipperman et al, 2017;Vázquez-Pérez et al, 2020;Wang et al, 2020;Cao et al, 2021;Kateete et al, 2021;Lin et al, 2021;Valdez-Palomares et al, 2021;Xiao et al, 2022;Ye et al, 2022;Zhang et al, 2022). Created with BioRender.com.…”