Species-level evaluation of the human respiratory microbiome

Abstract

Background Changes to human respiratory tract microbiome may contribute significantly to the progression of respiratory diseases. However, there are few studies examining the relative abundance of microbial communities at the species level along the human respiratory tract. Findings Bronchoalveolar lavage, throat swab, mouth rinse, and nasal swab samples were collected from 5 participants. Bacterial ribosomal operons were sequenced using the Oxford Nanopore MinION to determine the relative abundance of bacterial species in 4 compartments along the respiratory tract. More than 1.8 million raw operon reads were obtained from the participants with ∼600,000 rRNA reads passing quality assurance/quality control (70–95% identify; >1,200 bp alignment) by Discontiguous MegaBLAST against the EZ BioCloud 16S rRNA gene database. Nearly 3,600 bacterial species were detected overall (>750 bacterial species within the 5 dominant phyla: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria. The relative abundance of bacterial species along the respiratory tract indicated that most microbes (95%) were being passively transported from outside into the lung. However, a small percentage (<5%) of bacterial species were at higher abundance within the lavage samples. The most abundant lung-enriched bacterial species were Veillonella dispar and Veillonella atypica while the most abundant mouth-associated bacterial species were Streptococcus infantis and Streptococcus mitis. Conclusions Most bacteria detected in lower respiratory samples do not seem to colonize the lung. However, >100 bacterial species were found to be enriched in bronchoalveolar lavage samples (compared to mouth/nose) and may play a substantial role in lung health.

Veillonellaceae family members uniquely alter the cervical metabolic microenvironment in a human three-dimensional epithelial model

“…Histamine, a key metabolite involved in local host responses, was significantly accumulated by infection with V. atypica and V. montpellierensis. Other studies have found that histamine can decrease the expression of tight junctional proteins (ZO-1 in nasal epithelial cells and E-cadherin in epithelial pulmonary cells) 61 . Therefore, an increase in histamine may increase epithelial permeability, although this would need to be tested in the context of the cervicovaginal epithelium to confirm the role of histamine in barrier function within the cervicovaginal mucosa.…”

An observational study of anaerobic bacteria in cystic fibrosis lung using culture dependant and independent approaches

“…In our study, there is a tendency of association of the species V. dispar with a better lung function (non-significant association). The lung role of this species in PWCF is as yet unknown but a recent study in healthy people has shown that lung bacteria are the same as oral or nasal bacteria, but that some, like V. dispar , are enriched in the healthy lung 40 . This finding suggests that V. dispar may play an important role in lung health 40 , which needs further investigation.…”

“…The lung role of this species in PWCF is as yet unknown but a recent study in healthy people has shown that lung bacteria are the same as oral or nasal bacteria, but that some, like V. dispar , are enriched in the healthy lung 40 . This finding suggests that V. dispar may play an important role in lung health 40 , which needs further investigation. These results also pave the way for discussion of the protective role of anaerobic bacteria.…”

Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?

“…Along similar lines, Ibironke et al . ( 2020 ) examined the bacterial component in four compartments in the human respiratory system (lung [via lavage], throat, mouth and nose) from five subjects. The aim was to delineate the microbes that colonize the lungs, rather than being passively transported via inhalation.…”