Abstract
Rationale Microbiome studies of the lower airway based on bacterial 16S rRNA gene sequencing assess microbial community structure but can only infer functional characteristics. Microbial products, such as short chain fatty acids (SCFAs), in the lower airways have significant impact on the host's immune tone. Thus, functional approaches to the analyses of the microbiome are necessary.
Methods Here we used upper and lower airway samples from a research bronchoscopy smoker cohort. In addition, we validated our results in an experimental mouse model.
Measurements We extended our microbiota characterisation beyond 16S rRNA gene sequencing with the use of whole genome (WGS) and RNA metatranscriptome sequencing. Short chain fatty acids (SCFA) were also measured in lower airway samples and correlated with each of the sequencing datasets. In the mouse model, 16S rRNA gene and RNA metatranscriptome sequencing were performed.
Main Results Functional evaluations of the lower airway microbiota using inferred metagenome, WGS and metatranscriptome were dissimilar. Comparison with measured levels of SCFAs shows that the inferred metagenome from the 16S rRNA gene sequencing data was poorly correlated, while better correlations were noted when SCFAs levels were compared with WGS and metatranscriptome. Modelling lower airway aspiration with oral commensals in a mouse model showed that the metatranscriptome most efficiently captures transient active microbial metabolism, which was overestimated by 16S rRNA gene sequencing.
Conclusions Functional characterisation of the lower airway microbiota through metatranscriptome identify metabolically active organisms capable of producing metabolites with immunomodulatory capacity such as SCFAs.
Footnotes
This manuscript has recently been accepted for publication in the European Respiratory Journal. It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Please open or download the PDF to view this article.
Conflict of interest: Dr. Funke-Chambour reports grants from roche, grants and personal fees from Boehringer Ingelheim, outside the submitted work;. Dr. Funke-Chambour reports grants from roche, grants and personal fees from Boehringer Ingelheim, outside the submitted work;.
Conflict of interest: Dr. SULAIMAN has nothing to disclose.
Conflict of interest: Dr. WU has nothing to disclose.
Conflict of interest: Dr. LI has nothing to disclose.
Conflict of interest: Dr. Tsay has nothing to disclose.
Conflict of interest: Dr. Sauthoff has nothing to disclose.
Conflict of interest: Dr. Scott has nothing to disclose.
Conflict of interest: Dr. Ji has nothing to disclose.
Conflict of interest: Dr. Koralov has nothing to disclose.
Conflict of interest: Dr. Weiden has nothing to disclose.
Conflict of interest: Dr. Clemente has nothing to disclose.
Conflict of interest: Dr. Jones has nothing to disclose.
Conflict of interest: Dr. Huang has nothing to disclose.
Conflict of interest: Dr. Stringer has nothing to disclose.
Conflict of interest: Dr. Zhang has nothing to disclose.
Conflict of interest: Dr. Geber has nothing to disclose.
Conflict of interest: Dr. Banakis has nothing to disclose.
Conflict of interest: Dr. Tipton has nothing to disclose.
Conflict of interest: Dr. Ghedin has nothing to disclose.
Conflict of interest: Dr. SEGAL has nothing to disclose.
- Received October 16, 2020.
- Accepted December 19, 2020.
- ©The authors 2021. For reproduction rights and permissions contact permissions{at}ersnet.org
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