Abstract
Background Microbiome studies of the lower airways 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. We extended our microbiota characterisation beyond 16S rRNA gene sequencing with the use of whole-genome shotgun (WGS) and RNA metatranscriptome sequencing. SCFAs 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.
Results Functional evaluations of the lower airway microbiota using inferred metagenome, WGS and metatranscriptome data 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 SCFA levels were compared with WGS and metatranscriptome data. 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 data identifies metabolically active organisms capable of producing metabolites with immunomodulatory capacity, such as SCFAs.
Abstract
This study shows that both whole-genome shotgun and RNA metatranscriptome sequencing can be done on lower airway samples and can provide valuable information on bacterial function https://bit.ly/3hNmZfi
Footnotes
Data availability: All data is publicly available in the Sequence Read Archive under accession numbers PRJNA603592, PRJNA573853 and PRJNA603675. All codes utilised for the analysis included in this article are available at: www.github.com/segalmicrobiomelab/functional_microbiomics
Author contributions: Conception and design: I. Sulaiman and L.N. Segal. Acquisition of data: B.G. Wu, Y. Li, A.S. Scott, K. Ji, A. Geber, S. Banakis, E. Ghedin, I. Sulaiman and L.N. Segal. Analysis and interpretation of data: B.G. Wu, J-C. Tsay, M. Sauthoff, M. Weiden, J.C. Clemente, D. Jones, Y.J. Huang, K.A. Stringer, L. Zhang, L. Tipton, E. Ghedin, I. Sulaiman and L.N. Segal. Drafting or revising the manuscript: I. Sulaiman, B.G. Wu, Y. Li, M. Sauthoff, A.S. Scott, J-C. Tsay, S.B. Koralov, M. Sauthoff, M. Weiden, J.C. Clemente, D. Jones, Y.J. Huang, K.A. Stringer, E. Ghedin and L.N. Segal. Final approval of the manuscript: I. Sulaiman and L.N. Segal.
This article has supplementary material available from erj.ersjournals.com This article has an editorial commentary: https://doi.org/10.1183/13993003.00321-2021
Conflict of interest: I. Sulaiman has nothing to disclose.
Conflict of interest: B.G. Wu has nothing to disclose.
Conflict of interest: Y. Li has nothing to disclose.
Conflict of interest: J-C. Tsay has nothing to disclose.
Conflict of interest: M. Sauthoff has nothing to disclose.
Conflict of interest: A.S. Scott has nothing to disclose.
Conflict of interest: K. Ji has nothing to disclose.
Conflict of interest: S.B. Koralov has nothing to disclose.
Conflict of interest: M. Weiden has nothing to disclose.
Conflict of interest: J.C. Clemente has nothing to disclose.
Conflict of interest: D. Jones has nothing to disclose.
Conflict of interest: Y.J. Huang has nothing to disclose.
Conflict of interest: K.A. Stringer has nothing to disclose.
Conflict of interest: L. Zhang has nothing to disclose.
Conflict of interest: A. Geber has nothing to disclose.
Conflict of interest: S. Banakis has nothing to disclose.
Conflict of interest: L. Tipton has nothing to disclose.
Conflict of interest: E. Ghedin has nothing to disclose.
Conflict of interest: L.N. Segal has nothing to disclose.
Support statement: R37 CA244775 (L.N. Segal, National Institutes of Health/National Cancer Institute), R01 HL125816 (S.B. Koralov and L.N. Segal, National Institutes of Health/National Heart, Lung, and Blood Institute), R01 GM111400 (K.A. Stringer, National Institutes of Health/National Institute of General Medical Sciences), Stony Wold (I. Sulaiman), Chest Foundation Grant (I. Sulaiman), Flight Attendant Medical Research Institute (B.G. Wu), PACT grant (L.N. Segal, Foundation for the National Institutes of Health (FHIH)), R01AI129958 (Y.J. Huang). Financial support for the PACT project is made possible through funding support provided to the FNIH by AbbVie Inc., Amgen Inc., Boehringer Ingelheim Pharma GmbH & Co. KG, Bristol-Myers Squibb, Celgene Corporation, Genentech Inc., Gilead, GlaxoSmithKline plc, Janssen Pharmaceutical Companies of Johnson & Johnson, Novartis Institutes for Biomedical Research, Pfizer Inc. and Sanofi. Funding information for this article has been deposited with the Crossref Funder Registry.
- Received October 16, 2020.
- Accepted December 19, 2020.
- Copyright ©The authors 2021. For reproduction rights and permissions contact permissions{at}ersnet.org