Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota

Whelan, Fiona J.; Waddell, Barbara; Syed, Saad A.; Shekarriz, Shahrokh; Rabin, Harvey R.; Parkins, Michael D.; Surette, Michael G.

Abstract

Amplicon sequencing (for example, of the 16S rRNA gene) identifies the presence and relative abundance of microbial community members. However, metagenomic sequencing is needed to identify the genetic content and functional potential of a community. Metagenomics is challenging in samples dominated by host DNA, such as those from the skin, tissue and respiratory tract. Here, we combine advances in amplicon and metagenomic sequencing with culture-enriched molecular profiling to study the human microbiota. Using the cystic fibrosis lung as an example, we cultured an average of 82.13% of the operational taxonomic units representing 99.3% of the relative abundance identified in direct sequencing of sputum samples; importantly, culture enrichment identified 63.3% more operational taxonomic units than direct sequencing. We developed the PLate Coverage Algorithm (PLCA) to determine a representative subset of culture plates on which to conduct culture-enriched metagenomics, resulting in the recovery of greater taxonomic diversity—including of low-abundance taxa—with better metagenome-assembled genomes, longer contigs and better functional annotations when compared to culture-independent methods. The PLCA is also applied as a proof of principle to a previously published gut microbiota dataset. Culture-enriched molecular profiling can be used to better understand the role of the human microbiota in health and disease.

Citation

Whelan, F. J., Waddell, B., Syed, S. A., Shekarriz, S., Rabin, H. R., Parkins, M. D., & Surette, M. G. (2020). Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota. Nature Microbiology, 5, 379-390. https://doi.org/10.1038/s41564-019-0643-y

• Journal Article Type: Article
• Acceptance Date: Nov 18, 2019
• Online Publication Date: Jan 20, 2020
• Publication Date: 2020-02
• Deposit Date: Feb 4, 2020
• Publicly Available Date: Jul 21, 2020
• Journal: Nature Microbiology
• Electronic ISSN: 2058-5276
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 5
• Pages: 379-390
• DOI: https://doi.org/10.1038/s41564-019-0643-y
• Keywords: Immunology; Microbiology (medical); Applied Microbiology and Biotechnology; Genetics; Cell Biology; Microbiology
• Public URL: https://nottingham-repository.worktribe.com/output/3882308
• Publisher URL: https://www.nature.com/articles/s41564-019-0643-y
• Additional Information: Received: 5 November 2018; Accepted: 18 November 2019; First Online: 20 January 2020; : The authors declare no competing interests.