Untangling species-level composition of complex bacterial communities through a novel metagenomic approach
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Date
2020
Authors
Milani, Christian
Alessandri, Giulia
Mangifesta, Marta
Mancabelli, Leonardo
Lugli, Gabriele Andrea
Fontana, Federico
Longhi, Giulia
Anzalone, Rosaria
Viappiani, Alice
Duranti, Sabrina
Journal Title
Journal ISSN
Volume Title
Publisher
American Society for Microbiology
Published Version
Abstract
16S small-subunit (SSU) rRNA gene-based bacterial profiling is the gold standard for cost-effective taxonomic reconstruction of complex bacterial populations down to the genus level. However, it has been proven ineffective in clinical and research settings requiring higher taxonomic resolution. We therefore developed a bacterial profiling method based on the internal transcribed spacer (ITS) region employing optimized primers and a comprehensive ITS database for accurate cataloguing of bacterial communities at (sub)species resolution. Performance of the microbial ITS profiling pipeline was tested through analysis of host-associated, food, and environmental matrices, while its efficacy in clinical settings was assessed through analysis of mucosal biopsy specimens of colorectal cancer, leading to the identification of putative novel biomarkers. The data collected indicate that the proposed pipeline represents a major step forward in cost-effective identification and screening of microbial biomarkers at (sub)species level, with relevant impact in research, industrial, and clinical settings.
Description
Keywords
Metagenomics , ITS , Profiling
Citation
Milani, C., Alessandri, G., Mangifesta, M., Mancabelli, L., Lugli, G.A., Fontana, F., Longhi, G., Anzalone, R., Viappiani, A., Duranti, S., Turroni, F., Costi, R., Annicchiarico, A., Morini, A., Sarli, L., Ossiprandi, M.C., Van Sinderen, D. and Ventura, M. (2020) ‘Untangling species-level composition of complex bacterial communities through a novel metagenomic approach’, mSystems. 5(4), e00404-20 (12 pp). doi: 10.1128/mSystems.00404-20