Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches

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Date
2019-05-16
Authors
Lugli, Gabriele Andrea
Milani, Christian
Duranti, Sabrina
Alessandri, Giulia
Turroni, Francesca
Mancabelli, Leonardo
Tatoni, Danilo
Ossiprandi, Maria Cristina
van Sinderen, Douwe
Ventura, Marco
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Publisher
BioMed Central Ltd.
Published Version
10.1186/s13059-019-1711-6
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Abstract
Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method.
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Keywords
Genomics , Metagenomics , Microbiota , Human gut commensals
Citation
Lugli, G.A., Milani, C., Duranti, S., Alessandri, G., Turroni, F., Mancabelli, L., Tatoni, D., Ossiprandi, M.C., van Sinderen, D. and Ventura, M. (2019). 'Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches'. Genome biology, 20(1), 96. (6pp.) DOI:10.1186/s13059-019-1711-6
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https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1711-6
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https://hdl.handle.net/10468/9129
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APC Microbiome Ireland - Journal Articles
Microbiology - Journal Articles
Copyright
© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.