Reference : Identification, recovery, and refinement of hitherto undescribed population-level gen...
Scientific journals : Article
Life sciences : Microbiology
Systems Biomedicine
http://hdl.handle.net/10993/27978
Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract
English
Laczny, Cedric C. [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)]
Muller, Emilie mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Heintz-Buschart, Anna mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Herold, Malte mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Lebrun, Laura mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Hogan, Angela [Integrated Biobank of Luxembourg]
May, Patrick mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
de Beaufort, Carine mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Wilmes, Paul mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
2016
Frontiers in Microbiology
7
884
Yes
International
1664-302X
[en] Linking taxonomic identity and functional potential at the population-level is important for the study of mixed microbial communities and is greatly facilitated by the availability of microbial reference genomes. While the culture-independent recovery of population-level genomes from environmental samples using the binning of metagenomic data has expanded available reference genome catalogs, several microbial lineages remain underrepresented. Here, we present two reference-independent approaches for the identification, recovery, and refinement of hitherto undescribed population-level genomes. The first approach is aimed at genome recovery of varied taxa and involves multi-sample automated binning using CANOPY CLUSTERING complemented by visualization and human-augmented binning using VIZBINpost hoc. The second approach is particularly well-suited for the study of specific taxa and employs VIZBINde novo. Using these approaches, we reconstructed a total of six population-level genomes of distinct and divergent representatives of the Alphaproteobacteria class, the Mollicutes class, the Clostridiales order, and the Melainabacteria class from human gastrointestinal tract-derived metagenomic data. Our results demonstrate that, while automated binning approaches provide great potential for large-scale studies of mixed microbial communities, these approaches should be complemented with informative visualizations because expert-driven inspection and refinements are critical for the recovery of high-quality population-level genomes.
Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) ; Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) ; Luxembourg Centre for Systems Biomedicine (LCSB): Medical Translational Research (J. Schneider Group)
Fonds National de la Recherche - FnR
Researchers
http://hdl.handle.net/10993/27978
10.3389/fmicb.2016.00884
http://www.frontiersin.org/microbial_physiology_and_metabolism/10.3389/fmicb.2016.00884/abstract
FnR ; FNR10404839 > Emilie Muller > LEGeLiS (for Linking Environment - Genome - Lifestyle Strategy) > Linking environmental condition to lifestyle strategies and to population-level genetic heterogeneity > 01/12/2015 > 30/11/2017 > 2015

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