[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.
Research center :
- 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)
Disciplines :
Microbiology
Author, co-author :
Laczny, Cedric Christian ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Muller, Emilie ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Heintz, Anna ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Herold, Malte ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Lebrun, Laura ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Hogan, Angela; Integrated Biobank of Luxembourg
May, Patrick ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
de Beaufort, Carine ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Wilmes, Paul ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
External co-authors :
no
Language :
English
Title :
Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract
FNR10404839 - Linking Environmental Condition To Lifestyle Strategies And To Population-level Genetic Heterogeneity, 2015 (01/12/2015-14/09/2018) - Paul Wilmes