title: Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract.
abstract: 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 VIZBIN post hoc. The second approach is particularly well-suited for the study of specific taxa and employs VIZBIN de 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.
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg Belvaux, Luxembourg.
authors.forename: Cedric C
authors.initials: CC
authors.lastname: Laczny
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg Belvaux, Luxembourg.
authors.forename: Emilie E L
authors.initials: EE
authors.lastname: Muller
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg Belvaux, Luxembourg.
authors.forename: Anna
authors.initials: A
authors.lastname: Heintz-Buschart
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg Belvaux, Luxembourg.
authors.forename: Malte
authors.initials: M
authors.lastname: Herold
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg Belvaux, Luxembourg.
authors.forename: Laura A
authors.initials: LA
authors.lastname: Lebrun
authors.affiliation: Integrated Biobank of Luxembourg Luxembourg, Luxembourg.
authors.forename: Angela
authors.initials: A
authors.lastname: Hogan
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg Belvaux, Luxembourg.
authors.forename: Patrick
authors.initials: P
authors.lastname: May
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of LuxembourgBelvaux, Luxembourg; Centre Hospitalier de LuxembourgLuxembourg, Luxembourg.
authors.forename: Carine
authors.initials: C
authors.lastname: de Beaufort
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg Belvaux, Luxembourg.
authors.forename: Paul
authors.initials: P
authors.lastname: Wilmes
keywords: binning; genome recovery; metagenome; reference genomes; refinement