Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract

Cedric C. Laczny, Emilie E.L. Muller, Anna Heintz-Buschart, Malte Herold, Laura A. Lebrun, Angela Hogan, Patrick May, Carine de Beaufort, Paul Wilmes*

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

8 Citations (Scopus)


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.

Original languageEnglish
Article number884
JournalFrontiers in Microbiology
Issue numberJUN
Publication statusPublished - 2016


  • Binning
  • Genome recovery
  • Metagenome
  • Reference genomes
  • Refinement


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