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.

The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder

“…Metagenomic reads were processed and assembled using the metaomic pipeline, IMP, and genome reconstructions were performed as described . Functional annotations of genes were assigned as described . For details, see Supplementary Information.…”

“…38 Functional annotations of genes were assigned as described. 38,46 For details, see Supplementary Information.…”

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

“…According to the strategy used for binning [72], these can be classified into three main groups: nucleotide composition-based, abundance-based and hybrid methods. Nucleotide composition-based methods assume that the oligonucleotide composition of fragments from the same genome is more similar than that of different genomes [73, 74]. Examples are Metawatt [75], SCIMM [76], or LikelyBin [77].…”

Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages

“…Methods for molecular [ 18 , 19 , 20 ] and computational [ 21 , 22 , 23 ] assessment of viral communities are being continuously developed and refined. The aforementioned methods, as well as other approaches employed in studies (e.g., clustering contigs based upon nucleotide usage and/or coverage (see review [ 24 ]), have resulted in the generation of numerous complete or near complete genomes of uncultivated prokaryotes [ 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 ] and viruses [ 11 , 28 , 30 , 34 , 38 , 39 , 40 ]. Additionally, complete phage genomes have been assembled from viral metagenomes through manual curation and BLAST searches [ 11 , 15 , 33 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 ].…”