Fig. 1

Reconstruction of 1321 high-quality (HQ) E. rectale genomes from 6775 fecal metagenomes. a The parameters for the binning step of our reference-based workflow (average identity and fraction of contig aligned) were chosen using E. rectale-free metagenomic assemblies spiked with E. rectale sequences obtained from isolate genomes (“Materials and methods”). We report the median number of false positive (FP) bases (binned contigs not coming from spike-in) and false negative (FN) bases (contigs coming from spike-in that were not binned). FP and FN values are scaled with respect to the average E. rectale isolate genome size. The red square indicates the parameter value combination used in this study. b Estimation of completeness and contamination for all extracted genomes using CheckM [17]. c Comparison of genome characteristics for E. rectale isolate genomes, genomes from metagenomes reconstructed with a semi-supervised approach (MCR), and the large set of automatically reconstructed genomes (HQ). d, e Completeness and contamination estimates for bins extracted using the reference-based binning approach used in this study and bins produced by a reference-independent pipeline using metaBAT2 [2, 18]. Only genomes with > 90% completeness and < 5% contamination in both approaches are shown. f The sizes of the E. rectale genomes reconstructed with the reference-based pipeline are very consistent with the genome sizes (gray area) from cultured isolate sequencing (gray shading) while the reference-independent pipeline produces genomes of smaller size. g Pan-genome characteristics for seven E. rectale isolate genomes from NCBI available at the time of processing (Additional file 3: Table S2) as well as seven genomes from the reference-based binning and from Pasolli et al. [2]. For both binning methods, we considered the same seven, randomly selected European metagenomes as well as all seven cultured isolate genomes originating from studies in Europe/North America