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. 2021 Aug 24;6(4):e00729-21. doi: 10.1128/mSystems.00729-21

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FIG 5 — Proteobacteria was the main reservoir of IncI1 plasmids carried by broiler chickens. (a) Percentage of metagenomic reads assigned to the top 20 bacterial genera of the phylum Proteobacteria present in samples Hi-IC4 and Hi-IC6. Only reads assigned to phylum Proteobacteria (70.9% of the metagenomic reads) were used and zoomed in to show 0% to 1% of total reads within phylum Proteobacteria (96.7% of reads within phylum Proteobacteria were assigned to Komagataeibacter). (b and c) IncI1 contig hosts found by Hi-C contacts. IncI1-derived contigs (horizontal axis of heatmap) show specific Hi-C associations with metagenome-assembled genomes (MAGs) present in samples Hi-IC4 (a) and Hi-IC6 (b) (vertical axis of heatmap). MAGs are derived from Hi-C deconvolution of the metagenome assembly and placed into a bacterial phylogeny using Mash and CheckM. Cluster.10 in each sample is an Escherichia coli genome. In Hi-IC4, one MAG (cluster.82) representing an extremely fragmented and partially contaminated Escherichia coli genome is omitted for clarity (due to its contamination, this cluster was placed in Clostridia by CheckM). Heatmap values indicate transformed counts of Hi-C read contacts (indicating intracellular physical proximity of IncI1 contigs to those genomes). Heatmap values were pseudocounted to facilitate plotting of log-transformed data, including zeroes.