PMC

Canonical correspondence analysis of functions in four groups of MAGs. The 39 significant functional subcategories are shown

Similarity between donor and recipient samples before and after FMT. Non-metric multidimensional scaling based on mean coverage of 92 MAGs and based on microbial community profiles from this study and 151 HMP metagenomes at the genus level of short reads annotated by MetaPhlAn. Clustering employed average linkage with Bray-Curtis similarity index on square-root normalized values. Labels represent the recipients (R01, R02) before FMT (pre-FMT), 4 weeks (W4) and 8 weeks after FMT (W8). Gray circles represent HMP metagenomes. Panel a displays changes in recipient microbial community profiles after FMT based on coverage values of donor MAGs. Panel b displays the organization of samples based on the genus-level taxonomy of all short metagenomic reads in each sample. In contrast, Panel c displays the genus organization of samples based on the genus-level taxonomy of only short metagenomic reads that do not match donor MAGs

Distribution of MAGs across samples and HMP metagenomes. a The 92 MAGs and their level of detection in four donor samples (four inner circles) as well as two recipients (R01 and R02) before FMT (pre-FMT), 4 weeks after FMT (W4), and 8 weeks after FMT (W8). Rectangles with red and blue colors in donor and recipient layers indicate the level of detection of a given MAG in a given sample. The outermost two layers display the genus- and order-level taxonomy for each MAG. Selections in a represent four groups of MAGs based on their distribution patterns: group I with 20 MAGs that colonized both recipients, group II with 11 MAGs that colonized only R01, group III with 8 MAGs that colonized only R02, and finally, group IV with 13 MAGs that colonized neither recipient. b The detection for each contig in two example MAGs summarized to a single detection value in a. c The coverage of each nucleotide position in two example contigs from the MAGs displayed in b. d The prevalence of MAGs in groups I and IV across 151 HMP gut metagenomes and detection of MAG 54 (group I) and MAG 26 (group IV) in HMP gut metagenomes as two examples