Fig. 4: Conservation and expression of PULs in P. copri MAGs and isolates.
From: Bioactive glycans in a microbiome-directed food for children with malnutrition
a, PUL conservation in P. copri MAGs identified in study participants (blue font) and in P. copri isolates cultured from Bangladeshi children (red font). The marker-gene-based phylogenetic tree (left) indicates the relatedness of P. copri MAGs and isolates. The β1(WLZ) coefficient for each MAG is shown on the right; significant associations (q < 0.05) are indicated by asterisks. The matrix in the centre depicts PUL conservation among P. copri MAGs and cultured isolates relative to Bg0019. The number of differentially expressed PUL transcripts in MAGs Bg0018 and Bg0019 are shown within the coloured cells (identified from comparisons of MDCF-2- versus RUSF-treated participants, and/or from MDCF-2-treated participants in the WLZ-response upper versus lower quartiles; transcript annotations are shown in Supplementary Table 15). b, The relationship between PUL conservation in the 11 P. copri MAGs identified in study participants and the association of each MAG abundance with WLZ. The grey ribbon indicates the 95% confidence interval. c,d, In vitro growth assays for five P. copri isolates in defined medium supplemented with individual purified glycans representative of those in MDCF-2. n = 3 replicates per condition; two independent experiments were performed; representative results from one are shown. c, The results obtained with P. copri BgF5_2, the isolate of which the PUL profile is most similar to MAGs Bg0019/Bg0018. Data are the mean ± s.d. (grey ribbons) optical density at 600 nm (OD600). d, Summary of PUL conservation and growth rates for the five P. copri strains tested (Extended Data Fig. 5a). Each coloured box lists PULs in each strain (rows) that are predicted to metabolize each carbohydrate. PULs are denoted as functionally conserved (black, bold), structurally distinct but functionally similar (black, not bold) or not conserved (grey) according to the scheme shown in a. The colour intensity surrounding each box indicates the mean maximum growth rate for each isolate in the presence of each glycan.
