Extended Data Fig. 4: Expression of P. copri and P. stercorea PULs and targeted mass spectrometric analysis of their predicted targets.

(a,b) GSEA of expression of PULs shared by P. copri Bg131 (panel a) and P. stercorea (panel b) in the two Prevotella-containing arms of the experiment described in Fig. 1 (n = 8 and 5 offspring for arms 1 and 2 respectively). Benjamini-Hochberg adjusted P-values were calculated using GSEA ranking genes by their mean log₂ TPM across the Prevotella-colonized samples in Arms 1 and 2, with each PUL comprising a gene set against the background of all predicted PUL genes. Violin plots show the log₂ TPM of all genes assigned to any of the PULs in each isolate; plots are split to show the indicated PUL. The exact adjusted P-value for PUL27a in Arm 2 (panel a) is 3x10^-4. (c) UHPLC-QqQ-MS-based quantitation of levels of total mannose, N-acetylglucosamine, and N-acetylgalactosamine in cecal glycans collected at P53 (n = 8, 5, and 7 offspring for arms 1, 2, and 3 respectively). Mean values ± SD are shown. Each dot represents an individual animal. P-values were calculated by the Kruskal-Wallis test followed by post-hoc Dunn’s test with Bonferroni correction.