Fig. 4: Host-synthesized compounds enhance S. alvi growth in vitro.

a, Schematic diagram depicting growth and spent supernatant analysis. The Bee9 medium was derived from M9 base medium (Supplementary Information). b, The maximum growth rate across single carbon sources with (+) or without (−) citrate added to the medium, reveals that growth on citrate + 3Hmg was faster than for all other conditions, including ‘All’, where all substrates were pooled together. The average value (bars) was calculated from independent biological replicates (citrate (+), n = 3; citrate (−), n = 4). Adjusted significance values were calculated using two-sided Wilcoxon rank sum test with BH correction, using the growth on citrate (+) as the reference state (dotted line), *P < 0.05 (Supplementary Table 3). c, Abundances of carboxylic acids in the spent supernatant, relative to growth on citrate alone, vary with growth substrates. While some carboxylic acids including α-ketoglutarate and malate are produced across most conditions, acetate is a growth substrate but only produced with either pyruvate or 3Hmg in the media. Average fold changes calculated from n = 3 replicates. d, Addition of kynurenine to the medium leads to the production of anthranilate, kynurenic acid and l-tryptophan. Significant changes between fresh and spent media were calculated using a two-sided, paired t-test from n = 3 independent samples (anthranilate, *P = 0.015; kynurenate, **P = 0.004; l-tryptophan, *P = 0.039). GC–MS schematic in a created with BioRender.com.