European Molecular Biology Laboratory, Heidelberg, Germany.
Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.
Mol Syst Biol. 2023 Apr 12;19(4):e11501. doi: 10.15252/msb.202211501. Epub 2023 Feb 13.
Cross-feeding is fundamental to the diversity and function of microbial communities. However, identification of cross-fed metabolites is often challenging due to the universality of metabolic and biosynthetic intermediates. Here, we use C isotope tracing in peptides to elucidate cross-fed metabolites in co-cultures of Saccharomyces cerevisiae and Lactococcus lactis. The community was grown on lactose as the main carbon source with either glucose or galactose fraction of the molecule labelled with C. Data analysis allowing for the possible mass-shifts yielded hundreds of peptides for which we could assign both species identity and labelling degree. The labelling pattern showed that the yeast utilized galactose and, to a lesser extent, lactic acid shared by L. lactis as carbon sources. While the yeast provided essential amino acids to the bacterium as expected, the data also uncovered a complex pattern of amino acid exchange. The identity of the cross-fed metabolites was further supported by metabolite labelling in the co-culture supernatant, and by diminished fitness of a galactose-negative yeast mutant in the community. Together, our results demonstrate the utility of C-based proteomics for uncovering microbial interactions.
共代谢是微生物群落多样性和功能的基础。然而，由于代谢物和生物合成中间产物的普遍性，交叉喂养代谢物的鉴定往往具有挑战性。在这里，我们使用 C 同位素追踪肽来阐明酿酒酵母和乳酸乳球菌共培养物中的交叉喂养代谢物。该群落以乳糖作为主要碳源生长，其中分子的葡萄糖或半乳糖部分用 C 标记。数据分析允许可能的质量转移，产生了数百种肽，我们可以为其分配物种身份和标记程度。标记模式表明，酵母利用了半乳糖和乳酸作为碳源，尽管程度较小，这些乳酸是由乳酸乳球菌共享的。虽然酵母向细菌提供了必需氨基酸，这是预期的，但数据还揭示了氨基酸交换的复杂模式。共培养物上清液中的代谢物标记以及在群落中缺乏半乳糖的酵母突变体的适应性降低进一步支持了交叉喂养代谢物的身份。总之，我们的结果证明了基于 C 的蛋白质组学在揭示微生物相互作用方面的实用性。
