Melkonian Chrats, Gottstein Willi, Blasche Sonja, Kim Yongkyu, Abel-Kistrup Martin, Swiegers Hentie, Saerens Sofie, Edwards Nathalia, Patil Kiran R, Teusink Bas, Molenaar Douwe
Systems Bioinformatics, VU University Amsterdam, Amsterdam, Netherlands.
European Molecular Biology Laboratory, Heidelberg, Germany.
Front Microbiol. 2019 Jun 25;10:1347. doi: 10.3389/fmicb.2019.01347. eCollection 2019.
Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition by end-products, but also by their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible for food fermentations. Their niche in a community depends on their own properties as well as those of the other species. Here, we apply a computational approach, which uses only genomic and metagenomic information and functional annotation of genes, to find properties that distinguish a species from others in the community, as well as to follow individual species in a community. We analyzed isolated and sequenced strains from a kefir community, and metagenomes from wine fermentations. We demonstrate how the distinguishing properties of an organism lead to experimentally testable hypotheses concerning the niche and the interactions with other species. We observe, for example, that , a dominant organism in kefir, stands out among the because it potentially has more amino acid auxotrophies. Using metagenomic analysis of industrial wine fermentations we investigate the role of an inoculated in malolactic fermentation. We observed that thrives better on white than on red wine fermentations and has the largest number of phosphotransferase system among the bacteria observed in the wine communities. Also, together with , and genera had the highest number of genes involved in biosynthesis of amino acids.
微生物生命通常发生在一个群落中，个体之间通过争夺营养物质、交叉取食、被终产物抑制以及空间分布等方式相互作用。乳酸菌是负责食品发酵的微生物群落中的重要成员。它们在群落中的生态位取决于自身特性以及其他物种的特性。在此，我们应用一种计算方法，该方法仅使用基因组和宏基因组信息以及基因的功能注释，来寻找区分群落中一个物种与其他物种的特性，以及追踪群落中的单个物种。我们分析了来自开菲尔群落的分离和测序菌株，以及葡萄酒发酵的宏基因组。我们展示了一种生物的独特特性如何导致关于其生态位以及与其他物种相互作用的可通过实验验证的假设。例如，我们观察到，开菲尔中的优势生物，在 中脱颖而出，因为它可能有更多的氨基酸营养缺陷型。通过对工业葡萄酒发酵的宏基因组分析，我们研究了接种的 在苹果酸乳酸发酵中的作用。我们观察到， 在白葡萄酒发酵中比在红葡萄酒发酵中生长得更好，并且在葡萄酒群落中观察到的细菌中，它拥有最多的磷酸转移酶系统。此外， 与 属和 属一起，参与氨基酸生物合成的基因数量最多。
