微生物生活通常发生在个体互动的社区中,通过对营养的竞争,交叉喂食,最终产品的抑制作用,还有它们的空间分布。乳酸菌是负责食物发酵的微生物群落的重要成员。它们在社区中的生态位取决于它们自己的属性以及其他物种的属性。这里,我们应用了一种计算方法,只使用基因组和宏基因组信息以及基因的功能注释,为了找到将一个物种与社区中的其他物种区分开的属性,以及跟随社区中的单个物种。我们分析了从开菲尔群落中分离和测序的菌株,和来自葡萄酒发酵的宏基因组。我们证明了生物体的独特特性如何导致有关生态位以及与其他物种的相互作用的实验可测试的假设。我们观察,例如,L.kiferanofaciens,开菲尔中的优势生物,在乳杆菌中脱颖而出,因为它可能具有更多的氨基酸营养缺陷。使用工业葡萄酒发酵的宏基因组分析,我们研究了接种的植物乳杆菌在苹果酸乳酸发酵中的作用。我们观察到,植物乳杆菌在白葡萄酒上的生长比在红葡萄酒发酵上更好,并且在葡萄酒群落中观察到的细菌中,磷酸转移酶系统的数量最多。此外,植物乳杆菌与泛菌,Erwinia,Asaia,葡糖酸杆菌,和Komagataeibacter属具有最多的参与氨基酸生物合成的基因。
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 L. kefiranofaciens, a dominant organism in kefir, stands out among the Lactobacilli because it potentially has more amino acid auxotrophies. Using metagenomic analysis of industrial wine fermentations we investigate the role of an inoculated L. plantarum in malolactic fermentation. We observed that L. plantarum 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, L. plantarum together with Pantoea, Erwinia, Asaia, Gluconobacter, and Komagataeibacter genera had the highest number of genes involved in biosynthesis of amino acids.