Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture
Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture
复制标题
寻找微生物群落中物种之间的功能差异：葡萄酒发酵和开菲尔培养的案例研究
DOI：
10.3389/fmicb.2019.01347
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发表时间：
2019
影响因子：
5.2
通讯作者：
D. Molenaar
中科院分区：
文献类型：
--
作者：
Chrats Melkonian;W. Gottstein;Sonja Blasche;Yongkyu Kim;Martin Abel;H. Swiegers;S. Saerens;N. Edwards;K. Patil;B. Teusink;D. Molenaar
微生物生活通常发生在一个社区中，其中个体通过竞争营养物质，交叉喂养，最终产品的抑制以及它们的空间分布而相互作用。乳酸菌是负责食品发酵的微生物群落的重要成员。它们在群落中的生态位取决于它们自己的特性以及其他物种的特性。在这里，我们应用一种计算方法，它只使用基因组和宏基因组信息和功能注释的基因，找到属性，区分一个物种从其他社区，以及在一个社区中的个别物种。我们分析了从开菲尔社区分离和测序的菌株，和葡萄酒发酵的宏基因组。我们展示了如何区分性质的生物体导致实验验证的假设有关的生态位和与其他物种的相互作用。例如，我们观察到L.开菲尔中占优势的生物体开菲尔产酸菌在乳杆菌中脱颖而出，因为它潜在地具有更多的氨基酸营养缺陷型。使用宏基因组分析的工业葡萄酒发酵，我们调查的作用，接种L。plantarum在苹果酸-乳酸发酵中的作用。我们观察到L.植物菌在白色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具有最大数量的磷酸转移酶系统。此外，L。plantarum与泛菌属、欧文氏菌属、Asaia属、葡糖酸杆菌属和Komagataeibacter属一起具有参与氨基酸生物合成的最高数量的基因。
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.
影响因子：
5.6
作者：
Zomorrodi AR;Segrè D
通讯作者：
Segrè D
DOI：
--
发表时间：
--
期刊：
--
影响因子：
--
作者：
Systems Biology
通讯作者：
Systems Biology
影响因子：
8.8
作者：
Harcombe WR;Riehl WJ;Dukovski I;Granger BR;Betts A;Lang AH;Bonilla G;Kar A;Leiby N;Mehta P;Marx CJ;Segrè D
通讯作者：
Segrè D