Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that consumption of these foods helps to address the negative consequences of “industrialization” of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented-food microbiota to better harness desirable traits. Here, we considerably expand the understanding of fermented-food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity, and functional potential (including antimicrobial resistance and carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from a number of countries. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined data set, 127 high-quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Companilactobacillus, Leuconostoc, and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than nonfermented equivalents, with water kefirs, sauerkrauts, and kvasses containing the greatest numbers of potentially health-associated gene clusters. Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date and yields novel information regarding their relative health-promoting potential.

中文翻译：

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发酵食品宏基因组学揭示了分类学中与底物相关的差异以及与健康相关和抗生素耐药性决定因素


由于据称具有健康益处，发酵食品已成为人们越来越关注的焦点。事实上，有人认为食用这些食物有助于解决西方社会人类肠道微生物群“工业化”的负面后果。然而，由于发酵食品中的微生物改善健康的机制尚不清楚，因此有必要了解发酵食品微生物群的组成和功能，以更好地利用所需的特性。在这里，我们通过采用鸟枪法宏基因组测序来全面了解多种微生物的微生物组成、多样性和功能潜力（包括抗菌素耐药性以及碳水化合物降解和健康相关基因含量），从而大大扩展了对发酵食品微生物组的理解。来自多个国家的手工生产商的 58 种发酵食品。食品类型，即乳制品、糖类或盐水类发酵食品，是微生物组成的主要驱动因素，其中乳制品的微生物多样性最低。从组合数据集中，生成了 127 个高质量的宏基因组组装基因组 (MAG)，其中 10 个 MAG 代表了醋杆菌、酸球菌、葡糖杆菌、 Companilactobacillus 、明串珠菌和Rouxiella的推定新物种。潜在的健康促进属性在发酵食品中比非发酵食品更常见，其中水开菲尔、酸菜和格瓦斯含有最多数量的潜在健康相关基因簇。 最终，这项研究提供了迄今为止对发酵食品微生物组最全面的了解，并提供了有关其相对健康促进潜力的新信息。