The food we eat includes complex microbiomes, but the diversity of these food microbiomes has not been explored fully. In a new study published in Cell, the microbial diversity of >2,500 food metagenomes has been assessed and analysed in connection with the human microbiome, generating a new open access resource, the curatedFoodMetagenomicData (cFMD). “We all knew how food microbes are important for the food itself — quality, conservation, health-promoting properties — and food microbiologists studied some of such microbes, but it was surprising no comprehensive efforts at characterizing the food microbiome across food types and geography were available,” explains author Nicola Segata.

The investigators also assessed the overlap between food and human microbiomes, examining 19,833 previously sequenced human metagenomes (gut and oral samples from individuals across 39 different countries). Interestingly, food-associated microbial species comprised approximately 3% of the gut microbiome in adults and >50% in newborn babies, with food and human microbial species having more substantial overlap in infants than in adults or school-age children. Some food microbial species were consistently detected across age categories in humans, including Bifidobacterium longum and Escherichia coli, among others. Moreover, strain-level analyses indicated potential food-to-gut transmission and gut colonization (for example, Lacticaseibacillus paracasei, a strain prevalent in dairy, fermented beverages and water kefir), although food-borne pathogens (such as Listeria monocytogenes) were rarely detected. Finally, fungal taxa were widespread members of the food metagenomes, with the highest prevalences in alcoholic beverages, fermented beverages and fermented meats.

我们吃的食物包括复杂的微生物组，但这些食物微生物组的多样性尚未得到充分探索。在发表在《细胞》上的一项新研究中，已经对 >2,500 个食物宏基因组的微生物多样性进行了与人类微生物组相关的评估和分析，从而产生了一个新的开放获取资源，即 curatedFoodMetagenomicData （cFMD）。“我们都知道食品微生物对食品本身的重要性——质量、保存、促进健康的特性——食品微生物学家研究了其中一些微生物，但令人惊讶的是，没有全面的努力来表征不同食物类型和地理的食品微生物组，”作者 Nicola Segata 解释说。

研究人员还评估了食物和人类微生物组之间的重叠，检查了 19,833 个先前测序的人类宏基因组（来自 39 个不同国家/地区的个体的肠道和口腔样本）。有趣的是，食物相关微生物物种约占成人肠道微生物组的 3%，占新生儿肠道微生物组的 >50%，婴儿的食物和人类微生物物种比成人或学龄儿童有更大的重叠。在人类的各个年龄类别中一致检测到一些食品微生物物种，包括长双歧杆菌和大肠杆菌 等。此外，菌株水平分析表明潜在的食物到肠道传播和肠道定植（例如，副干酪乳杆菌，一种普遍存在于乳制品、发酵饮料和水开菲尔中的菌株），尽管很少检测到食源性病原体（如单核细胞增生李斯特菌）。最后，真菌类群是食物宏基因组的广泛成员，在酒精饮料、发酵饮料和发酵肉类中的患病率最高。