Parente Eugenio, Ricciardi Annamaria
Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy.
Foods. 2024 May 28;13(11):1689. doi: 10.3390/foods13111689.
Amplicon-targeted metagenomics is now the standard approach for the study of the composition and dynamics of food microbial communities. Hundreds of papers on this subject have been published in scientific journals and the information is dispersed in a variety of sources, while raw sequences and their metadata are available in public repositories for some, but not all, of the published studies. A limited number of web resources and databases allow scientists to access this wealth of information but their level of annotation on studies and samples varies. Here, we report on the release of FoodMicrobionet v5, a comprehensive database of metataxonomic studies on bacterial and fungal communities of foods. The current version of the database includes 251 published studies (11 focusing on fungal microbiota, 230 on bacterial microbiota, and 10 providing data for both bacterial and fungal microbiota) and 14,035 samples with data on bacteria and 1114 samples with data on fungi. The new structure of the database is compatible with interactive apps and scripts developed for previous versions and allows scientists, R&D personnel in industries and regulators to access a wealth of information on food microbial communities.
扩增子靶向宏基因组学现已成为研究食品微生物群落组成和动态的标准方法。关于这一主题的数百篇论文已发表在科学期刊上，信息分散在各种来源中，而原始序列及其元数据仅在部分（而非全部）已发表研究的公共存储库中可用。数量有限的网络资源和数据库使科学家能够获取这些丰富的信息，但它们对研究和样本的注释水平各不相同。在此，我们报告FoodMicrobionet v5的发布，这是一个关于食品细菌和真菌群落元分类学研究的综合数据库。该数据库的当前版本包括251项已发表研究（11项关注真菌微生物群，230项关注细菌微生物群，10项同时提供细菌和真菌微生物群的数据）以及14,035个有细菌数据的样本和1114个有真菌数据的样本。该数据库的新结构与为先前版本开发的交互式应用程序和脚本兼容，使科学家、行业研发人员和监管机构能够获取有关食品微生物群落的丰富信息。
