{"id":761,"date":"2015-02-02T18:11:36","date_gmt":"2015-02-02T17:11:36","guid":{"rendered":"http:\/\/www2.unibas.it\/parente\/wordpress\/?page_id=761"},"modified":"2025-11-18T16:23:22","modified_gmt":"2025-11-18T15:23:22","slug":"foodmicrobionet-2","status":"publish","type":"page","link":"https:\/\/web.unibas.it\/parente\/?page_id=761","title":{"rendered":"FoodMicrobionet"},"content":{"rendered":"\n<p>Our research group proudly maintains FoodMicrobionet, a metataxonomic database on the composition of bacterial and fungal communities of foods and food environments. The structure of the database and its relationships with external databases is shown below:<\/p>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"769\" src=\"http:\/\/web.unibas.it\/parente\/wp-content\/upLoads\/table_structure_v5-1024x769.jpg\" alt=\"FMBN v5 table structure\" class=\"wp-image-2273\" srcset=\"https:\/\/web.unibas.it\/parente\/wp-content\/upLoads\/table_structure_v5-1024x769.jpg 1024w, https:\/\/web.unibas.it\/parente\/wp-content\/upLoads\/table_structure_v5-300x225.jpg 300w, https:\/\/web.unibas.it\/parente\/wp-content\/upLoads\/table_structure_v5-768x577.jpg 768w, https:\/\/web.unibas.it\/parente\/wp-content\/upLoads\/table_structure_v5-400x300.jpg 400w, https:\/\/web.unibas.it\/parente\/wp-content\/upLoads\/table_structure_v5.jpg 1120w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure><\/div>\n\n\n<p><a href=\"http:\/\/web.unibas.it\/parente\/?attachment_id=1882\" rel=\"attachment wp-att-1882\"><br><\/a><\/p>\n\n\n\n<p>Current version (5.1.2) includes 302 studies with 17,174 samples for bacteria and 3,175 samples for fungi: it is arguably the largest and best annotated database on the structure of food bacterial communities.<\/p>\n\n\n\n<p>The database and scripts for FoodMicrobionet are publicly available on <a href=\"https:\/\/github.com\/ep142\/FoodMicrobionet\">GitHub<\/a>. In addition, the interactive Shiny app (ShinyFMBN) which allows a simplified access to the database (for searching, selecting studies and samples, expiring data and visualising and exporting graphs is also available on <a href=\"https:\/\/data.mendeley.com\/datasets\/8fwwjpm79y\/7\">Mendeley data (DOI 10.17632\/8fwwjpm79y.7)<\/a>. Finally, processed studies using to feed FoodMicrobionet are available on <a href=\"https:\/\/doi.org\/10.5281\/zenodo.6954040\">Zenodo<\/a>&nbsp;(DOI 10.5281\/zenodo.6954040) as R lists.<\/p>\n\n\n\n<p>If you want to keep up to date with latest developments visit the <a href=\"https:\/\/github.com\/ep142\/FoodMicrobionet\">GitHub<\/a> repository or search this site using FMBN as a tag.<\/p>\n\n\n\n<p>If you want to learn more about FoodMicrobionet and how it can be used for meta studies read our publications:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Parente, E., Ricciardi, A., 2024. A comprehensive view of food microbiota: introducing FoodMicrobionet v5. Foods 13, 1689. <a href=\"https:\/\/doi.org\/10.3390\/foods13111689\">https:\/\/doi.org\/10.3390\/foods1311168<\/a><\/li>\n\n\n\n<li><div class=\"nova-legacy-e-text nova-legacy-e-text--size-m nova-legacy-e-text--family-sans-serif nova-legacy-e-text--spacing-s nova-legacy-e-text--color-inherit redraft-text\">Parente, E., Zotta, T., Giavalisco, M., Ricciardi, A., 2023. Metataxonomic insights in the distribution of <em>Lactobacillaceae<\/em> in foods and food environments. Int J Food Microbiol 110124. <a class=\"nova-legacy-e-link nova-legacy-e-link--color-inherit nova-legacy-e-link--theme-decorated\" href=\"https:\/\/www.researchgate.net\/deref\/https%3A%2F%2Fdoi.org%2F10.1016%2Fj.ijfoodmicro.2023.110124\" target=\"_blank\" rel=\"noopener\">https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2023.110124<\/a><\/div><\/li>\n\n\n\n<li><span class=\"csl-entry\">Parente, E., Zotta, T., Ricciardi, A., 2022. FoodMicrobionet v4: A large, integrated, open and transparent database for food bacterial communities. Int J Food Microbiol 372, 109696. <a href=\"https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2022.109696\">https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2022.109696<\/a><\/span><\/li>\n\n\n\n<li><span class=\"csl-entry\">Parente, E., Zotta, T., Ricciardi, A., 2022. A review of methods for the inference and experimental confirmation of microbial association networks in cheese. Int J Food Microbiol 368, 109618. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2022.109618<\/span><\/li>\n\n\n\n<li><span class=\"csl-entry\">Parente, E., Ricciardi, A., Zotta, T., 2020. The microbiota of dairy milk: A review. Int Dairy J 107, 104714. <a href=\"https:\/\/doi.org\/10.1016\/j.idairyj.2020.104714\">https:\/\/doi.org\/10.1016\/j.idairyj.2020.104714<\/a><\/span><\/li>\n\n\n\n<li><span class=\"csl-entry\">Parente, E., De Filippis, F., Ercolini, D., Ricciardi, A., Zotta, T., 2019. Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database. International Journal of Food Microbiology 305, 108249. <a href=\"https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2019.108249\">https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2019.108249<\/a><\/span><\/li>\n\n\n\n<li><span class=\"csl-entry\">De Filippis, F., Parente, E., Zotta, T., Ercolini, D., 2018. A comparison of bioinformatic approaches for 16S rRNA gene profiling of food bacterial microbiota. International Journal of Food Microbiology 265, 9\u201317. <a href=\"https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2017.10.028\">https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2017.10.028<\/a><\/span><\/li>\n\n\n\n<li><span class=\"csl-entry\">Parente, E., Zotta, T., Faust, K., De Filippis, F., Ercolini, D., 2018. Structure of association networks in food bacterial communities. Food microbiology 73, 49\u201360. <a href=\"https:\/\/doi.org\/10.1016\/j.fm.2017.12.010\">https:\/\/doi.org\/10.1016\/j.fm.2017.12.010<\/a><\/span><\/li>\n\n\n\n<li><span class=\"csl-entry\">Parente, E., Cocolin, L., De Filippis, F., Zotta, T., Ferrocino, I., O\u2019Sullivan, O., Neviani, E., De Angelis, M., Cotter, P.D., Ercolini, D., 2016. FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis. International Journal of Food Microbiology 219, 28\u201337. <a href=\"https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2015.12.001\">https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2015.12.001<\/a><\/span><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Our research group proudly maintains FoodMicrobionet, a metataxonomic database on the composition of bacterial and fungal communities of foods and food environments. The structure of the database and its relationships with external databases is shown below: Current version (5.1.2) includes &hellip; <a href=\"https:\/\/web.unibas.it\/parente\/?page_id=761\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":26,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-761","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/pages\/761","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=761"}],"version-history":[{"count":27,"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/pages\/761\/revisions"}],"predecessor-version":[{"id":2275,"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/pages\/761\/revisions\/2275"}],"up":[{"embeddable":true,"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/pages\/26"}],"wp:attachment":[{"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=761"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}