Category Archives: Uncategorized

Making the most of FoodMicrobionet – a webinar

Posted on by

It is almost time for the webinar, which will take place on Tuesday, April 21st, 2026 15:00 CET (this is to allow people from the USA and Alberta to attend without having to wake up before sunrise…). A few things worth knowing:

  • you can find FoodMicrobionet and related scripts in my GitHub repository. You may want to check out how to clone a repository, and how to download a folder or a raw file.
  • you can find a downloadable version of the ShinyFMBN app on Mendeley data and on GitHub: you are strongly encouraged to download the app because running it locally is much faster
  • you can run the app on Shinyapps.io by clicking on this link
  • further resources (studies with ASVs) are available on Zenodo
  • I will make available more example scripts next week so check the GitHub repository just before the webinar for the most recent version of the scripts

If you are one of the few people left in the world who still reads manuals:

  • Table specifications for FoodMicrobionet are here
  • Instruction manual for the ShinyFMBN app are here

Please note: I will be accepting people in the webinar (you should be logged in the browser with the address you have used for registering) in the first 15 minutes

The following scientific papers are related to FoodMicrobionet

  • Parente, E., Cocolin, L., Filippis, F.D., Zotta, T., Ferrocino, I., O’Sullivan, O., Neviani, E., Angelis, M.D., 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, 28–37. https://doi.org/10.1016/j.ijfoodmicro.2015.12.001
  • Parente, E., Filippis, F.D., 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. https://doi.org/10.1016/j.ijfoodmicro.2019.108249
  • Parente, E., Ricciardi, A., Zotta, T., 2020. The microbiota of dairy milk: A review. Int Dairy J 107, 104714. https://doi.org/10.1016/j.idairyj.2020.104714
  • Parente, E., Zotta, T., Ricciardi, A., 2021. Microbial association networks in cheese: a meta-analysis. Biorxiv 2021.07.21.453196. https://doi.org/10.1101/2021.07.21.453196
  • Zotta, T., Ricciardi, A., Condelli, N., Parente, E., 2022. Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture. Crit Rev Food Sci 62, 3898–3912. https://doi.org/10.1080/10408398.2020.1870927
  • 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
  • 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. https://doi.org/10.1016/j.ijfoodmicro.2022.109696
  • Parente, E., Zotta, T., Giavalisco, M., Ricciardi, A., 2023. Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments. Int J Food Microbiol 391, 110124. https://doi.org/10.1016/j.ijfoodmicro.2023.110124
  • Parente, E., Ricciardi, A., 2024. A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5. Foods 13, 1689. https://doi.org/10.3390/foods13111689
  • Ricciardi, A., López, F.N.A., Giavalisco, M., Pietrafesa, R., Parente, E., 2025. Determining the core bacterial and fungal genera in table olive fermentations. Int. J. Food Microbiol. 442, 111344. https://doi.org/10.1016/j.ijfoodmicro.2025.111344

Fondamenti di analisi del rischio degli alimenti – AA 2025-2026 – Inizio corsi

Posted on by

Il corso di Fondamenti di Analisi del Rischio degli Alimenti degli per il Corso di Laurea Magistrale in Scienze e Tecnologie Alimentari inizierà il giorno 1 ottobre 2025 nell’aula A15 alle 9.30 e proseguirà con il seguente orario:

  • martedì 11.30-13.30 aula A15
  • mercoledì 9.30-11.30 aula A15

Gli studenti devono iscriversi autonomamente alla piattaforma di e-learning seguendo questo link a partire dal 1/10/2026.

Inoltre gli studenti devono autonomamente iscriversi al gruppo Google del corso.

Microbiologia degli alimenti, AA 2025-2026, inizio corsi

Posted on by

Il corso di Microbiologia degli Alimenti per il Corso di Studi in Tecnologie Alimentari inizierà il giorno 1 ottobre 2025 nell’aula A7 alle 11.30 e proseguirà con il seguente orario:

  • mercoledì 11.30-13.30 aula A16
  • giovedì 11.30-13.30 aula A16

Gli studenti devono iscriversi autonomamente alla piattaforma di e-learning seguendo questo link a partire dal 1/10/2026.

Inoltre gli studenti devono autonomamente iscriversi al gruppo Google del corso.

Advances in the microbiology of table olives: Meet links to the workshop sessions

Posted on by

If you are attending remotely to the meeting you can connect to the following links:

Netiquette: Unfortunately, Meet only allows direct access to the meetings if you have an invitation and if you are logged to your browser with the address which received the invitation. Since this is not practical (most people would incorrectly set their browser) you will be able to participate as a guest. Please join with your microphone muted by clicking on the link of the active session (you can activate your microphone during the question time), a moderator will let you in as soon as possible. This will usually happen within 1-2 minutes: if it doesn’t close the connection and join again. If your microphone is active during a talk, if you are not a speaker for that session your microphone will be muted by the videoconference moderator; if you turn it on again we will be forced to close your connection. You can keep your video feed on if you wish but, since all sessions will be recorded and made available on the workshop web page, we assume that if your video is on, you accept that your streaming is included in the recording.

e-posters will be shown in a loop during the e-poster sessions with the following schedule (clicl on the title to download the poster):

SessionAuthorsCorresponding author affiliationTitle
1/9/2025 13:30-14:00 Poster viewing https://meet.google.com/snw-ofsz-xbvPietrafesa, R. (1)*, Ricciardi, A. (1), Alessandra De Vivo (2), Labella, Maria Grazia (1), Parente, E. (1)Università degli Studi della Basilitaca, DAFECulturable yeasts in table olives: the METAolive collection
1/9/2025 13:30-14:00 Poster viewing https://meet.google.com/snw-ofsz-xbvPietrafesa, R. (1)*, Ricciardi, A. (1), De Vivo. A. (2), Labella, Maria Grazia (1), Parente, E. (1)Dept. of Agricultural, Food, Forestry and Environmental Sciences, University of Basilicata, Potenza, ItalyWL (Wallerstein Laboratory) Nutrient Agar of any use in differentiation of colonies of yeasts from table olives?
1/9/2025 13:30-14:00 Poster viewing https://meet.google.com/snw-ofsz-xbvParente, E. (1)*, Arroyo López, F. N. (2), Ricciardi, A. (1)Dept. of Agricultural, Food, Forestry and Environmental Sciences, University of Basilicata, Potenza, ItalyOliveFMBN: an extensively annotated database of the microbiota of table olives
1/9/2025 13:30-14:00 Poster viewing https://meet.google.com/snw-ofsz-xbvParente, E.(1), Ricciardi, A.1)*, Labella Maria Grazia (1)Dept. of Agricultural, Food, Forestry and Environmental Sciences, University of Basilicata, Potenza, ItalyModelling the effect of NaCl on the growth of selected Lactiplantibacillus pentosus strains.
1/9/2025 13:30-14:00 Poster viewing https://meet.google.com/snw-ofsz-xbvAlfonzo, A. (1)*, Alongi, D. (1), Perricone, G. (1), Naselli, V. (1), Irene, D. (1), Viola, E. (1), La Croce, F. (2),  Settanni, L. (1), Moschetti, G. (1), Francesca, N. (1)Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, Viale delle Scienze, Building 5, 90128, Palermo, ItalyBioprotection of Nocellara del Belice table olives: effects of Candida boidinii LC1 and Candida norvegica OC10 under different thermal storage conditions
1/9/2025 16:30 – 17:00 Poster viewing https://meet.google.com/knm-sbpx-suoAlongi, D. (1)*, Perricone, G. (1), Pirrone, A. (1), Naselli, V. (1), Azzurra, V. (1), Micaela, C. (1), Settanni, L. (1), Moschetti, G. (1), Francesca, N. (1), Alfonzo, A. (1)Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, Viale delle Scienze, Building 5, 90128, Palermo, ItalyBioprotective co-inoculation strategies for optimising the fermentation of Nocellara del Belice table olive
1/9/2025 16:30 – 17:00 Poster viewing https://meet.google.com/knm-sbpx-suoBonatsou, S. (1), Panagou,E.Z. (1)(1) Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrion, Agricultural University of Athens, Athens, GreeceControlled Fermentation of Kalamata Olives Using Multifunctional Yeast Starters: The Role of Yeasts in Enhancing Process Control and Product Stability
1/9/2025 16:30 – 17:00 Poster viewing https://meet.google.com/knm-sbpx-suoMartínez, A.(1), Pérez-Nevado, A.(2)(3)*, Ramírez, M.(1)Dept. de Producción Animal y Ciencia de los Alimentos, Universidad de Extremadura, Badajoz, Spain.Co-Inoculation of Lachancea thermotolerans and Lactobacillus plantarum enhances the Fermentation and Quality of Spanish-Style Table Olives
1/9/2025 16:30 – 17:00 Poster viewing https://meet.google.com/knm-sbpx-suoAMIN, A. (1) *, AMIN, S. (1), PASHA, I. (1)National Institute of Food Science and Technology, Faculty of Food Nutrition and Home Sciences, University of Agriculture, Faisalabad, PakistanIntegrative Microbiome Engineering and Nanobiotechnology Approaches for Precision-Controlled Fermentation of Table Olives
2/9/2025 11:30 – 12:00 Poster viewing https://meet.google.com/kqr-hxvy-dhpKazou, M. (1)*, Psarafti, A. (1), Papantoni, A. (2), Mallouchos, A. (2), Panagou, E.Z. (1)Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of AthensThe impact of different starter cultures on the microbiome and volatilome profile of cv. Kalamata natural black olives during fermentation
2/9/2025 11:30 – 12:00 Poster viewing https://meet.google.com/kqr-hxvy-dhpTsobi, I.(1)*, Kazou, M.(1), Panagou, E.Z. (1)Laboratory of Microbiology and Biotechnology of Foods, Dept. of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of Athens, Athens, GreeceImpact of partial substitution of NaCl with KCl on the microbial dynamics and physicochemical attributes of Kalamata natural black olives fermented at semi-industrial scale
2/9/2025 11:30 – 12:00 Poster viewing https://meet.google.com/kqr-hxvy-dhpOikonomou, M.V.(1) *, Kollia, E.(1), Roumani, F.(1), Panagou, E.Z. (2) Dasenaki, M. (1),  Valdramidis, V. (1)(1) Dept. of Chemistry, Food Chemistry, National and Kapodistrian University of Athens,  Greece  (2) Dept. of Food Science and Human Nutrition, Argicultural University of AthensMicrobial and Physico-chemical Dynamics During the Fermentation of Conservolea  and Kalamàta table olives

If you are attending in person or remotely and you want to pose questions to the corresponding author of the poster, you will need to do so during that session. It is safer if you send an email to the corresponding author of the poster. The e-mails are available in the abstract book.

FoodMicrobionet 4.2.1 is now available

Posted on by

I have just released a new version of FoodMicrobionet. Version 4.2.1 includes 233 studies and 13895 food and food environment samples. New tables have been added (Abstracts table) and metadata for studies (a study_type field now provides a classification in longitudinal cross-sectional or mixed for the study design) have been improved. You can access the new version:

  • on GitHub: data in the the_real_thing folder, plus a bunch of scripts
  • on Zenodo: here you can find the mindata files, with ASV sequences
  • on Mendeley data (the most recent version is in moderation, reserved DOI 10.17632/8fwwjpm79y.8)

Share (using the DOIs provided by Mendeley data and Zenodo) and enjoy. You can find the most recent publications on FMBN here.

pigR

Posted on by

“pigR: R per pigri” è stato finalmente pubblicato. Lo trovate qui. Potete scaricare una copia del libro (basta scaricare l’intera cartella dal nome pigR_251123) o il codice dei singoli capitoli nel mio repository GitHub. Grazie:

  • alla persona che più di tutte mi sopporta
  • al Prof. Fulvio Delle Donne, coordinatore del comitato scientifico di Basilicata University Press
  • agli editori anonimi che hanno avuto la pazienza di leggere le bozze

Spero vi piaccia e, soprattutto, che sia utile nel tempo (abbastanza breve) che ci metterà ad essere obsoleto.