FoodMicrobionet 5.0: mindata files

This folder contains mindata objects for FoodMicrobionet v5.0. These objects allow, via the NCBI accession number, direct access to information on individual studies. Each object is a R list containing:

• Study_accn = the study accession number,
• study_df = a data frame with the study information,
• overlap = a logical flag indicating if overlapping paired sequences were used,
• pend = a logical flag indicating if paired sequences were used,
• physeq = a phyloseq object with sample, taxa, OTU tables and, when available, a phylogenetic tree,
• rev_compl = a flag indicating if the sequences need to be transformed in reverse complement before taxonomic assignment

Both data for bacteria (SILVA database) and fungi (UNITE database) are available in two separate folders within the compressed folder. This version is currently co-funded by Ministero dell'Università e della Ricerca PRIN 2022 PNRR, proposal P20229JMMH, Mining the biodiversity of non conventional yeasts as bioresources for innovative fermented beverages through a genomics, and received funding from the European Union Next-GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR)) CUP C53D23007560001

Refer to this publication for further detail on v4.1 of FoodMicrobionet:

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