FoodMicrobionet 5.1.2: mindata files

This folder contains mindata objects for FoodMicrobionet v5.1.2. 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, v138.1 and v 138.2) and fungi (UNITE database, SILVA SSU and LSU) are available in 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 bioinformatics approach”, 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 v5.0 of FoodMicrobionet:

Parente, E., Ricciardi, A., 2024. A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5. Foods 13, 1689. https://doi.org/10.3390/foods13111689