Quarto scripts that have be used for the publication Microbial community transfers across a pilot ripening cellar are increased by cheese wiping.

The folder zip archive contains 4 folder:

Metabarcoding analyses (16S) = MetaB16S Metabarcoding analyses (ITS) = MetaBITSS Analyses from culture-depend data and from gases data (CO2) = Microbiology_gases All data = Raw_data

Metab16S

In the MetaB16S folder ==> 2 documents, the quarto file and the html version, related with analyses of bacterial composition and diversity from all environments (cheese, cloth, air and wall's cellars). The quarto file contains the following analyses.

Cheese microbial characteristics

Barpolt of composition of short-ripened cheese and long-ripened cheese (separeted by time and cellars) Alpha diversity was measured with the Shannon and Richness observed indexes by ripening stage, time and cellar Beta diversity analyses were generated by ripening stage, time and cellar (+ Permanova analyses and pairwise adonis when necessary)

All env microbial characteristics

Same analyses as for cheese microbial characteristics were performed to describe microbial evolution for all environments (cheese, cloths, air and wall'cellars)

Flux - all environments

Microbial transfers between all environments ==> heatmap from ASVs at least shared with two environments and gather at species level and then at order level. In this heatmap, we can see the prevalence (Blue = weak, red = strong) of thoses ASVs at different relative abundance (absciss axe) for 6 environments (long-ripened cheese, short-ripened cheese, long-ripened cheese cloth, short-ripened cheese cloth, air and wall). This heatmap was generated for the three cellar separately.

MetaBITS

In the MetaBITS files there are two documents (quarto file with the script and the html version) related with bacterial composition of all environments (cheese, cloth, air and wall's cellars) In the quarto file, the phyloseq files was loaded to generate the following figures. Same analyses as MetaB16S were generated for fungal community.

Differential analyses

Differential analyses performed on cheese samples ==> (short-ripened cheeses stored with vs without long-ripened cheeses)

Microbiology_gases

In this this barplot of levels of molds in the air according wiping activity ==> comparison of 2 media (OGA vs MEA) A figure of the evolution of CO2 during one day in one cave was generated. On this figure we can see the concentration of CO2 increasing when cheeses were being wiped and its diminution. Then there is zoom on some specific period when the CO2 increased when cheese were not being wiped.

Raw_data

2023-06-07_synthese_microbio_SN_1204file (.xlsx) , sheet = Microbiologie ==> data related with enumeration for each environment + metadata (date of sampling, cellar, wiping conditions...) 2024-10-10_Phyloseq_SN_16S file (.Rdata) ==> phyloseq file use to performed analyses MetaB16S 2024-10-10_Phyloseq_SN_ITS file (.Rdata) ==> phyloseq file use to performed analyses MetaBITS 2024-10-14_Synthese_gases_all_cellars1 file (.xlsx)==> several sheets:

`Evolution of CO2C2, Cave 3 and Cave 4` = Evolution of CO2, relative humidity, temperature and atmospheric pressure from 12/04/2023 to 17/05/2023.
`CO2_suivi_C2, CO2_suivi_C3 and CO2_suivi_C4` = For each cellar (C2,C3 and C4) ==\> focus evolution on of CO2, relative humidity, temperature and atmospheric pressure on 1 day
`NH3` = Evolution of NH3 from 12/04/2023 to 12/05/2023

EBI BioProject

R, 4.1.0