This repository contains all R-markdown files and HTML-files of the submitted manuscript entitled:

Carrot juice fermentations as man-made microbial ecosystems dominated by lactic acid bacteria

Sander Wuyts (1,2), Eline F.M. Oerlemans (1), Wannes Van Beeck (1), Stijn Wittouck (1), Ingmar J.J. Claes (1), Ilke De Boeck (1), Stefan Weckx (2), Bart Lievens (3), Luc De Vuyst (2), Sarah Lebeer (1)*

1 University of Antwerp, Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, Groenenborgerlaan 171, B-2020 Antwerp, Belgium

2 Vrije Universiteit Brussel, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Pleinlaan 2, B-1050 Brussels, Belgium

3 KU Leuven, Campus De Nayer, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), Fortsesteenweg 30A, B-2860 Sint-Katelijne-Waver, Belgium

(*) Corresponding author

Here you can find:

• LF1_LF2_HF
  Processing of sequence and taxonomy table of all household fermentations (HF) and laboratory fermentation 1 & 2 (LF1 & LF2) using Phyloseq and ggplot2
• LF3
  Processing of sequence and taxonomy table of laboratory fermentation 3 (LF3) which compares the DNA-based versus the RNA-based 16S rRNA sequencing of the fermentation
• Phylogenetic placement
  All necessary scripts for running the phylogenetic placement of the ASVs on a 16S rRNA tree. A huge thank you to Stijn Wittouck for conceptualising and performing this analysis