Overview

This is the accompanying code repository for the paper Schropp et al. (under revision) - "The Impact of Regular Sauerkraut Consumption on the Human Microbiota: a Cross-Over Intervention Trial".

The code contains the data and R code for all relevant analyses in the paper, including the supplementary material. Data and code are published under the CC BY 4.0 license.

Folder structure

• code (helpers): Helper functions for the main code, in form of an R package. The package can be locally installed by calling devtools::install("code (helpers)/sauerkrautTaxonomyBuddy").
• code (main): Main R code files (using Quarto reports) reproducing all analyses and figures shown in the paper.
• data: Data folder (see descriptions below)
• figures: Figure files produced by the code.

Data description

• 1a - group info.Rdata: Information to which intervention group (A or B, receiving the fresh or pasteurized sauerkraut intervention first, respectively) each participant belongs.
• 1b - participant data.Rdata: Several datasets containing general participant information like which intervention was received at which timepoint and general information like BMI, weight, etc.
• 1c - sample IDs.xlsx: General base information on observations, including some information on duplicate measurements (which were measured in duplicate for estimating the measuring reliability)
• 1d - food frequency questionnaire.csv: Food questionnaire responses
• 1e - food frequency questionnaire (nutrients).csv: Nutrient data based on the food questionnaire responses
• 1f - opinion questionnaire.xlsx: Opinion questionnaire responses, with explanations of the items in file 1f - lookup for opinion questionnaire.xlsx.
• 1g - blood markers.xlsx: Blood marker measurements (glucose, CRP, etc.)
• 1h - body measurements.xlsx: Body measurements (BMI, blood pressure, etc.)
• 1i - symptom diaries.xlsx: Symptom diary data
• 2a - stool taxonomy (absolute abundances).tsv: Taxonomic stool measurements (absolute abundances)
• 2b - stool taxonomy (relative abundances).tsv: Taxonomic stool measurements (relative abundances)
• 2c - meta information blood and stool samples.xlsx: Meta information on blood and stool samples and duplicate measurements (measured for estimating measuring reliability)
• 2d - meta information sauerkraut samples.xlsx: Some (quite unstructured) general information on the taxonomic samples which were no human stool samples, but taxonomic samples taken from some sauerkraut jars
• 3a - KEGG genes.txt: KEGG KO data on genes in the stool samples
• 3b - KEGG pathways.txt: KEGG data on pathways in the stool samples
• 4a - blood data part 1.Rdata: Further blood measurements (TNFR2, RAGE, etc.)
• 4b - blood data part 2.Rdata: Further blood measurements (glucose, sCRP, etc.)
• 4c - blood data part 1 including duplicates.xlsx: Blood measurements (TNFR2, RAGE, etc.), also including the duplicate samples (used for estimating measuring reliability)
• 4d - blood data part 2 including duplicates.xlsx: Blood measurements (glucose, sCRP, etc.), also including the duplicate samples (used for estimating measuring reliability)
• 5a - blood SCFAs.xlsx: Blood SCFA measurements
• 5b - stool SCFAs.xlsx: Stool SCFA measurements