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.
code (helpers): Helper functions for the main code, in form of an R package. The package can be locally installed by callingdevtools::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.
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 responses1e - food frequency questionnaire (nutrients).csv: Nutrient data based on the food questionnaire responses1f - opinion questionnaire.xlsx: Opinion questionnaire responses, with explanations of the items in file1f - 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 data2a - 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 jars3a - KEGG genes.txt: KEGG KO data on genes in the stool samples3b - KEGG pathways.txt: KEGG data on pathways in the stool samples4a - 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 measurements5b - stool SCFAs.xlsx: Stool SCFA measurements