***Title of the dataset / Data underlying the publication: ‘Effects of E. coli Nissle 1917 on the Porcine Gut Microbiota and Immune System in Early Life’***

***Creators***
Mirelle Geervliet 1,†, Hugo de Vries 2,3,†, Christine A. Jansen 1,4, Victor P.M.G. Rutten 4,5, Hubèrt van Hees 6, Caifang Wen 3, 
Kerstin Skovgaard 7, Giacomo Antonello 8, Huub F.J. Savelkoul 1, Hauke Smidt 3, Edwin Tijhaar 1,†, and Jerry M. Wells2,†,*

1	Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, The Netherlands; mirelle.geervliet@wur.nl; huub.savelkoul@wur.nl; edwin.tijhaar@wur.nl; christine.jansen@wur.nl 
2	Host-Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands; jerry.wells@wur.nl
3	Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands; hugo.devries@wur.nl; caifang.wen@wur.nl; hauke.smidt@wur.nl 
4	Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands; v.rutten@uu.nl 
5	Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa; v.rutten@uu.nl 
6	Research and Development, Trouw Nutrition, Amersfoort, The Netherlands; hubert.van.hees@trouwnutrition.com
7       Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; kesk@dtu.dk
8       Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy; giacomo.antonello@unitn.it

* Correspondence: jerry.wells@wur.nl

† These authors have contributed equally to this work and share first or last authorship.

***Related publication***
Title: Effects of E. coli Nissle 1917 on the Porcine Gut Microbiota and Immune System in Early Life
DOI: 10.3389/fcimb.2022.842437
Received: December 23th, 2021; Accepted: February 1st, 2022; Published: 2022

***General Introduction***
This dataset contains data collected during an in vivo experiment with pigs at the Wageningen University as part of the PhD Thesis Projects of Mirelle Geervliet and Hugo de Vries (first authors of the manuscript). 
This research project was made possible by The Netherlands Organisation for Scientific Research and Vereniging Diervoeders Nederland (VDN).

***Key words***
E. coli Nissle 1917, porcine, gastro-intestinal tract, gut microbiota, immune system, early life, immunomodulation, probiotic 

***Spatial coverage*** 
Swine Research Centre, St. Antonis, The Netherlands

***Temporal coverage*** 
September 2018 until November 2018

***Purpose of the study***
We hypothesized that early life consumption of E. coli Nissle 1917 (EcN) alters the porcine gut microbiota development (composition), the intestinal epithelial barrier and the immune system. 
In addition, we examined the temporal dynamics of these complex systems. A more developed and mature gut microbiota and immune system in early life could make the animals more resilient against invasive pathogens during the weaning phase and later in life.

***Description of the data in this dataset***
The data included in this dataset has been organized by folders which includes raw data of one or multiple figures. Every folder contains a separate README.txt file with a description of the file structure.
Please note that there is not a folder named 'Figure 1, Figure S1, Figure S3 and Figure S4' as these figures do not present results from obtained data (explanatory information only).

Every Figure has its own folder, each containing subfolders with separate readme files. 

In addition to data belonging to the figures, the folder named 'Data_analysis_in_R_Studio' contains all files related to the analyses performed in R.

Alternatively, all files can be found under the following Github page: https://github.com/mibwurrepo/Geervliet-et-al-2022-porcine-study-EcN

***Instructions***
1. Download the repository and unzip.
2. Inspect the figure folders individually to assess the raw figures, the final figures and data files corresponding to each figure.
3. Open the HTML file named 'Porcine_study_EcN_R_analyses_nov2020_markdown_file' for a complete overview of the analyses in R or alternatively open the 'Data_analyses_in_R_Studio_EcN_study' folder and run the analyses yourself in R-Studio.

This dataset is published under the CC BY SA license 
