***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 README file corresponds to the data corresponding to Figure S7 of the manuscript.
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).

***Purpose of analysis***
To investigate whether EcN is present in digesta of jejunum, ileum and caecum segments of the porcine GIT, at three different timepoints: d27, d44, and d70.

***Methodological information***
DNA was extracted from digesta samples, then PCR amplification was carried out with barcoded primers directed to the V4 region 
of the bacterial and archaeal 16 S rRNA gene. Samples were sent for Illumina HiSeq sequencing after which amplicon sequence data were processed and analysed using NG-Tax 2.0 and annotated using the SILVA 132 database.
Resulting data was imported into R-studio together with a metadata file to perform analyses and generate figures.

***Data specific information***
Folder 'Figure S7' contains two subfolders:

1. Unprocessed_Figure:
This folder contains a PDF file with the figure as generated by R. 
This PDF file was used to create final Figure S7. 

2. Final_Figure:
This folder contains the final figure as presented in the manuscript. 
The final figure is prepared in Adoble Illustrator. 

Raw_data:
Raw Illumina sequencing data has been uploaded to the European Nucleotide Archive (ENA), and can be found under the following accession numbers: PRJEB40329 and PRJEB45986

R script can be found under the following folder: Data_analyses_in_R_Studio
This folder also contains the data files used in the subfolder 'input_data'. This includes the metadata file, the .biom file and the .tre file.


