Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties
Authors: Sudarshan A. Shetty1#⸸, Ioannis Kostopoulos1#⁋, Sharon Geerlings1#, Hauke Smidt 1, Willem M. de Vos1,2* , Clara Belzer*1
1Laboratory of Microbiology, Wageningen University & Research
2Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
⸸Present address: University Medical Center Utrecht, Utrecht, The Netherlands & Rijksinstituut voor Volksgezondheid en Milieu, Bilthoven, The Netherlands
⁋Present address: Danone Nutricia Research, Utrecht, The Netherlands
#Shared first authors; These authors contributed equally.
*Co-Corresponding authors; These authors contributed equally.
Manuscript Correspondence:
Sudarshan A. Shetty; sudarshanshetty9[@]gmail[.]com
Clara Belzer; clara.belzer[@]wur[dot]nl
Hauke Smidt; hauke.smidt[@]wur[dot]nl
Willem M. de Vos; willem.devos[@]wur[dot]nl
This repository contains codes for analysis done in the research article by Sudarshan A. Shetty1#⸸*, Ioannis Kostopoulos1#⁋, Sharon Geerlings1#, Hauke Smidt*1, Willem M. de Vos1,2, Clara Belzer1 (2022). Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties. accepted ISME Journal.
We developed syncomR package as a research compendium for organizing and sharing files processed files and custom functions
For re-running the analysis, first install syncomR package from GitHub
install.packages("devtools")
devtools::install_github("microsud/syncomR")
The scripts that we used for processing raw reads are in amp_seq/ (dada2, raw reads to ASVs --> transferred to syncomR) and rna_seq/ (modified samsa2, raw reads to gene count tables --> transferred to syncomR). The main analysis codes and figures reported in the manuscript are located in analysis/, codes/, and data/ folders.
Correspondence for analysis:
Author: Sudarshan A. Shetty
Contact: sudarshanshetty9[at]gmail[dot]com