The syncomR package is developed to analyse and visualize temporal microbial community profiles. The development was done for and using the human gut synthetic microbial community designed to investigate ecophysiological properties of core human gut microbes by Sudarshan A. Shetty, Ioannis Kostopoulos, Sharon Geerlings, Hauke Smidt, Willem M. de Vos, Clara Belzer (2022). Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties. accepted ISME Journal. The package requires phyloseq-class object of microbial community profile for most of the analysis aimed at the ecological aspects. In addition, package data includes metatranscriptomics data, metabolites data, and gut microbiota module expression data. The focus is to analyse temporal dynamics of microbial community, test changes in abundances, overall community variability, resistance and resilience properties of the microbial communities. The ecological stability properties are calculated using the modified R code from Liu et al., 2018. Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry, while community level temporal variability and succession is calculated with modified R code from Guittar J et al., 2019. Trait-based community assembly and succession of the infant gut microbiome.
Additional functions are provided for data handling and formatting. Visualization tools are provided to explore the microbial community dynamics, including area, bar and line plot for composition, ordination plots for visualizing movement of community in and out of reference phase.
The package is mainly accompanying the research article "Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties" Shetty SA., Kostopoulos I., Geerlings SY., et al 2020. Therefore, the functions have been tested using a synthetic minimal microbiome that was assembled in three bioreactors. Therefore, this package should mostly be considered as a research compendium for organizing and sharing codes and files pertaining to the said research article.
Before installing syncomR, you will need to install R (3.5.1 or later) and RStudio (1.1.463 or later). Windows users also have to install RTools. Then open RStudio as administrator and in the console panel run the commands below to install syncomR:
install.packages("devtools")
devtools::install_github("microsud/syncomR")
Sudarshan A. Shetty (sudarshanshetty9[@]gmail[dot]com)