Guanidine as the sole nitrogen source enables growth in Alphaproteobacteria
Read the manuscript » (pending publication)
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This repository contains the raw data, and scripts that were written during my MSc internship project at the Monier group at the Living Systems Institute.
The main objective of the internship was to identifying whether guanidine hydrolase (gdmH) allows for the utilisation of guanidine as the sole nitrogen source in Alphaproteobacteria. The key findings of the project are:
- gdmH+ Alphaproteobacteria grow on guanidine as the sole nitrogen source.
- gdmH is widely, but sporadically distributed in Alphaproteobacteria.
- gdmH occurs across diverse bacterial and eukaryotic lineages.
For more information and a closer look at the findings, please read the manuscript (pending publication).
To be able to run the scripts and recreate the analyses, follow the steps below.
First, clone the repository onto your machine (note that the scripts were written and tested in a Linux environment, I will assume that you will clone the repository to a Linux system as well).
- Cloning the repository
git clone https://github.com/Tomersardjoe/MSc-internship.gitThe first thing you will want to do is to retrieve all the dependencies. For convenience, the project uses Conda environments for this.
Create the Conda environments from the environments .yml files. These files can be found in the conda_envs directory and the environments can be created like so:
conda env create -f ncbi_tools.yml
conda env create -f phylo.ymlThe phylo environment should be activated for the R scripts, the ncbi_tools environment should be activated for all other scripts.
Now, the project environment is ready for the analyses.
The repository is divided into two main parts; data and scripts.
The data directory contains data that was generated from experiments in the lab or analyses based on those experiments (data that cannot be found anywhere else), and is therefore uploaded to the repository. Some of the data is used as input for analyses scripts.
The scripts directory contains support scripts, used to download or reformat data for subsequent analyses. The analyses directory contains the scripts that were used to generate the main figures in the manuscript.
Distributed under the GPL-3.0 license. See LICENSE for more information.
Tomer Sardjoe - tomer.sardjoe@wur.nl
Project Link: https://github.com/Tomersardjoe/MSc-internship
The authors thank Marnix Medema for reviewing the manuscript and his helpful feedback. Additionally, we would like to express our gratitude to Victoria Jackson for transporting the Roscoff Culture Collection strains from France to the LSI.