A social niche breadth score reveals niche range strategies of generalists and specialists

Abstract

Generalists can survive in many environments whereas specialists are restricted to a single environment. Although a classical concept in ecology, niche breadth has remained challenging to quantify for microbes because it depends on an objective definition of the environmental conditions. Here, by defining the environment of a microbe as the community it resides in, we integrated information from over 22 thousand environmental sequencing samples to derive a quantitative measure of the niche, which we call ‘social niche breadth’. At the level of genera, we explored niche range strategies throughout the prokaryotic tree of life. We found that social generalists include opportunists that stochastically dominate local communities, while social specialists are stable but low in abundance. Social generalists have a more diverse and open pan genome than social specialists, but we found no global correlation between social niche breadth and genome size. Instead, we observed two distinct evolutionary strategies, where specialists have relatively small genomes in habitats with low local diversity, but relatively large genomes in habitats with high local diversity. Together, our analysis shines data-driven light on microbial niche range strategies.

Inside this repository

This is the directory structure and code used to generate all data and figures in the paper "A social niche breadth score reveals niche range strategies of generalists and specialists" by F. A. Bastiaan von Meijenfeldt, Paulien Hogeweg, and Bas E. Dutilh. The code was made by F. A. Bastiaan von Meijenfeldt.

The code inside the ./MGnify directory was used to download the MGnify data.

The code inside the ./niche_breadth directory was used to generate all other data and uses the MGnify data.

The code inside the ./figures directory was used to generate all figures.

Each directory in ./MGnify and ./niche_breadth contains a commands.sh that if run, and if source files are present, will generate all content in that directory. No files are written outside the directory. For example running ./MGnify/commands.sh will generate all files within ./MGnify. The generated files are source files for some of the scripts in ./MGnify/2019-08-20_extra and ./MGnify/2019-08-20_extra/commands.sh can now be run to generate all files within. Source files for the ./niche_breadth subdirectories can be from the ./MGnify directory or from other subdirectories within ./niche_breadth.

The ./figures directory and its subdirectories contain *.ipynb Jupyter Notebook files that if run, and source files are present, will generate the vector files that were used as raw input for the final figures.

The file ./figures/mappings.Figure_to_Notebook.txt contains the mapping of the figure to the notebook that was used to generate the figure. In some cases only part of the notebook output was used in the final figures.