BacMGEnet

Inference of bacteria-phage interactions using CRISPR

This package contains computational tools for inference of bacteria-phage interactions using CRISPR arrays. The tools have been extensively tested on Ubuntu linux systems.

The tools are oganized into two main pipelines (available under pipelines/)

crispr_ann.py

This pipeline is for generating CRISPR arrays given a list of genomes/metagenome

mge_net.py

This pipeline generates bacteria-phage network using the CRISPR arrays created by crispr_ann.py

MGE database

To run the second pipeline (mgenet.py), a MGE database is needed. We provide a curated MGE database (including phage and plasmid sequences), which you can download and place it under the BacMGEnet/ folder (as follows) or somewhere else.

For example, after git clone the BacMGEnet to your local machine, go under the BacMGEnet folder,

mkdir mgedb

cd mgedb

wget https://omics.informatics.indiana.edu/mg/packages/mgedb.tar.gz

tar zxvf mgedb.tar.gz

then you have the MGE database for running the pipeline.

We note the MGE database we provide was curated for discovery of phage-bacteria interactions that are involved with gut microbiomes. If a user is interested in using our pipeline for microbial species associated with other environments, they may want to curate their own databases (blastn database).

Dependencies

Python: python 3

NetworkX: a python package for network based analysis

CRISPRone: a pipeline for CRISPR-Cas system annotation, included in this repository under the CRISPRone

Sample usage using a toy example

Please go to examples/ to see how it works using a toy example, and what the pipelines output.

Outputs

The main outputs are the predicted CRISPR-Cas systems (and CRISPR arrays), putative MGEs (phages and pladmids) that have traces caught in the CRISPR-Cas systems, and putative interaction network of the genomes/metagenomes and the MGEs (in GML format).

For the toy example, the results are under examples/ folder.

crisprone/

crisprone/crispr -- CRISPR-Cas prediction results (annotations in gff file, and predicted cas genes)

crisprone/spacer_graph/module.all.ori -- CRISPR arrays

mgenet/

mgenet/protospacer_w_multihits-greedy.gff -- identified phages with protospacer information (in gff format)

mgenet/spacer2mge.gml -- spacer and MGE network (below shows a visualization of the network in Cytoscape when this style file is applied)

In this figure, the green rectanges are the genomes (hosts), yellow ovals are phages and red ovals are plasmids.

Sample results

Phocaeicola vulgatus

See results/pvulgatus

human gut MAGs

See results/gut

wound microbiome

See results/wound