Engineered live biotherapeutic product (eLBP) prevents antibiotic-induced dysbiosis: metagenomics analysis

This repository contains code needed to reproduce metagenomics (i.e., shotgun sequencing) analyses described in “An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis” (Cubillos-Ruiz et al. 2022).

Installation & requirements

This repository, including all code needed to reproduce analyses, can be installed using:

git clone https://github.com/maalcantar/engineered-probiotic-prevents-dysbiosis-metagenomics-analysis.git
cd engineered-probiotic-prevents-dysbiosis-metagenomics-analysis
pip install -r requirements_python.txt #requirements for Jupyter Notebooks 

R requirements:

• broom v0.7.9
• cowplot v1.1.1
• ggplot2 v3.3.5
• multcomp v1.4-17
• phyloseq v1.30.0
• plyr v1.8.6
• rmarkdown v2.10
• tidyverse v1.3.1

Additional requirements:

• Bowtie2 v2.2.6
• Samtools v1.6

The majority of the metagenomic sequence processing and analyses were conducted using the Commonwealth Computational Cloud for Data Driven Biology (C3DDB) cluster.

Directory structure

source code

All code is in src/, which contains a combination of bash, python (in Jupyter Notebooks), and R scripts. The numbering at the beginning of each file name indicates the order in which that script should be run.

data

All data files are found in and/or will be written to data/

• data/card/
  • contains both the native CARD database (protein homolog model version v3.0.9.) and the custom CARD database (which includes SpTEM1 B-lactamase and chloramphenicol resistance used in this study).
• data/custom_card_db_data/
  • folder where ARG analyses (based in custom card database) are written to.
• data/reference_genomes/
  • directory where mouse reference genome should be stored. mouse reference genome can be downloaded from: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/all_assembly_versions/GCF_000001635.26_GRCm38.p6/
  • the actual genome file is called: GCF_000001635.26_GRCm38.p6_genomic.fna.gz
• data/sequencing/
  • contains sequencing data and results for some analysis applied to sequencing data.

Metagenomics sequencing data is not included in this repository due to their large file sizes; however, all data are publicly available under NCBI Bioproject PRJNA803721.

figures

Figures created with R can be found in figs/. The majority of figures shown in the publication were recreated using PRISM.

Please feel free to reach out if you have any questions about implementation or reproducing analyses! (alcantar [at] mit [dot] edu).