Microbial Index of Pathogenic bacteria (MIP)

Contents

• Introduction
• Software Requirement and Dependency
• Installation guide
• Basic Usage
• Batch Processing
• Example dataset

Introduction

Microbial Index of Pathogenic bacteria (MIP) is an easy-to-use bioinformatic package that calculates the quantitative microbial pathogenic risk. MIP assesses the disease risk to human from a microbiome sample and reports the quantitative indices from multiple aspects using a reference pathogen database and an artificially curated pathogen-disease interaction network. MIP works as a plug-in tools of Parallel-META 3, and supports 16S rRNA amplicon sequences as input.

Software Requirement and Dependency

MIP requires Parallel-Meta-Suite, please refer to https://github.com/qdu-bioinfo/parallel-meta-suite#installation-guide for installation.

Installation Guide

MIP provides a fully automatic installer for easy installation.

a. Download the package

git clone https://github.com/qdu-bioinfo/mip.git	

b. Install by installer

cd mip
source install.sh

The package should take less than 1 minute to install on a computer with the specifications recommended above.

The example dataset could be found at “example” folder. Check the “example/Readme” for details about the demo run.

Basic Usage

With a input 16S rRNA amplicon sequence file, e.g. sample1.fasta:

a. Profiling by Parallel-META using MIP database

PM-parallel-meta -r sample1.fasta -D P -f F -o sample1.out

The “sample1.out” folder is the profiling result.

b. Parse out the microbial index of pathogenic bacteria

PM-parse-mip -i sample1.out/classification.txt -o sample1.mip

The output contains 5 files：

sample1.mip.summary.out: The overall MIP;
sample1.mip.taxa.out: The relative abundance of species contributed to the overall MIP (MIP LV1);
sample1.mip.OTU.Abd.out: The relative abundance of reference OTUs contributed to the overall MIP (MIP LV1);
sample1.mip.infection.out: Human diseases associated with the identified pathogenic bacteria (MIP LV2);
sample1.mip.site.out: Targeted human organs or body sites (MIP LV3).

Batch Processing

MIP also supports the batch input of profiling results by the following alternative two forms (compatible with Parallel-META 3):

a. Sample list

PM-parse-mip -l samples.list -o samples.mip

in which parameter “-l” assigns the file list of profiling results of multiple samples. The format of a sample list:

Sample1	/home/data/sample1.out/classification.txt
Sample2	/home/data/sample2.out/classification.txt
...	
SampleN	/home/data/sampleN.out/classification.txt

b. Abundance tables

PM-parse-mip -T samples.OTU.Abd -o samples.mip

in which parameter “-T” assigns the profiling result of OTU table of multiple samples. The format of a OTU table:

		OTU_1	OTU_2	OTU_3	…	OTU_M
Sample1		100	200	0	…	50
Sample2		0	300	600	…	100
…		…	…	…	…	60
SampleN		50	80	0	…	200

Example Dataset

Here we provide a demo dataset with profiling results of 20 microbiome. To run the demo, you can either run the script “Readme”:

cd example
sh Readme

or type the following command:

PM-parse-mip -l samples.list -o samples.mip