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'NetShift': a methodology for understanding 'driver microbes' from healthy and disease microbiome datasets
Bhusan K Kuntal1,2, Pranjal Chandrakar1,3, Sudipta Sadhu1
1Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India.
The ISME Journal
|October 6, 2018
Summary
This study introduces NetShift, a method to analyze microbial association networks and identify key microbial drivers of disease. It quantifies network changes, offering new insights into human health and disease states.
Area of Science:
- Microbiology
- Bioinformatics
- Computational Biology
Background:
- Microbial communities significantly impact human health.
- Analyzing microbial taxonomic abundance is common for identifying disease markers.
- Inter-microbial associations are crucial for community-based health inferences.
Purpose of the Study:
- To introduce NetShift, a novel methodology for quantifying changes in microbial association networks.
- To develop a scoring system for identifying 'driver' microbial taxa associated with disease transitions.
- To provide a web-based application for accessible analysis of microbial network rewiring.
Main Methods:
- Development of the NetShift algorithm to quantify network rewiring and community shifts.
- Design of a scoring system to identify key microbial taxa driving transitions from healthy to disease states.
- Validation of the methodology using simulated scenarios and real-world metagenomic datasets.
Main Results:
- NetShift effectively quantifies microbial association network changes between healthy and disease states.
- The developed score successfully identifies significant microbial drivers.
- The methodology is applicable to real metagenomic data, providing actionable insights.
Conclusions:
- Quantifying changes in inter-microbial associations is essential for understanding health and disease.
- NetShift offers a robust approach to analyze microbial network dynamics.
- The tool facilitates the identification of microbial drivers, advancing microbiome research.