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‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets

The ISME Journal (2018) | Download Citation

Abstract

The combined effect of mutual association within the co-inhabiting microbes in human body is known to play a major role in determining health status of individuals. The differential taxonomic abundance between healthy and disease are often used to identify microbial markers. However, in order to make a microbial community based inference, it is important not only to consider microbial abundances, but also to quantify the changes observed among inter microbial associations. In the present study, we introduce a method called ‘NetShift’ to quantify rewiring and community changes in microbial association networks between healthy and disease. Additionally, we devise a score to identify important microbial taxa which serve as ‘drivers’ from the healthy to disease. We demonstrate the validity of our score on a number of scenarios and apply our methodology on two real world metagenomic datasets. The ‘NetShift’ methodology is also implemented as a web-based application available at https://web.rniapps.net/netshift

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Acknowledgements

We acknowledge Mr. Pramod Nanadikar and Mr. Govind Gopal for their help in deploying the web application. We also acknowledge Dr. Anirban Dutta and Dr. Swadha Anand for their help in preparing the figures and proofreading the manuscript. Kuntal Kumar Bhusan is an industry sponsored PhD student at Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory (NCL), Pune 411008 (India) and would like to acknowledge the Academy of Scientific and Innovative Research (AcSIR) and NCL for its support.

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    • Pranjal Chandrakar

    Present address: Decision Sciences, Indian Institute of Management Bangalore, Bannerghatta Road, Bengaluru, Karnataka, 560076, India

Affiliations

  1. Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India

    • Bhusan K. Kuntal
    • , Pranjal Chandrakar
    • , Sudipta Sadhu
    •  & Sharmila S. Mande
  2. Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory Campus, Pune, 411 008, India

    • Bhusan K. Kuntal

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The authors declare that they have no conflict of interest.

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Correspondence to Sharmila S. Mande.

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DOI

https://doi.org/10.1038/s41396-018-0291-x

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Enrolled as an industry sponsored PhD candidate: Bhusan K. Kuntal