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IPCO: Inference of Pathways from Co-variance analysis.

Mrinmoy Das1,2, Tarini Shankar Ghosh1,2, Ian B Jeffery3,4

  • 1APC Microbiome Ireland, University College Cork, Cork, Ireland.

BMC Bioinformatics
|February 20, 2020
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Summary

IPCO, a novel method, infers microbiome functionality from 16S data without reference genomes, outperforming existing tools. This advance aids microbiome functional profiling and discovery.

Keywords:
Co-varianceFunctionalityMicrobiomeNovel methodPrediction

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Area of Science:

  • Microbiome Research
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate microbiome analysis requires both taxonomic identification and functional profiling.
  • 16S ribosomal DNA sequencing is common for taxonomic profiling but lacks functional insights.
  • Current functional prediction tools often depend on reference genomes, limiting their scope.

Purpose of the Study:

  • To introduce IPCO (Inference of Pathways from Co-variance analysis), a novel method for inferring microbiome functionality from 16S data.
  • To develop a tool that does not require reference genomes for functional prediction.
  • To improve the accuracy and applicability of functional profiling in microbiome research.

Main Methods:

  • IPCO utilizes biological co-variance between paired taxonomic and functional profiles.
  • The method analyzes co-variance within the queried dataset for functional inference.
  • It is implemented in R for accessibility.

Main Results:

  • IPCO demonstrates superior performance in both sample and feature profile prediction compared to established methods.
  • Validation confirmed IPCO's ability to replicate biological associations observed in shotgun and metabolite profiles.
  • Existing 16S-based functional prediction tools showed significantly lower performance and correlation with shotgun data.

Conclusions:

  • IPCO effectively infers functionality from 16S datasets, surpassing current tools.
  • The method offers a genome-independent approach to microbiome functional profiling.
  • IPCO is available as an R package for broader scientific use.