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Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt.
Gavin M Douglas1, Robert G Beiko2, Morgan G I Langille3,4
1Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.
Methods in Molecular Biology (Clifton, N.J.)
|October 10, 2018
Summary
Marker-gene sequencing offers a cost-effective way to profile microbial communities. The PICRUSt tool infers functional genes from marker gene sequences, enabling predictions of community functional potential.
Area of Science:
- Microbial ecology
- Bioinformatics
- Genomics
Background:
- Marker-gene sequencing is a cost-effective method for microbial community taxonomic profiling.
- It does not directly reveal functional genes, unlike metagenomics.
- Inferring function from marker genes is possible using reference genomes.
Purpose of the Study:
- To describe the PICRUSt method for predicting functional gene abundances from marker gene data.
- To explain how to use PICRUSt for inferring microbial community functional potential.
- To detail the ancestral state reconstruction approach used in PICRUSt.
Main Methods:
- Utilizes a reference phylogeny including taxa with and without sequenced genomes.
- Employs a modified ancestral state reconstruction (ASR) method to infer functional categories.
- Leverages sequence similarity to reference genomes for functional inference.
Main Results:
- PICRUSt predicts functional category abundances based on input marker gene data.
- Inferred functional profiles can be cross-referenced with other datasets.
- This enables rapid generation of predictions for community functional potential.
Conclusions:
- PICRUSt provides a valuable approach to predict microbial community functional potential from marker gene data.
- The method enhances the utility of cost-effective marker-gene sequencing.
- This facilitates deeper insights into microbial community functions.
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