Abstract
BackgroundKey aspects of microbiome research are the accurate identification of taxa and the profiling of their functionality. Amplicon profiling based on the 16S ribosomal DNA sequence is a ubiquitous technique to identify and profile the abundance of the various taxa. However, it does not provide information on their encoded functionality. Predictive tools that can accurately extrapolate the functional information of a microbiome based on taxonomic profile composition are essential. At present, the applicability of these tools is limited due to requirement of reference genomes from known species. We present IPCO (Inference of Pathways from Co-variance analysis), a new method of inferring functionality for 16S-based microbiome profiles independent of reference genomes. IPCO utilises the biological co-variance observed between paired taxonomic and functional profiles and co-varies it with the queried dataset.ResultsIPCO outperforms other established methods both in terms of sample and feature profile prediction. Validation results confirmed that IPCO can replicate observed biological associations between shotgun and metabolite profiles. Comparative analysis of predicted functionality profiles with other popular 16S-based functional prediction tools showed significantly lower performances with predicted functionality showing little to no correlation with paired shotgun features across samples.ConclusionsIPCO can infer functionality from 16S datasets and significantly outperforms existing tools. IPCO is implemented in R and available from https://github.com/IPCO-Rlibrary/IPCO.
Highlights
Key aspects of microbiome research are the accurate identification of taxa and the profiling of their functionality
The study of microbiome communities fundamentally falls under two strategies: the taxonomic composition is determined by either amplicon sequencing (16S marker gene) or metagenomic whole genome shotgun sequencing with the latter providing additional information on the functional capabilities which allows the identification of genes and pathways
No significant differences were observed for feature correlation using a reference size of at least 30% or larger in the KEGG pathway analysis and 50% or more for MetaCyc at the different taxonomic levels investigated
Summary
Key aspects of microbiome research are the accurate identification of taxa and the profiling of their functionality. Amplicon profiling based on the 16S ribosomal DNA sequence is a ubiquitous technique to identify and profile the abundance of the various taxa It does not provide information on their encoded functionality. Despite the availability of mWGS, amplicon sequencing still remains popular due to its relatively low cost, quicker computation time, lower disk space requirements, and ability to detect a diverse set of taxa, including those with a low abundance based only on the marker gene. Reviews of these two approaches have discussed both the advantages and disadvantages of these methods [3, 4]. The major limitation of PICRUSt comes forth in the case of 16S sequences, which do not have sequenced/
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