KAUST Metagenomic Analysis Platform (KMAP), Enabling Access to Massive Analytics of Re-Annotated Metagenomic Data.

Abstract

Exponential rise of metagenomics sequencing is delivering massive functional environmental genomics data. However, this also generates a procedural bottleneck for on-going re-analysis as reference databases grow and methods improve, and analyses need be updated for consistency, which require acceess to increasingly demanding bioinformatic and computational resources. Here, we present the KAUST Metagenomic Analysis Platform (KMAP), a new integrated open web-based tool for the comprehensive exploration of shotgun metagenomic data. We illustrate the capacities KMAP provides through the re-assembly of ~27,000 public metagenomic samples captured in ~450 studies sampled across ~77 diverse habitats, resulting in 36 new habitat-specific gene catalogs, all based on full-length (complete) genes. Extensive taxonomic and gene annotations are stored in Gene Information Tables (GITs), a simple tractable data integration format useful for analysis through command line or for database management. KMAP facilitates the exploration and comparison of microbial GITs across different habitats with over 275 million genes.

Phylogeny analysis of whole protein-coding genes in metagenomic data detected an environmental gradient for the microbiota

“…Therefore, metagenomic shotgun sequencing analysis can detect unique metabolic pathways, new species, and novel functional genes in addition to taxonomic identification. These multidimensional data have been integrated into publicly available databases such as KEGG (Kyoto Encyclopedia of Genes and Genomes) [ 8 ], MAPLE (microbiome analysis pipeline) [ 9 ], and KMAP (KAUST metagenomic analysis platform) [ 10 ] for functional analysis.…”