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. A small subset of these metagenomic assemblies is used in this pilot study grouped into 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 pilot study provides the exploration and comparison of microbial GITs across different habitats with over 275 million genes. KMAP access to data and analyses is available at https://www.cbrc.kaust.edu.sa/aamg/kmap.start.

Phylogeny-metabolism dual-directed single-cell genomics for dissecting and mining ecosystem function

“…From the KMAP metagenomic database which includes MAG-derived genes of diverse environments (including marine, soil, rhizosphere, lake, wastewater, saltmarsh, etc ( 69, 70 )), a search for CYP236A P450 subfamily enzymes revealed only eight such genes, and they all originated from seawater, marine sediment or freshwater ( Table S5 ). Moreover, from the Ocean Microbial Reference Catalog v2 (OM-RGC.v2; ( 71 )) and Ocean Gene Atlas v2.0 116 ( Fig.…”

“…( ii ) The sequences of P450 PsFu (in SAG m1 and m7), P450 ZoGa (WP_013995999.1) and P450 FoAg (WP_038530297.1) were compared using MAFFT v7.508 ( 111 ) and visualized using the R package ggmsa (https://cloud.r-project.org/package=ggmsa). ( iii ) The CYP236A P450 subfamily proteins were searched in the environmental metagenomic databases of KMAP ( 69 ) and OM-RGC.v2 ( 71 ) using P450 PsFu as the query. Initially, candidate CYP236A proteins were selected based on homology comparisons using blastp ( 113 ) or diamond blastp ( 114 ); then, the sequence identities between P450 PsFu and all candidate CYP236A proteins were calculated using ggsearch36 ( 115 ); finally, proteins in the CYP236A P450 subfamily were filtered out (with a criterion of protein identities > 55%) using custom scripts.…”