IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes

Abstract

The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source datasets include those generated by the DOE’s Joint Genome Institute (JGI), submitted by external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed through the IMG annotation pipeline and then loaded into the IMG data warehouse. IMG’s web user interface provides a variety of analytical and visualization tools for comparative analysis of isolate genomes and metagenomes in IMG. IMG/M allows open access to all public genomes in the IMG data warehouse, while its expert review (ER) system (IMG/MER: https://img.jgi.doe.gov/mer/) allows registered users to access their private genomes and to store their private datasets in workspace for sharing and for further analysis. IMG/M data content has grown by 60% since the last report published in the 2017 NAR Database Issue. IMG/M v.5.0 has a new and more powerful genome search feature, new statistical tools, and supports metagenome binning.

l‐Rhamnose catabolism in archaea

“…BlastP analyses were performed using the RefSeq and MGI/M databases (O’Leary et al , ; Chen et al , ). Sequence alignments were generated with ClustalX 2.1 using default parameters and are provided with ESPRIPT (Larkin et al , ; Robert and Gouet, ).…”

Geologic legacy spanning >90 years explains unique Yellowstone hot spring geochemistry and biodiversity

“…Following preliminary gene predictions and annotations for MAGs using Prodigal v.2.6.3, gene functions were further examined using the Kyoto Encyclopedia of Genes and Genomes (KEGG) function database (Kanehisa and Goto, ) using the KEGG Automatic Annotation Server (KAAS) (Moriya et al ., ). The results from the KAAS‐based analyses were also cross‐referenced against KEGG annotations after annotation of the assembled metagenome via the Joint Genome Institute (JGI) Integrated Microbial Genomes (IMG) pipeline (Chen et al ., ). MAGs were also queried via BLASTp for specific gene functions to screen for specified sulphur cycling functions, as guided by gene contents of closely related genomes.…”

Genome Sequence of Segmented Filamentous Bacteria Present in the Human Intestine

“…To verify that SFB-human-IMAG resides in the human intestine, we searched for it among published metagenomes from the human gut. The genome was first BLAST-searched against an integrated catalogue of reference genes in the human gut microbiome (IGC 9.9) 31 , which consists of 9.9 million genes assembled from 1,267 human faecal samples. Only fourteen of the IGC genes gave matches to the genome when requiring ≥95% identity and ≥70% of the IGC gene's bases aligned.…”