#8 · Tools & infrastructure
Curated microbial genome and metagenome resources support strain, plasmid and metabolic…
The dominant thread is curated, reusable reference infrastructure organizing microbial genomes and metagenomic data by host or environmental context. BacMap 3.0 integrates annotated bacterial and archaeal genomes, AnnelidaDB couples multi-omic data and symbiont genomes for 1121 annelid species, and CAnDi catalogues anaerobic digestion microbiomes. PLATE applies this model to 4,690 food metagenomes, producing plasmid contig catalogs with host, taxonomy and AMR annotations. The preprints are more heterogeneous but add inference on top of such data: SYMBIO-SCAN uses full-length long-read 16S for beetle symbiont detection, 550 soil MAG-derived metabolic models support FBA predictions of conserved amino acid fermentation fluxes, and sourmash benchmarks report gene content recovery with F1 of 0.942-0.998 on long-read metagenomes.
Published papers
BacMap 3.0: a comprehensive knowledgebase of annotated bacterial genomes.
BacMap 3.0 (https://bacmap.ca) is a comprehensive, freely accessible resource integrating 23 524 bacterial and archaeal species, 32 866 genomes, >100 million ge
AnnelidaDB: a comprehensive platform of taxonomic and multi-omic resources across annelids.
AnnelidaDB is a species-centred database integrating genomes, transcriptomes, proteomes, epigenomes, single-cell data and symbiont genomes for 1121 annelid…
CAnDi: a global catalogue of anaerobic digestion microbiomes.
Methanogenic environments harbour complex prokaryotic consortia that drive the anaerobic conversion of organic matter into methane and carbon dioxide.
Preprints
SYMBIO-SCAN, a full-length 16S rRNA gene-based workflow optimized for bacterial symbiont detection and discovery from long read sequencing
SYMBIO-SCAN is a long-read full-length 16S rRNA workflow for detecting bacterial symbionts in beetles, validated on a mock community and revealing novel…
Genome-scale metabolic models reveal phylogenetic conservation of amino acid fermentation-linked metabolic traits in soil bacteria
Presents 550 genome-scale metabolic models from soil MAGs across the US; FBA predicts conserved amino acid and fermentation fluxes, identifying candidate…
PLATE: a global atlas of food metaplasmidomes
PLATE is a curated global resource of 4,690 food metagenomes yielding plasmid contig catalogs with metadata, host, taxonomy, and AMR/functional annotations.
Sourmash accurately profiles strains from long-read metagenomes preserving gene content
Benchmarks sourmash k-mer sketch profiling on long-read metagenome mock communities, finding strain ID, gene content recovery (F1 0.942-0.998), and abundance…
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