MCycDB

MCycDB catalogs methane-cycling gene families and reference sequences to enable profiling and taxonomic assignment of methane metabolism across environmental microbiomes and linkages to carbon, nitrogen, sulfur, and metal biogeochemical cycles.

Key Features:

• Gene family coverage: Contains 298 methane cycling gene families spanning 10 distinct methane metabolic pathways.
• Sequence collection: Includes 610,208 representative sequences alongside reference sequences sourced from the NCBI RefSeq database.
• Taxonomic breadth: Covers 48 phyla and 2,197 genera, with specific representation of five bacterial phyla and 100 archaeal genera.
• Orthology integration: Integrates homologous groups identified from public orthology databases to reduce false positive assignments and improve specificity.
• Biogeochemical scope: Supports analysis of methane metabolism in the context of carbon, nitrogen, sulfur, and metal cycles.

Scientific Applications:

• Microbial community profiling: Enables profiling of methane-cycling microbial communities across diverse environmental samples.
• Methanogenesis detection: Has been used to identify abundance of methanogenesis-related gene families in hot spring sediments.
• Aerobic methane oxidation detection: Has been used to detect prevalence of aerobic methane oxidation genes in permafrost and peatland environments.

Methodology:

Compilation of representative sequences and reference sequences from NCBI RefSeq and integration of homologous groups from public orthology databases to reduce false positives and increase assignment specificity.