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. Beyond being key to the global carbon cycle, such processes have been steered into powerful biotechnologies for energy production in bioreactors. Decoding the functional and taxonomic landscape of these communities requires comprehensive surveys, including bacteriophages and plasmids, which, however, remain vastly underrepresented in current databases. Here, we present the microbial Catalogue of Anaerobic Digestion (CAnDi), a database comprising 36 480 prokaryotic genomes spanning 11 149 species recovered from 1256 metagenomic samples collected across bioreactors worldwide. The reconstructed metagenomes also encode ∼1.9 million viral and over 130 000 plasmid sequences. Identity clustering revealed ∼536 000 candidate viral species, of which 85% are novel relative to existing databases, as well as over 15 000 unique plasmids. Clusters of viral and plasmid proteins were generated de novo, totalling 1 721 182 and 123 813 distinct protein families, respectively. Together, these resources substantially advance previous systematic approaches to characterize anaerobic digestion microbiomes, providing an expanded foundation for investigating the ecological and evolutionary roles of the virome and plasmidome in methane-producing ecosystems. CAnDi is accessible via https://www.candi-db.org/.