BIOM 2.1 with metadata structure updates are coming on June 30th
The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing counts of observations (e.g., OTUs, KO categories, lipid types) in one or more biological samples (e.g., microbiome samples, genomes, metagenomes).
Further details can be found at http://biom-format.org.