Make biom fails to correctly format taxonomic data.

[cErikson]

I have a problem with make_biom failing to create the correct format in the json for the taxanomic data.

I want my observation metadata to have the following format in the json.
{"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}

If I run the following code

rich_sparse_file = system.file("extdata", "rich_sparse_otu_table.biom", package = "biom")
biom_in=read_biom(rich_sparse_file)
counts=biom_data(biom_in)
taxa=observation_metadata(biom_in)
metadata=sample_metadata(biom_in)
biom_out=make_biom(counts,sample_metadata = metadata, observation_metadata = taxa)
write_biom(biom_out,'~/tmp/out.biom')

The result is not the same as the input.

{
 "id": "GG_OTU_5",
"metadata": {
 "taxonomy1": "k__Bacteria",
"taxonomy2": "p__Proteobacteria",
"taxonomy3": "c__Gammaproteobacteria",
"taxonomy4": "o__Enterobacteriales",
"taxonomy5": "f__Enterobacteriaceae",
"taxonomy6": "g__Escherichia",
"taxonomy7": "s__" 
} 

This is causing a number of programs such as phinch to fail to parse the biom file.