Hi,
I used dada2 for analyzing the 16S dataset and now I am trying to predict high-level phenotypes in the data using Bugbase. But while outputting the biom file I am facing some problems. I am not sure whether this is the correct forum for posting the question or not but any help will be appreciated.

Bugbase supports BIOM file in JSON format and with both counts and taxonomy. When I am trying to output biom file using package biomformat with both counts and taxonomy it is ouputting a file but not recognized by Bugbase. The code I am using for outputting the file is :

biom16S <- make_biom(count_tab16s, observation_metadata = tax_gg )
biom_file <- biom16S
outfile = tempfile()
write_biom(biom_file, outfile)

where count_tab16S is the count file with ASV IDS in rows and sample names in columns and tax_gg is the file with ASV IDS in rows and their hierarchy (from kingdom to Species) in columns.

May I get some help on where I am going wrong or what is the correct way to merge counts and taxonomic information from dada2 to a biom file?

Thanks,

Sandipan