[dsugarman]

I've worked on some metagenomics projects in the past, I admit I don't know too much about uBiome, but what I do know is that it is really hard to figure out what bacteria, archaea and fungi are in a given stomach.

consider that you can only cultivate a very small % of bacteria and archaea which means you can only find the genome of a given species that is living in a natural environment (often a very extreme environment). to figure out the genome, you have to sequence them all at the same time, but you can only read 1k-2k base pairs at one time, which means you need to bin these sequences into what you (educatedly) guess is the right organism and then sequence the genome. overtime, our understanding of these genomes should increase but I wonder what the current provable accuracy is using uBiome.

[sakai]

16S reads should be fine for basic characterization. The bioinformatics tools for sequence classification of short reads from a full sequencing run have also improved dramatically recently. Especially in terms of speed (100-1000X improvements).

(Plug) I just launched a site last week that demos this and links to a few other academic works in the field (check the FAQ): https://helix.io

[aroch]

They're doing 16S sequencing, so short reads are fine and still diagnostic