Wow. 113 mb is huge. May I ask how many samples and how many OTUs?
Sorry to be so nosy. Part of the reason I ask is that you mentioned you are using fasta + qual files. These are common formats for 454 data, which is error prone, which could lead to more 'noise' or 'error' OTUs, which could lead to a large .biom table.
Thanks for telling me more about your project. Let me know how I can help,