I have just published a new script to transform an edge table in an OTU abundance table. Using this you can (if you so wish) transform the whole FoodMicrobionet dataset (or part of it) in a very large abundance table. A newer version of the script, which comes handy when using FMBN 2.0 edge tables and allows to generate files which can be used with the package Bipartite of R (more on this later) is available here. Be careful with this script, however, it must be run in pieces.