As @andresrcs says, it's difficult to follow what you intend since there's so much code, but let me see if I understand a little about what your difficulty is:
It seems that to apply your analysis, you need two tables, one a table you call 'Family', which contains bacteria counts from several samples, and a second table you call 'Metadata' which contains non-count information about the samples, like when they were taken.
Is what you want a table like your 'Family' table, but, say, only with count data from the month of July?
Unrelated to your question, I noticed a couple of things I wasn't sure about. One is that 'Family' contains two columns with the same name (at the least the one you gave with tribble()), and the other is that the calculations intended to remove rare bacteria don't match the verbal instructions for removing them.