Gut bacteria reportedly fell with onset of acidosis (5)
I believe the answer is:
flora
'gut bacteria' is the definition.
'reportedly fell with onset of acidosis' is the wordplay.
'reportedly fell' becomes 'flor' (I am not sure about this - if you are sure you should give a lot more credence to this answer).
'with' means one lot of letters go next to another.
'onset of' indicates taking the first letters.
The first letter of 'acidosis' is 'a'.
'flor'+'a'='FLORA'
(Other definitions for flora that I've seen before include "growing flowers" , "__ MacDonald, heroine of the 1745 Jacobite rising" , "vegetation" , "A region's plants" , "Plants collectively" .)