RNA was extracted from clarified fecal suspensions using four different commercial protocols. Samples were extracted in parallel to eliminate storage related differences [19] . Extractions were performed according to manufacturers' instructions except that RNA was extracted from 50 ml of stool suspension for all four protocols with addition of respective suspension buffer to reach the recommended aqueous volumes listed above. The RNA was stored at 270uC pending analysis and between analyses (See Fig. S2 ). Samples 1 to 93 were also extracted by protocol D as above, except that exogenous MS2 was omitted from the lysis buffer.