“…Only Bacteroides, Roseburia, and Blautia oligotype patterns were significantly affected by treatment. After the initial round of oligotyping, high-entropy positions were chosen (-C option): 2, 27, 30, 31, 32, 94, 114, 120, and 291 (Bacteroides); 1,2,12,27,28,30,56,57,58,61,82,101,103,157,160,170,172,174,176,184,191,213,215,220,235,237,273,274,293,343,347,371, and 409 (Blautia); and 2, 28, 57, 215, 272, 369, 370, 409, and 410 (Roseburia). To minimize the impact of sequencing errors, we required an oligotype to be represented by at least 100 reads (-M option).…”