Table 1.

Summary statistics of sequences analysed including average OTU numbers detected and microbial diversity covered. For each chicken breed or line, the sequencing reads of all three primer pairs were merged and OTUs were clustered at > 97% similarity using QIIME

Location	Breed/line	Total sequences	Av. sequences/ sample	Av. no. OTUs	Average microbial diversity covered (% Good’s coverage)
1	Aseel	839,375	55,958	1134	94.6
	Kadaknath	1,042,538	69,503	816	95.9
	Cobb400	679,158	45,277	1273	94.1
2	Aseel	2,775,511	185,034	735	95.7
	Kadaknath	2,548,471	164,390	833	95.6
	Ross 308	2,465,845	169,898	645	97.0