Metagenomic Characterization of Poultry Cloacal and Oropharyngeal Swabs in Kenya Reveals Bacterial Pathogens and Their Antimicrobial Resistance Genes

Table 3

OTUs (0.05% coverage) and diversity indices from cloacal samples from different poultry species.

Sample	Number of observed OTUs	Chao1	ACE	Shannon	Inverse Simpson
CNP1	35	38.00	40.23	2.548	8.310
CNP2	12	13.00	16.09	1.261	2.544
CNP4	11	11.00	11.69	1.146	2.414
CNP5	23	25.50	27.06	1.244	2.245
CNP6	31	35.20	35.12	1.929	4.112
DKP1	27	27.33	29.03	2.498	7.513
DKP2	32	32.50	33.68	2.009	4.195
DKP4	23	23.00	23.88	1.761	2.989
GSP1	43	58.60	55.18	2.150	5.237
GSP2	18	18.00	18.42	1.651	2.985
GFP1	23	23.60	25.37	1.612	2.852
PNP2	3	3.00	3.00	0.405	1.294
PNP3	3	3.00	NaN	0.913	2.198
TYP1	17	17.50	17.75	1.939	5.419
Total	301