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

Table 4

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

Sample	Number of observed OTUs	Chao1	ACE	Shannon	Inverse Simpson
CNP7	14	14.33	15.46	1.367	3.144
CNP8	40	42.63	45.61	2.742	9.568
CNP9	28	35.50	32.88	1.810	3.072
CNP12	11	11.20	12.61	0.501	1.263
DKP5	38	53.00	49.56	2.267	5.232
DKP6	14	14.33	14.90	0.386	1.143
GFP2	20	20.00	20.00	1.674	2.985
GSP3	29	36.50	33.04	2.141	5.608
GSP4	47	54.33	57.58	2.420	7.230
PNP4	5	5.00	5.00	0.416	1.262
PNP5	7	7.00	8.243	1.276	3.157
PNP6	4	4.00	NaN	0.9769	2.372
TYP2	18	28.00	23.40	1.6760	3.767
Total	275