Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing

Table 2 Percent hits for BLASTn and MetaPhlAn analysis of cilantro shotgun metagenomes to Salmonella

Cilantro sample	FL8K^a		MI2J^a		NY7J^a		MI6F^b,f		NY3F^c	OH6F^c,f
Time point	T0^d,	T24^e,	T0	T24	T0	T24	S2_T24	S3_T24	T24	S1_T24	S2_T24	S3_T24
No. of samples in MiSeq run	1	1	6	6	6	6	2	2	1	6	6	6
Total reads	2,566,734	9,146,885	1,212,903	2,009,022	683,454	1,767,923	5,450,586	4,990,831	10,622,374	3,347,897	2,082,712	1,988,350
BLASTn^g
SalC 102 (Newport) (%)	2.383	16.135	0.008	1.042	0.029	0.145	3.959	1.377	0.227	0.128	0.084	0.183
SalC 13 (Newport) (%)	2.347	15.779	0.008	1.016	0.028	0.144	4.099	1.419	0.228	0.126	0.082	0.183
SalC 77 (Tennessee) (%)	1.785	11.994	0.008	0.788	0.024	0.139	3.061	1.077	0.215	0.110	0.074	0.214
SalC AVG (%)	2.172	14.636	0.008	0.949	0.027	0.143	3.706	1.291	0.223	0.121	0.080	0.193
MetaPhlAn
S. enterica (%)	4.870	13.658	0.000	0.000	0.000	0.000	4.282	1.790	0.000	0.000	0.000	0.000
Salmonella_unclassified (%)	14.626	34.269	0.000	7.770	0.000	0.000	15.717	6.490	0.000	0.000	0.000	0.448

^aCilantro sample culture positive for SalC 102
^bCilantro samples culture positive for SalC 13
^cCilantro samples culture positive for SalC 77
^dT0 = time zero
^eT24 = 24-hour
^fSubsets of a single cilantro samples are indicated by S1 S2 and S3
^gBolded numbers indicate results with S. enterica isolate cultured from the cilantro

ISSN: 1471-2180