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

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

Cilantro sample FL8Ka MI2Ja NY7Ja MI6Fb,f NY3Fc OH6Fc,f
Time point T0d, T24e, 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
BLASTng
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
  1. aCilantro sample culture positive for SalC 102
  2. bCilantro samples culture positive for SalC 13
  3. cCilantro samples culture positive for SalC 77
  4. dT0 = time zero
  5. eT24 = 24-hour
  6. fSubsets of a single cilantro samples are indicated by S1 S2 and S3
  7. gBolded numbers indicate results with S. enterica isolate cultured from the cilantro