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Table 2 Genes significantly down-regulated in Escherichia coli O157:H7 EDL933 in samples with microbiota compared to those without microbiota

From: Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat

Locus (Z #) Gene name Mean of normalized counts FCa adj. p b Function or product
Nitrate metabolism and nitrite detoxification
 1107 hcp 270 −2.5 3.2E-08 Hybrid-cluster [4Fe-2S-2O] protein in anaerobic terminal reductases
Amino acid transport and metabolism
 0037 carA 369 −2.3 1.8E-07 Carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
 1090 artJ 1305 −4.0 8.4E-15 Arginine transporter subunit; periplasmic-binding component of ABC superfamily
 1093 artI 407 −2.0 0.0002 Arginine transporter subunit; periplasmic-binding component of ABC superfamily
 3181 hisG 221 −2.0 0.001 ATP phosphoribosyltransferase
 3569 hisM 208 −2.0 0.0008 Histidine/lysine/arginine/ornithine transporter subunit; membrane component of ABC superfamily
 4135 argA 737 −2.5 2.7E-07 Fused acetylglutamate kinase homolog (inactive); amino acid N-acetyltransferase
 4534 argG 972 −3.0 9.9E-12 Argininosuccinate synthetase
 5285 ilvC 773 −2.0 2.1E-05 Ketol-acid reductoisomerase. NAD(P)-binding
 5515 argE 448 −2.5 2.8E-09 Acetylornithine deacetylase
 5516 argC 1480 −3.7 1.4E-16 N-acetyl-gamma-glutamylphosphate reductase, NAD(P)-binding
 5517 argB 533 −2.8 1.1E-09 Acetylglutamate kinase
 5518 argH 1496 −2.5 7.2E-06 Argininosuccinate lyase
 5719 adiA 539 −2.1 0.001 Biodegradative arginine decarboxylase
 5866 argI 404 −2.5 0.0006 Ornithine carbamoyltransferase 1
bacterial pathogenicity
 3200 peR 739 −2.0 6.9E-05 Perosamine synthetase Per
  1. aFC is the fold change of the genes that exhibit significant (FC ≤ −2, false discovery rate (FDR) ≤ 0.005, minimum normalized read count = 10) differential expression. Only genes discussed in our study are shown on this table
  2. bAdjusted p-value for multiple testing with the Benjamini-Hochberg procedure which controls FDR