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

Table 4 Genes significantly up-regulated in E. coli O157:H7 EDL933 in samples with microbiota compared to those without microbiota

Locus (Z #)	Gene name	Mean of normalized counts	FC^a	adj. p ^b	Function or product
Antibiotic resistance
2169	marB	78	2.6	8.2E-06	Conserved hypothetical protein associated with multiple antibiotic resistance operon
2170	marA	133	2.1	2.1E-05	DNA-binding transcriptional dual activator of multiple antibiotic resistance
Response to stress
2478	pspD	74	2.6	2.2E-05	Peripheral inner membrane phage-shock protein
Hypothetical proteins
1402	ymcB	102	2.1	0.0004	Conserved hypothetical protein
2695	ydhS	1115	2.0	0.0001	Conserved hypothetical protein; putative FAD/NAD(P)-binding domain
2774	ydjR	206	2.3	0.0004	Conserved hypothetical protein
3175	yeeE	143	2.8	1.7E-07	Conserved hypothetical protein; putative inner membrane protein
5712	yjcZ	173	2.1	0.0002	Conserved hypothetical protein
Other up-regulated genes
0043	caiC	204	2.0	0.0005	Putative crotonobetaine CoA ligase:carnitine CoA ligase
1987	ldrB	176	2.0	0.001	Fragment of small toxic polypeptide (partial)
3266	yegX	100	2.3	0.0002	Putative membrane-bound hydrolase
3660	yfeA	3551	2.0	2.9E-05	Putative diguanylate cyclase

^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 passed the filter are shown on this table. Expected genes to be differentially expressed due to the possibility of spurious alignment, and crosstalk between the reference genome and other similar genomes identified at genus level by 16S meta-genomic analysis, were discarded from this study (For discarded genes see Additional file 8: Table S8)
^bAdjusted p-value for multiple testing with the Benjamini-Hochberg procedure which controls FDR

ISSN: 1471-2164