Table 4.

DEGs (up- or down-regulated) in different groups.

	Name	Length	Log2 Fold Change	Q-value	Product or description
TB vs. TF	fimH	1008	5.3012	1.39E−117	Adhesin
	fimF	519	4.3905	1.68E−64	Adhesin
	prpD	1452	3.0211	1.24E−40	2-methylcitrate dehydratase
	prpE	1887	2.9446	6.61E−43	Propionate–CoA ligase
	RS06450	993	1.9846	1.45E−34	RNA polymerase sigma factor RpoS
	RS02175	891	−8.4037	4.66E−101	Hypothetical protein
	RS21920	555	−8.1927	1.44E−289	Hypothetical protein
	RS02245	1272	−8.1116	0	Hypothetical protein
	fliA	720	−4.3271	4.90E−37	RNA polymerase sigma factor FliA
	flgK	1662	−3.2153	3.52E−25	Flagellar hook-associated protein 1
aTB vs. aTF	prpD	1452	5.8943	1.78E−44	2-methylcitrate dehydratase
	prpE	1887	5.2302	7.25E−38	Propionate–CoA ligase
	fimH	1008	3.6608	4.75E−130	Adhesin
	fimF	519	3.3435	1.076E−43	Adhesin
	RS06450	993	2.3788	1.76E−77	RNA polymerase sigma factor RpoS
	RS02245	1272	−7.2526	9.40E−245	Hypothetical protein
	RS02175	891	−6.2471	7.40E−77	Hypothetical protein
	RS02240	549	−6.1948	0	Hypothetical protein
	fliA	720	−2.3034	8.24E−05	RNA polymerase sigma factor FliA
	flgk	1662	−1.4816	8.66E−40	Flagellar hook-associated protein 1
aTF vs. TF	RS03030	282	4.254	8.84E−67	Outer membrane protein
	RS06065	411	3.7112	9.30E−74	Formate hydrogenlyase maturation protein HycH
	hycI	471	3.2794	9.20E−74	Hydrogenase 3 maturation endopeptidase HycI
	rbsC	966	2.8462	1.51E−32	Ribose ABC transporter permease
	RS06100	462	2.644	4.19E−51	Formate hydrogenlyase regulatory protein HycA
aTB vs. TB	RS06320	1119	2.813	3.45E−34	Invasion protein InvE
	RS00680	327	2.7514	5.43E−26	Type III secretion system chaperone SseA
	RS00655	417	2.4205	1.68E−13	Pathogenicity island 2 effector protein SseE
	RS00665	1455	2.3799	5.26E−16	Pathogenicity island 2 effector protein SseC