Changes in the colon microbiota and intestinal cytokine gene expression following minimal intestinal surgery

Table 1 List of primer sequences and Universal ProbeLibrary combinations used in this study

Primer	Sequence 5’ to 3’	UPL Probe
RPL32 Forward	AACTGGCCATCAGGGTCAC	#64
RPL32 Reverse	CACAACTGGAACTCCTGTCTATTC
TNF Forward	TTGTCGCTACATCGCTGAAC	#32
TNF Reverse	CCAGTAGGGCGGTTACAGAC
IL1β Forward	CCAATTCAGGGACCCTACC	#19
IL1β Reverse	CATGGCTGCTTCAGAAACCT
IL18 Forward	ACTTTACTTTGTAGCTGAAAACGATG	#85
IL18 Reverse	TTTAGGTTCAAGCTTGCCAAA
IL12 Forward	GAGGGTGAGTGAGTGCCTTG	#62
IL12 Reverse	ACTCCGCCTAGGTTCGACTT
IL8 Forward	TTCTTCTTTATCCCCAAACTGG	#41
IL8 Reverse	CCACATGTCCTCAAGGTAGGA
IL6 Forward	TGAACTCCCTCTCCACAAGC	#7
IL6 Reverse	GGCAGTAGCCATCACCAGA
IL10 Forward	TCCAGTTTTACCTGGAAGACG	#8
IL10 Reverse	CCTTGATATCCTCCCCATCA

Table 2 Relative abundance of bacterial species at the family level in colonic content samples obtained from no-surgery control animals (n = 6) or animals who have undergone a transaction surgery (n = 5)

Phylum level	Family level	Control (Rel. Abundance)	Transection (Rel. Abundance)	P value
Proteobacteria	Enterobacteriaceae	22.95 + 5.27	2.07 + 0.72a	0.0104
	Desulfovibrionaceae	2.89 + 1.26	2.95 + 1.16	0.9716
	Moraxellaceae	0.69 + 0.55	8.81 + 8.72	0.4501
	Pseudoalteromonadaceae	0.55 + 0.43	1.42 + 1.42	0.5844
	Vibrionaceae	0.52 + 0.37	6.03 + 5.91	0.4038
Bacteriodetes	Rikenallaceae	6.00 + 1.87	3.70 + 1.31	0.3416
	Porphyromonadaceae	2.33 + 0.76	4.50 + 1.78	0.3080
	Prevotellaceae	2.76 + 0.39	8.05 + 2.60	0.1105
	Bacteroidaceae	2.54 + 0.56	0.86 + 0.43a	0.0432
Firmicutes	Ruminococcaceae	19.97 + 2.01	15.26 + 4.71	0.3962
	Veillonellaceae	14.19 + 4.12	22.40 + 7.73	0.3834
	Lachnospiraceae	7.63 + 2.31	6.19 + 2.00	0.6475
	Peptostreptococcaceae	3.19 + 1.06	1.52 + 1.08	0.2991
	Erysipeolotrichales Incertae Sedis	1.78 + 0.61	1.03 + 0.53	0.3809
	Clostridiaceae	1.45 + 0.35	0.73 + 0.36	0.1843
	Lactobacillaceae	1.09 + 0.45	1.58 + 0.83	0.6197
	Streptococcaceae	0.13 + 0.06	1.56 + 1.54	0.4056
Actinobacteria	Micrococcinea	0.07 + 0.07	1.54 + 1.54	0.3926
Fusobacteria	Fusobacteriaceae	0.98 + 0.44	3.85 + 3.09	0.4079
Spirochaetes	Spirochaetaceae	1.83 + 1.15	0.09 + 0.08	0.1898
Other		6.49 + 1.09	5.84 + 1.41	0.7245

Data are expressed as mean + SEM (%).

^aP < 0.05 vs control. Bacterial species whose relative abundance was < 1% in both the control and transaction surgery group are compiled within the “other” category. Significant changes in bacteria whose relative abundance was < 1% are detailed within the text.

Table 3 Relative abundance of bacterial species at the genus level in colonic content samples obtained from no-surgery control animals (n = 6) or animals who have undergone a transaction surgery (n = 5)

Phylum	Genus level	Control (Rel. Abundance)	Transection (Rel. Abundance)	P value
Proteobacteria	Members of the Enterobacteriaceae	29.20 + 6.74	2.88 + 1.08a	0.0108
	Desulfovibrio	2.08 + 0.68	2.74 + 0.78	0.5389
	Bilophila	1.48 + 0.81	1.13 + 0.95	0.7847
	Psychrobacter	0.90 + 0.72	9.13 + 9.01	0.4136
	Vibrio	0.62 + 0.46	5.89 + 5.70	0.4105
	Pseudoalteromonas	0.15 + 0.12	1.47 + 1.47	0.4192
Bacteriodetes	Alistipes	4.82 + 1.73	0.18 + 0.13a	0.0441
	Prevotella	3.61 + 0.59	11.11 + 3.68	0.1110
	Bacteroides	3.25 + 0.71	1.24 + 0.63	0.0625
	Parabacteroides	2.88 + 0.65	5.59 + 2.41	0.3313
	Lachnospitaceae Incertae sedis	2.50 + 1.02	1.10 + 0.47	0.2548
Firmicutes	Megasphaera	9.71 + 3.87	14.18 + 4.01	0.4434
	Phascolartobacterium	4.07 + 1.00	6.90 + 1.89	0.2330
	Rumminococcaceae Incertae sedis	2.94 + 0.71	1.78 + 0.47	0.2106
	peptostreptococcaceae incertae sedis	2.79 + 1.23	1.80 + 1.49	0.6208
	Subdoligranulum	2.49 + 0.99	1.28 + 0.57	0.3264
	Acidaminococcus	2.40 + 0.71	3.53 + 1.82	0.5866
	Erysipelotrichales incertae sedis	2.28 + 0.77	1.48 + 0.78	0.4859
	Lactobacillus	1.96 + 0.74	2.15 + 1.16	0.8958
	Clostridium	1.86 + 0.45	1.05 + 0.52	0.2732
	Anaerotruncus	2.23 + 0.71	0.97 + 0.31	0.1501
	Oribacterium	0.63 + 0.25	1.88 + 0.88	0.2341
	Lactococcus	0.06 + 0.06	1.60 + 1.58	0.3860
	Mitsuokella	0.05 + 0.05	1.90 + 1.82	0.3664
Actinobacteria	Microccoccaceae	0.07 + 0.07	1.38 + 1.38	0.3959
Fusobacteria	Fusobacterium	1.27 + 0.60	5.43 + 4.39	0.3986
Spirochaetes	Treponema	2.29 + 1.44	0.13 + 0.11	0.1951
Uncult. Clone	EU774397	1.43 + 0.73	0.05 + 0.05	0.1178
	AF371921	1.43 + 0.47	2.18 + 0.99	0.5217
	AF371920	0.24 + 0.14	1.11 + 0.79	0.3315
Other		8.05 + 0.69	6.66 + 1.21	0.3549

Data are expressed as mean + SEM (%).

^aP < 0.05 vs control. Bacterial species whose relative abundance was < 1% in both the control and transaction surgery group are compiled within the “other” category. Significant changes in bacteria whose relative abundance was < 1% are detailed within the text.