Mucosal healing progression after acute colitis in mice

Table 5 Mucosa-adherent microbiota composition and cecal bacterial metabolic activity

Parameter		d0	d7	d7 vs d0	d10	d10 vs d7	d13	d13 vs d10	d28	d28 vs d0	Statistical effect (time)
Total bacteria (log/g mucosal content)		9.36 ± 0.35	10.4 ± 0.14a	↑	9.92 ± 0.16b	↓	10.6 ± 0.22ac	↑	10.2 ± 0.24ac	↑	< 0.001
Shannon index		6.46 ± 0.07	4.75 ± 0.32a	↓	4.56 ± 0.28a	-	4.44 ± 0.26a	-	5.03 ± 0.29a	↓	< 0.001
Chao index		794 ± 55.2	633 ± 43.7a	↓	593 ± 31.1a	-	635 ± 34.4a	-	606 ± 51.6a	↓	< 0.01
Actinobacteria (%)
Bifidobacteriaceae		0.02 ± 0.01	0.01 ± 0.00	-	0.01 ± 0.01	-	0.00 ± 0.00	-	0.60 ± 0.28abcd	↑	< 0.001
Coriobacteriaceae		0.01 ± 0.02	0.04 ± 0.02	-	0.07 ± 0.04	-	0.06 ± 0.04	-	0.83 ± 0.31abcd	↑	< 0.001
Bacteroidetes (%)
Bacteroidaceae		4.35 ± 1.24	5.6 ± 1.34	-	11.55 ± 2.77b	↑	3.08 ± 1.08c	↓	20.1 ± 4.98cd	↑	< 0.05
Porphyromonadaceae		12.1 ± 2.55	7.40 ± 2.08	-	2.53 ± 1.29	-	1.03 ± 0.35ab	-	12.1 ± 5.18d	-	< 0.001
Prevotellaceae		1.06 ± 0.33	0.01 ± 0.00a	↓	0.01 ± 0.01a	-	0.02 ± 0.01a	-	0.01 ± 0.01a	↓	< 0.01
	Alloprevotella	1.04 ± 0.32	0.00 ± 0.00a	↓	0.01 ± 0.01a	-	0.01 ± 0.01a	-	0.00 ± 0.00a	↓	< 0.05
Rikenelleceae		9.64 ± 1.79	0.33 ± 0.24a	↓	0.33 ± 0.24a	-	0.31 ± 0.26a	-	2.04 ± 1.20a	↓	< 0.001
	Alistipes	9.48 ± 0.72	1.04 ± 0.51a	↓	0.24 ± 0.15a	-	0.13 ± 0.09a	-	1.98 ± 1.20a	↓	< 0.001
Deferribacterres (%)				↓
Deferribacteraceae	Mucispirillum	3.53 ± 1.86	9.98 ± 2.33a	↑	10.16 ± 3.04a	-	14.82 ± 2.80a	-	3.49 ± 0.76bcd	-	< 0.001
Firmicutes (%)
Clostridiaceae	Roseburia	0.80 ± 0.17	0.01 ± 0.00a	↓	0.01 ± 0.01a	-	0.01 ± 0.01a	-	0.03 ± 0.01a	↓	< 0.001
	Clostridium XIVa	6.07 ± 0.84	1.09 ± 0.35a	↓	5.56 ± 2.73b	↑	8.54 ± 2.80abc	↑	4.01 ± 1.64b	-	< 0.05
	Butyrivibrio	0.28 ± 0.21	0.00 ± 0.00a	↓	0.00 ± 0.00a	-	0.00 ± 0.00a	-	0.00 ± 0.00a	↓	< 0.01
Eubacteriaceae		0.17 ± 0.05	0.04 ± 0.02a	↓	0.00 ± 0.00a	-	0.00 ± 0.00a	-	0.00 ± 0.00a	↓	< 0.001
Lachnospiraceae		35.0 ± 4.85	13.5 ± 2.91a	↓	21.7 ± 4.25a	-	23.2 ± 4.49a	-	23.6 ± 4.69	-	< 0.01
	Acetitafactor	5.46 ± 1.47	1.28 ± 0.55a	↓	0.30 ± 0.13a	-	1.11 ± 0.63a	-	1.00 ± 0.63a	↓	< 0.001
Lactobacillaceae		0.42 ± 0.19	0.24 ± 0.12	-	3.41 ± 2.82	-	0.63 ± 0.26	-	1.44 ± 0.88	-	NS
Ruminococcaceae		24.7 ± 4.5	30.4 ± 6.4	-	18.2 ± 3.6b	↓	26.7 ± 4.0	-	21.1 ± 4.0	-	< 0.05
Proteobacteria (%)
Desulfovibrionaceae		1.94 ± 0.39	1.68 ± 0.32	-	3.06 ± 0.64	-	3.64 ± 0.95ab	-	1.30 ± 0.31d	-	< 0.01
Enterobacteriaceae		0.24 ± 0.04	14.38 ± 5.93a	↑	6.28 ± 2.59a	-	5.99 ± 3.80a	-	0.55 ± 0.16bcd	-	< 0.01
	Escherichia Shigella	0.05 ± 0.03	14.08 ± 5.83a	↑	6.02 ± 2.53a	-	5.47 ± 3.46bc	-	0.30 ± 0.11bc	-	< 0.01
Pseudomonadaceae		0.11 ± 0.04	0.06 ± 0.01	-	0.06 ± 0.02	-	0.18 ± 0.09	-	0.21 ± 0.12	-	NS
Sutterellaceae		0.05 ± 0.40	1.02 ± 0.42	-	2.87 ± 0.87	-	4.97 ± 1.93	-	7.39 ± 2.97	-	NS
Rhodospirillaceae		0.14 ± 0.05	0.51 ± 0.26a	↑	0.02 ± 0.02b	↓	0.00 ± 0.00b	-	0.04 ± 0.02b	-	< 0.001
Tenericutes (%)
Anaeroplasmataceae		0.23 ± 0.13	0.00 ± 0.00a	↓	0.00 ± 0.00a	-	0.01 ± 0.01a	-	0.00 ± 0.00a	↓	< 0.01
Total SCFA (µmol/g)		12.4 ± 1.63	1.13 ± 0.78a	↓	0.06 ± 0.04a	-	0.14 ± 0.07a	-	4.88 ± 1.08abcd	↓	< 0.001
	Acetate	8.95 ± 1.16	0.94 ± 0.67a	↓	0.04 ± 0.04ab	↓	0.14 ± 0.07ab	-	3.40 ± 0.71abcd	↓	< 0.001
	Propionate	1.93 ± 0.29	0.04 ± 0.04a	↓	0.00 ± 0.00a	-	0.00 ± 0.00a	-	0.90 ± 0.26abcd	↓	< 0.001
	Butyrate	1.51 ± 0.22	0.15 ± 0.11a	↓	0.01 ± 0.01a	-	0.00 ± 0.00a	-	0.59 ± 0.13abcd	↓	< 0.001

Quantification of total bacteria in the mucosa adherent microbiota was determined by real-time qPCR. Values are expressed as log of gene copy numbers of the different bacterial groups per gram of mucosal content. Evolution of the relative abundance of mucosa-adherent microbiota families was assessed by Illumina MiSeq sequencing. Cecal short chain fatty acids concentrations were obtained by gas chromatography after esterification. Values are means ± SE (n = 8-12).

^aP < 0.05 vs day 0;

^bP < 0.05 vs day 7;

^cP < 0.05 vs day 10;

^dP < 0.05 vs day 13. NS: Non-significant difference; SCFA: Short chain fatty acids.