Table 3.

Estimated fold changes, 95% confidence intervals [], and p- values of significant interactions from the Gut Microbiotassay

Primer set	Gut section: status estimate (ileum, diarrhoeic)	Gut section: status estimate (colon, diarrhoeic)	Gut section: status p- value	Status: age estimate, day 3	Status: age estimate, day 4	Status: age estimate, day 5	Status: age estimate, day 6	Status: age estimate, day 7	Status: age estimate, mean age	Status: age p -value
Family Clostridium cluster I	0.07 [0.01,0.31]	0.27 [0.04,1.39]	0.01							NS
Species Cl. perfringens	0.33 [0.13,0.80]	1.41 [0.51,3.16]	0.04							NS
Phylum Bacteroidetes	1.00 [0.39,2.42]	0.12 [0.05,0.26]	0.0009							NS
Genus Bacteroides	0.73 [0.13,0.80]	0.20 [0.08,0.43]	0.04							NS
Class Beta- and Gammaproteobacteria			NS	3.12	5.63	10.21	18.60	34.37	4.52 [5.05,11.64]	0.0007
Family Enterobacteriaceae			NS	1.81	3.80	8.07	17.29	38.07	4.52 [3.19,9.69]	<0.0001
Species E. coli			NS	1.98	4.38	9.81	22.42	53.95	4.47 [3.39,11.85]	0.0004

This table is an extension of Table 2, and the estimated fold changes are the estimates of the exponentiated effect parameter.