Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study

Table 4 Differential abundance of members of the family Enterobacteriaceae in DA-DTT versus DA-U

	DA-DTT (n = 43) vs. DA-U (n = 112)
Taxonomy	Average relative abundance % DA-DTT^a	Average relative abundance % DA-U^a	Fold Change (calculated from the GLM)^b	P-value	FDR P-value
c_Gammaproteobacteria, o_Enterobacteriales, f_Enterobacteriaceae	19.193	6.068	5.46	5.13E-4	1.47E-3
f_Enterobacteriaceae, g_unknown	14.984	5.227	17.00	2.72E-8	1.21E-7
f_Enterobacteriaceae, g_Klebsiella	3.812	0.784	24.10	7.13E-7	2.73E-6
f_Enterobacteriaceae, g_Providencia	0.224	0.00025	13.57	< 0.0001	< 0.0001
f_Enterobacteriaceae, g_Morganella	0.018	0.006	36.71	1.18E-9	5.81E-9
f_Enterobacteriaceae, g_Salmonella	0.006	0.001	3.71	0.01	0.02

P-value< 0.05 and FDR P-value< 0.05 are shown in bold. ^aThe relative abundances were calculated from the original counts (number of sequences in the OTU table). ^bFold changes were calculated from the GLM, which corrects for differences in library size between the samples and the effects of confounding factors. It is therefore not possible to derive these fold changes from the original counts (number of sequences in the OTU table) by simple algebraic calculations

ISSN: 1471-2180