Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome

Table 2 This table shows the average clr-transformed abundances for select bacteria genera, chosen because they were found previously to associate with IBD

Genus	p-value	Control	IBD	UC	CD	Previous Association	Agreement
Clostridium	<0.001	3.785	4.898	4.397	5.331	Decreased in IBD	No
Ruminococcus	<0.001	2.895	-0.352	0.517	-1.102	Decreased in IBD	Strong
Lactobacillus	0.006	1.352	2.202	1.586	2.733	Decreased in IBD	No
Fusobacterium	0.012	-2.560	-1.866	-2.336	-1.460	Present in IBD	Strong
Bifidobacterium	0.097	3.179	3.417	4.262	2.686	Decreased in IBD	Mixed
Bacteroides	0.199	5.698	4.939	5.142	4.764	Decreased in IBD	Weak

Since abundance is expressed relative to the per-sample mean, positive values signify above-average presence for samples within that group. The evidence for previous association is taken from [42]. All p-values are FDR-adjusted. Two genera, Ruminococcus and Fusobacterium, show an association that agrees with past literature