TABLE 8.

DESeq2 analysis of the operational taxonomic units (OTUs) that showed the most significant (A) increase, or (B) decrease, in abundance from the neat inocula to the end of the first 48 h fermentation (CBC1) for Experiment 2.

A)		Increased from neat inoculum to end of CBC1
		Genus	Foldchangea	P−valueb
	OTU 2	Fibrobacter	9.79	< 0.001
	OTU 7	Ruminococcus 1	6.63	< 0.001
	OTU 9	Anaeroplasma	6.18	< 0.001
	OTU 4	Pseudobutyrivibrio	5.45	< 0.001
	OTU 19	Bacteroidales S24-7 group unclassified	9.01	< 0.001
	OTU 1	Fibrobacter	6.54	< 0.001
	OTU 47	Bacteroidales S24-7 group unclassified	6.56	< 0.001
	OTU 28	Prevotella 1	4.83	< 0.001
	OTU 6	Oribacterium	5.30	< 0.001
	OTU 61	Ruminococcus 1	5.20	< 0.001
(B)		Decreased from neat inoculum to end of CBC1
		Genus	Foldchangea	P−valueb
	OTU 35	Candidate division SR1 unclassified	–5.09	< 0.001
	OTU 127	Prevotella 1	–5.41	< 0.001
	OTU 119	[Eubacterium] coprostanoligenes group	–4.65	< 0.001
	OTU 130	Prevotella 1	–4.45	< 0.001
	OTU 196	Candidate division SR1 unclassified	–4.29	0.002
	OTU 125	Prevotella 1	–4.76	0.002
	OTU 328	Prevotella 1	–5.17	0.003
	OTU 226	Bacteroidales BS11 gut group unclassified	–4.31	0.003
	OTU 320	p-1088-a5 gut group	–4.99	0.003
	OTU 277	WA aaa01f12 unclassified	–4.41	0.004

^aLog2 fold change ^bP-values shown are corrected for multiple testing using the Benjamin-Hochberg correction.