Eight nonlactating Danish Holstein cows were fed a control diet with a forage-to-concentrate ratio of 78:22 (DM basis) for several weeks, before a SARA challenge was conducted in 4 cows. This challenge was conducted by gradually substituting 45% of the DM of the control diet with pellets containing 50% wheat and 50% barley over a 4 d. Control cows received the control diet throughout. All cows were slaughtered after the SARA cows had received the full challenge for 2 d. Biopsies of epithelia were collected from different sites of the digestive tract. Extracted DNA from these biopsies were analyzed using MiSeq Illumina sequencing of the V4 region of the bacterial 16S rRNA gene. Rarefaction analysis was performed on observed species and Chao1 estimates of species richness and Shannon estimate of evenness at an even sequencing depth of 8000 per sample. The SARA challenge reduced (P < 0.01) the mean daily rumen pH from 6.6 to 5.8, and increased (P < 0.01) the duration of the rumen pH below 5.6 from 15 to 509 min/d, and the daily average rumen concentration L-lactate from 0.45 to 27.57 nmol/L, without affecting this concentration of total VFA. The challenge decreased the α-diversity along the digestive tract, with the exception of the middle jejunum. Principal coordinate analyses (PCoA) of weighted UniFrac distances and hierarchical clustering of the abundant taxa (>0.1%) revealed distinct clustering patterns (P < 0.05) by diet for all sites. On the rumen epithelium, the challenge increased (P < 0.05) the relative abundance of Streptococcaceae, Bifidobacterium and Lactobacillales taxa, whereas it reduced (P < 0.05) Clostridia, Butyrivibrio, Ruminoccocus, Bacteroidales and Fibrobacter taxa. In conclusion, the challenge caused mostly adverse changes in epimural microbiota throughout the digestive tract. Table 1.

	Shannon				Chao1				Observed species
	Control	SARA	P-value		Control	SARA	P-value		Control	SARA	P-value
Rumen	8.74	6.09	0.04		2,991	1,196	0.001		1,603	733	0.001
Duodenum	8.24	6.37	0.05		1,049	838	0.68		837	617	0.31
Jejunum, prox.	7.96	5.77	0.04		888	577	0.88		720	465	0.92
Jejunum, middle	7.52	6.55	0.22		612	675	0.88		509	525	0.91
Jelunum, distal	7.01	4.79	0.04		805	492	0.05		618	345	0.001
Ileum	7.61	4.98	0.01		999	713	0.001		766	501	0.001
Cecum	8.46	5.77	0.21		2,666	1,238	0.001		1,468	722	0.001
Colon	8.48	6.01	0.02		2,405	993.4	0.001		1,388	603	0.005