Effect of induced hindgut acidosis on gastrointestinal tract microbiome.

The objective was to determine the effects of induced hindgut acidosis in sheep on rumen, cecal, and fecal microbiome. Ruminally and cecally cannulated ewes [n = 11; body weight (BW) = 49 ± 4 kg] were assigned to one of two treatments: control (CON; n = 5) or induced hindgut acidosis (HGA; n = 6). To induce hindgut acidosis, 3 g wheat starch/kg BW per 24 h was continuously infused via the cecal cannula for 4 d. Control ewes received a constant infusion of deionized water. The diet contained 40% grass hay pellets, 35% whole shelled corn, 15% dried distillers grains, and 10% alfalfa cubes. On d 0, 2, and 4, immediately before feeding, and 12 h after feeding, rumen fluid, cecal fluid, and fecal samples were frozen in liquid nitrogen and stored at -80°C. Microbial DNA from samples were extracted using the QIAamp PowerFecal Pro DNA Kit. Full length 16S rRNA amplicon libraries were prepared using Kinnex kits and then sequenced on the PacBio Revio platform. Reads were analyzed using DADA2 and QIIME2. Statistical analysis was performed with the GLIMMIX procedure of SAS 9.4 (SAS Inst. Inc., Cary, NC) with the fixed effect of treatment, time, and their interaction. Data from d 0 was utilized as a covariate. There was a treatment effect (P < 0.01) for relative abundance of Christensenellaceae R7 group, Bacteroides, Akkermansia, Ruminococcus, and Treponema in cecal contents, with CON ewes having greater relative abundance than HGA ewes. Conversely, HGA had greater (P < 0.01) relative abundance of Bifidobacterium, Streptococcus, and Limosilactobacillus in cecal contents than CON ewes. Fusobacterium necrophorum was detected in all cecal samples after h 0 averaging 4.3% of reads, but was not affected by treatment, time, or their interaction. Trueperella pyogenes was detected in more than 80% of cecal samples after h 0 and averaged 0.25% of detected reads. In feces, there was a treatment effect (P < 0.01) for relative abundance of Bacteroides, Akkermansia, and Treponema, with CON ewes having greater relative abundance than HGA ewes. Relative abundance of Bifidobacterium and Streptococcus were greater (P < 0.01) in HGA feces than CON. A treatment by time interaction (P = 0.02) was observed for both fecal Ruminococcus and Christensenellaceae R7 group relative abundance, as relative abundance did not change in CON ewes but decreased in HGA after h 24. There were no effects of treatment, time, or their interaction (P ≥ 0.15) for relative abundance of Prevotella, Ruminococcus, Christensenellaceae R7 group, Selenomonas, or Rikenellaceae RC9 gut group in rumen fluid. Prevotellaceae UCG-001 relative abundance was affected (P = 0.04) by treatment with CON ewes having greater relative abundance than HGA ewes. Induced hindgut acidosis drastically altered the microbiome composition of cecal contents and feces. [ABSTRACT FROM AUTHOR]