Comparison of bacterial diversity in the rumen of sheep and in Rusitec fermenters as assessed by ARISA–PCR

Abstract

This study was designed to compare the effects of 4 diets on bacterial communities in bacterial pellets (BP) isolated from the solid (SAB) and liquid phase (LAB) of the rumen of sheep with those observed in Rusitec fermenters. The 4 experimental diets had forage:concentrate ratios (F:C) of 70:30 (HF) or 30:70 (HC) and alfalfa hay or grass hay as forage (FOR). SAB and LAB were isolated from each sheep (4 per diet) and fermenter (n = 4) immediately before feeding, and bacterial diversity was analyzed by ARISA-PCR of the 16S ribosomal DNA. A total of 170 peaks were detected in the ARISA electropherograms across the full set of 64 BP. The number of peaks (NP) in BP from sheep ranged from 42 to 82 for LAB, and from 31 to 81 for SAB (168 peaks in total). In fermenters, NP ranged from 53 to 79 for LAB, and from 21 to 69 for SAB (162 peaks in total). No effect of F:C (P > 0.05) on NP or Shannon index (SI) was observed on LAB in any system. F:C did not affect SAB profile in fermenters, but NP and SI were greater (P < 0.05) in SAB from sheep fed HF diets compared with those from HC-sheep. Feeding grass hay diets promoted greater (P < 0.01) SAB diversity in both systems compared with alfalfa hay diets. FOR did not (P > 0.05) affect LAB profile in sheep, but grass hay-fed fermenters had greater (P < 0.01) LAB diversity compared with fermenters fed alfalfa hay diets. The results indicate that bacterial diversity was more markedly affected by FOR than by F:C. There was a positive relationship (P = 0.001) between the NP in LAB and that in SAB in Rusitec, but no relationship (P = 0.72) was found in sheep; this would indicate that dietary effects on bacterial diversity were similar in LAB and SAB in fermenters, but contrasting in sheep. When all samples were analyzed together by clustering analysis, 2 distinct clusters were observed for in vivo and in vitro BP, which suggests a different structure of the bacterial communities in sheep and fermenters.