Pyrosequencing reveals shifts in the bacterial epimural community relative to dietary concentrate amount in goats

Abstract

Ecological balance in the rumen is highly sensitive to concentrate-rich diets. Yet the effects of these feeding practices on the caprine bacterial epimural microbiome (CBEM), a microbial community with putative important physiological functions in the rumen, are largely unexplored. This study aimed to investigate the effect of dietary concentrate amount on ruminal CBEM. Seventeen growing goats were fed diets with 0 [n=5; 6.2MJ of metabolizable energy (ME)/d], 30 (n=6; 7.3MJ of /d), or 60% (n=6; 10.2MJ of ME/d) concentrate for 6 wk. Two hours after their last feeding, goats were euthanized and tissue samples of the ventral rumen wall were collected, washed in phosphate-buffered saline to detach loosely attached bacteria, and stored at -20°C for further processing. Genomic DNA was isolated from thawed rumen mucosa samples and used for Roche/454 Life Science (Branford, CT) 16S rRNA gene amplicon pyrosequencing yielding 122,458 reads. Pyrosequencing data were clustered into 1,879 operational taxonomic units (OTU; 0.03 distance level). Pyrosequencing revealed Proteobacteria, Bacteroidetes, Firmicutes, and Spirochaetes as the most abundant phyla (97.7%). Compared with the 30% group, both the 60 and 0% concentrate groups harbored significantly more Firmicutes and SR1, respectively. On an OTU level, a Bergeriella-related OTU was most abundant in the CBEM, followed by 2 Campylobacter OTU, which responded differently to diets: 1 OTU was significantly increased whereas the other significantly decreased with highest concentrate amount in the diet. At the genus level, the 0% concentrate group harbored increased Kingella-like sequences compared with the other feeding groups. Furthermore, the 0% concentrate group tended to have more Bergeriella than the 30 and 60% concentrate groups. The genus Bergeriella was significantly decreased in the 60% feeding group compared with the other diets. In conclusion, this is the first report of CBEM using deep-sequencing methods on the genus and OTU level, and our study revealed major shifts in the CBEM in response to concentrate-rich diets with potential health relevance in goats.

Characterizing the bacterial community across the gastrointestinal tract of goats: Composition and potential function

“…The present study showed that the metabolic functions of the bacteria in the goat GIT, such as carbohydrate metabolism, amino acid metabolism, and energy metabolism, were highly represented, which was consistent with the results from previous studies (Wetzels et al., ). The findings of the present study revealed significant differences ( p < 0.002) in bacterial function among the GIT regions of goats (Figure c).…”

Effect of Dietary Fat on the Metabolism of Energy and Nitrogen, Serum Parameters, Rumen Fermentation, and Microbiota in twin Hu Male Lambs

“…Jami and Mizrahi [40] reported that the proportion of Bacteroidetes was higher than Firmicutes , which is consistent with our results. Previous research shows that Proteobacteria is dominant in newborn lambs, followed by a sharp decline where it becomes the lowest proportion and Bacteroidetes becomes the highest [41,42]. In our study, the proportion of Proteobacteria and Fibrobacteres phylum was still high in HF group, which is similar to the study on the gut microbiome of mice fed with high fat diet by Hildebrandt [43].…”

Effects of replacing Leymus chinensis with whole-crop wheat hay on Holstein bull apparent digestibility, plasma parameters, rumen fermentation, and microbiota

“…The dominant microbes must take the responsibility for a large amount of the transformation of ingested forage, especially of protein, cellulose, starch, and so on, because these are the principal energy-yielding substrates that are used for the growth of microorganisms 50 . In this study, the most abundant phyla were Bacteroidetes , Firmicutes , and Proteobacteria , which are the main bacterial phyla and play important roles in rumen fermentation 51–53 . Based on the data set presented in the current study, Bacteroidetes was more predominant than Firmicutes , consistent with the result of Jami and Mizrahi 54 , who reported that the rumen pH was approximately 6.51 and the Bacteroidetes proportion (50%) was higher than that of Firmicutes (43%).…”