A rapid shift to high-grain diet results in dynamic changes in rumen epimural microbiome in sheep

Abstract

The rapid shift to high-grain (HG) diets in ruminants can affect the function of the rumen epithelium, but the dynamic changes in the composition of the epithelium-associated (epimural) bacterial community in sheep still needs further investigation. Twenty male lambs were randomly allocated to four groups (n = 5). Animals of the first group received hay diet and represented a control group (CON). Simultaneously, animals in the other three groups (HG groups) were rapidly shifted to an HG diet (60% concentrate)which continued for 7 (HG7), 14 (HG14) and 28 (HG28) days, correspondingly. Results showed that ruminal pH dramatically decreased due to the rapid shift to the HG diet (P <0.001), while, the concentrations of butyrate (P <0.001), lactate (P = 0.001), valerate (P = 0.008) and total volatile fatty acids (P = 0.001) increased. Diversity estimators showed a dramatic decrease after the shift without recovering as the HG feeding continued. The principal coordinates analysis showed that CON group clustered separately from all HG groups with the presence of significant difference only between HG7 and HG28 (P = 0.034). The non-parametric multivariate analysis (npmv R-package) deduced that the primary significant differences in phyla and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt)-predicted Kyoto Encyclopedia of Genes and Genomes (KEGGs) was attributed mainly to the diet composition (P <0.001, P = 0.001) compared to its application period (P = 0.140, 0.545) which showed a significant effect only on the genus (P = 0.001) and the operational taxonomic units (OTUs) level (P = 0.011). The Kruskal–Wallis test deduced that six phyla showed a significant effect due to the shift in diet composition. At the genus level, HG feeding altered the abundance of 12 taxa, four of which showed a significant variation due to the duration of the HG diet application. Similarly, we found that 21 OTUs showed significant variations due to the duration of the HG diet application. Furthermore, the genes abundance predicted by PICRUSt revealed that the HG feeding significantly affected seven metabolic pathways identified in the KEGG. Particularly, the abundance of gene families associated with carbohydrates metabolism were significantly higher in HG feeding groups (P = 0.027). Collectively, these results revealed that the rapid transition to an HG diet causes dramatic alterations in ruminal fermentation and the composition and function of ruminal epithelium-associated microbiome in sheep, while, the duration of the HG diet application causes drastic alterations to the abundance of some species.

Effects of dietary energy levels on rumen fermentation, microbiota, and gastrointestinal morphology in growing ewes

“…The present study showed that the genes responsible for glycolysis/ gluconeogenesis, pentose phosphate pathway, glycerolipid metabolism, and biosynthesis of ansamycins were upregulated in high energy feeding which indicates an enhanced fermentation rate performed by the rumen microbiota, with a decrease in the general function prediction only, arginine and proline metabolism, drug metabolism‐other enzymes, riboflavin metabolism, amino acid metabolism, novobiocin biosynthesis, and glutamatergic synapse‐related genes. These results are inconsistent with that of previous research (Seddik et al., 2018). The current study implied that feeding a high energy diet by using corn as the main energy source and decreasing the roughage percentage alters the ruminal microbial composition and the inferred microbial functions.…”

“…The current study also identified the changes of the represented genera in the rumen between the different dietary ME levels. For instance, unidentified Ruminococcaceae comprised 5.23%–7.02% of the relative abundance, which was inconsistent with previous studies (Seddik et al., 2018; Wang, et al., 2017). Ruminococcaceae strains play a critical role in energy and lipid metabolism, and its relative abundance is negatively associated with vascular sclerosis (Menni et al., 2018).…”

Microbiome–host co-oscillation patterns in remodeling of colonic homeostasis during adaptation to a high-grain diet in a sheep model

“…Not surprisingly, after abruptly switching to an HG diet, the colonic niche underwent comprehensive modification that included increased dietary starch content, enhanced total VFA production, promoted lactate, and decreased pH. These results were also mirrored by our previous study in rumen, which described a hallmark of the significant increased concentrations of ruminal butyrate, valerate, lactate and total VFA in the HG groups compared to their levels in the CON group [ 26 ]. Additionally, the high-starch diet drove clearly distinguishable changes in colon microbial ecosystems, and the duration of the HG-diet regulated the divergence and convergence of diet-microbe fingerprints in this study.…”

Effect of different glucogenic to lipogenic nutrient ratios on rumen fermentation and bacterial community in vitro

“…In the results, the most abundant functional categories contained amino acid metabolism, carbohydrate metabolism, replication and repair, membrane transport and translation, which were proved to be fundamental for the growth and reproduction of bacteria (Seddik et al . 2019). The G diet was predicted to lower the pathway of membrane transport than other diets.…”