Characterization of Microbial Intolerances and Ruminal Dysbiosis Towards Different Dietary Carbohydrate Sources Using an in vitro Model

Animal board invited review: The effect of diet on rumen microbial composition in dairy cows

Ruminants play an important part in the food supply chain, and manipulating rumen microbiota is important to maximising ruminants' production. Rumen microbiota through rumen fermentation produces as major end products volatile fatty acids that provide animal's energy requirements, and microbial CP. Diet is a key factor that can manipulate rumen microbiota, and each variation of the physical and chemical composition creates a specific niche that selects specific microbes. Alteration in the chemical composition of forage, the addition of concentrates in the diet, or the inclusion of plant extract and probiotics, can induce a change in rumen microbiota. High-throughput sequencing technologies are the approaches utilised to investigate the microbial system. Also, the application of omics technologies allows us to understand rumen microbiota composition and these approaches are useful to improve selection programmes. The aim of this review was to summarise the knowledge about rumen microbiota, its role in nutrient metabolism, and how diet can influence its composition.

Integrated microbiota-host-metabolome approaches reveal adaptive ruminal changes to prolonged high-grain feeding and phytogenic supplementation in cattle

Diets rich in readily fermentable carbohydrates primarily impact microbial composition and activity, but can also impair the ruminal epithelium barrier function. By combining microbiota, metabolome, and gene expression analysis, we evaluated the impact of feeding a 65% concentrate diet for 4 weeks, with or without a phytogenic feed additive (PFA), on the rumen ecosystem of cattle. The breaking point for rumen health seemed to be the second week of high grain (HG) diet, with a dysbiosis characterized by reduced alpha diversity. While we did not find changes in histological evaluations, genes related with epithelial proliferation (IGF-1, IGF-1R, EGFR, and TBP) and ZO-1 were affected by the HG feeding. Integrative analyses allowed us to define the main drivers of difference for the rumen ecosystem in response to a HG diet, identified as ZO-1, MyD88, and genus Prevotella 1. PFA supplementation reduced the concentration of potentially harmful compounds in the rumen (e.g. dopamine and 5-aminovaleric acid) and increased the tolerance of the epithelium toward the microbiota by altering the expression of TLR-2, IL-6, and IL-10. The particle-associated rumen liquid microbiota showed a quicker adaptation potential to prolonged HG feeding compared to the other microenvironments investigated, especially by the end of the experiment.

Effects of partially replacing dietary corn with sugars in a dual-flow continuous culture system on the ruminal microbiome

The objective of this study was to evaluate the effects of feeding sugars as a replacement for starch on the ruminal microbiome using a dual-flow continuous culture system. Four periods of 10 days each were conducted with 8 fermenters in a 4 × 4 replicated Latin square design. Treatments included: 1) control with corn-CON, 2) molasses-MOL, 3) untreated condensed whey permeate-CWP, and 4) CWP treated with a caustic agent-TCWP as a partial substitute for corn. Sugars were defined as the water-soluble carbohydrates (WSC) concentration. Diets were formulated by replacing 4% of the diet DM in the form of starch from corn with the sugars in byproducts. Microbial samples for DNA analysis were collected from the solid and liquid effluent containers at 3, 6, and 9 h after feeding. Bacterial community composition was analyzed with sequencing the V4 region of the 16S rRNA gene using Illumina MiSeq platform. Data were analyzed with R 4.1.3 packages vegan, lmer, and ggplot to determine the effects of treatment on the relative abundance of taxa in the solid and liquid fractions, as well as the correlation of Acetate: Propionate ratio and pH to taxa relative abundance. Treatments did not affect alpha or beta diversity. At the phylum level the relative abundance of Proteobacteria was increased in CON compared to sugars in the solid fraction. In the liquid fraction, Firmicutes had greater relative abundance in sugar treatments while Bacteroidota and Spirochaetota were present in lower relative abundance in CWP. For solid and liquid samples, the family Lachnospiraceae had greater relative abundance in sugar treatments compared to CON. The decreased relative abundance of Christensenellaceae and Rikenellaceae paired with the greater relative abundance of Selenomonadaceae in CWP could help explain greater propionate molar proportion and decreased ruminal pH previously observed for this treatment. The genera Olsenella a lactic acid-producing bacterium, had the greatest relative abundance in MOL. Incorporating TCWP or MOL as a partial replacement for starch was more conservative of fibrolytic bacterial taxa compared to CWP. Additionally, TCWP did not increase bacterial taxa associated with synthesis of lactate as compared to MOL. Overall, replacing starch with sugars is mostly conservative of the ruminal microbiome; however, changes observed coincide with differences observed in acetate and propionate proportions and ruminal pH.

Impact of ileal indigestible protein on fecal nitrogen excretion and fecal microbiota may be greater compared with total protein concentration of diets in growing pigs

In the current study, we hypothesized that an increase in dietary ileal indigestible protein concentration induces an increase in hindgut nitrogen utilization and nitrogen excretion and a shift in fecal microbiota in growing pigs, when compared to pigs given a high total protein diet. Three diets were prepared: 1) standard protein diet based on corn and soybean meal, 2) high-indigestible protein diet in which autoclaved, low-digestible soybean meal replaced soybean meal in the first diet, and 3) high protein diet where the inclusion rate of soybean meal was greater than that of the other diets. The 3 diets were fed to 18 barrows that were fitted with T-cannula at the ileo-cecal junction (initial body weight = 63.4 ± 8.0 kg) in a randomized complete block design with body weight as a blocking factor. Pigs were individually housed in pens and the experiment lasted for 23 d. On days 7 and 21, fecal samples were collected by rectal massage for microbiota analysis. Grab samples of feces were collected on days 20 and 21, and ileal digesta were collected on days 22 and 23 for the determination of energy and nitrogen utilization. Lower apparent ileal digestibility of nitrogen in the high-indigestible protein diet containing autoclaved soybean meal resulted in greater ileal indigestible nitrogen concentration (P < 0.05). Apparent total tract digestibility of nitrogen was lower (P < 0.05), and correspondingly nitrogen concentration and daily fecal nitrogen output were greater (P < 0.05) in the high-indigestible protein diet compared with the other diets. Apparent post-ileal digestibility and hindgut disappearance of nitrogen and gross energy were the greatest (P < 0.05) in the high protein diet, whereas a statistical difference was not observed in those variables between the standard protein diet and the high-indigestible protein diet. Beta diversity metrics of feces in the high-indigestible protein diet on day 21 were different (q < 0.05) from those in the other two diets, which indicates a shift in microbial communities. According to the results of the DESeq2, the direction of microbiota shift induced by the high-indigestible protein diet may have reduced fiber utilization in the hindgut. In conclusion, an increase in dietary ileal indigestible protein concentration increased fecal nitrogen excretion and shifted fecal microbial communities but did not increase nitrogen utilization in the hindgut.