Effects of dilution rate and retention time of concentrate on efficiency of microbial growth, methane production, and ruminal fermentation in Rusitec fermenters

Effects of Garlic Oil and Cinnamaldehyde on Sheep Rumen Fermentation and Microbial Populations in Rusitec Fermenters in Two Different Sampling Periods

Garlic oil (GO) and cinnamaldehyde (CIN) have shown potential to modify rumen fermentation. The aim of this study was to assess the effects of GO and CIN on rumen fermentation, microbial protein synthesis (MPS), and microbial populations in Rusitec fermenters fed a mixed diet (50:50 forage/concentrate), as well as whether these effects were maintained over time. Six fermenters were used in two 15-day incubation runs. Within each run, two fermenters received no additive, 180 mg/L of GO, or 180 mg/L of CIN. Rumen fermentation parameters were assessed in two periods (P1 and P2), and microbial populations were studied after each of these periods. Garlic oil reduced the acetate/propionate ratio and methane production (p < 0.001) in P1 and P2 and decreased protozoal DNA concentration and the relative abundance of fungi and archaea after P1 (p < 0.05). Cinnamaldehyde increased bacterial diversity (p < 0.01) and modified the structure of bacterial communities after P1, decreased bacterial DNA concentration after P2 (p < 0.05), and increased MPS (p < 0.001). The results of this study indicate that 180 mg/L of GO and CIN promoted a more efficient rumen fermentation and increased the protein supply to the animal, respectively, although an apparent adaptive response of microbial populations to GO was observed.

Appropriate particle size of rice straw promoted rumen fermentation and regulated bacterial microbiota in a rumen simulation technique system

The purpose of this study is to reveal the effects of different particle sizes of rice straw on the rumen protozoa count, nutrient disappearance rate, rumen fermentation, and microbial community in a rumen simulation technique (RUSITEC) system. In this experiment, a single-factor random trial design was adopted. According to the different particle sizes of rice straw, there were three treatments with three replies in each treatment. Three kinds of goat total mixed ration (TMR), with the same nutrients were used to carry out a 10 days in vitro fermentation experiment using the rumen simulation system developed by Hunan Agricultural University, including 6 days the pretrial period and 4 days formal period. This study found that the organic matter disappearance rate, concentrations of total volatile fatty acids (VFAs), acetate, propionate, and iso-butyrate were greatest in the 4 mm group (p < 0.05). There were no significant differences in the alpha diversity, among the three groups (p > 0.05). The relative abundance of Treponema and Ruminococcus of the 2 mm group increased; the relative abundance of Butyrivibrio and Prevotella in samples increased in the 4 mm group. In addition, the results of correlation analysis showed that Prevotella and Ruminococcus was positively correlated with butyrate, ammonia-N, dOM and d ADF (p < 0.05) and negatively correlated with valerate (p < 0.05); Oscillospira was positively correlated with valerate (p < 0.01) and negatively correlated with propionate, butyrate, ammonia-N, dOM and dADF (p < 0.05). The present results imply that compared to the other groups, rice straw particle size of 4 mm may improve the disappearance rate of nutrients and promote the production of volatile fatty acids by regulating ruminal microorganisms.

Effect of dietary peNDF levels on digestibility and rumen fermentation, and microbial community in growing goats

Physically effective neutral detergent fiber (peNDF) is a concept that accounts for the particle length of NDF in diets, sustaining the normal chewing behavior and rumen fermentation of ruminants. Specifically, peNDF>1.18 is the commonest one that is calculated from NDF and the percentage of feed dry matter left on the 1.18, 8.00, and 19.00 mm sieves. This study aimed to investigate the effects of different levels of peNDF>1.18 on the rumen microbiome and its correlation with nutrient digestibility and rumen fermentation in goats. A total of 30 Lezhi black goats were randomized and blocked to five dietary treatments (n = 6). All the diets were identical in composition but varied in hay lengths, leading to the different peNDF>1.18 content of the diets: 32.97, 29.93, 28.14, 26.48, and 24.75%. The results revealed that the nutrient digestibility increased when dietary peNDF>1.18 levels decreased from 32.97% to 28.14%, with the highest digestibility at 28.14% peNDF>1.18 treatment, after which nutrient digestibility decreased with the decreasing of dietary peNDF levels. Ruminal NH3-N concentrations in the 29.93% and 28.14% groups were higher than that in the 24.75% group (p < 0.05). Ruminal microbial protein concentration was the highest in the 32.97% group (p < 0.05). Daily CH4 production in the 32.97% and 24.75% peNDF>1.18 treatments was lower than that in the 26.48% group (p < 0.05) and no differences were observed among other groups. The relative abundance of rumen fungi at the phylum and genus levels and archaea at the species were affected by dietary peNDF>1.18 content. In conclusion, decreasing dietary peNDF>1.18 levels within a certain range can improve nutrient digestibility and change the rumen microbial community structure of goats. Dietary peNDF>1.18 level should be 28.14% (roughage length around 1 cm) among the five levels for 4 months Lezhi black goats with the purpose of optimal nutrient digestibility.

Effects of Dilution Rate on Fermentation Characteristics of Feeds With Different Carbohydrate Composition Incubated in the Rumen Simulation Technique (RUSITEC)

This study investigated the impact of carbohydrate source and fluid passage rate (dilution rate) on ruminal fermentation characteristics and microbial crude protein (MCP) formation. Three commonly used feeds (barley grain [BG], beet pulp [BP], and soybean hulls [SBH]), which differ considerably in their carbohydrate composition, were incubated together with a mixture of grass hay and rapeseed meal in two identical Rusitec apparatuses (each 6 vessels). Differences in fluid passage rate were simulated by infusing artificial saliva at two different rates (1.5% [low] and 3.0% [high] of fermenter volume per h). This resulted in six treatments (tested in 3 runs): BGhigh, BGlow, BPhigh, BPlow, SBHhigh and SBHlow. The system was adapted for 7 d, followed by 4 d of sampling. Production of MCP (mg/g degraded organic matter [dOM]; estimated by 15N analysis) was greater with high dilution rate (DL; p &lt; 0.001) and was higher for SBH compared to both BG and BP (p &lt; 0.001). High DL reduced OM degradability (OMD) compared to low DL (p &lt; 0.001), whereas incubation of BG resulted in higher OMD compared to SBH (p &lt; 0.002). Acetate:propionate ratio decreased in response to high DL (p &lt; 0.001). Total gas and methane production (both /d and /g dOM) were lower with high DL (p &lt; 0.001). In our study increasing liquid passage rate showed the potential to increase MCP and decrease methane production simultaneously. Results encourage further studies investigating these effects on the rumen microbial population.

Dose-Response Effects of 3-Nitrooxypropanol Combined with Low- and High-Concentrate Feed Proportions in the Dairy Cow Ration on Fermentation Parameters in a Rumen Simulation Technique

Methane (CH4) from ruminal feed degradation is a major pollutant from ruminant livestock, which calls for mitigation strategies. The purpose of the present 4 × 2 factorial arrangement was to investigate the dose-response relationships between four doses of the CH4 inhibitor 3-nitrooxypropanol (3-NOP) and potential synergistic effects with low (LC) or high (HC) concentrate feed proportions (CFP) on CH4 reduction as both mitigation approaches differ in their mode of action (direct 3-NOP vs. indirect CFP effects). Diet substrates and 3-NOP were incubated in a rumen simulation technique to measure the concentration and production of volatile fatty acids (VFA), fermentation gases as well as substrate disappearance. Negative side effects on fermentation regarding total VFA and gas production as well as nutrient degradability were observed for neither CFP nor 3-NOP. CH4 production decreased from 10% up to 97% in a dose-dependent manner with increasing 3-NOP inclusion rate (dose: p < 0.001) but irrespective of CFP (CFP × dose: p = 0.094). Hydrogen gas accumulated correspondingly with increased 3-NOP dose (dose: p < 0.001). In vitro pH (p = 0.019) and redox potential (p = 0.066) varied by CFP, whereas the latter fluctuated with 3-NOP dose (p = 0.01). Acetate and iso-butyrate (mol %) decreased with 3-NOP dose, whereas iso-valerate increased (dose: p < 0.001). Propionate and valerate varied inconsistently due to 3-NOP supplementation. The feed additive 3-NOP was proven to be a dose-dependent yet effective CH4 inhibitor under conditions in vitro. The observed lack of additivity of increased CFP on the CH4 inhibition potential of 3-NOP needs to be verified in future research testing further diet types both in vitro and in vivo.

The effects of rumen nitrogen balance on intake, nutrient digestibility, chewing activity, and milk yield and composition in dairy cows vary with dietary protein sources

The objective was to study the interaction effects of rumen nitrogen balance (RNB) and dietary protein source on feed intake, apparent total-tract digestibility (ATTD), eating and ruminating activity, milk yield (MY), and milk composition in lactating dairy cows. Twenty-four lactating Holstein cows were divided in 4 groups, which were randomly assigned to the dietary treatments included in a replicated 4 × 4 Latin square experimental design that consisted of four 20-d periods, each with 12 d of adaptation to the experimental diets and 8 d of sampling. The dietary treatments followed a 2 × 2 factorial arrangement with 2 main protein sources, faba bean grain (FB) and SoyPass (SP; Beweka Kraftfutterwerk GmbH), offered at 2 dietary RNB levels: RNB0 (RNB of 0 g/kg of dry matter) and RNB- (RNB of -3.2 g/kg of dry matter; i.e., 4 treatments). The composition of concentrate mixtures was adjusted to create diets with the desired RNB levels. Each of the protein sources supplied ≥35% of the total dietary crude protein (CP). Both diets within a protein source had similar forage sources and forage to concentrate ratios and were iso-energetic, but differed in CP concentrations. The main effects of RNB, protein source, and their interactions were tested by PROC MIXED in SAS 9.4 (SAS Institute Inc.). Interaction effects were observed for daily dry matter intake and energy-corrected MY, which were lower for RNB- than RNB0 in diets containing FB (23.5 vs. 24.4 kg dry matter/d; 28.6 vs. 30.6 kg milk/d), but similar in diets containing SP (24.2 vs. 24.3 kg dry matter/d; 31.3 vs. 31.7 kg milk/d). The ATTD of NDF was lower for RNB- compared with RNB0 in the FB (44.9 vs. 49.1 g/100 g) and SP (48.5 vs. 51.9 g/100 g) diets, and greater for the SP than for FB diets. There were interaction effects for ATTD of CP and concentrations of milk urea nitrogen, which were lower for RNB- compared with RNB0 in both, FB (55 vs. 63.1 g/100 g of CP; 5.65 vs. 11.3 mg/dL milk) and SP diets (60 vs. 64.4 g/100 g of CP; 8.74 vs. 13.4 mg/dL milk). However, differences between RNB levels were greater for FB than for SP diets. Furthermore, proportions of milk fatty acids followed the same pattern as that of dietary fatty acids, but biohydrogenation appeared to be greater for RNB- than RNB0 for both protein sources and in FB than in SP diets for both RNB levels. There was an interaction effect on total number of chews per unit of NDF intake, which was greater for RNB- compared with RNB0 for both protein sources. However, the differences between RNB levels were greater in FB than in SP diets. Overall, differences in the animal responses to negative RNB between FB and SP diets suggest a need to better understand the effect of negative RNB levels with different dietary ingredients at similar utilizable CP supply.

Ruminal resistome of dairy cattle is individualized and the resistotypes are associated with milking traits

BACKGROUND

Antimicrobial resistance is one of the most urgent threat to global public health, as it can lead to high morbidity, mortality, and medical costs for humans and livestock animals. In ruminants, the rumen microbiome carries a large number of antimicrobial resistance genes (ARGs), which could disseminate to the environment through saliva, or through the flow of rumen microbial biomass to the hindgut and released through feces. The occurrence and distribution of ARGs in rumen microbes has been reported, revealing the effects of external stimuli (e.g., antimicrobial administrations and diet ingredients) on the antimicrobial resistance in the rumen. However, the host effect on the ruminal resistome and their interactions remain largely unknown. Here, we investigated the ruminal resistome and its relationship with host feed intake and milk protein yield using metagenomic sequencing.

RESULTS

The ruminal resistome conferred resistance to 26 classes of antimicrobials, with genes encoding resistance to tetracycline being the most predominant. The ARG-containing contigs were assigned to bacterial taxonomy, and the majority of highly abundant bacterial genera were resistant to at least one antimicrobial, while the abundances of ARG-containing bacterial genera showed distinct variations. Although the ruminal resistome is not co-varied with host feed intake, it could be potentially linked to milk protein yield in dairy cows. Results showed that host feed intake did not affect the alpha or beta diversity of the ruminal resistome or the abundances of ARGs, while the Shannon index (R² = 0.63, P < 0.01) and richness (R² = 0.67, P < 0.01) of the ruminal resistome were highly correlated with milk protein yield. A total of 128 significantly different ARGs (FDR < 0.05) were identified in the high- and low-milk protein yield dairy cows. We found four ruminal resistotypes that are driven by specific ARGs and associated with milk protein yield. Particularly, cows with low milk protein yield are classified into the same ruminal resistotype and featured by high-abundance ARGs, including mfd and sav1866.

CONCLUSIONS

The current study uncovered the prevalence of ARGs in the rumen of a cohort of lactating dairy cows. The ruminal resistome is not co-varied with host feed intake, while it could be potentially linked to milk protein yield in dairy cows. Our results provide fundamental knowledge on the prevalence, mechanisms and impact factors of antimicrobial resistance in dairy cattle and are important for both the dairy industry and other food animal antimicrobial resistance control strategies.

Replacing Forage by Crude Olive Cake in a Dairy Sheep Diet: Effects on Ruminal Fermentation and Microbial Populations in Rusitec Fermenters

Olive oil extraction generates large amounts of a highly pollutant by-product called olive cake (OC), and its use in ruminant feeding could be an alternative. This study was designed to evaluate the effects of partially replacing forage by crude OC (COC) in a mixed dairy diet on rumen fermentation and microbial populations in Rusitec fermenters. The COC replaced 33% of the forage (66% maize silage and 33% barley straw) and was included at 16.6% of the total diet. Four fermenters were used in a cross-over design with two 13-day incubation periods. Experimental diets had a 50:50 forage-to-concentrate ratio and were formulated to contain the same protein (16.0%) and neutral detergent fiber (32.5%) levels. Compared with control fermenters, those fed the COC diet showed greater (p ≤ 0.02) pH (6.07 vs. 6.22), diet disappearance (0.709 vs. 0.748), and butyrate proportions (18.0 vs. 19.4), but there were no differences in volatile fatty acids and ammonia production. Microbial growth, bacterial diversity, protozoal abundance, and relative abundance of fungi and archaea were unaffected by diet, although the solid phase of COC-fed fermenters showed greater (p = 0.01) bacterial abundance than control ones. Results indicate that COC could replace 33% of the forage in a mixed dairy diet.

Effects of Replacing Extruded Maize by Dried Citrus Pulp in a Mixed Diet on Ruminal Fermentation, Methane Production, and Microbial Populations in Rusitec Fermenters

Citrus pulp is a highly abundant by-product of the citrus industry. The aim of this study was to assess the effects of replacing extruded maize (EM; 20% of total diet) by dried citrus pulp (DCP; 20%) in a mixed diet on rumen fermentation and microbial populations in Rusitec fermenters. The two diets contained 50% alfalfa hay and 50% concentrate, and the same protein level. Four Rusitec fermenters were used in a cross-over design with two 13-d incubation runs. After 7-d of diet adaptation, diet disappearance, fermentation parameters, microbial growth, and microbial populations were assessed. Fermenters receiving the DCP showed greater pH values and fiber disappearance (p < 0.001) and lower methane production (p = 0.03) than those fed EM. Replacing EM by DCP caused an increase in the proportions of propionate and butyrate (p < 0.001) and a decrease in acetate (p = 0.04). Microbial growth, bacterial diversity, and the quantity of bacteria and protozoa DNA were not affected by the diet, but the relative abundances of fungi and archaea were greater (p < 0.03) in solid and liquid phases of DCP fermenters, respectively. Results indicate that DCP can substitute EM, promoting a more efficient ruminal fermentation.

Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle

BACKGROUND

Microorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbiome and its association with host feed efficiency is unknown. Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics, aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome.

RESULTS

Rumen metagenomes were more closely clustered together and thus more conserved among individuals than metatranscriptomes, suggesting that inter-individual functional variations at the RNA level were higher than those at the DNA level. However, while mRNA enrichment significantly increased the sequencing depth of mRNA and generated similar functional profiles to total RNA-based metatranscriptomics, it led to biased abundance estimation of several transcripts. We observed divergent rumen microbial composition (metatranscriptomic level) and functional potentials (metagenomic level) among three breeds, but differences in functional activity (metatranscriptomic level) were less apparent. Differential rumen microbial features (e.g., taxa, diversity indices, functional categories, and genes) were detected between cattle with high and low feed efficiency, and most of them were breed-specific.

CONCLUSIONS

Metatranscriptomes represent real-time functional activities of microbiomes and have the potential to better associate rumen microorganisms with host performances compared to metagenomics. As total RNA-based metatranscriptomics seem to avoid potential biases caused by mRNA enrichment and allow simultaneous use of rRNA for generation of compositional profiles, we suggest their use for linking the rumen microbiome with host phenotypes in future studies. However, if exploration of specific lowly expressed genes is desired, mRNA enrichment is recommended as it will enhance the resolution of mRNA. Finally, the differential microbial features observed between efficient and inefficient steers tended to be specific to breeds, suggesting that interactions between host breed genotype and the rumen microbiome contribute to the variations in feed efficiency observed. These breed-associated differences represent an opportunity to engineer specific rumen microbiomes through selective breeding of the hosts.

Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle

Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and cattle feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n = 10; inefficient, n = 10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic data sets. In total, six bacterial phyla (Proteobacteria, Firmicutes, Bacteroidetes, Spirochaetes, Cyanobacteria, and Synergistetes), eight bacterial families (Succinivibrionaceae, Prevotellaceae, Ruminococcaceae, Lachnospiraceae, Veillonellaceae, Spirochaetaceae, Dethiosulfovibrionaceae, and Mogibacteriaceae), four archaeal clades (Methanomassiliicoccales, Methanobrevibacter ruminantium, Methanobrevibacter gottschalkii, and Methanosphaera), 112 metabolic pathways, and 126 CAZymes were identified as core components of the active rumen microbiome. As determined by comparative analysis, three bacterial families (Lachnospiraceae, Lactobacillaceae, and Veillonellaceae) tended to be more abundant in low-feed-efficiency (inefficient) animals (P < 0.10), and one archaeal taxon (Methanomassiliicoccales) tended to be more abundant in high-feed-efficiency (efficient) cattle (P < 0.10). Meanwhile, 32 microbial metabolic pathways and 12 CAZymes were differentially abundant (linear discriminant analysis score of >2 with a P value of <0.05) between two groups. Among them, 30 metabolic pathways and 11 CAZymes were more abundant in the rumen of inefficient cattle, while 2 metabolic pathways and 1 CAZyme were more abundant in efficient animals. These findings suggest that the rumen microbiomes of inefficient cattle have more diverse activities than those of efficient cattle, which may be related to the host feed efficiency variation.IMPORTANCE This study applied total RNA-based metatranscriptomics and showed the linkage between the active rumen microbiome and feed efficiency (residual feed intake) in beef cattle. The data generated from the current study provide fundamental information on active rumen microbiome at both compositional and functional levels, which serve as a foundation to study rumen function and its role in cattle feed efficiency. The findings that the active rumen microbiome may contribute to variations in feed efficiency of beef cattle highlight the possibility of enhancing nutrient utilization and improve cattle feed efficiency through modification of rumen microbial functions.

Lower Methane Emissions from Yak Compared with Cattle in Rusitec Fermenters

Globally methane (CH₄) emissions from ruminant livestock account for 29% of total CH₄ emissions. Inherited variation about CH₄ emissions of different animal species might provide new opportunity for manipulating CH₄ production. Six rumen-simulating fermenters (Rusitec) were set up for this study lasting for 16 d. The diet consisted of forage to concentrate ratio of 50:50 with barley straw as the forage. Treated vessels were supplied with rumen fluid from yak or cattle (3 vessels per animal species). Microbial growth was measured using ¹⁵N as a marker. The microbial community structure from liquid- and solid-fraction of each vessel was determined based on the 16S rRNA genes targeting both bacteria and archaea with MiSeq platform. CH₄ yield was lower when the inoculum used from yak than that from cattle (0.26 and 0.33 mmol CH₄/g dry matter intake, respectively). Lower H₂ production was observed in Rusitec fermenters with rumen fluid from yak compare with that from cattle (0.28 and 0.86 mmol/d, respectively). The apparent digestibility of neutral detergent fiber, the isovalerate percentage with respect to the total amount of volatile fatty acids, the hydrogen recovery, and the proportion of liquid-associated microbial nitrogen derived from ammonia-nitrogen were higher in Rusitec fermenters incubated with rumen fluid from cattle than that from yak. The relative abundances of methanogens were no difference between two animal species. We hypothesize that more H₂ production contributes to the higher methane emissions in cattle compare with yak.

Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. II. Protozoa population and diversity of bacterial communities

Four ruminally and duodenally cannulated sheep and 8 Rusitec fermenters were used to determine the effects of dietary characteristics on microbial populations and bacterial diversity. The purpose of the study was to assess how closely fermenters can mimic the differences between diets found in vivo. The 4 experimental diets contained forage to concentrate (F:C) ratios of 70:30 (high forage; HF) or 30:70 (high concentrate; HC) with either alfalfa hay (A) or grass hay (G) as the forage. Total bacterial numbers were greater in the rumen of sheep fed HF diets compared with those fed HC diets, whereas the opposite was found in fermenters. The numbers of cellulolytic bacteria were not affected by F:C ratio in any fermentation system, but cellulolytic numbers were 2.7 and 1.8 times greater in sheep than in fermenters for HF and HC diets, respectively. Neither total bacterial nor cellulolytic numbers were affected by the type of forage in sheep or fermenters. Decreasing F:C ratio increased total protozoa and Entodiniae numbers in sheep by about 29 and 25%, respectively, but it had no effect in fermenters. Isotrichidae and Ophryoscolecinae numbers in sheep were not affected by changing F:C ratio, but both disappeared completely from fermenters fed HC diets. Total protozoa and Entodiniae numbers were greater in sheep fed A diets than in those fed G diets, whereas the opposite was found in fermenters. Results indicate that under the conditions of the present study, protozoa population in Rusitec fermenters was not representative of that in the rumen of sheep fed the same diets. In addition, protozoa numbers in fermenters were 121 and 226 times lower than those in the sheep rumen for HF and HC diets, respectively. The automated ribosomal intergenic spacer analysis of the 16S ribosomal DNA was used to analyze the diversity of liquid- and solid-associated bacteria in both systems. A total of 170 peaks were detected in the automated ribosomal intergenic spacer analysis electropherograms of bacterial pellets across the full set of 64 samples, from which 160 were detected in at least 1 individual from each system (sheep or fermenter). Diversity of liquid-associated bacterial pellets was greater with G diets in fermenters but seemed to be unaffected by diet in sheep. Bacterial diversity in solid-associated bacteria pellets was greater for G diets compared with A diets in sheep and fermenters. Different conditions in the fermenters compared with sheep rumen might have caused a selection of some bacterial strains.