Effect of donor animals and their diet on in vitro nutrient degradation and microbial protein synthesis using grass and corn silages

Effects of diets for three growing stages by rumen inocula donors on in vitro rumen fermentation and microbiome

Hanwoo and Jeju Black cattle (Jeju Black) are native breeds of Korean cattle. Jeju Black cattle are recognized as natural monuments and are known to exhibit slower growth rates compared to Hanwoo. While several studies have analyzed the genetic characteristics of these cattle, there has been limited research on the differences in their microbiome. In this study, rumen fluid was obtained from three Hanwoo steers and three Jeju Black steers, and three different diets (total mixed rations [TMRs] for growing, early fattening, and late fattening periods) were used as substrates for in vitro fermentation. The in vitro incubation was conducted for 3 h and 24 h following a 2 × 3 factorial arrangement. After both incubation periods, fermentation characteristics were analyzed, and ruminal microbiome analysis was performed using 16S rRNA gene sequencing, employing both QIIME2 and PICRUSt2. The results revealed significant differences in the ruminal microbiota due to the inoculum effect. At the phylum level, Patescibacteria and Synergistota were found to be enriched in the Jeju Black inoculum-treated group. Additionally, using different inocula also affected the relative abundance of major taxa, including Ruminococcus, Pseudoramibacter, Ruminococcaceae CAG-352, and the [Eubacterium] ruminantium group. These microbial differences induced by the inoculum may have originated from varying levels of domestication between the two subspecies of donor animals, which mainly influenced the fermentation and microbiome features in the early incubation stages, although this was only partially offset afterward. Furthermore, predicted commission numbers of microbial enzymes, some of which are involved in the biosynthesis of secondary metabolites, fatty acids, and alpha amylase, differed based on the inoculum effect. However, these differences may account for only a small proportion of the overall metabolic pathway. Conversely, diets were found to affect protein biosynthesis and its related metabolism, which showed differential abundance in the growing diet and were potentially linked to the growth-promoting effects in beef cattle during the growing period. In conclusion, this study demonstrated that using different inocula significantly affected in vitro fermentation characteristics and microbiome features, mainly in the early stages of incubation, with some effects persisting up to 24 h of incubation.

Is there a difference in ruminal fermentation control between cattle and sheep? A meta-analytical test of a hypothesis on differential particle and fluid retention

Ruminant species differ in digestive physiology. The species-specific ratio of mean retention time of particles and fluid (MRT_particle/MRT_fluid) in the reticulorumen has been interpreted as controlling ruminal fermentation: a higher ratio indicates of a more distinct 'washing' of particulate digesta by liquid. This should increase the harvest of microbes from the reticulorumen, and keep the microbiome in a state of more intense growth; at the same time, this should increase the metabolic losses of faecal nitrogen of microbial origin, leading to lower values for the apparent digestibility of crude protein (aD CP). A systematic difference has been hypothesized between cattle (higher ratio) and sheep (lower ratio), with a lower MRT_fluid in cattle due to a higher saliva production. Here, we test these hypotheses in a meta-analysis, using only studies that investigated cattle and sheep simultaneously. The datasets included 12 studies on MRT (of which 11 contained information on feed intake), yielding 102 (or 89) individual data; and 26 studies on protein digestibility (of which 18 contained information on intake), yielding 349 individual data. Cattle had a higher MRT_particle/MRT_fluid (2.1) than sheep (1.7), mainly due to longer MRT_particle; only if body mass was included in the model, MRT_fluid was significantly shorter in cattle in the larger MRT dataset (and tended to be shorter in the slightly smaller dataset). Cattle had a significantly lower aD CP than sheep, while there was no such difference in overall (dry or organic matter) digestibility. The dataset confirms a shift in fermentation strategy towards microbial production in cattle. While this has been suggested for ruminants in general, cattle appear particularly far on an evolutionary trajectory of maximizing microbial yield from the forestomach. The application of more specific digestive physiology data (like endogenous losses) gained from sheep to cattle should be done bearing these differences in mind.

Modulation of rumen bacterial community and feed utilization in camel and sheep using combined supplementation of live yeast and microalgae

The combination of live yeast and microalgae as feed supplementation could improve rumen fermentation and animal productivity. This study aimed to investigate the impact of a mixture of (YA) yeast (Saccharomyces cerevisiae) and microalgae (Spirulina platensis and Chlorella vulgaris) as feed supplementation on feed intake, rumen disappearance of barley straw, bacteria, and fermentation, blood parameters of camels and sheep. Three fistulated camels and three fistulated rams were fed a concentrates mixture and ad libitum barley straw as a basal diet alone or supplemented with YA mixture. The dietary supplementation improved the feed intake, rumen disappearance of barley straw nutrients, and the blood immunity parameters. The YA supplementation affected rumen fermentation as well as the composition and diversity of rumen bacteria; however, the response to the supplementation varied according to animal species. Principle Coordinate Analysis (PCoA) separated bacterial communities based on animal species and feeding treatment. Phylum Bacteroidetes and Firmicutes dominated the bacterial community; and the dominant genera were Prevotella, RC9_gut_group, Butyrivibrio, Ruminococcus, Saccharofermentans, Christensenellaceae_R-7_group, and Succiniclasticum. Our results suggest positive impacts of YA supplementation in rumen fermentation and animal performance.

Effects of Different Formulations of Glyphosate on Rumen Microbial Metabolism and Bacterial Community Composition in the Rumen Simulation Technique System

The use of the herbicide glyphosate and its formulations on protein-rich feedstuff for cattle leads to a considerable intake of glyphosate into the rumen of the animals, where glyphosate may potentially impair the 5-enolpyruvylshikimate-3-phosphate pathway of the commensal microbiota, which could cause dysbiosis or proliferation of pathogenic microorganisms. Here, we evaluated the effects of pure glyphosate and the formulations Durano TF and Roundup® LB plus in different concentrations on the fermentation pattern, community composition and metabolic activity of the rumen microbiota using the Rumen Simulation Technique (RUSITEC). Application of the compounds in three concentrations (0.1 mg/l, 1.0 mg/l or 10 mg/l, n = 4 each) for 9 days did not affect fermentation parameters such as pH, redox potential, NH3-N concentration and production of short-chain fatty acids compared to a control group. Microbial protein synthesis and the degradation of different feed fractions did not vary among the treatments. None of the used compounds or concentrations did affect the microbial diversity or abundance of microbial taxa. Metaproteomics revealed that the present metabolic pathways including the shikimate pathway were not affected by addition of glyphosate, Durano TF or Roundup® LB plus. In conclusion, neither pure glyphosate, nor its formulations Durano TF and Roundup® LB plus did affect the bacterial communities of the rumen.

Longitudinal Characterization of the Gut Bacterial and Fungal Communities in Yaks

Development phases are important in maturing immune systems, intestinal functions, and metabolism for the construction, structure, and diversity of microbiome in the intestine during the entire life. Characterizing the gut microbiota colonization and succession based on age-dependent effects might be crucial if a microbiota-based therapeutic or disease prevention strategy is adopted. The purpose of this study was to reveal the dynamic distribution of intestinal bacterial and fungal communities across all development stages in yaks. Dynamic changes (a substantial difference) in the structure and composition ratio of the microbial community were observed in yaks that matched the natural aging process from juvenile to natural aging. This study included a significant shift in the abundance and proportion of bacterial phyla (Planctomycetes, Firmicutes, Bacteroidetes, Spirochaetes, Tenericutes, Proteobacteria, and Cyanobacteria) and fungal phyla (Chytridiomycota, Mortierellomycota, Neocallimastigomycota, Ascomycota, and Basidiomycota) across all development stages in yaks. As yaks grew older, variation reduced, and diversity increased as compared to young yaks. In addition, the intestine was colonized by a succession of microbiomes that coalesced into a more mature adult, including Ruminococcaceae_UCG-005, Romboutsia, Prevotellaceae_UCG-004, Blautia, Clostridium_sensu_stricto_1, Ruminococcus_1, Ruminiclostridium_5, Rikenellaceae_RC9_gut_group, Alloprevotella, Acetitomaculum, Lachnospiraceae_NK3A20_group, Bacteroides, Treponema_2, Olsenella, Escherichia-Shigella, Candidatus_Saccharimonas, and fungal communities Mortierella, Lomentospora, Orpinomyces, and Saccharomyces. In addition, microorganisms that threaten health, such as Escherichia-Shigella, Mortierella, Lomentospora and Hydrogenoanaerobacterium, Corynebacterium_1, Trichosporon, and Coprinellus, were enriched in young and old yaks, respectively, although all yaks were healthy. The significant shifts in microflora composition and structure might reflect adaptation of gut microbiome, which is associated with physicochemical conditions changes and substrate availability in the gut across all development periods of yaks.

PacBio and Illumina MiSeq Amplicon Sequencing Confirm Full Recovery of the Bacterial Community After Subacute Ruminal Acidosis Challenge in the RUSITEC System

The impact of subacute rumen acidosis (SARA) on the rumen bacterial community has been frequently studied in in vivo trials. Here we investigated whether these alterations can be mirrored by using the rumen simulation technique (RUSITEC) as an in vitro model for this disease. We hypothezised that the bacterial community fully recovers after a subacute ruminal acidosis challenge. We combined a PacBio nearly full-length 16S rRNA gene analysis with 16S rRNA gene Illumina MiSeq sequencing of the V4 hypervariable region. With this hybrid approach, we aimed to get an increased taxonomic resolution of the most abundant bacterial groups and an overview of the total bacterial diversity. The experiment consisted of a control period I and a SARA challenge and ended after a control period II, of which each period lasted 5 d. Subacute acidosis was induced by applying two buffer solutions, which were reduced in their buffering capacity (SARA buffers) during the SARA challenge. Two control groups were constantly infused with the standard buffer solution. Furthermore, the two SARA buffers were combined with three different feeding variations, which differed in their concentrate-to-hay ratio. The induction of SARA led to a decrease in pH below 5.8, which then turned into a steady-state SARA. Decreasing pH values led to a reduction in bacterial diversity and richness. Moreover, the diversity of solid-associated bacteria was lower for high concentrate groups throughout all experimental periods. Generally, Firmicutes and Bacteroidetes were the predominant phyla in the solid and the liquid phase. During the SARA period, we observed a decrease in fibrolytic bacteria although lactate-producing and -utilizing families increased in certain treatment groups. The genera Lactobacillus and Prevotella dominated during the SARA period. With induction of the second control period, most bacterial groups regained their initial abundance. In conclusion, this in vitro model displayed typical bacterial alterations related to SARA and is capable of recovery from bouts of SARA. Therefore, this model can be used to mimic SARA under laboratory conditions and may contribute to a reduction in animal experiments.

Effects of Microalgae Species on In Vitro Rumen Fermentation Pattern and Methane Production

This experiment was conducted to establish the effects of two types of microalgae [Chlorella vulgaris (AI), C. variabilis (AII) and their combination (AI+AII)] with two substrates (wheat and corn silages) on rumen fermentation, gas and methane production. To each substrate, one of 3 algae treatment was supplemented at 0% and 25% of the total incubated dry matter. A series of 5 measurement points (3, 6, 12, 24 and 48 h) were completed and the gas production was monitored. The proximate and mineral composition of microalgae and substrates were examined. At 48 h incubation rumen fermentation variables and CH4 production were also assessed. When compared with wheat silage, corn silage caused an increase in gas production (P<0.05). Ruminal gas production decreased in the algae groups when compared to the controls (0% algae, wheat and corn silages, P<0.05). Among algae, C. vulgaris had the strongest effect, decreasing gas production by 34%. Among algae, the total volatile fatty acids (VFA) and CH4 production were found to be lower in C. variabilis (P<0.001). Ammonia-N increased with the algae inclusion (P<0.05). But, the ruminal gas production, pH, acetate, the total VFA, CH4 and rumen fermentation efficiency were not affected by the substrate and algae interaction (P>0.05). The propionate was the highest (P<0.05) for corn silage when incubated with C. vulgaris. Ruminal butyrate was the lowest for the wheat silage when incubated with the mixture of algae (P<0.05). The NH3-N was the highest in corn silage when incubated with all algae types (P<0.05). Careful selection and combination of substrate and algae may positively manipulate rumen fermentation and may inhibit CH4 production. Further research is needed to validate these results in vivo.

The effect of diet of the donor cows on in vitro measurements of methane production from wheat and corn incubated in various forage-to-grain ratios

BACKGROUND

Supplementation of ruminant diets with wheat and corn grains influences ruminal fermentation. In vitro fermentation is a methodology that can be used to screen feeds for their potential to produce enteric methane. However, there is evidence that the diet of the donor cows could impact the results of in vitro analysis. This research investigated the in vitro fermentation of wheat and corn grain when incubated in ruminal fluid from cows fed different grain types and different forage-to-grain ratios.

RESULTS

The type of grain fed to the donor cows, as well as forage-to-grain ratio, affected the outcome of fermentation of wheat and corn grain. Differences in methane production (MP) between grains were only observed when incubated with ruminal fluid adapted to each specific grain type. Increasing proportions of wheat but not of corn decreased in vitro MP in a linear manner compared with MP produced from forage only.

CONCLUSIONS

Wheat grain has a greater in vitro antimethanogenic effect than corn. However, to detect the different fermentations between wheat and corn, grains should be incubated in ruminal fluid from cows adapted to that specific grain type. © 2019 Society of Chemical Industry.

Evaluation of sources of variation on in vitro fermentation kinetics of feedstuffs in a gas production system

The aim of this study was to evaluate the effect of different sources of variation in gas production technique on the in vitro gas production kinetics of feedstuffs. Triplicates of commercial concentrate, grass silage, grass hay and grass pasture were incubated in three experiments: experiment 1 assessed two agitation methods; experiment 2 evaluated different rumen inocula (pooled or different donor cows for each incubation run); and experiment 3 used Goering-Van Soest or Mould buffers for media preparation. Gas production data were fitted into the Michaelis-Menten model and then subjected to analysis of variance. Gas production (GP) at 48 h and asymptote gas production (A) were lower when bottles were continuously under horizontal movement. Time to produce half and 75% of A, and A were affected by rumen inocula, while buffer type affected time to produce half and 25% of A and GP. No interactions between substrates and sources of variation were observed, suggesting that the effects of substrates on GP parameters were not modified. It is concluded that comparison of numerical data from in vitro experiments that follow different protocols must be done carefully. However, the ranking of different substrates is more robust and less affected by the sources of variation.

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 rumen in vitro fermentation of temperate pastures using different batch culture systems

In vitro batch culture systems are popular because they are relatively inexpensive and allow the screening and testing of large amounts of samples in a short time. Most of the batch culture systems have been designed for the evaluation of gas produced during fermentation of substrates and different designs have been compared between laboratories, but very little work is published where methane production or volatile fatty acid production is compared. The aim of this study was to determine the degree of agreement between two different in vitro batch culture systems, from different laboratories when measuring in vitro fermentation kinetics and end products using pasture samples as substrates. The two systems were a manual and a fully automated pressure-based system. Duplicates of pasture samples were incubated in three consecutive runs. Concordance correlation coefficients between systems and estimates of variance components (pasture, incubation run and random error) for each system were determined for all measured variables. There were poor correlations between systems for most of the variables except for time to produce half of the asymptotic gas production and acetate molar proportion of volatile fatty acids. However, for both systems most of variance was due to pasture sample and then incubation run. The poor agreement between systems might be explained by the different laboratory protocols. Therefore, comparisons of absolute values from different batch culture systems or experiments must be done carefully. Alternatively, more standardisation in terms of sample preparation and incubation procedure may be needed to compare in vitro fermentation products among systems.

Changes in Rumen Microbial Community Composition during Adaption to an In Vitro System and the Impact of Different Forages

This study examined ruminal microbial community composition alterations during initial adaption to and following incubation in a rumen simulation system (Rusitec) using grass or corn silage as substrates. Samples were collected from fermenter liquids at 0, 2, 4, 12, 24, and 48 h and from feed residues at 0, 24, and 48 h after initiation of incubation (period 1) and on day 13 (period 2). Microbial DNA was extracted and real-time qPCR was used to quantify differences in the abundance of protozoa, methanogens, total bacteria, Fibrobacter succinogenes, Ruminococcus albus, Ruminobacter amylophilus, Prevotella bryantii, Selenomonas ruminantium, and Clostridium aminophilum. We found that forage source and sampling time significantly influenced the ruminal microbial community. The gene copy numbers of most microbial species (except C. aminophilum) decreased in period 1; however, adaption continued through period 2 for several species. The addition of fresh substrate in period 2 led to increasing copy numbers of all microbial species during the first 2–4 h in the fermenter liquid except protozoa, which showed a postprandial decrease. Corn silage enhanced the growth of R. amylophilus and F. succinogenes, and grass silage enhanced R. albus, P. bryantii, and C. aminophilum. No effect of forage source was detected on total bacteria, protozoa, S. ruminantium, or methanogens or on total gas production, although grass silage enhanced methane production. This study showed that the Rusitec provides a stable system after an adaption phase that should last longer than 48 h, and that the forage source influenced several microbial species.

Effects of mineral and rapeseed phosphorus supplementation on phytate degradation in dairy cows

The objective of this study was to evaluate the effects of diet composition on phytate (InsP6) degradation in dairy cows. In Experiment 1, four diets that differed in the amount and source of phosphorus (P) were fed to 24 lactating cows in a 4 × 4 Latin Square design. The control diet (Diet C) contained 4.18 g P/kg dry matter (DM). Diet MP contained additional mineral P (5.11 g P/kg DM), Diet RS contained rapeseed and rapeseed meal as organic P sources (5.26 g P/kg DM) and Diet RSM contained rapeseed meal and rapeseed oil (5.04 g P/kg DM). Total P (tP) and InsP6 excretion in faeces were measured. In Experiment 2, we used a rumen simulation technique (Rusitec) to estimate ruminal disappearance of tP and InsP6 from Diets C, MP and RSM. In Experiment 1, tP concentration in faeces increased with tP intake and was highest for Diets RS and RSM. The source of supplemented P had no influence on tP digestibility, but tP digestibility was reduced for Diets MP, RS and RSM in comparison to that for Diet C. InsP6 disappearance decreased in Diet MP (85.0%) and increased in Diets RS (92.7%) and RSM (94.0%) compared to that in Diet C (90.0%). In Experiment 2, P source influenced ruminal tP disappearance (Diet MP, 78.6%; Diet RSM, 75.3%). InsP6 disappearance for Diet C (98.1%) was higher than that for Diets MP (95.6%) and RSM (94.9%). The results confirmed the high potential of ruminants to degrade InsP6, but differences in diet composition influenced InsP6 disappearance. Further studies of the site of InsP6 degradation are required to understand the relevance of InsP6 degradation for the absorption of P.