A systems biology approach reveals differences in the dynamics of colonization and degradation of grass vs. hay by rumen microbes with minor effects of vitamin E supplementation

Increasing the efficiency of utilization of fresh and preserved forage is a key target for ruminant science. Vitamin E is often used as additive to improve product quality but its impact of the rumen function is unknown. This study investigated the successional microbial colonization of ryegrass (GRA) vs. ryegrass hay (HAY) in presence of zero or 50 IU/d supplementary vitamin E, using a rumen simulation technique. A holistic approach was used to link the dynamics of feed degradation with the structure of the liquid-associated (LAB) and solid-associated bacteria (SAB). Results showed that forage colonization by SAB was a tri-phasic process highly affected by the forage conservation method: Early colonization (0?2 h after feeding) by rumen microbes was 2? faster for GRA than HAY diets and dominated by Lactobacillus and Prevotella which promoted increased levels of lactate (+56%) and ammonia (+18%). HAY diets had lower DM degradation (-72%) during this interval being Streptococcus particularly abundant. During secondary colonization (4?8 h) the SAB community increased in size and decreased in diversity as the secondary colonizers took over (Pseudobutyrivibrio) promoting the biggest differences in the metabolomics profile between diets. Secondary colonization was 3? slower for HAY vs. GRA diets, but this delay was compensated by a greater bacterial diversity (+197 OTUs) and network complexity resulting in similar feed degradations. Tertiary colonization (>8 h) consisted of a slowdown in the colonization process and simplification of the bacterial network. This slowdown was less evident for HAY diets which had higher levels of tertiary colonizers (Butyrivibrio and Ruminococcus) and may explain the higher DM degradation (+52%) during this interval. The LAB community was particularly active during the early fermentation of GRA and during the late fermentation for HAY diets indicating that the availability of nutrients in the liquid phase reflects the dynamics of feed degradation. Vitamin E supplementation had minor effects but promoted a simplification of the LAB community and a slight acceleration in the SAB colonization sequence which could explain the higher DM degradation during the secondary colonization. Our findings suggest that when possible, grass should be fed instead of hay, in order to accelerate feed utilization by rumen microbespublishersversionPeer reviewe

An Integrated Multi-Omics Approach Reveals the Effects of Supplementing Grass or Grass Hay with Vitamin E on the Rumen Microbiome and Its Function

Rumen function is generally suboptimal leading to losses in methane and nitrogen. Analysis of the rumen microbiome is thus important to understanding the underlying microbial activity under different feeding strategies. This study investigated the effect of forage conservation method and vitamin E supplementation on rumen function using a rumen simulation technique. Ryegrass (GRA) or ryegrass hay (HAY) was supplemented with 20% concentrate containing zero or 50 IU/d vitamin E, as α-tocopheryl acetate, according to a 2 × 2 factorial design. The forage conservation method did not substantially change the nutrient composition but had a profound impact on the structure and diversity of the rumen microbiome. HAY diets promoted a more complex bacterial community (+38 OTUs) dominated by Firmicutes. This bacterial adaptation, together with increased rumen protozoa levels and methanogen diversity, was associated with greater fiber disappearance (+12%) in HAY diets, but also with greater rumen true N degradability (+7%) than GRA diets. HAY diets also had a higher metabolic H recovery and methane production (+35%) suggesting more efficient inter-species H transfer between bacteria, protozoa and methanogens. Contrarily, GRA diets promoted more simplified methanogen and bacterial communities, which were dominated by Bacteroidetes and Lactobacillus, thus lactate formation may have acted as an alternative H sink in GRA diets. Moreover the structure of the bacterial community with GRA diets was highly correlated with N utilization, and GRA diets promoted greater bacterial growth and microbial protein synthesis (+16%), as well as a more efficient microbial protein synthesis (+22%). A dose-response experiment using batch cultures revealed that vitamin E supplementation increased rumen fermentation in terms of total VFA and gas production, with protozoal activity higher when supplying α-tocopheryl acetate vs. α-tocopherol. Moreover, α-tocopheryl acetate promoted a small increase in feed degradability (+8%), possibly as a result of its antioxidant properties which led to higher bacterial and protozoal levels. Vitamin E supplementation also modified the levels of some methanogen species indicating that they may be particularly sensitive to oxidative stresses. Our findings suggested that when possible, grass should be fed instead of grass hay, in order to improve rumen function and to decrease the environmental impact of livestock agriculture

Effect of progressive inoculation of fauna-free sheep with holotrich protozoa and total-fauna on rumen fermentation, microbial diversity and methane emissions

Rumen methanogenesis represents an energy waste for the ruminant and an important source of greenhouse gas; thus, integrated studies are needed to fully understand this process. Eight fauna-free sheep were used to investigate the effect of successive inoculation with holotrich protozoa then with total fauna on rumen methanogenesis. Holotrichs inoculation neither altered rumen fermentation rate nor diet digestibility, but increased concentrations of acetate (+15%), butyrate (+57%), anaerobic fungi (+0.82 log), methanogens (+0.41 log) and methanogenesis (+54%). Further inoculation with total fauna increased rumen concentrations of protozoa (+1.0 log), bacteria (+0.29 log), anaerobic fungi (+0.78 log), VFA (+8%), ammonia and fibre digestibility (+17%) without affecting levels of methanogens or methanogenesis. Rumen methanogens population was fairly stable in terms of structure and diversity, while the bacterial community was highly affected by the treatments. Inoculation with holotrich protozoa increased bacterial diversity. Further inoculation with total fauna lowered bacterial diversity but increased concentrations of certain propionate and lactate-producing bacteria, suggesting that alternative H(2) sinks could be relevant. This experiment suggests that holotrich protozoa have a greater impact on rumen methanogenesis than entodiniomorphids. Thus, further research is warranted to understand the effect of holotrich protozoa on methane formation and evaluate their elimination from the rumen as a potential methane mitigation strategy

A metagenomics approach to evaluate the impact of dietary supplementation with Ascophyllum nodosum or Laminaria digitata on rumen function in Rusitec fermenters

There is an increasing need to identify alternative feeds for livestock that do not compete with foods for humans. Seaweed might provide such a resource, but there is limited information available on its value as an animal feed. Here we use a multi-omics approach to investigate the value of two brown seaweeds, Ascophyllum nodosum (ASC) and Laminaria digitata (LAM), as alternative feeds for ruminants. These seaweeds were supplemented at 5% inclusion rate into a control diet (CON) in a rumen simulation fermenter. The seaweeds had no substantial effect on rumen fermentation, feed degradability or methane emissions. Concentrations of total bacteria, anaerobic fungi, biodiversity indices and abundances of the main bacterial and methanogen genera were also unaffected. However, species-specific effects of brown seaweed on the rumen function were noted: ASC promoted a substantial decrease in N degradability (-24%) due to its high phlorotannins content. Canonical correspondence analysis of the bacterial community revealed that low N availability led to a change in the structure of the bacterial community. ASC also decreased the concentration of Escherichia coli O157:H7 post-inoculation. In contrast, LAM which has a much lower phlorotannin content did not cause detrimental effects on N degradability nor modified the structure of the bacterial community in comparison to CON. This adaptation of the microbial community to LAM diets led to a greater microbial ability to digest xylan (+70%) and carboxy-methyl-cellulose (+41%). These differences among brown seaweeds resulted in greater microbial protein synthesis (+15%) and non-ammonia N flow (+11%) in LAM than in ASC diets and thus should led to a greater amino acid supply to the intestine of the animal. In conclusion, it was demonstrated that incorporation of brown seaweed into the diet can be considered as a suitable nutritional strategy for ruminants; however special care must be taken with those seaweeds with high phlorotannin concentrations to prevent detrimental effects on N metabolism. This study highlights the value of combining fermentation and enzyme activity data with molecular characterization of the rumen microbiome in evaluating novel feeds for ruminants. Further experiments are required to determine the maximum seaweed inclusion rate tolerated by rumen microbes

An evaluation of equity premium prediction using multiple kernel learning with financial features

This paper introduces and extensively explores a forecasting procedure based on multivariate dynamic kernels to re-examine –under a non-linearframework– the experimental tests reported by Welch and Goyal (Review of Financial Studies 21(4),1455-1508, 2008) showing that several variables proposed in the finance literature are of no use as exogenous information to predict the equity premium under linear regressions. For this non-linear approach to equity premium forecasting, kernel functions for time series are used with multiple kernel learning(MKL) in order to represent the relative importance of each of the variables. We find that, in general, the predictive capabilities of the MKL models do not improve consistently with the use of some or all of the variables, nor does the predictability by single kernels, as determined by different resampling procedures that we implement and compare. This fact tends to corroborate the instability already observed by Welch and Goyal for the predictive power of exogenous variables, now in a non-linear modelling frameworkPeer ReviewedPostprint (author's final draft

A multi-kingdom study reveals the plasticity of the rumen microbiota in response to a shift from non-grazing to grazing diets in sheep

Increasing feed efficiency is a key target in ruminant science which requires a better understanding of rumen microbiota. This study investigated the effect of a shift from a non-grazing to a grazing diet on the rumen bacterial, methanogenic archaea, fungal, and protozoal communities. A systems biology approach based on a description of the community structure, core microbiota, network analysis, and taxon abundance linked to the rumen fermentation was used to explore the benefits of increasing depth of the community analysis. A total of 24 sheep were fed ryegrass hay supplemented with concentrate (CON) and subsequently ryegrass pasture (PAS) following a straight through experimental design. Results showed that concentrate supplementation in CON-fed animals (mainly starch) promoted a simplified rumen microbiota in terms of network density and bacterial, methanogen and fungal species richness which favored the proliferation of amylolytic microbes and VFA production (+48%), but led to a lower (ca. 4-fold) ammonia concentration making the N availability a limiting factor certain microbes. The adaptation process from the CON to the PAS diet consisted on an increase in the microbial concentration (biomass of bacteria, methanogens, and protozoa), diversity (+221, +3, and +21 OTUs for bacteria, methanogens, and fungi, respectively), microbial network complexity (+18 nodes and +86 edges) and in the abundance of key microbes involved in cellulolysis (Ruminococcus, Butyrivibrio, and Orpinomyces), proteolysis (Prevotella and Entodiniinae), lactate production (Streptococcus and Selenomonas), as well as methylotrophic archaea (Methanomassiliicoccaceae). This microbial adaptation indicated that pasture degradation is a complex process which requires a diverse consortium of microbes working together. The correlations between the abundance of microbial taxa and rumen fermentation parameters were not consistent across diets suggesting a metabolic plasticity which allowed microbes to adapt to different substrates and to shift their fermentation products. The core microbiota was composed of 34, 9, and 13 genera for bacteria, methanogens, and fungi, respectively, which were shared by all sheep, independent of diet. This systems biology approach adds a new dimension to our understanding of the rumen microbial interactions and may provide new clues to describe the mode of action of future nutritional interventions.</p

Study of methanogen communities associated with different rumen protozoal populations

Protozoa-associated methanogens (PAM) are considered one of the most active communities in the rumen methanogenesis. This experiment investigated whether methanogens are sequestrated within rumen protozoa, and structural differences between rumen free-living methanogens and PAM. Rumen protozoa were harvested from totally faunated sheep, and six protozoal fractions (plus free-living microorganisms) were generated by sequential filtration. Holotrich-monofaunated sheep were also used to investigate the holotrich-associated methanogens. Protozoal size determined the number of PAM as big protozoa had 1.7–3.3 times more methanogen DNA than smaller protozoa, but also more endosymbiotic bacteria (2.2- to 3.5-fold times). Thus, similar abundance of methanogens with respect to total bacteria were observed across all protozoal fractions and free-living microorganisms, suggesting that methanogens are not accumulated within rumen protozoa in a greater proportion to that observed in the rumen as a whole. All rumen methanogen communities had similar diversity (22.2 ± 3.4 TRFs). Free-living methanogens composed a conserved community (67% similarity within treatment) in the rumen with similar diversity but different structures than PAM (P < 0.05). On the contrary, PAM constituted a more variable community (48% similarity), which differed between holotrich and total protozoa (P < 0.001). Thus, PAM constitutes a community, which requires further investigation as part of methane mitigation strategies

Enhancing rumen microbial diversity and its impact on energy and protein metabolism in forage-fed goats

Introduction: This study explores if promoting a complex rumen microbiota represents an advantage or a handicap in the current dairy production systems in which ruminants are artificially reared in absence of contact with adult animals and fed preserved monophyte forage. Methods: In order to promote a different rumen microbial diversity, a total of 36 newborn goat kids were artificially reared, divided in 4 groups and daily inoculated during 10 weeks with autoclaved rumen fluid (AUT), fresh rumen fluid from adult goats adapted to forage (RFF) or concentrate (RFC) diets, or absence of inoculation (CTL). At 6 months of age all animals were shifted to an oats hay diet to determine their ability to digest a low quality forage. Results and discussion: Early life inoculation with fresh rumen fluid promoted an increase in the rumen overall microbial diversity which was detected later in life. As a result, at 6 months of age RFF and RFC animals had higher bacterial (+50 OTUs) and methanogens diversity (+4 OTUs) and the presence of a complex rumen protozoal community (+32 OTUs), whereas CTL animals remained protozoa-free. This superior rumen diversity and presence of rumen protozoa had beneficial effects on the energy metabolism allowing a faster adaptation to the forage diet, a higher forage digestion (+21% NDF digestibility) and an energetically favourable shift of the rumen fermentation pattern from acetate to butyrate (+92%) and propionate (+19%) production. These effects were associated with the presence of certain rumen bacterial taxa and a diverse protozoal community. On the contrary, the presence of rumen protozoa (mostly Entodinium) had a negative impact on the N metabolism leading to a higher bacterial protein breakdown in the rumen and lower microbial protein flow to the host based on purine derivatives urinary excretion (-17% to -54%). The inoculation with autoclaved rumen fluid, as source of fermentation products but not viable microbes, had smaller effects than using fresh inoculum. These findings suggest that enhancing rumen microbial diversity represents a desirable attribute when ruminants are fed forages in which the N supply does not represent a limiting factor for the rumen microbiota