Nitrogen metabolism and rumen microbial enumeration in lactating cows with divergent residual feed intake fed high-digestibility pasture

Effects of rumen-bypass protein supplement on growth performance, hepatic mitochondrial protein complexes, and hepatic immune gene expression of beef steers with divergent residual feed intake

We investigated the impact of a rumen-bypass protein (RBP) supplement on growth performance, plasma and urinary N (UN) concentration, hepatic mitochondrial protein complexes, and hepatic mRNA expression of immune genes of beef steers with negative or positive residual feed intake (RFI) phenotype. Forty crossbred beef steers with an average body weight (BW) of 492 ± 36 kg were subjected to a generalized randomized block design over a 42-day experimental period. This study followed a 2 × 2 factorial arrangement of treatments. The factors evaluated were: 1) RFI classification (low-RFI (-2.12 kg/d) vs. high-RFI (2.02 kg/d), and 2) rumen-bypass protein supplement: RBP supplement (RBP; 227 g/steer/d) vs. control diet (CON; 0 g/d), resulting in four distinct treatments: LRFI-CON (n = 10), LRFI-RBP (n = 10), HRFI-CON (n = 10), and HRFI-RBP (n = 10). The RBP supplement (84% crude protein) is a mixture of hydrolyzed feather meal, porcine blood meal, and DL-methionine hydroxy analogue. The beef steers were stratified by BW, randomly assigned to treatments, and housed in four pens (1 treatment/pen) equipped with two GrowSafe feed bunks each to measure individual dry mater intake (DMI). Body weight was measured every 7 d. Liver tissue samples were collected on d 42 from all the beef steers. These samples were used for mRNA expression analysis of 16 immune-related genes and for evaluating the mitochondrial protein complexes I - V. No significant effects due to RBP supplementation or RFI × RBP interactions (P > 0.05) were observed for average daily gain (ADG) and DMI. However, compared to high-RFI steers, low-RFI steers showed a trend towards reduced DMI (12.9 vs. 13.6 kg/d; P = 0.07) but ADG was similar for the two RFI groups. Regardless of RFI status, supplemental RBP increased blood urea nitrogen (BUN) (P = 0.01), with a lower BUN concentration in low-RFI steers compared to high-RFI ones. A tendency for interaction (P = 0.07) between RFI and RBP was detected for the UN concentrations; feeding the dietary RBP increased the UN concentration in high-RFI beef steers (209 vs. 124 mM), whereas the concentration was lower than that of the CON group for low-RFI beef steers (86 vs. 131 mM). Interactions of RBP and RFI were observed (P ≤ 0.05) for mitochondrial activities of complexes IV, V, and mRNA expressions of some immune genes such as TLR2, TLR3, and IL23A. In conclusion, while RBP supplementation did not alter growth performance, its observed effects on hepatic immune gene expression, mitochondrial protein complexes, BUN, and UN depended on the beef steers' RFI phenotype. Therefore, the RFI status of beef steers should be considered in future studies evaluating the effects of dietary protein supplements.

The impact of twice daily 3-nitroxypropanol supplementation on enteric methane emissions in grazing dairy cows

Although 3-NOP has been proven to reduce enteric methane (CH4) by ∼30% in indoor systems of dairying when the additive is mixed throughout a total mixed ration (TMR), there has been very limited research to date in grazing systems in which the most convenient method of additive supplementation is at milking twice daily. To investigate the effect of twice daily 3-NOP supplementation on enteric CH4 emissions, a 12-week study was undertaken in which treatment cows (n = 26) were supplemented with 3-NOP (80 mg per kg dry matter intake; DMI) twice daily at morning and evening milking, while control cows (n = 26) received no additive supplementation. Enteric CH4, hydrogen (H2) and carbon dioxide (CO2) were measured using GreenFeed units, while milk production, body weight (BW), body condition score (BCS) and DMI were monitored to determine the effect of 3-NOP supplementation on productivity. There was no significant effect of 3-NOP supplementation on any of the aforementioned parameters with the exception of CH4 and H2 production, respectively. Cows supplemented with 3-NOP produced ∼36% more H2 (P < 0.001) across a 24-h period, with reductions in CH4 production of 28.5% recorded in the 3 h after additive consumption (P < 0.001), however, levels of CH4 production returned to that of the control group thereafter. When CH4 production was considered across the entire 24-h period, the cows offered 3-NOP produced ∼5% less CH4 than the control (P < 0.050). Future research should focus on methods to increase the efficacy of the additive throughout the day which would include the deployment of a slow-release form or an out of parlor feeding system that allows animals consume the product at additional time points.

Integrating microbial abundance time series with fermentation dynamics of the rumen microbiome via mathematical modelling

The rumen represents a dynamic microbial ecosystem where fermentation metabolites and microbial concentrations change over time in response to dietary changes. The integration of microbial genomic knowledge and dynamic modelling can enhance our system-level understanding of rumen ecosystem's function. However, such an integration between dynamic models and rumen microbiota data is lacking. The objective of this work was to integrate rumen microbiota time series determined by 16S rRNA gene amplicon sequencing into a dynamic modelling framework to link microbial data to the dynamics of the volatile fatty acids (VFA) production during fermentation. For that, we used the theory of state observers to develop a model that estimates the dynamics of VFA from the data of microbial functional proxies associated with the specific production of each VFA. We determined the microbial proxies using CowPi to infer the functional potential of the rumen microbiota and extrapolate their functional modules from KEGG (Kyoto Encyclopedia of Genes and Genomes). The approach was challenged using data from an in vitro RUSITEC experiment and from an in vivo experiment with four cows. The model performance was evaluated by the coefficient of variation of the root mean square error (CRMSE). For the in vitro case study, the mean CVRMSE were 9.8% for acetate, 14% for butyrate and 14.5% for propionate. For the in vivo case study, the mean CVRMSE were 16.4% for acetate, 15.8% for butyrate and 19.8% for propionate. The mean CVRMSE for the VFA molar fractions were 3.1% for acetate, 3.8% for butyrate and 8.9% for propionate. Ours results show the promising application of state observers integrated with microbiota time series data for predicting rumen microbial metabolism.

Fecal microbiota colonization dynamics in dairy heifers associated with early-life rumen microbiota modulation and gut health

Early-life modulation of rumen microbiota holds promise for enhancing calf growth, health, and long-term production in ruminants. However, limited attention has been given to the impact of rumen microbiota modulation on the establishment of hindgut microbiota. In this study, fecal microbiota development was examined in identical twin calves for 12 months. The treatment group (T-group) received adult cow fresh rumen liquid inoculum during the pre-weaning period, while the control group did not (C-group). The effects of inoculum were assessed on calf gut health and as microbial seeding route into the hindgut. The early rumen modulation had no effect on age-related fecal microbiota development. The fecal bacterial community evolved gradually following dietary changes and categorized into pre-weaning and post-weaning communities. Bacterial richness increased with age and stabilized at month 9, while between-sample variation reduced in post-weaning samples. Archaeal load in fecal samples increased after month 4, while archaeal richness increased and stabilized in both groups by month 9. Between-sample similarity was higher during the pre-weaning period, with increased dissimilarity from month 4 onward. Anaerobic fungi were detected in feces at month 4, with richness peaking at month 7. Before month 6, fungal community composition distinctly differed from mature communities. When colostrum, calf rumen, and donor inoculum were evaluated as seeding sources for hindgut colonization, the calf's own rumen was identified as the primary seeding source for fecal bacteria and fungi. Colostrum was a source for several bacteria detected in feces, but these were of temporary importance until weaning. The donor inoculum had limited impact on gut health as diarrhea rates were similar between the T-group and C-group. In conclusion, early-life microbiota modulation shows potential in ruminant development. However, a more targeted approach with bacteria adapted to the hindgut environment may be necessary to modulate hindgut effectively. This research contributes to our understanding of the complex relationship between gut microbiota and calf health and growth.

The intestinal digesta microbiota of tropical marine fish is largely uncultured and distinct from surrounding water microbiota

Studying the gut microbes of marine fishes is an important part of conservation as many fish species are increasingly threatened by extinction. The gut microbiota of only a small fraction of the more than 32,000 known fish species has been investigated. In this study we analysed the intestinal digesta microbiota composition of more than 50 different wild fish species from tropical waters. Our results show that the fish harbour intestinal digesta microbiota that are distinct from that of the surrounding water and that location, domestication status, and host intrinsic factors are strongly associated with the microbiota composition. Furthermore, we show that the vast majority (~97%) of the fish-associated microorganisms do not have any cultured representative. Considering the impact of the microbiota on host health and physiology, these findings underpin the call to also preserve the microbiota of host species, especially those that may be exposed to habitat destruction.

The effects of residual energy intake on nutrient use, methane emissions and microbial composition in dairy cows

For sustainable food production selection and breeding of feed efficient animals is crucial. The objective of this study was to evaluate whether multiparous dairy cows, ranked during their first lactation based on residual energy intake (REI) as efficient (low; L-REI) or inefficient (high; H-REI), differ in terms of nutrient use efficiency, methane emissions, rumen fermentation, and gut microbiota composition. Six L-REI and 6 H-REI cows were offered two diets with either a low or high proportion of concentrates (30 vs. 50% of DM) on two consecutive periods of 21 d. Gas exchanges, milk yield, feces and urine excretions were measured in open-circuit respiratory chambers. The results indicated that L-REI cows had higher methane yields (22.6 vs. 20.4 g/kg DM intake) and derived more energy (energy balance - 36.6 vs. - 16.9 MJ/d) and protein (N balance - 6.6 vs. 18.8 g/d) from the tissues to support similar milk yields compared to H-REI cows. Nutrient intake and digestibility were not affected by REI, and there were no interactions between REI and diet. Milk yield, milk production efficiency, and milk composition were not affected by REI except for milk urea concentration that was higher for L-REI cows (14.1 vs. 10.8 mg/100 ml). The rumen and fecal microbiota community structure and function were associated with both the diet and REI, but the diet effect was more pronounced. The current study identified several physiological mechanisms underlying the differences between high and low REI cows, but further studies are needed to distinguish the quantitative role of each mechanism.

Effect of a garlic and citrus extract supplement on performance, rumen fermentation, methane production, and rumen microbiome of dairy cows

The aim of this trial was to determine the effect of a garlic and citrus extract supplement (GCE) on the performance, rumen fermentation, methane emissions, and rumen microbiome of dairy cows. Fourteen multiparous Nordic Red cows in mid-lactation from the research herd of Luke (Jokioinen, Finland) were allocated to 7 blocks in a complete randomized block design based on body weight, days in milk, dry matter intake (DMI), and milk yield. Animals within each block were randomly allocated to a diet with or without GCE. The experimental period for each block of cows (one for each of the control and GCE groups) consisted of 14 d of adaptation followed by 4 d of methane measurements inside the open circuit respiration chambers, with the first day being considered as acclimatization. Data were analyzed using the GLM procedure of SAS (SAS Institute Inc.). Methane production (g/d) and methane intensity (g/kg of energy-corrected milk) were lower by 10.3 and 11.7%, respectively, and methane yield (g/kg of DMI) tended to be lower by 9.7% in cows fed GCE compared with the control. Dry matter intake, milk production, and milk composition were similar between treatments. Rumen pH and total volatile fatty acid concentrations in rumen fluid were similar, whereas GCE tended to increase molar propionate concentration and decrease the molar ratio of acetate to propionate. Supplementation with GCE resulted in greater abundance of Succinivibrionaceae, which was associated with reduced methane. The relative abundance of the strict anaerobic Methanobrevibacter genus was reduced by GCE. The change in microbial community and rumen propionate proportion may explain the decrease in enteric methane emissions. In conclusion, feeding GCE to dairy cows for 18 d modified rumen fermentation and microbiota, leading to reduced methane production and intensity without compromising DMI or milk production in dairy cows. This could be an effective strategy for enteric methane mitigation of dairy cows.

Fermented Total Mixed Ration Alters Rumen Fermentation Parameters and Microbiota in Dairy Cows

This study aimed to determine changes and interactions of ruminal microbiota and chemical parameters in dairy cows fed FTMR. Twelve multiparous Holstein dairy cows (Body weight = 616 ± 13.4 kg; day in milk = 106 ± 7.55 d; and parity = 2.31 ± 0.49; mean ± standard deviation) were divided randomly into two treatments depending on the day in milk, milk production, and parity. The two treatments were: (1) total mixed ration (TMR) and (2) FTMR. Illumina MiSeq sequencing was used to explore the changes in the ruminal microbiota. The results revealed that the bacterial and fungal diversity of the FTMR group were significantly higher than the TMR group. The predominant microbiota phyla in the bacteria and fungi showed significant differences between TMR and FTMR, as follows: Verrucomicrobia (p = 0.03) and Tenericutes (p = 0.01), Ascomycota (p = 0.04) and Basidiomycota (p = 0.04). The dominant bacterial genera in the bacteria, fungi, protozoan, and archaea that showed significant differences between TMR and FTMR were Unclassified_Bacteroidales (p = 0.02), Unclassified_RFP12 (p = 0.03), Candida (p = 0.0005), Bullera (p = 0.002), Cryptococcus (p = 0.007), and Ostracodinium (p = 0.01). LefSe analysis was performed to reveal the biomarker genera of the rumen microbiota community (bacteria, fungi, protozoan, and archaea) in the TMR and FTMR were the genera Shuttleworthia, Ruminococcus, Cryptococcus, Mycosphaerella, Bullera, Candida, and Ostracodinium. NH3-N concentration (p < 0.0001), total VFA concentration (p = 0.003), and molar proportion in total VFA of acetate (p = 0.01) were higher for the cows fed FTMR compared with the cows fed the TMR. Several bacterial genera showed significant correlations with rumen fermentation parameters. The genus Unclassified_Bacteroidales and Bullera were positively correlated with total volatile fatty acids (VFA) and acetate, whereas Candida and Ostracodinium showed negative correlations. Meanwhile, propionate was positively correlated with Candida and negatively correlated with Bullera. The PICRUSt functional profile prediction indicated that the xenobiotics biodegradation and metabolism, the lipid, amino acid, terpenoids, and polyketides metabolisms of the FTMR group were significantly higher than that of the TMR group. The results imply that FTMR can increase lipid and amino acid metabolism, and modulate the rumen microbiome and improve ruminal fermentation.

Long-term effects of early-life rumen microbiota modulation on dairy cow production performance and methane emissions

Rumen microbiota modulation during the pre-weaning period has been suggested as means to affect animal performance later in life. In this follow-up study, we examined the post-weaning rumen microbiota development differences in monozygotic twin-heifers that were inoculated (T-group) or not inoculated (C-group) (n = 4 each) with fresh adult rumen liquid during their pre-weaning period. We also assessed the treatment effect on production parameters and methane emissions of cows during their 1st lactation period. The rumen microbiota was determined by the 16S rRNA gene, 18S rRNA gene, and ITS1 amplicon sequencing. Animal weight gain and rumen fermentation parameters were monitored from 2 to 12 months of age. The weight gain was not affected by treatment, but butyrate proportion was higher in T-group in month 3 (p = 0.04). Apart from archaea (p = 0.084), the richness of bacteria (p < 0.0001) and ciliate protozoa increased until month 7 (p = 0.004) and anaerobic fungi until month 11 (p = 0.005). The microbiota structure, measured as Bray-Curtis distances, continued to develop until months 3, 6, 7, and 10, in archaea, ciliate protozoa, bacteria, and anaerobic fungi, respectively (for all: p = 0.001). Treatment or age × treatment interaction had a significant (p < 0.05) effect on 18 bacterial, 2 archaeal, and 6 ciliate protozoan taxonomic groups, with differences occurring mostly before month 4 in bacteria, and month 3 in archaea and ciliate protozoa. Treatment stimulated earlier maturation of prokaryote community in T-group before month 4 and earlier maturation of ciliate protozoa at month 2 (Random Forest: 0.75 month for bacteria and 1.5 month for protozoa). No treatment effect on the maturity of anaerobic fungi was observed. The milk production and quality, feed efficiency, and methane emissions were monitored during cow's 1st lactation. The T-group had lower variation in energy-corrected milk yield (p < 0.001), tended to differ in pattern of residual energy intake over time (p = 0.069), and had numerically lower somatic cell count throughout their 1st lactation period (p = 0.081), but no differences between the groups in methane emissions (g/d, g/kg DMI, or g/kg milk) were observed. Our results demonstrated that the orally administered microbial inoculant induced transient changes in early rumen microbiome maturation. In addition, the treatment may influence the later production performance, although the mechanisms that mediate these effects need to be further explored.

Host Age Prediction from Fecal Microbiota Composition in Male C57BL/6J Mice

The lifelong relationship between microorganisms and hosts has a profound impact on the overall health and physiology of the holobiont. Microbiome composition throughout the life span of a host remains largely understudied. Here, the fecal microbiota of conventionally raised C57BL/6J male mice was characterized throughout almost the entire adult life span, from "maturing" (9 weeks) until "very old" (112 weeks) age. Our results suggest that microbiota changes occur throughout life but are more pronounced in maturing to middle-age mice than in mice later in life. Phylum-level analysis indicates a shift of the Bacteroidota-to-Firmicutes ratio in favor of Firmicutes in old and very old mice. More Firmicutes amplicon sequence variants (ASVs) were transient with varying successional patterns than Bacteroidota ASVs, which varied primarily during maturation. Microbiota configurations from five defined life phases were used as training sets in a Bayesian model, which effectively enabled the prediction of host age. These results suggest that age-associated compositional differences may have considerable implications for the interpretation and comparability of animal model-based microbiome studies. The sensitivity of the age prediction to dietary perturbations was tested by applying this approach to two age-matched groups of C57BL/6J mice that were fed either a standard or western diet. The predicted age for the western diet-fed animals was on average 27 ± 11 (mean ± standard deviation) weeks older than that of standard diet-fed animals. This indicates that the fecal microbiota-based predicted age may be influenced not only by the host age and physiology but also potentially by other factors such as diet. IMPORTANCE The gut microbiome of a host changes with age. Cross-sectional studies demonstrate that microbiota of different age groups are distinct but do not demonstrate the temporal change that a longitudinal study is able to show. Here, we performed a longitudinal study of adult mice for over 2 years. We identified life stages where compositional changes were more dynamic and showed temporal changes for the more abundant species. Using a Bayesian model, we could reliably predict the life stages of the mice. Application of the same training set to mice fed different dietary regimens revealed that life-stage age predictions were possible for mice fed the same diet but less so for mice fed different diets. This study sheds light on the temporal changes that occur within the gut microbiota of laboratory mice over their life span and may inform researchers on the appropriate mouse age for their research.

Low-cost sample preservation methods for high-throughput processing of rumen microbiomes

Background

The use of rumen microbial community (RMC) profiles to predict methane emissions has driven interest in ruminal DNA preservation and extraction protocols that can be processed cheaply while also maintaining or improving DNA quality for RMC profiling. Our standard approach for preserving rumen samples, as defined in the Global Rumen Census (GRC), requires time-consuming pre-processing steps of freeze drying and grinding prior to international transportation and DNA extraction. This impedes researchers unable to access sufficient funding or infrastructure. To circumvent these pre-processing steps, we investigated three methods of preserving rumen samples for subsequent DNA extraction, based on existing lysis buffers Tris-NaCl-EDTA-SDS (TNx2) and guanidine hydrochloride (GHx2), or 100% ethanol.

Results

Rumen samples were collected via stomach intubation from 151 sheep at two time-points 2 weeks apart. Each sample was separated into four subsamples and preserved using the three preservation methods and the GRC method (n = 4 × 302). DNA was extracted and sequenced using Restriction Enzyme-Reduced Representation Sequencing to generate RMC profiles. Differences in DNA yield, quality and integrity, and sequencing metrics were observed across the methods (p < 0.0001). Ethanol exhibited poorer quality DNA (A260/A230 < 2) and more failed samples compared to the other methods. Samples preserved using the GRC method had smaller relative abundances in gram-negative genera Anaerovibrio, Bacteroides, Prevotella, Selenomonas, and Succiniclasticum, but larger relative abundances in the majority of 56 additional genera compared to TNx2 and GHx2. However, log₁₀ relative abundances across all genera and time-points for TNx2 and GHx2 were on average consistent (R² > 0.99) but slightly more variable compared to the GRC method. Relative abundances were moderately to highly correlated (0.68 ± 0.13) between methods for samples collected within a time-point, which was greater than the average correlation (0.17 ± 0.11) between time-points within a preservation method.

Conclusions

The two modified lysis buffers solutions (TNx2 and GHx2) proposed in this study were shown to be viable alternatives to the GRC method for RMC profiling in sheep. Use of these preservative solutions reduces cost and improves throughput associated with processing and sequencing ruminal samples. This development could significantly advance implementation of RMC profiles as a tool for breeding ruminant livestock.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00190-z.

Fresh Rumen Liquid Inoculant Enhances the Rumen Microbial Community Establishment in Pre-weaned Dairy Calves

The development of the functional rumen in calves involves a complex interplay between the host and host-related microbiome. Attempts to modulate rumen microbial community establishment may therefore have an impact on weaning success, calf health, and animal performance later in life. In this experiment, we aimed to elucidate how rumen liquid inoculum from an adult cow, provided to calves during the pre-weaning period, influences the establishment of rumen bacterial, archaeal, fungal, and ciliate protozoan communities in monozygotic twin calves (n = 6 pairs). The calves were divided into treatment (T-group) and control (C-group) groups, where the T-group received fresh rumen liquid as an oral inoculum during a 2-8-week period. The C-group was not inoculated. The rumen microbial community composition was determined using bacterial and archaeal 16S ribosomal RNA (rRNA) gene, protozoal 18S rRNA gene, and fungal ITS1 region amplicon sequencing. Animal weight gain and feed intake were monitored throughout the experiment. The T-group tended to have a higher concentrate intake (Treatment: p < 0.08) and had a significantly higher weekly weight gain (Treatment: p < 0.05), but no significant difference in volatile fatty acid concentrations between the groups was observed. In the T-group, the inoculum stimulated the earlier establishment of mature rumen-related bacterial taxa, affecting significant differences between the groups until 6 weeks of age. The inoculum also increased the archaeal operational taxonomic unit (OTU) diversity (Treatment: p < 0.05) but did not affect the archaeal quantity. Archaeal communities differed significantly between groups until week 4 (p = 0.02). Due to the inoculum, ciliate protozoa were detected in the T-group in week 2, while the C-group remained defaunated until 6 weeks of age. In week 8, Eremoplastron dilobum was the dominant ciliate protozoa in the C-group and Isotricha sp. in the T-group, respectively. The Shannon diversity of rumen anaerobic fungi reduced with age (Week: p < 0.01), and community establishment was influenced by a change of diet and potential interaction with other rumen microorganisms. Our results indicate that an adult cow rumen liquid inoculum enhanced the maturation of bacterial and archaeal communities in pre-weaning calves' rumen, whereas its effect on eukaryotic communities was less clear and requires further investigation.

Apart From the Diet, the Ruminal Microbiota of Lambs Is Modified in Relation to Their Genetic Potential for Feed Efficiency or Feeding Behavior

Using two successive types of diets (100% concentrate and 67% forage), this study explores the relationship between the ruminal microbiota of 78 Romane lambs and their feed efficiency (residual feed intake trait) or feeding behavior (feeding rate trait). Analysis was carried out phenotypically by correlating feed efficiency or feeding behavior traits with the relative abundance of bacteria at the phylum, family, and genus levels, and then genetically by comparing the microbiota of lambs selected for extreme breeding values for residual feed intake or feeding rate. Our results confirmed the major effect of diet on the ruminal microbiota composition. The microbiota of lambs consuming a forage-based diet was distinguished by higher microbial diversity and also by higher relative abundance of Firmicutes, whereas Bacteriodetes and Actinobacteria were relatively more abundant in the microbiota of lambs consuming a concentrate-based diet. Moreover, the comparison of lambs divergent for residual feed intake breeding values revealed that regardless of diet, more efficient lambs possessed a ruminal microbiota enriched in Coprococcus, Moryella, [Eubacterium] Brachy group, and [Eubacterium] hallii group, but depleted in Lachnospiraceae FD2005 and Shuttleworthia. The connection between microbiota composition and feeding rate was more tenuous, with no link between the abundance of particular genera and lambs genetically divergent for feeding rate.

Effect of Divergent Feeding Regimes During Early Life on the Rumen Microbiota in Calves

The objective of this study was to determine whether divergent feeding regimes during the first 41 weeks of the life of a calf are associated with long-term changes in the rumen microbiota and the associated fermentation end-products. Twenty-four calves (9 ± 5 days of age) were arranged in a 2 × 2 factorial design with two divergent treatments across three dietary phases. In phase 1 (P01), calves were offered a low-milk volume/concentrate starter diet with early weaning (CO) or high-milk volume/pasture diet and late weaning (FO). In phase 2 (P02), calves from both groups were randomly allocated to either high-quality (HQ) or low-quality (LQ) pasture grazing groups. In phase 3 (P03), calves were randomly allocated to one of two grazing groups and offered the same pasture-only diet. During each dietary phase, methane (CH₄) and hydrogen (H₂) emissions and dry matter intake (DMI) were measured in respiration chambers, and rumen samples for the evaluation of microbiota and short-chain fatty acid (SCFA) characterizations were collected. In P01, CO calves had a higher solid feed intake but a lower CH₄ yield (yCH₄) and acetate:propionate ratio (A:P) compared with FO calves. The ruminal bacterial community had lower proportions of cellulolytic bacteria in CO than FO calves. The archaeal community was dominated by Methanobrevibacter boviskoreani in CO calves and by Mbb. gottschalkii in FO calves. These differences, however, did not persist into P02. Calves offered HQ pastures had greater DMI and lower A:P ratio than calves offered LQ pastures, but yCH₄ was similar between groups. The cellulolytic bacteria had lower proportions in HQ than LQ calves. In all groups, the archaeal community was dominated by Mbb. gottschalkii. No treatment interactions were observed in P02. In P03, all calves had similar DMI, CH₄ and H₂ emissions, SCFA proportions, and microbial compositions, and no interactions with previous treatments were observed. These results indicate that the rumen microbiota and associated fermentation end-products are driven by the diet consumed at the time of sampling and that previous dietary interventions do not lead to a detectable long-term microbial imprint or changes in rumen function.

Seasonal Variation in the Faecal Microbiota of Mature Adult Horses Maintained on Pasture in New Zealand

Simple Summary

Ten horses were kept on pasture for one year, with hay provided from June to October. Each month we measured how much pasture was present and collected pasture and hay samples to assess their nutrient content, and faecal samples from all horses to investigate the diversity of the bacterial species present using next-generation sequencing technology. The population of faecal bacteria was more diverse during the months when the horses were kept exclusively on pasture compared to the months when pasture was supplemented with hay. The diet offered, and the season and the month we sampled the paddock all had a major influence on the diversity of the species of bacteria in the faeces. While there were some differences between the horses, generally the bacterial populations could be grouped together in samples obtained during May, June, and July (late-autumn to winter period), and January, February, and March (a period of drought). More specifically we were able to show an association between specific bacterial species, nutrients (dry matter, protein, and structural carbohydrates), and climatic conditions (rainfall and temperature). Our study showed that the diversity and composition of the bacterial population of horses kept on pasture changes over a 12-month period, and this reflects changes in the nutrient composition of the pasture, which in turn is influenced by climate. The findings of this study may have implications for managing horses on pasture and the use of forages for horses susceptible to digestive problems.

Abstract

Seasonal variation in the faecal microbiota of forage-fed horses was investigated over a 12-month period to determine whether the bacterial diversity fluctuated over time. Horses (n = 10) were maintained on pasture for one year, with hay supplemented from June to October. At monthly intervals, data were recorded on pasture availability and climate (collected continuously and averaged on monthly basis), pasture and hay samples were collected for nutrient analysis, and faecal samples were collected from all horses to investigate the diversity of faecal microbiota using next-generation sequencing on the Illumina MiSeq platform. The alpha diversity of bacterial genera was high in all samples (n = 118), with significantly higher Simpson’s (p < 0.001) and Shannon-Wiener (p < 0.001) diversity indices observed during the months when horses were kept exclusively on pasture compared to the months when pasture was supplemented with hay. There were significant effects of diet, season, and month (ANOSIM, p < 0.01 for each comparison) on the beta diversity of bacterial genera identified in the faeces. While there was some inter-horse variation, hierarchical clustering of beta diversity indices showed separate clades originating for samples obtained during May, June, and July (late-autumn to winter period), and January, February, and March (a period of drought), with a strong association between bacterial taxa and specific nutrients (dry matter, protein, and structural carbohydrates) and climate variables (rainfall and temperature). Our study supports the hypothesis that the diversity and community structure of the faecal microbiota of horses kept on pasture varied over a 12-month period, and this variation reflects changes in the nutrient composition of the pasture, which in turn is influenced by climatic conditions. The findings of this study may have implications for grazing management and the preparation of conserved forages for those horses susceptible to perturbations of the hindgut microbiota.

Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal Tract

Dietary changes are known to alter the composition of the gut microbiome. However, it is less understood how repeatable and reversible these changes are and how diet switches affect the microbiota in the various segments of the gastrointestinal tract. Here, a treatment group of conventionally raised laboratory mice is subjected to two periods of western diet (WD) interrupted by a period of standard diet (SD) of the same duration. Beta-diversity analyses show that diet-induced microbiota changes are largely reversible (q = 0.1501; PERMANOVA, weighted-UniFrac comparison of the treatment-SD group to the control-SD group) and repeatable (q = 0.032; PERMANOVA, weighted-UniFrac comparison of both WD treatments). Furthermore, we report that diet switches alter the gut microbiota composition along the length of the intestinal tract in a segment-specific manner, leading to gut segment-specific Firmicutes/Bacteroidota ratios. We identified prevalent and distinct Amplicon Sequencing Variants (ASVs), particularly in genera of the recently described Muribaculaceae, along the gut as well as ASVs that are differentially abundant between segments of treatment and control groups. Overall, this study provides insights into the reversibility of diet-induced microbiota changes and highlights the importance of expanding sampling efforts beyond the collections of fecal samples to characterize diet-dependent and segment-specific microbiome differences.

Assessing feed efficiency in early and mid lactation and its associations with performance and health in Holstein cows

Objectives were to evaluate the associations between residual dry matter (DM) intake (RFI) and residual N intake (RNI) in early lactation, from 1 to 5 wk postpartum, and in mid lactation, from 9 to 15 wk postpartum, and assess production performance and risk of diseases in cows according to RFI in mid lactation. Data from 4 experiments including 399 Holsteins cows were used in this study. Intakes of DM and N, yields of milk components, body weight, and body condition were evaluated daily or weekly for the first 105 d postpartum. Milk yield by 305 d postpartum was also measured. Incidence of disease was evaluated for the first 90 d postpartum and survival up to 300 d postpartum. Residual DM and N intake were calculated in early and mid lactation as the observed minus the predicted values, which were based on linear models that accounted for major energy or N sinks, including daily milk energy or N output, metabolic body weight, and daily body energy or N changes, and adjusting for parity, season of calving, and treatment within experiment. Cows were ranked by RFI and RNI in mid lactation and categorized into quartiles (Q1 = smallest RFI, to Q4 = largest RFI). Increasing efficiency in mid lactation resulted in linear decreases in RFI (depicted from Q1 to Q4; -0.93, -0.05, -0.04, and 0.98 kg/d), DMI (16.0, 16.9, 17.3, and 18.4 kg/d), net energy for lactation (NE_L) intake (26.8, 28.4, 29.0, and 30.8 Mcal/d), and NE_L balance (-9.0, -8.1, -8.2, and -5.5 Mcal/d) during early lactation, but no differences were observed in body NE_L or N changes or yield of energy-corrected milk in the first 5 wk of lactation. Residual DM intake in mid lactation was associated with RFI (Pearson r = 0.43, and Spearman ρ = 0.32) and RNI (r = 0.44, ρ = 0.36) in early lactation, and with RNI in mid lactation (r = 0.91, ρ = 0.84). Similarly, RNI in mid lactation was associated with RNI in early lactation (r = 0.42, ρ = 0.35). During the first 15 wk postpartum, more efficient cows in mid lactation consumed 3.5 kg/d less DM (Q1 = 19.3 vs. Q4 = 22.8 kg/d) and were more N efficient (Q1 = 31.6 vs. Q4 = 25.8%), at the same time that yields of milk (Q1 = 39.0 vs. Q4 = 39.4 kg/d), energy-corrected milk (Q1 = 38.6 vs. Q4 = 39.3 kg/d), and milk components did not differ compared with the quartile of least efficient cows. Furthermore, RFI in mid lactation was not associated with 305-d milk yield, incidence of diseases in the first 90 d postpartum, or survival by 300 d postpartum. Collectively, rankings of RFI and RNI are associated and repeatable across lactation stages. The most feed-efficient cows were also more N efficient in early and mid lactation. Phenotypic selection of RFI based on measurements in mid lactation is associated with improved efficiency without affecting production or health in dairy cows.

Effects of long-acting, broad spectra anthelmintic treatments on the rumen microbial community compositions of grazing sheep

Anthelmintic treatment of adult ewes is widely practiced to remove parasite burdens in the expectation of increased ruminant productivity. However, the broad activity spectra of many anthelmintic compounds raises the possibility of impacts on the rumen microbiota. To investigate this, 300 grazing ewes were allocated to treatment groups that included a 100-day controlled release capsule (CRC) containing albendazole and abamectin, a long-acting moxidectin injection (LAI), and a non-treated control group (CON). Rumen bacterial, archaeal and protozoal communities at day 0 were analysed to identify 36 sheep per treatment with similar starting compositions. Microbiota profiles, including those for the rumen fungi, were then generated for the selected sheep at days 0, 35 and 77. The CRC treatment significantly impacted the archaeal community, and was associated with increased relative abundances of Methanobrevibacter ruminantium, Methanosphaera sp. ISO3-F5, and Methanomassiliicoccaceae Group 12 sp. ISO4-H5 compared to the control group. In contrast, the LAI treatment increased the relative abundances of members of the Veillonellaceae and resulted in minor changes to the bacterial and fungal communities by day 77. Overall, the anthelmintic treatments resulted in few, but highly significant, changes to the rumen microbiota composition.

Characterization of the rumen microbiota and its relationship with residual feed intake in sheep

Feed efficiency is a highly important economic trait in sheep production and has a significant impact on the economic benefits of sheep farming. Microbial fermentation of the rumen has a vital role in the host's nutrition; the rumen microbiota might affect host feed efficiency. However, the relationship between the rumen microbiota and feed efficiency in sheep is unclear. In the present study, the microbiota of 195 Hu sheep was investigated and their residual feed intake (RFI), a commonly used measure of feed efficiency, was determined. From birth, all sheep were subjected to the same management practices. At slaughter, samples of liquid rumen contents were collected and subjected to amplicon sequencing for the 16S rDNA gene on the IonS5™XL platform. To identify the bacterial taxa differentially represented at the genus or higher taxonomy levels, we used linear discriminant analysis coupled with effect size and curve fitting. In the sheep rumen, the four most abundant phyla were Firmicutes, Bacteroidetes, Fibrobacteres, and Proteobacteria; and the dominant genera were unidentified Prevotellaceae, Fibrobacter, unidentified Lachnospiraceae, Saccharofermentans, and Succinivibrio. Pathway analysis of the 16S rDNA sequencing data from the rumen microbiota identified that carbohydrate metabolism was enriched. Using α-diversity analysis, we further identified that Observed species, ACE, Good's coverage, and Chao1 are more abundant (P < 0.01) in the low-RFI (L-RFI) group compared to the high-RFI (H-RFI) group. High-RFI sheep had a higher abundance of three bacterial taxa (Prevotellaceae, Negativicutes, and Selenomonadales), and one taxa was overrepresented in the L-RFI sheep (Succinivibrio), respectively. Furthermore, model fitting showed that Veillonellaceae, Sphaerochaeta, Negativibacillus, Saccharofermentans, and members of the Tenericutes, Kiritimatiellaeota, Deltaproteobacteria, and Campylobacterales were correlated with the sheep RFI classification and thus were indicative of a role in animal efficiency. Tax4Fun analysis revealed that metabolic pathways such as "energy metabolism," "metabolism of cofactors and vitamins," "poorly characterized," and "replication recombination and repair proteins" were enriched in the rumen from H-RFI sheep, and "genetic information processing" and "lipopolysaccharide biosynthesis" were overrepresented in L-RFI sheep rumen. In addition, six Kyoto Encyclopedia of Genes and Genomes orthology pathways were identified as different between H-RFI and L-RFI groups. In conclusion, the low RFI phenotype (efficient animals) consistently (or characteristically) exhibited a more abundant and diverse microbiome in sheep.

Effect of zeolite administration on nitrogen metabolism and excretion in lactating dairy cows offered pasture herbage

Context Due to high protein concentrations in pastures, dairy cows offered a pasture-based diet often consume excess nitrogen (N), which leads to high ruminal ammonia concentrations and excessive urinary N excretion, thereby contributing to pasture N leaching. Aims To study the effect of administration of natural zeolite on ruminal pH and ammonia production and N excretion in lactating cows offered an all-pasture herbage diet. Methods In a metabolism stall trial using a crossover trial design, rumen-cannulated Friesian cows were administered either zero (Control, n = 16) or 400 g/day of zeolite (Zeolite; n = 16). Zeolite was divided into two equal portions and administered directly into the rumen before feeding fresh-cut ryegrass-clover herbage at 07:30 and 15:30 hours. Cows were kept in the metabolism stalls for two measurement periods of 5 days each, with each period preceded by an adaptation/washout period of 2 weeks. Feed intake, milk yield, total urine and faecal outputs were measured daily. During the last day of each measurement period ruminal fluid and blood were frequently sampled. Key results Zeolite administered at 2.2% of dry matter intake (DMI) did not affect daily DMI. Moreover, milk yield and milk composition, including milk urea, were not affected by zeolite administration. In cows administered zeolite the mean 24-h ruminal ammonia concentration was reduced by 1.5 mmol/L (9%) and the ruminal pH pattern in zeolite-administered cows over 24 h was above that of Control cows, but the overall effect on pH was not significant. Zeolite had no effect on plasma urea, total urinary N excreted or faecal N. Of the total N excreted across the groups, 21.7, 50.6 and 27.7% was excreted into milk, urine and faeces respectively. Conclusions Zeolite administration reduced ruminal ammonia concentration but this did not result in reduced urinary N excretion in dairy cows offered pasture. Implications Dietary supplementation with zeolite may help to improve aspects of ruminal function in cows consuming pasture, but is unlikely to be an effective tool for reducing N leaching from pastures.

Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach

The lactobacilli identified to date encompass more than 270 closely related species that were recently reclassified into 26 genera. Because of their relevance to industry, there is a need to distinguish between closely related and yet metabolically and regulatory distinct species, e.g., during monitoring of biotechnological processes or screening of samples of unknown composition. Current available methods, such as shotgun metagenomics or rRNA gene-based amplicon sequencing, have significant limitations (high cost, low resolution, etc.). Here, we generated a phylogeny of lactobacilli based on phenylalanyl-tRNA synthetase (pheS) genes and, from it, developed a high-resolution taxonomic framework which allows for comprehensive and confident characterization of the community diversity and structure of lactobacilli at the species level. This framework is based on a total of 445 pheS gene sequences, including sequences of 276 validly described species and subspecies (of a total of 282, including the proposed L. timonensis species and the reproposed L. zeae species; coverage of 98%), and allows differentiation between 265 species-level clades of lactobacilli and the subspecies of L. sakei The methodology was validated through next-generation sequencing of mock communities. At a sequencing depth of ∼30,000 sequences, the minimum level of detection was approximately 0.02 pg per μl DNA (equaling approximately 10 genome copies per μl template DNA). The pheS approach, along with parallel sequencing of partial 16S rRNA genes, revealed considerable diversity of lactobacilli and distinct community structures across a broad range of samples from different environmental niches. This novel complementary approach may be applicable to industry and academia alike.IMPORTANCE Species formerly classified within the genera Lactobacillus and Pediococcus have been studied extensively at the genomic level. To accommodate their exceptional functional diversity, the over 270 species were recently reclassified into 26 distinct genera. Despite their relevance to both academia and industry, methods that allow detailed exploration of their ecology are still limited by low resolution, high cost, or copy number variations. The approach described here makes use of a single-copy marker gene which outperforms other markers with regard to species-level resolution and availability of reference sequences (98% coverage). The tool was validated against a mock community and used to address diversity of lactobacilli and community structure in various environmental matrices. Such analyses can now be performed at a broader scale to assess and monitor the assembly, structure, and function of communities of lactobacilli at the species level (and, in some cases, even at the subspecies level) across a wide range of academic and commercial applications.

Association between residual feed intake, digestion, ingestive behavior, enteric methane emission and nitrogen metabolism in Nellore beef cattle

This study aimed to evaluate nutrient intake and digestibility, enteric methane emission and nitrogen utilization efficiency in Nellore cattle ranked by residual feed intake (RFI). Twenty-four Nellore bulls at 466 ± 24 days of age and with 352 ± 14.6 kg of body weight, classified as low and high RFI, were evaluated. Animals were kept in individual pens for three periods of 28 days and variables were measured. Data were analyzed as repeated measures over time, considering as fixed effects RFI class, period and RFI class x period interaction, and linear (co)variate of age. No significant differences in dry matter or nutrient intake were detected between RFI classes, but total digestible nutrients intake tended to be lower in low RFI animals, and apparent nutrient digestibility was higher in high RFI animals. Partial efficiency of growth tended to be lower in high RFI animals. RFI class did not interfere with enteric methane production or microbial protein synthesis, but fecal nitrogen output was higher in low RFI animals. The greater efficiency of low RFI animals is consequence of lower maintenance requirements, since energy from higher nutrients digestibility in high RFI animals was spent on metabolic processes other than body tissue deposition.

Rumen metabolism, omasal flow of nutrients, and microbial dynamics in lactating dairy cows fed fresh perennial ryegrass (Lolium perenne L.) not supplemented or supplemented with rolled barley grain

The objective of this study was to evaluate the effect of rolled barley grain (RB) supplementation on rumen metabolism, omasal flow of nutrients, and microbial dynamics in lactating dairy cows fed fresh perennial ryegrass (Lolium perenne L.; PRG)-based diets. Ten ruminally cannulated Holstein cows averaging (mean ± standard deviation) 49 ± 23 d in milk and 513 ± 36 kg of body weight were assigned to 1 of 2 treatments in a switchback design. The treatment diets were PRG only (G) or PRG plus 3.5 kg of dry matter RB (G+RB). The study consisted of three 29-d periods where each period consisted of 21 d of diet adaptation and 8 d of data and sample collection. A double marker system was used to quantify nutrient flow entering the omasal canal along with labeled ¹⁵N-ammonium sulfate to measure bacterial, protozoal, and nonmicrobial N flow. Rumen evacuation techniques were used to determine nutrient and microbial pool size, allowing the calculation of fractional rates of digestion and microbial growth. There was no difference in daily milk yield or energy-corrected milk yield between treatments. Milk fat concentration and milk urea N decreased, whereas milk protein concentration increased in cows fed the G+RB diet. During the omasal sampling phase, dry matter intake was higher in cows fed the G+RB diet. Ruminal and total-tract neutral detergent fiber digestibility was lower in G+RB cows; however, no difference was observed in reticulorumen pH. The rumen pool size of fermentable carbohydrate was increased in cows fed the G+RB diet; however, the fractional rate of digestion was decreased. Flow of nonammonia N and bacterial N at the omasal canal increased in cows fed the G+RB diet compared with the G diet. Protozoa N flow was not different between diets; however, protozoa appeared to supply a much larger amount of microbial N and exhibited shorter generation time than previously considered. Feed N ruminal digestibility, corrected for microbial contribution, was similar for both treatments (88.4 and 89.0% for G and G+RB, respectively). In conclusion, RB supplementation did not benefit overall animal performance; however, it reduced ruminal neutral detergent fiber digestibility and increased bacterial N flow. The results demonstrate the large dependence of cows consuming PRG-based diets on microbial N as the main source of nonammonia N supply. Additional quantitative research is required to further describe the supply of nutrients and microbial dynamics in cows consuming PRG-based diets in an effort to determine most limiting nutrients.

Investigation into the effect of divergent feed efficiency phenotype on the bovine rumen microbiota across diet and breed

The relationship between rumen microbiota and host feed efficiency phenotype, for genetically divergent beef cattle breeds is unclear. This is further exacerbated when different growth stages, chemically diverse diets and production systems are considered. Residual feed intake (RFI), a measure of feed efficiency, was calculated for individually fed Charolais (CH) and Holstein-Friesian (HF) steers during each of four 70-day (excluding adaptation) successive dietary phases: namely, high-concentrate, grass silage, fresh zero-grazed grass and high-concentrate again. Rumen fluid from the ten highest- (HRFI) and ten lowest-ranking (LRFI) animals for RFI, within breed, during each dietary phase was collected using a trans-oesophageal sampler and subjected to 16S rRNA amplicon sequencing and metabolic profiling. The datasets were analysed to identify microbial and rumen fermentation markers associated with RFI status. Age, dietary phase and breed were included in the statistical model. Within breed, for each dietary phase, mid-test metabolic weight and average daily gain did not differ (P > 0.05) between HRFI and LRFI steers; however, for the initial high-concentrate, grass silage, fresh grass herbage and final high-concentrate dietary phases, HRFI HF steers consumed 19, 23, 18 and 27% more (P < 0.001) than their LRFI counterparts. Corresponding percentages for CH HRFI compared to CH LRFI steers were 18, 23, 13 and 22%. Ten OTUs were associated with RFI (q < 0.05) independent of the other factors investigated. Of these Methanomassiliicoccaceae, Mogibacteriaceae and the genus p-75-a5 of Erysipelotrichaceae and were negatively associated (q < 0.05) with RFI. The results gave evidence that microbial species could potentially be an indicator of RFI in ruminants rather than broader microbiome metrics; however, further research is required to elucidate this association.

Grouping crossbred Holstein x Gyr heifers according to different feed efficiency indexes and its effects on energy and nitrogen partitioning, blood metabolic variables and gas exchanges

The objectives of this study were: i) to classify animals into groups of high and low feed efficiency (FE) using three FE indexes (Residual feed intake (RFI), Residual weight gain (RG) and Feed conversion efficiency (FCE)), and ii) to evaluate whether crossbreed Holstein x Gyr heifers divergent for FE indexes exhibit differences in nutrient intake and digestibility, energy partitioning, heat production, methane emissions, nitrogen partitioning and blood parameters. Thirty-five heifers were housed in a tie-stall, received ad libitum TMR (75:25, corn silage: concentrate) and were ranked and classified into high (HE) or low efficiency (LE) for RFI, RG and FCE. The number of animals for each HE group were 13 (< 0.5 standard deviation (SD) for RFI, 11 for RG and 11 for FCE (> 0.5 SD) and for the LE were 10 (> 0.5 SD) for RFI, 11 for RG and 12 for FCE (< 0.5 SD). Gas exchanges (O₂ consumption, CO₂ and CH₄ production) in open-circuit respiratory chambers and whole tract digestibility trial was performed. A completely randomized experimental design was used and the data were analyzed by ANOVA and correlation study. High efficiency animals for RFI produced less CO_2, consumed less O₂ and had lower heat production (HP). Methane production was positively correlated with RFI. High efficiency RG had higher O₂ consumption and CO₂ production in relation to LE-RG. High efficiency FCE had greater NFC digestibility, higher positive energy balance (EB) and excreted (11.4 g/d) less nitrogen in urine. High efficiency RG and FCE groups emitted less CH₄ per kg of weight gain than LE animals. Animals HE for RFI and FCE had lower β-hydroxybutyrate and higher glucose concentrations, respectively. The differences in intake, digestibility, energy and nitrogen partition, CH₄ emission, blood metabolic variables and heat production between the HE and LE groups varied according to the efficiency indexes adopted. The HP (kcal/d/BW^0.75) was lower for HE animals for RFI and FCE indexes.

A comparative study on rumen ecology of water buffalo and cattle calves under similar feeding regime

In all, 12 male water buffalo (Bubalusbubalis) calves and Holstein (Bostaurus) calves of similar age (10 ± 5 days) were selected to explore the mechanism underlying the differences in growth performance and feed conversion ratio between the two species. The experiment contains 33 days of sucking period and 40 days of post‐weaning period. Both calves were fed the same amounts of milk in sucking period, and starter and oat grass were supplied ad libitum both before and after the weaning period. Feed intake, growth performance, ruminal fermentation parameters and the ruminal microbial community were measured the during experiment period. Results showed no differences in growth performance and feed intake between the two species in sucking period; however, the feed/gain ratio (F/G) of the water buffalo was higher than that of Holstein calve (p > 0.05). After weaning, the intake of starter by the Holstein calf was higher while intake of grass by the water buffalo was higher resulting in higher growth performance of and a lower F/G ratio for Holstein (p < 0.05). The rumen of Holstein calf showed higher levels of propionate, lower levels of acetate and branched‐chain fatty acids than that of water buffalo during both periods (p < 0.05). The rumen of water buffalo showed a higher number of observed bacterial species and Shannon diversity as compared with that of Holstein calf. The members belonging to the bacterial phylum Bacteroides and genus Prevotella in the rumen of Holstein calf were higher (p < 0.05), while Firmicutes and fibrolytic bacteria Ruminobacter and Ruminococcus were lower (p < 0.05) than that of water buffalo. In conclusion, the water buffalo calves demonstrated clearly of having significant population of bacterial community and better fibre digestion than those of cattle calves.

The use of milk Fourier transform mid-infrared spectra and milk yield to estimate heat production as a measure of efficiency of dairy cows

Background

Transformation of feed energy ingested by ruminants into milk is accompanied by energy losses via fecal and urine excretions, fermentation gases and heat. Heat production may differ among dairy cows despite comparable milk yield and body weight. Therefore, heat production can be considered an indicator of metabolic efficiency and directly measured in respiration chambers. The latter is an accurate but time-consuming technique. In contrast, milk Fourier transform mid-infrared (FTIR) spectroscopy is an inexpensive high-throughput method and used to estimate different physiological traits in cows. Thus, this study aimed to develop a heat production prediction model using heat production measurements in respiration chambers, milk FTIR spectra and milk yield measurements from dairy cows.

Methods

Heat production was computed based on the animal’s consumed oxygen, and produced carbon dioxide and methane in respiration chambers. Heat production data included 168 24-h-observations from 64 German Holstein and 20 dual-purpose Simmental cows. Animals were milked twice daily at 07:00 and 16:30 h in the respiration chambers. Milk yield was determined to predict heat production using a linear regression. Milk samples were collected from each milking and FTIR spectra were obtained with MilkoScan FT 6000. The average or milk yield-weighted average of the absorption spectra from the morning and afternoon milking were calculated to obtain a computed spectrum. A total of 288 wavenumbers per spectrum and the corresponding milk yield were used to develop the heat production model using partial least squares (PLS) regression.

Results

Measured heat production of studied animals ranged between 712 and 1470 kJ/kg BW^0.75. The coefficient of determination for the linear regression between milk yield and heat production was 0.46, whereas it was 0.23 for the FTIR spectra-based PLS model. The PLS prediction model using weighted average spectra and milk yield resulted in a cross-validation variance of 57% and a root mean square error of prediction of 86.5 kJ/kg BW^0.75. The ratio of performance to deviation (RPD) was 1.56.

Conclusion

The PLS model using weighted average FTIR spectra and milk yield has higher potential to predict heat production of dairy cows than models applying FTIR spectra or milk yield only.

Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation

Ruminant methane production is a significant energy loss to the animal and major contributor to global greenhouse gas emissions. However, it also seems necessary for effective rumen function, so studies of anti-methanogenic treatments must also consider implications for feed efficiency. Between-animal variation in feed efficiency represents an alternative approach to reducing overall methane emissions intensity. Here we assess the effects of dietary additives designed to reduce methane emissions on the rumen microbiota, and explore relationships with feed efficiency within dietary treatment groups. Seventy-nine finishing steers were offered one of four diets (a forage/concentrate mixture supplemented with nitrate (NIT), lipid (MDDG) or a combination (COMB) compared to the control (CTL)). Rumen fluid samples were collected at the end of a 56 d feed efficiency measurement period. DNA was extracted, multiplexed 16s rRNA libraries sequenced (Illumina MiSeq) and taxonomic profiles were generated. The effect of dietary treatments and feed efficiency (within treatment groups) was conducted both overall (using non-metric multidimensional scaling (NMDS) and diversity indexes) and for individual taxa. Diet affected overall microbial populations but no overall difference in beta-diversity was observed. The relative abundance of Methanobacteriales (Methanobrevibacter and Methanosphaera) increased in MDDG relative to CTL, whilst VadinCA11 (Methanomassiliicoccales) was decreased. Trimethylamine precursors from rapeseed meal (only present in CTL) probably explain the differences in relative abundance of Methanomassiliicoccales. There were no differences in Shannon indexes between nominal low or high feed efficiency groups (expressed as feed conversion ratio or residual feed intake) within treatment groups. Relationships between the relative abundance of individual taxa and feed efficiency measures were observed, but were not consistent across dietary treatments.

Relationship of residual feed intake and protein efficiency in lactating cows fed high- or low-protein diets

Our objectives were to determine the repeatability of residual feed intake (RFI) across dietary protein levels and to determine the association between RFI and protein efficiency in lactating cows. Holstein cows (n = 166; 92 primiparous, 74 multiparous) with initial milk yield 41.3 ± 9.8 kg/d were fed diets with high or low protein in peak lactation. Experiments were conducted as crossovers with 2 treatment periods of 28 to 35 d. Production of 69 of the 166 cows (42 primiparous, 27 multiparous) was also measured in late lactation. Low-protein diets were 14% crude protein (CP) in peak lactation and 13% CP in late lactation and were formulated to contain adequate rumen-degradable protein to maintain rumen function. High-protein diets were 18% CP in peak lactation and 16% CP in late lactation and contained extra expeller soybean meal to increase absorbed protein. Cows were milked twice daily; DMI and milk yield were recorded daily. Milk composition was measured over 4 consecutive milkings weekly, and body weight (BW) was measured 3 times weekly. Fixed effects of diet, parity, and treatment period, interaction of parity and diet, and random effects of experiment and cow nested within experiment were included in the model to compare intake and production performance between cows fed different levels of CP. The RFI value was calculated for each cow on each treatment based on the actual intake, milk energy output, metabolic BW, and body energy (calculated from BW change and body condition score over the treatment period) change. Ranking of cows for RFI was moderately repeatable across dietary protein in peak lactation (r = 0.59) but less repeatable in late lactation (r = 0.41). Negative correlation was observed between RFI and protein efficiency values (dietary protein captured in milk) for cows in both peak lactation (r = -0.42) and late lactation (r = -0.24), which suggested that cows with higher energy efficiency had greater protein efficiency. In conclusion, RFI was repeatable across dietary protein levels within lactation stage, and cows with lower RFI values utilized protein more efficiently.

Insights into the microbiome of farmed Asian sea bass (Lates calcarifer) with symptoms of tenacibaculosis and description of Tenacibaculum singaporense sp. nov

Outbreaks of diseases in farmed fish remain a recurring problem despite the development of vaccines and improved hygiene standards on aquaculture farms. One commonly observed bacterial disease in tropical aquaculture of the South-East Asian region is tenacibaculosis, which is attributed to members of the genus Tenacibaculum (family Flavobacteriaceae, phylum Bacteroidetes), most notably Tenacibaculum maritimum. The impact of tenacibaculosis on the fish microbiota remains poorly understood. In this study, we analysed the microbiota of different tissues of commercially reared Asian seabass (Lates calcarifer) that showed symptoms of tenacibaculosis and compared the microbial communities to those of healthy and experimentally infected fish that were exposed to diseased farmed fish. The relative abundance of Tenacibaculum species in experimentally infected fish was significantly lower than in commercially reared diseased fish and revealed a higher prevalence of different Tenacibaculum species. One isolated strain, TLL-A2^T, shares 98.7% 16S rRNA gene identity with Tenacibaculum mesophilum DSM 13764^T. The genome of strain TLL-A2^T was sequenced and compared to that of T. mesophilum DSM 13764^T. Analysis of average nucleotide identity and comparative genome analysis revealed only 92% identity between T. mesophilum DSM 13764^T and strain TLL-A2^T and differences between the two strains in predicted carbohydrate activating enzymes respectively. Phenotypic comparison between strain TLL-A2^T and T. mesophilum DSM 13764^T indicated additional differences, such as growth response at different salt concentrations. Based on molecular and phenotypic differences, strain TLL-A2^T (=DSM 106434^T, KCTC 62393^T) is proposed as the type strain of Tenacibaculum singaporense sp. nov.

Rumen digesta and products of fermentation in cows fed varying proportions of fodder beet (Beta vulgaris) with fresh pasture or silage or straw

Context Fodder beet (FB) is a popular feed for dairy cows in temperate climates due to its high yields, high digestibility, low nitrogen (N) content in the dry matter (DM) and convenience of feeding (grazing in situ). However, the risk of ruminal acidosis requires research to design feeding regimes that capture these benefits without compromising animal health. Aims To understand aspects of rumen function when FB is offered in conditions representative of practical feeding in temperate pastoral systems. Methods Two indoor experiments were undertaken; one with cows in late lactation fed fresh perennial ryegrass with three proportions of FB (0, 0.23 and 0.45) and another with non-lactating cows fed pasture silage with 0.65 FB or barley straw with 0.86 FB. Measurements included rumen pH, short-chain fatty acid (SCFA) and ammonia concentrations determined at 2-h intervals, as well as daily individual cow intakes, estimates of microbial growth and rumen dynamics. Key results The inclusion of 0, 0.23 and 0.45 FB with fresh pasture in the did not affect daily DM intakes (~14.6 kg), milk yield (~10.7 kg), microbial synthesis (129 g of N/d) or fractional outflow rates of digesta (0.16/h; 11.2 L/h) of lactating cows. The non-lactating cow ration comprising 0.86 FB with straw was inappropriate and resulted in low intakes and insufficient dietary N. Microbial growth was approximately one-third of that in cows fed pasture silage with 0.65 FB. The ruminal pH reached lower values in all treatments where FB was offered. Rumen ammonia concentrations averaged 4.4 mmol/L in cows fed pasture but was sometimes undetectable in lactating cows fed 0.45 FB and in non-lactating cows. The amount of FB in the diet affected the extent of the circadian changes in molar proportions of SCFA. Conclusions Based on the results presented here, feeding fresh FB to dairy cows should not exceed ~0.4 of their DMI with pasture (late lactation), or ~0.6 of their intake with silage (non-lactating). Implications These findings could support evidence-based recommendations for FB use, considering its effects on aspects of rumen function, such as microbial protein synthesis and pH.

Symposium review: Decomposing efficiency of milk production and maximizing profit

The dairy industry has focused on maximizing milk yield, as it is believed that this maximizes profit mainly through dilution of maintenance costs. Efficiency of milk production has received, until recently, considerably less attention. The most common method to determine biological efficiency of milk production is feed efficiency (FE), which is defined as the amount of milk produced relative to the amount of nutrients consumed. Economic efficiency is best measured as income over feed cost or gross margin obtained from feed investments. Feed efficiency is affected by a myriad of factors, but overall they could be clustered as follows: (1) physiological status of the cow (e.g., age, state of lactation, health, level of production, environmental conditions), (2) digestive function (e.g., feeding behavior, passage rate, rumen fermentation, rumen and hindgut microbiome), (3) metabolic partitioning (e.g., homeorhesis, insulin sensitivity, hormonal profile), (4) genetics (ultimately dictating the 2 previous aspects), and (5) nutrition (e.g., ration formulation, nutrient balance). Over the years, energy requirements for maintenance seem to have progressively increased, but efficiency of overall nutrient use for milk production has also increased due to dilution of nutrient requirements for maintenance. However, empirical evidence from the literature suggests that marginal increases in milk require progressively greater marginal increases in nutrient supply. Thus, the dilution of maintenance requirements associated with increases in production is partially overcome by a progressive diminishing marginal biological response to incremental energy and protein supplies. Because FE follows the law of diminishing returns, and because marginal feed costs increase progressively with milk production, profits associated with improving milk yield might, in some cases, be considerably lower than expected.

Associations between residual feed intake and apparent nutrient digestibility, in vitro methane-producing activity, and volatile fatty acid concentrations in growing beef cattle1

The objectives of this study were to examine the relationship between residual feed intake (RFI) and DM and nutrient digestibility, in vitro methane production, and volatile fatty acid (VFA) concentrations in growing beef cattle. Residual feed intake was measured in growing Santa Gertrudis steers (Study 1; n = 57; initial BW = 291.1 ± 33.8 kg) and Brangus heifers (Study 2; n = 468; initial BW = 271.4 ± 26.1 kg) fed a high-roughage-based diet (ME = 2.1 Mcal/kg DM) for 70 d in a Calan-gate feeding barn. Animals were ranked by RFI based on performance and feed intake measured from day 0 to 70 (Study 1) or day 56 (Study 2) of the trial, and 20 animals with the lowest and highest RFI were identified for subsequent collections of fecal and feed refusal samples for DM and nutrient digestibility analysis. In Study 2, rumen fluid and feces were collected for in vitro methane-producing activity (MPA) and VFA analysis in trials 2, 3, and 4. Residual feed intake classification did not affect BW or BW gain (P > 0.05), but low-RFI steers and heifers both consumed 19% less (P < 0.01) DMI compared with high-RFI animals. Steers with low RFI tended (P < 0.1) to have higher DM digestibility (DMD) compared with high-RFI steers (70.3 vs. 66.5 ± 1.6% DM). Heifers with low RFI had 4% higher DMD (76.3 vs. 73.3 ± 1.0% DM) and 4 to 5% higher (P < 0.01) CP, NDF, and ADF digestibility compared with heifers with high RFI. Low-RFI heifers emitted 14% less (P < 0.01) methane (% GE intake; GEI) calculated according to Blaxter and Clapperton (1965) as modified by Wilkerson et al. (1995), and tended (P = 0.09) to have a higher rumen acetate:propionate ratio than heifers with high RFI (GEI = 5.58 vs. 6.51 ± 0.08%; A:P ratio = 5.02 vs. 4.82 ± 0.14%). Stepwise regression analysis revealed that apparent nutrient digestibilities (DMD and NDF digestibility) for Study 1 and Study 2 accounted for an additional 8 and 6%, respectively, of the variation in intake unaccounted for by ADG and mid-test BW0.75. When DMD, NDF digestibility, and total ruminal VFA were added to the base model for Study 2, trials 2, 3, and 4, the R2 increased from 0.33 to 0.47, explaining an additional 15% of the variation in DMI unrelated to growth and body size. On the basis of the results of these studies, differences in observed phenotypic RFI in growing beef animals may be a result of inter-animal variation in apparent nutrient digestibility and ruminal VFA concentrations.

Digestibility contributes to between-animal variation in feed efficiency in beef cows

Residual feed intake (RFI) is an alternative measure of feed efficiency (FE) and is calculated as the difference between actual and expected feed intake. The biological mechanisms underlying animal-to-animal variation in FE are not well understood. The aim of this study was to investigate the digestive ability of beef cows selected for RFI divergence as heifers, using two contrasted diets. Fifteen 4-year-old beef cows were selected from a total of 69 heifers based on their RFI following the feedlot test. The selected heifers were ranked into high-RFI (+ 1.02 ± 0.28, n = 8) and low-RFI (-0.73 ± 0.28, n = 7), and a digestibility trial was performed after their first lactation. Both RFI groups were offered two different diets: 100% hay or a fattening diet which consisted of a DM basis of 67% whole-plant maize silage and 33% high starch concentrates over four experimental periods (two per diet). A diet effect was observed on feed intake and apparent digestibility, whereas no diet × RFI interaction was detected (P > 0.05). Intake and apparent digestibility were higher in cows fed the fattening diet than in those fed the hay diet (P < 0.0001). DM intake (DMI) and organic matter apparent digestibility (OMd) were repeatable and positively correlated between the two subsequent periods of measurements. For the hay and fattening diets, the repeatability between periods was r = 0.71 and r = 0.73 for DMI and r = 0.87 and r = 0.48 for OMd, respectively. Moreover, both intake (r = 0.55) and OMd (r = 0.54) were positively correlated (P < 0.05) between the hay and fattening diets. Significant differences between beef cows selected for divergence in RFI as heifers were observed for digestive traits (P < 0.05), DM and organic matter (OM) apparent digestibility being higher for low-RFI cows. Overall, this study showed that apparent digestibility contributes to between-animal variation in FE in beef cows.

Nitrogen partitioning and microbial protein synthesis in lactating dairy cows with different phenotypic residual feed intake

Background

Residual feed intake (RFI) is an inheritable measure of feed efficiency that is independent on level of production. However, physiological and metabolic mechanisms underlying divergent RFI are not fully elucidated. This study was conducted to investigate dietary nitrogen (N) partitioning and microbial protein synthesis in lactating dairy cows divergent in phenotypic RFI.

Results

Thirty Holstein dairy cows (milk yield = 35.3 ± 4.71 kg/d; milk protein yield = 1.18 ± 0.13 kg/d; mean ± standard deviation) were selected for the experiment to derive RFI. After the RFI measurement period of 50 d, the 10 lowest RFI cows and 8 highest RFI cows were selected. The low RFI cows had lower dry matter intake (DMI, P < 0.05) than the high RFI cows, but they produced similar energy-corrected milk. The ratios of milk to DMI (1.41 vs. 1.24, P < 0.01) and energy-corrected milk to DMI (1.48 vs. 1.36, P < 0.01) were greater in low RFI cows than those in the high RFI cows. The low RFI cows had lower milk urea nitrogen than that in the high RFI cows (P = 0.05). Apparent digestibility of nutrients did not differ between two groups (P > 0.10). Compared with high RFI animals, the low RFI cows had a lower retention of N (5.72 vs. 51.4 g/d, P < 0.05) and a higher partition of feed N to milk N (29.7% vs. 26.5%, P < 0.05).

Conclusions

The results suggest that differences in N partition, synthesis of microbial protein, and utilization of metabolizable protein could be part of the mechanisms associated with variance in the RFI.

Characterizing the metabotype and its persistency in lactating Holstein cows: An approach toward metabolic efficiency measures

The variation in feed efficiency among dairy cows is due to differences in fermentation and digestion characteristics, but recent studies have suggested that various aspects of postabsorptive metabolic processes including heat production or the metabolizable energy for maintenance are more crucial. Thus, metabolic efficiency largely determines feed efficiency, but whether divergent feed efficient cows differ in O₂ consumption and metabolic CO₂ production, directly determining the metabolic rate has not been investigated. Therefore, the objective of the present study was to determine whether variation in ME intake (MEI), O₂ consumption, and metabolic CO₂ production account for the variation in metabolic efficiency of dairy cows and whether this effect persists across the lactation cycle. Eighteen cows with different German breeding value functional herd life were kept in freestalls with ad libitum access to a total mixed ration that was kept constant in composition throughout the first lactation. Cows were blood sampled and weighed at wk 5, 13, and 42 postpartum (pp) and transferred into respiration chambers. Animals were retrospectively clustered according to MEI, O₂ consumption, and metabolic CO₂ production, each normalized to metabolic body weight (mBW). Cluster analysis revealed 9 high metabolically efficient (high-Meff) and 9 low metabolically efficient cows. The high-Meff cows had greater MEI and feed conversion efficiency, produced less metabolic CO₂ and methane, had a stronger negative energy balance, and tended to have a lower metabolic respiratory quotient. Further, high-Meff cows had lower residual MEI, less heat energy loss, and lower plasma glucose concentrations, but used a greater portion of body reserves instead of feed energy for milk synthesis, particularly at wk 5 and 13 pp. However, these group differences did not persist by wk 42 pp. Cow groups were not different in O₂ consumption, milk yield, metabolizable energy for maintenance, or the efficiency of tissue utilization for milk synthesis, but high-Meff cows tended to have the lower German relative breeding value functional herd life, indicating a link between metabolic performance and productive lifespan. In conclusion, the use of a clustering approach involving MEI/mBW, O₂/mBW, and CO₂/mBW seems to be a promising method to differentiate cows with divergent metabolic efficiency but does not allow identifying an individual metabotype that persists across the whole lactation cycle.

Hot topic: Selecting cattle for low residual feed intake did not affect daily methane production but increased methane yield

Reducing enteric methane (CH₄) production and improving feed conversion efficiency of dairy cows is of high importance. Residual feed intake (RFI) is one measure of feed efficiency, with low RFI animals being more efficient in feed conversion. Enteric CH₄ is an important source of digestible energy loss in ruminants and, because research in beef cattle has reported a positive relationship between RFI and daily CH₄ production, we hypothesized that low RFI dairy heifers, which are more feed efficient, would produce less CH₄/d. We measured the daily methane production (g of CH₄/d), methane yield [g of CH₄/kg of dry matter intake (DMI)], and CH₄ per kilogram of body weight (BW) gain for 56 heifers (20-22 mo old) in a 2 × 2 factorial arrangement: factors included 2 breeds (Holstein-Friesian and Jersey; n = 28/breed), with equal numbers of animals previously determined as being either high [+2.0 kg of dry matter (DM)/d] or low RFI (-2.1 kg of DM/d; n = 28/RFI category). All heifers were commingled and offered unrestricted access to the same diet of dried alfalfa cubes. Between RFI categories, heifers did not differ in BW or BW gain but low RFI heifers had 9.3 and 10.6% lower DMI and DMI/kg of BW, respectively, than high RFI heifers. Similarly, RFI category did not affect CH₄/d or CH₄/kg of BWg, but CH₄/kg of DMI was higher in low RFI heifers because of their lower DMI. These results might reflect more complete digestion of ingested feed in the more efficient, low RFI heifers, consistent with previous reports of greater apparent digestibility of organic matter. Holstein-Friesian heifers were heavier and consumed more total DM than Jersey heifers, but breed did not affect DMI/kg of BW or BWg. Jersey heifers produced less CH₄/d, but not CH₄/kg of DMI or CH₄/kg of BWg. We detected no interaction between breed and RFI category in any of the variables measured. In conclusion, differences in RFI in dairy heifers did not affect daily CH₄ production (g/d); however, low RFI heifers had a greater CH₄ yield (g/kg of DMI) on a high forage diet.

Digestion and nitrogen excretion by Holstein-Friesian cows fed grasses with lucerne or lucerne and plantain

Forages and forage mixtures with greater tolerance of dry conditions than perennial ryegrass (Lolium perenne L.) are desirable for dairy farming in New Zealand, and a low urinary nitrogen (N) excretion is desirable to lessen pollution of waterways and ground water, and nitrous oxide emissions. Measurements were undertaken with late-lactation Holstein-Friesian cows (5/treatment) fed tall fescue (Festuca arundinacea Schreb.) with a substantial incursion of weed grasses, as either a sole diet (Grass), or with lucerne (Medicago sativa L.) or lucerne and plantain (Plantago lancelota L.), in metabolism stalls. Approximate ratios (DM basis) of Grass with lucerne (GL) were 55:45, and Grass with lucerne and plantain (GLP) were 55:25:20. Measurements included intakes, production, digestion, rumen function, and urinary excretion, including the circadian patterns of metabolite excretion with a focus on nitrogenous aspects. The DM intakes (kg/day) of cows fed Grass, GL and GLP were 14.9, 12.7 and 15.0 (P = 0.006), and DM digestibility (%) was 58.0, 59.8 and 61.9 (P = 0.006), respectively. Milk yields (kg/day) were Grass, 9.0; GL, 8.7 and GLP, 11.7 (P = 0.003) but composition was not affected by diet. Rumen digesta weight was greatest in cows fed Grass, averaging 23.4% of liveweight after morning feeding. The microbial growth (g/kg organic matter digested) was 16.8 in cows fed Grass and ~24.0 in the other diets. Dietary crude protein concentrations (g/100 g DM) were Grass, 15.4, GL, 20.1 and GLP, 18.3 and urinary N excretion (g/day) was lowest with the Grass diet but urinary N concentration was lowest from cows fed GLP. Daily creatinine excretion was unaffected by diet but there was a 2-fold range in excretion rates within 24 h and values from cows fed fresh forages are lower than published values from cows fed dry diets. Results showed that supplementation of poor quality pasture with lucerne or lucerne with plantain had minor effects on digestibility, and measurements of urinary N suggest a need for caution when predicting urinary N excretion from spot urine sampling in grazing trials.

Digestion and nitrogen excretion by Holstein–Friesian cows in late lactation offered ryegrass-based pasture supplemented with fodder beet

Recent changes in New Zealand dairying have included incorporation of fodder beet (FB) into rations. The present trial explored the impact of substituting different proportions of ryegrass-based pasture with FB for cows fed ad libitum in late lactation. The objective was to measure effects of FB on intake, digestion and urinary nitrogen (N) excretion using 16 Holstein–Friesian cows with a permanent rumen fistula. Before the 9-day indoor measurement period, cows were adapted to feeding 0%, 20%, 40% or 60% FB (bulbs and tops) with medium quality ryegrass-based pasture (191 g CP and 517 g neutral detergent fibre (aNDF)/kg DM; DM digestibility 0.634) over 2 weeks. However, it became apparent that a diet of 60% FB was detrimental to cow health, with two cows developing acidosis. The allocation of FB was reduced and the actual intakes were 23% and 45% of DM intake during the trial. Feeding FB substantially reduced N intake and urinary N excretion. The lower level (23%) of FB resulted in greater DM digestibility, albeit with a small reduction in N and aNDF digestibility. However, the higher level (45%) of FB reduced N and aNDF digestibility by 7.1 and 12.1 percentage units respectively, relative to pasture. Daily creatinine excretion was lower than published measurements from cattle fed dry diets, and circadian variation in urinary N:creatinine ratios suggests a need for caution when attempting to predict daily urinary N excretion from spot samples.

Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes

Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not. We conducted shotgun sequencing of microbial DNA from the rumen contents of 16 sheep that differed in their residual feed intake (RFI), a measure of feed efficiency. Metagenomic reads from each sheep were mapped onto a database-derived microbial metabolic network, which was linked to the sheep metabolic network by interface metabolites (metabolites transferred from microbes to host). No single enzyme was identified as being significantly different in abundance between the low and high RFI animals (P > 0.05, Wilcoxon test). However, when we analyzed the metabolic network as a whole, we found several differences between efficient and inefficient animals. Microbes from low RFI (efficient) animals use a suite of enzymes closer in network space to the host's reactions than those of the high RFI (inefficient) animals. Similarly, low RFI animals have microbial metabolic networks that, on average, contain reactions using shorter carbon chains than do those of high RFI animals, potentially allowing the host animals to extract metabolites more efficiently. Finally, the efficient animals possess community networks with greater Shannon diversity among their enzymes than do inefficient ones. Thus, our system approach to the ruminal microbiome identified differences attributable to feed efficiency in the structure of the microbes' community metabolic network that were undetected at the level of individual microbial taxa or reactions.

Effects of short-term fasting on in vivo rumen microbiota and in vitro rumen fermentation characteristics

Objective

Fasting may lead to changes in the microbiota and activity in the rumen. In the present study, the effects of fasting on rumen microbiota and the impact of fasting on in vitro rumen fermentation were evaluated using molecular culture-independent methods.

Methods

Three ruminally cannulated Holstein steers were fed rice straw and concentrates. The ruminal fluids were obtained from the same steers 2 h after the morning feeding (control) and 24 h after fasting (fasting). The ruminal fluid was filtrated through four layers of muslin, collected for a culture-independent microbial analysis, and used to determine the in vitro rumen fermentation characteristics. Total DNA was extracted from both control and fasting ruminal fluids. The rumen microbiota was assessed using denaturing gradient gel electrophoresis (DGGE) and quantitative polymerase chain reaction. Microbial activity was evaluated in control and fasting steers at various intervals using in vitro batch culture with rice straw and concentrate at a ratio of 60:40.

Results

Fasting for 24 h slightly affected the microbiota structure in the rumen as determined by DGGE. Additionally, several microorganisms, including Anaerovibrio lipolytica, Eubacterium ruminantium, Prevotella albensis, Prevotella ruminicola, and Ruminobacter amylophilus, decreased in number after fasting. In addition, using the ruminal fluid as the inoculum after 24 h of fasting, the fermentation characteristics differed from those obtained using non-fasted ruminal fluid. Compared with the control, the fasting showed higher total gas production, ammonia, and microbial protein production (p<0.05). No significant differences, however, was observed in pH and dry matter digestibility.

Conclusion

When in vitro techniques are used to evaluate feed, the use of the ruminal fluid from fasted animals should be used with caution.

Genome wide transcriptome analysis provides bases on colonic mucosal immune system development affected by colostrum feeding strategies in neonatal calves

Background

Delivery of colostrum within the first several hours after birth is vital for establishing successful passive immunity in neonatal dairy calves. However, it is unclear whether a difference in colostrum feeding strategy can affect the development of the calf gastrointestinal tract. The aim of this study was to evaluate the effect of colostrum feeding time within the first 12 h after birth on the colonic mucosal immune system in neonatal calves using a genome wide transcriptome analysis.

Results

RNA sequencing-based transcriptome analysis of colon tissues collected from 27 male Holstein calves which were randomly assigned to one of three colostrum feeding strategies – (immediately after birth (TRT0); 6 h after birth (TRT6); 12 h after birth (TRT12)) – and euthanized at 51 h of age detected 15,935 ± 210, 15,332 ± 415, and 15,539 ± 440 expressed genes in the colon under three treatments, respectively. The core transcriptome of the colon included 12,678 genes, with enriched “cellular process” and “metabolic process” as the top two biological functions with 802 of them being immune function related genes. Principal component analysis of the colon transcriptomes did not display a clear separation by colostrum feeding strategy and differential abundance analyses showed no significant difference in the expression of immune related genes among the treatments. Additionally, a weighted gene co-expression network analysis identified 4 significant (|correlation| > 0.50 and p ≤ 0.05) gene modules consisting of 122 immune related genes, which were positively or negatively correlated with the abundance of Lactobacillus and Faecalibacterium prausnitzii in the colon.

Conclusion

Transcriptome analysis indicates that the development of the colonic mucosal immune system in neonatal calves may be independent of the timing of initial colostrum meal within 12 h after birth. Our results also provide a molecular understanding of colonic biological function in neonatal calves and extends knowledge on how host gene expression profiles are associated with the abundance of specific bacterial groups in the colon.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5017-y) contains supplementary material, which is available to authorized users.

Review: Biological determinants of between-animal variation in feed efficiency of growing beef cattle

Animal's feed efficiency in growing cattle (i.e. the animal ability to reach a market or adult BW with the least amount of feed intake), is a key factor in the beef cattle industry. Feeding systems have made huge progress to understand dietary factors influencing the average animal feed efficiency. However, there exists a considerable amount of animal-to-animal variation around the average feed efficiency observed in beef cattle reared in similar conditions, which is still far from being understood. This review aims to identify biological determinants and molecular pathways involved in the between-animal variation in feed efficiency with particular reference to growing beef cattle phenotyped for residual feed intake (RFI). Moreover, the review attempts to distinguish true potential determinants from those revealed through simple associations or indirectly linked to RFI through their association with feed intake. Most representative and studied biological processes which seem to be connected to feed efficiency were reviewed, such as feeding behaviour, digestion and methane production, rumen microbiome structure and functioning, energy metabolism at the whole body and cellular levels, protein turnover, hormone regulation and body composition. In addition, an overall molecular network analysis was conducted for unravelling networks and their linked functions involved in between-animal variation in feed efficiency. The results from this review suggest that feeding and digestive-related mechanisms could be associated with RFI mainly because they co-vary with feed intake. Although much more research is warranted, especially with high-forage diets, the role of feeding and digestive related mechanisms as true determinants of animal variability in feed efficiency could be minor. Concerning the metabolic-related mechanisms, despite the scarcity of studies using reference methods it seems that feed efficient animals have a significantly lower energy metabolic rate independent of the associated intake reduction. This lower heat production in feed efficient animals may result from a decreased protein turnover and a higher efficiency of ATP production in mitochondria, both mechanisms also identified in the molecular network analysis. In contrast, hormones and body composition could not be conclusively related to animal-to-animal variation in feed efficiency. The analysis of potential biological networks underlying RFI variations highlighted other significant pathways such as lipid metabolism and immunity and stress response. Finally, emerging knowledge suggests that metabolic functions underlying genetic variation in feed efficiency could be associated with other important traits in animal production. This emphasizes the relevance of understanding the biological basis of relevant animal traits to better define future balanced breeding programmes.