Abstract: The temporal sequence of microbial establishment in the rumen of the neonatal ruminant has important ecological and pathophysiological implications. In this study, we characterized the rumen microbiota of pre-ruminant calves fed milk replacer using two approaches, pyrosequencing of hypervariable V3-V5 regions of the 16S rRNA gene and whole-genome shotgun approach. Fifteen bacterial phyla were identified in the microbiota of pre-ruminant calves. Bacteroidetes was the predominant phylum in the rumen microbiota of 42-day-old calves, representing 74.8% of the 16S sequences, followed by Firmicutes (12.0%), Proteobacteria (10.4%), Verrucomicrobia (1.2%) and Synergistetes (1.1%). However, the phylum-level composition of 14-day-old calves was distinctly different. A total of 170 bacterial genera were identified while the core microbiome of pre-ruminant calves included 45 genera. Rumen development seemingly had a significant impact on microbial diversity. The dazzling functional diversity of the rumen microbiota was reflected by identification of 8298 Pfam and 3670 COG protein families. The rumen microbiota of pre-ruminant calves displayed a considerable compositional heterogeneity during early development. This is evidenced by a profound difference in rumen microbial composition between the two age groups. However, all functional classes between the two age groups had a remarkably similar assignment, suggesting that rumen microbial communities of pre-ruminant calves maintained a stable function and metabolic potentials while their phylogenetic composition fluctuated greatly. The presence of all major types of rumen microorganisms suggests that the rumen of pre-ruminant calves may not be rudimentary. Our results provide insight into rumen microbiota dynamics and will facilitate efforts in formulating optimal early-weaning strategies.

Abstract: MethanereductionontrulydegradedsubstratebasisOMD Organic matter digestibilityPSM Plant secondary metabolitesQSE Quillaja saponaria extractSCFAs Short-chain fatty acidsTP Total phenolsTT Total tanninsIntroductionThe ruminal methane production is a by-product of themicrobial digestive process and represents a loss of 2–12%of the feed energy. Furthermore, emission of methane isconsidered as one of the most important global environ-mental issues (IPCC 2001). Therefore, decreasing methaneproduction is desirable for reducing the greenhouse gasemission with improved efficiency of the digested energyutilization (Johnson and Johnson 1995). A previous reportby Kurihara et al. (1999) indicated that methane energy lossin cattle fed on tropical forage diets was higher than inthose fed on temperate forage diets, due to relative highlevels of fibre and lignin and a low level of non-fibrecarbohydrate in tropical forages. Also, the livestock indeveloping countries are predominantly maintained on ahigh-roughage diet with little or no concentrate resulting inincreased ruminal methanogenesis. Therefore, the use ofbrowse species containing secondary compounds as feedsupplement rich in plant secondary metabolites (PSM) forruminants in many parts of the tropics is increasing in orderto improve animal performance and reduce methane(Abdulrazak et al. 2000). Tannins and saponins constitutethe major classes of PSM that are currently under researchin a number of laboratories. The antimicrobial action andeffects on rumen fermentation of these compounds dependon their nature, activity and concentration in a plant or plant

Abstract: Feed-efficient animals have lower production costs and reduced environmental impact. Given that rumen microbial fermentation plays a pivotal role in host nutrition, the premise that rumen microbiota may contribute to host feed efficiency is gaining momentum. Since diet is a major factor in determining rumen community structure and fermentation patterns, we investigated the effect of divergence in phenotypic residual feed intake (RFI) on ruminal community structure of beef cattle across two contrasting diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were performed to profile the rumen bacterial population and to quantify the ruminal populations of Entodinium spp., protozoa, Fibrobacter succinogenes, Ruminococcus flavefaciens, Ruminococcus albus, Prevotella brevis, the genus Prevotella, and fungi in 14 low (efficient)- and 14 high (inefficient)-RFI animals offered a low-energy, high-forage diet, followed by a high-energy, low-forage diet. Canonical correspondence and Spearman correlation analyses were used to investigate associations between physiological variables and rumen microbial structure and specific microbial populations, respectively. The effect of RFI on bacterial profiles was influenced by diet, with the association between RFI group and PCR-DGGE profiles stronger for the higher forage diet. qPCR showed that Prevotella abundance was higher (P < 0.0001) in inefficient animals. A higher (P < 0.0001) abundance of Entodinium and Prevotella spp. and a lower (P < 0.0001) abundance of Fibrobacter succinogenes were observed when animals were offered the low-forage diet. Thus, differences in the ruminal microflora may contribute to host feed efficiency, although this effect may also be modulated by the diet offered.

Abstract: Belanche Gracia, A., Doreau, M., Edwards, J. E., Moorby, J. M., Pinloche, E., Newbold, C. J. (2012). Shifts in the rumen microbiota due to the type of carbohydrate and level of protein ingested by dairy cattle are associated with changes in rumen fermentation. The Journal of Nutrition, 142 (9), 1684-1692.

Abstract: The objective of this study was to determine the effect of dietary nitrate on methane emission and rumen fermentation parameters in Nellore × Guzera (Bos indicus) beef cattle fed a sugarcane based diet. The experiment was conducted with 16 steers weighing 283 ± 49 kg (mean ± SD), 6 rumen cannulated and 10 intact steers, in a cross-over design. The animals were blocked according to BW and presence or absence of rumen cannula and randomly allocated to either the nitrate diet (22 g nitrate/kg DM) or the control diet made isonitrogenous by the addition of urea. The diets consisted of freshly chopped sugarcane and concentrate (60:40 on DM basis), fed as a mixed ration. A 16-d adaptation period was used to allow the rumen microbes to adapt to dietary nitrate. Methane emission was measured using the sulfur hexafluoride tracer technique. Dry matter intake (P = 0.09) tended to be less when nitrate was present in the diet compared with the control, 6.60 and 7.05 kg/d DMI, respectively. The daily methane production was reduced (P < 0.01) by 32% when steers were fed the nitrate diet (85 g/d) compared with the urea diet (125 g/d). Methane emission per kilogram DMI was 27% less (P < 0.01) on the nitrate diet (13.3 g methane/kg DMI) than on the control diet (18.2 g methane/kg DMI). Methane losses as a fraction of gross energy intake (GEI) were less (P < 0.01) on the nitrate diet (4.2% of GEI) than on the control diet (5.9% of GEI). Nitrate mitigated enteric methane production by 87% of the theoretical potential. The rumen fluid ammonia-nitrogen (NH(3)-N()) concentration was significantly greater (P < 0.05) for the nitrate diet. The total concentration of VFA was not affected (P = 0.61) by nitrate in the diet, while the proportion of acetic acid tended to be greater (P = 0.09), propionic acid less (P = 0.06) and acetate/propionate ratio tended to be greater (P = 0.06) for the nitrate diet. Dietary nitrate reduced enteric methane emission in beef cattle fed sugarcane based diet.

Abstract: A strain of Clostridium kluyveri was isolated from the bovine rumen in a medium containing ethanol as an electron donor and acetate and succinate (common products of rumen fermentation) as electron acceptors. The isolate displayed a narrow substrate range but wide temperature and pH ranges atypical of ruminal bacteria and a maximum specific growth rate near the typical liquid dilution rate of the rumen. Quantitative real-time PCR revealed that C. kluyveri was widespread among bovine ruminal samples but was present at only very low levels (0.00002% to 0.0002% of bacterial 16S rRNA gene copy number). However, the species was present in much higher levels (0.26% of bacterial 16S rRNA gene copy number) in lucerne silage (but not maize silage) that comprised much of the cows’ diet. While C. kluyveri may account for several observations regarding ethanol utilization and volatile fatty acid production in the rumen, its population size and growth characteristics suggest that it is not a significant contributor to ruminal metabolism in typical dairy cattle, although it may be a significant contributor to silage fermentation. The ability of unadapted cultures to produce substantial levels (12.8 g L−1) of caproic (hexanoic) acid in vitro suggests that this strain may have potential for industrial production of caproic acid.

Abstract: The effects of the anti-methanogenic compound, bromochloromethane (BCM), on rumen microbial fermentation and ecology were examined in vivo. Japanese goats were fed a diet of 50 % Timothy grass and 50 % concentrate and then sequentially adapted to low, mid and high doses of BCM. The goats were placed into the respiration chambers for analysis of rumen microbial function and methane and H2 production. The levels of methane production were reduced by 5, 71 and 91 %, and H2 production was estimated at 545, 2941 and 3496 mmol/head per d, in response to low, mid and high doses of BCM, respectively, with no effect on maintenance feed intake and digestibility. Real-time PCR quantification of microbial groups showed a significant decrease relative to controls in abundance of methanogens and rumen fungi, whereas there were increases in Prevotella spp. and Fibrobacter succinogenes, a decrease in Ruminococcus albus and R. flavefaciens was unchanged. The numbers of protozoa were also unaffected. Denaturing gradient gel electrophoresis and quantitative PCR analysis revealed that several Prevotella spp. were the bacteria that increased most in response to BCM treatment. It is concluded that the methane-inhibited rumen adapts to high hydrogen levels by shifting fermentation to propionate via Prevotella spp., but the majority of metabolic hydrogen is expelled as H2 gas.

Abstract: Aims: To determine the effects of the removal of forage in high-concentrate diets on rumen fermentation conditions and rumen bacterial populations using culture-independent methods. Methods and Results: Detectable bacteria and fermentation parameters were measured in the solid and liquid fractions of digesta from cattle fed two dietary treatments, high concentrate (HC) and high concentrate without forage (HCNF). Comparison of rumen fermentation conditions showed that duration of time spent below pH 5·2 and rumen osmolality were higher in the HCNF treatment. Simpson’s index of 16S PCR-DGGE images showed a greater diversity of dominant species in the HCNF treatment. Real-time qPCR showed populations of Fibrobacter succinogenes (P = 0·01) were lower in HCNF than HC diets. Ruminococcus spp., F. succinogenes and Selenomonas ruminantium were at higher (P ≤ 0·05) concentrations in the solid vs the liquid fraction of digesta regardless of diet. Conclusions: The detectable bacterial community structure in the rumen is highly diverse. Reducing diet complexity by removing forage increased bacterial diversity despite the associated reduction in ruminal pH being less conducive for fibrolytic bacterial populations. Quantitative PCR showed that removal of forage from the diet resulted in a decline in the density of some, but not all fibrolytic bacterial species examined. Significance and Impact of the Study: Molecular techniques such as DGGE and qPCR provide an increased understanding of the impacts of dietary changes on the nature of rumen bacterial populations, and conclusions derived using these techniques may not match those previously derived using traditional laboratory culturing techniques.

Abstract: Variation of microorganism communities in the rumen of cattle (Bos taurus) is of great interest because of possible links to economically or environmentally important traits, such as feed conversion efficiency or methane emission levels. The resolution of studies investigating this variation may be improved by utilizing untargeted massively parallel sequencing (MPS), that is, sequencing without targeted amplification of genes. The objective of this study was to develop a method which used MPS to generate “rumen metagenome profiles”, and to investigate if these profiles were repeatable among samples taken from the same cow. Given faecal samples are much easier to obtain than rumen fluid samples; we also investigated whether rumen metagenome profiles were predictive of faecal metagenome profiles. Rather than focusing on individual organisms within the rumen, our method used MPS data to generate quantitative rumen micro-biome profiles, regardless of taxonomic classifications. The method requires a previously assembled reference metagenome. A number of such reference metagenomes were considered, including two rumen derived metagenomes, a human faecal microflora metagenome and a reference metagenome made up of publically available prokaryote sequences. Sequence reads from each test sample were aligned to these references. The “rumen metagenome profile” was generated from the number of the reads that aligned to each contig in the database. We used this method to test the hypothesis that rumen fluid microbial community profiles vary more between cows than within multiple samples from the same cow. Rumen fluid samples were taken from three cows, at three locations within the rumen. DNA from the samples was sequenced on the Illumina GAIIx. When the reads were aligned to a rumen metagenome reference, the rumen metagenome profiles were repeatable (P < 0.00001) by cow regardless of location of sampling rumen fluid. The repeatability was estimated at 9%, albeit with a high standard error, reflecting the small number of animals in the study. Finally, we compared rumen microbial profiles to faecal microbial profiles. Our hypothesis, that there would be a stronger correlation between faeces and rumen fluid from the same cow than between faeces and rumen fluid from different cows, was not supported by our data (with much greater significance of rumen versus faeces effect than animal effect in mixed linear model). We have presented a simple and high throughput method of metagenome profiling to assess the similarity of whole metagenomes, and illustrated its use on two novel datasets. This method utilises widely used freeware. The method should be useful in the exploration and comparison of metagenomes.

Abstract: The rumen bacterial composition of both pre- ruminant dairy calves and cows and beef steers was surveyed using pyrosequencing of the 16S rRNA gene. Sequences were analyzed using taxonomy-dependent and -independent clustering methods. The core rumen microbiome, regardless of the rumen developmental status or breeds, consisted of 8 phyla, 11 classes, 15 families, and 17 genera. Principal component analysis and clustering demonstrated that the bacterial communities in the rumen of pre-ruminant dairy calves, dairy cows, and beef steers were clearly distinguishable. Approximately 66% of phyla and 41% of Operational Taxonomic Units (OTUs) in a typical rumen bacterial community differed in relative abundance between the developing and mature rumen. Greater abundance of Fibrobacteraceae and Ruminococaceae in the rumen of beef steers likely reflected the need for enhanced fiber-digesting capacity in beef cattle. Our results should facilitate understanding of the structural and functional relationships in the rumen microbial ecosystem.

Abstract: Bacterial predation by protozoa has the most deleterious effect on the efficiency of N use within the rumen, but differences in activity among protozoal groups are not completely understood. Two in vitro experiments were conducted to identify the protozoal groups more closely related with rumen N metabolism. Rumen protozoa were harvested from cattle and 7 protozoal fractions were generated immediately after sampling by filtration through different nylon meshes at 39 °C, under a CO(2) atmosphere to maintain their activity. Protozoa were incubated with (14)C-labeled bacteria to determine their bacterial breakdown capacity, according to the amount of acid-soluble radioactivity released. Epidinium tended to codistribute with Isotricha and Entodinium with Dasytricha; therefore, their activity was calculated together. This study demonstrated that big Diplodiniinae had the greatest activity per cell (100 ng bacterial CP per protozoa and hour), followed by Epidinium plus Isotricha (36.4), small Diplodiniinae (34.2), and Entodinium plus Dasytricha (14.8), respectively. However, the activity per unit of protozoal volume seemed to vary, depending on the protozoal taxonomy. Small Diplodiniinae had the greatest activity per volume (325 ng bacterial CP per protozoal mm(3) and hour), followed by big Diplodiniinae (154), Entodinium plus Dasytricha (104), and Entodinium plus Dasytricha (25.6). A second experiment was conducted using rumen fluid from holotrich-monofaunated sheep. This showed that holotrich protozoa had a limited bacterial breakdown capacity per cell (Isotricha 9.44 and Dasytricha 5.81 ng bacterial CP per protozoa and hour) and per protozoal volume (5.97 and 76.9 ng bacterial CP per protozoal mm(3) and hour, respectively). Therefore, our findings indicated that a typical protozoal population (10(6) total protozoa/mL composed by Entodinium sp. 88%, Epidinium sp. 7%, and other species 4%) is able to break down ~17% of available rumen bacteria every hour. Entodinium sp. is responsible for most of this bacterial breakdown (70 to 75%), followed by Epidinium sp. (16 to 24%), big Diplodiniinae (4 to 6%), and small Diplodiniinae (2 to 6%), whereas holotrich protozoa have a negligible activity (Dasytricha sp. 0.6 to 1.2% and Isotricha sp. 0.2 to 0.5%). This in vitro information must be carefully interpreted, but it can be used to indicate which protozoal groups should be suppressed to improve microbial protein synthesis in vivo.

Abstract: Reducing methane emission from ruminant animals has implications not only for global environmental protection but also for efficient animal production. Tea saponins (TS) extracted from seeds, leaves or roots of tea plant are pentacyclic triterpenes. They have a lasting antiprotozoal effect, but little effect on the methanogen population in sheep. There was no significant correlation between the protozoa counts and methanogens. The TS decreased methanogen activity. It seems that TS influenced the activity of the methanogens indirectly via the depressed ciliate protozoal population. The TS addition decreased fungal population in the medium containing rumen liquor in in vitro fermentation, but no such effect was observed in the rumen liquor of sheep fed TS. Tea saponins had a minor effect on the pattern of rumen fermentation and hence on nutrient digestion. When added at 3 g/day in diets, TS could improve daily weight gain and feed efficiency in goats. No positive associative effect existed between TS and disodium fumarate or soybean oil on methane suppression. Inclusion of TS in diets may be an effective way for improving feed efficiency in ruminants.

Abstract: The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial proteins, short chain fatty acids and gases. In this study, metagenomic approaches were used to study the microbial populations and metabolic potential of the microbial community. DNA was extracted from Surti Buffalo rumen samples (four treatments diet) and sequenced separately using a 454 GS FLX Titanium system. We used comparative metagenomics to examine metabolic potential and phylogenetic composition from pyrosequence data generated in four samples, considering phylogenetic composition and metabolic potentials in the rumen may remarkably be different with respect to nutrient utilization. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of fermentation of carbohydrates in a high roughage diet. The distribution of phylotypes and environmental gene tags (EGTs) detected within each rumen sample were dominated by Bacteroidetes/Chlorobi, Firmicutes and Proteobacteria in all the samples. The results of this study could help to determine the role of rumen microbes and their enzymes in plant polysaccharide breakdown is fundamental to understanding digestion and maximising productivity in ruminant animals.

Abstract: Short-chain fatty acids (SCFAs), such as butyrate, produced by gut microorganisms, play a critical role in energy metabolism and physiology of ruminants as well as in human health. In this study, the temporal effect of elevated butyrate concentrations on the transcriptome of the rumen epithelium was quantified via serial biopsy sampling using RNA-seq technology. The mean number of genes transcribed in the rumen epithelial transcriptome was 17,323.63 ± 277.20 (±SD; N = 24) while the core transcriptome consisted of 15,025 genes. Collectively, 80 genes were identified as being significantly impacted by butyrate infusion across all time points sampled. Maximal transcriptional effect of butyrate on the rumen epithelium was observed at the 72-h infusion when the abundance of 58 genes was altered. The initial reaction of the rumen epithelium to elevated exogenous butyrate may represent a stress response as Gene Ontology (GO) terms identified were predominantly related to responses to bacteria and biotic stimuli. An algorithm for the reconstruction of accurate cellular networks (ARACNE) inferred regulatory gene networks with 113,738 direct interactions in the butyrate-epithelium interactome using a combined cutoff of an error tolerance ( = 0.10) and a stringent P-value threshold of mutual information (5.0 × 1011). Several regulatory networks were controlled by transcription factors, such as CREBBP and TTF2, which were regulated by butyrate. Our findings provide insight into the regulation of butyrate transport and metabolism in the rumen epithelium, which will guide our future efforts in exploiting potential beneficial effect of butyrate in animal well-being and human health.

Abstract: BACKGROUND: Plant tannins as rumen modifiers are better than chemicals or antibiotic-based modifiers since these compounds are natural products which are environmentally friendly and therefore have a better acceptance with regard to feed safety issues. Tropical plants containing phenols such as tannins were found to suppress or eliminate protozoa from the rumen and reduce methane and ammonia production. The screening of these plants is an important step in the identification of new compounds and feed additives which might contribute to mitigate rumen methanogenesis. The present study was carried out to determine the efficacy of tannins from tropical tree leaves for their methane reduction properties. RESULTS: Activity of tannins, as represented by the increase in gas volume with the addition of polyethylene glycol (PEG)-6000 as a tannin binder (tannin bioassay) was highest in Ficus bengalensis (555%), followed by Azardirachta indica (78.5%). PEG addition did not alter (P > 0.05) methane percentage in Ficus racemosa, Glyricidia maculata, Leucena leucocephala, Morus alba and Semaroba glauca, confirming that tannins in these samples did not affect methanogenesis. The increase (P 0.05) in the protozoa population in Autocarpus integrifolia, Ficus bengalensis, Jatropha curcus, Morus alba and Sesbania grandiflora, demonstrating that methane reduction observed in these samples per se was not due to defaunation effect of the tannin. The increase in total volatile fatty acid concentration in samples with PEG ranged from 0.6% to > 70%. The highest increase (%) in NH3-N was recorded in Azardirachta indica (67.4), followed by Ficus mysoriensis (35.7) and Semaroba glauca (32.6) leaves, reflecting strong protein binding properties of tannin. CONCLUSION: The results of our study established that in vitro methanogenesis was not essentially related to the density of protozoa population. Tropical tree leaves containing tannins such as Autocarpus integrifolia, Jatropha curcus and Sesbania grandiflora have the potential to suppress methanogenesis. Therefore tannins contained in these plants could be of interest in the development of new additives in ruminant nutrition. Copyright © 2012 Society of Chemical Industry