Changes in ruminal bacterial community composition following feeding of alfalfa ensiled with a lactic acid bacterial inoculant

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.

Effects of lactic acid bacteria in a silage inoculant on ruminal nutrient digestibility, nitrogen metabolism, and lactation performance of high-producing dairy cows

Silage treated with lactic acid bacteria inoculants has been reported to increase ruminal microbial biomass when tested in vitro. Therefore, we tested if alfalfa silage inoculated with Lactobacillus plantarum MTD-1 would improve ruminal N metabolism and increase milk production in high-producing dairy cows. Twenty-eight early lactation Holstein cows (8 ruminally cannulated) were blocked by DIM and milk production; animals were used in a double crossover design consisting of four 28-d periods. Animals in each block were randomly assigned to 2 treatments: a diet containing uninoculated alfalfa silage (control) and a diet containing alfalfa silage inoculated with L. plantarum MTD-1 (LP). Diets were formulated to contain 50% of alfalfa silage, 16% crude protein, and 25% neutral detergent fiber (dry matter basis). Milk production and dry matter intake were recorded in the last 14 d of each period. Milk samples were collected twice at both daily milkings on d 20, 21, 27, and 28 of each period. On d 22, omasal samples were collected from the cannulated animals over a period of 3 d to quantify ruminal digestibility and nutrient flows. Data were analyzed using mixed models of SAS 9.4 (SAS Institute). Compared to the control, cows receiving the LP treatment had greater milk production (40.4 vs. 39.6 kg/d) and lower milk urea nitrogen concentration (11.6 vs. 12.7 mg/dL), despite minor changes in energy-corrected milk. Milk lactose concentration was greater in the milk produced by cows fed the LP treatment, which reflected a tendency for increased milk lactose yield. Although milk true protein concentration was lower for cows in the LP treatment, milk true protein yield was the same on both control and LP treatments. Improvements in milk production of animals under the LP treatment were associated with greater organic matter truly digested in the rumen, especially ruminal neutral detergent fiber digestion. Minor changes were observed in total omasal microbial nonammonia N flow in cows receiving the LP treatment. Therefore, alfalfa silage treated with L. plantarum MTD-1 may improve ruminal fermentation and milk production; however, because of a lack of response in ruminal N metabolism, these changes did not result in greater energy-corrected milk in high-producing dairy cows.

Identifying and exploring biohydrogenating rumen bacteria with emphasis on pathways including trans-10 intermediates

Background

Bacteria involved in ruminal formation of trans-10 intermediates are unclear. Therefore, this study aimed at identifying rumen bacteria that produce trans-10 intermediates from 18-carbon unsaturated fatty acids.

Results

Pure cultures of 28 rumen bacterial species were incubated individually in the presence of 40 μg/mL 18:3n-3, 18:2n-6 or trans-11 18:1 under control or lactate-enriched (200 mM Na lactate) conditions for 24 h. Of the 28 strains, Cutibacterium acnes (formerly Propionibacterium acnes) was the only bacterium found to produce trans-10 intermediates from 18:3n-3 and 18:2n-6, irrespective of the growth condition. To further assess the potential importance of this species in the trans-11 to trans-10 shift, different biomass ratios of Butyrivibrio fibrisolvens (as a trans-11 producer) and C. acnes were incubated in different growth media (control, low pH and 22:6n-3 enriched media) containing 40 μg/mL 18:2n-6. Under control conditions, a trans-10 shift, defined in the current study as trans-10/trans-11 ≥ 0.9, occurred when the biomass of C. acnes represented between 90 and 98% of the inoculum. A low pH or addition of 22:6n-3 inhibited cis-9, trans-11 CLA and trans-10, cis-12 CLA formation by B. fibrisolvens and C. acnes, respectively, whereby C. acnes seemed to be more tolerant. This resulted in a decreased biomass of C. acnes required at inoculation to induce a trans-10 shift to 50% (low pH) and 90% (22:6n-3 addition).

Conclusions

Among the bacterial species studied,C. acnes was the only bacterium that have the metabolic ability to produce trans-10 intermediates from 18:3n-3 and 18:2n-6. Nevertheless, this experiment revealed that it is unlikely that C. acnes is the only or predominant species involved in the trans-11 to trans-10 shift in vivo.

Invited review: Role of rumen biohydrogenation intermediates and rumen microbes in diet-induced milk fat depression: An update

To meet the energy requirements of high-yielding dairy cows, grains and fats have increasingly been incorporated in ruminant diets. Moreover, lipid supplements have been included in ruminant diets under experimental or practical conditions to increase the concentrations of bioactive n-3 fatty acids and conjugated linoleic acids in milk and meat. Nevertheless, those feeding practices have dramatically increased the incidence of milk fat depression in dairy cattle. Although induction of milk fat depression may be a management tool, most often, diet-induced milk fat depression is unintended and associated with a direct economic loss. In this review, we give an update on the role of fatty acids, particularly originating from rumen biohydrogenation, as well as of rumen microbes in diet-induced milk fat depression. Although this syndrome seems to be multi-etiological, the best-known causal factor remains the shift in rumen biohydrogenation pathway from the formation of mainly trans-11 intermediates toward greater accumulation of trans-10 intermediates, referred to as the trans-11 to trans-10 shift. The microbial etiology of this trans-11 to trans-10 shift is not well understood yet and it seems that unraveling the microbial mechanisms of diet-induced milk fat depression is challenging. Potential strategies to avoid diet-induced milk fat depression are supplementation with rumen stabilizers, selection toward more tolerant animals, tailored management of cows at risk, selection toward more efficient fiber-digesting cows, or feeding less concentrates and grains.

Effect of 2-hydroxy-4-(methylthio) butanoate (HMTBa) supplementation on rumen bacterial populations in dairy cows when exposed to diets with risk for milk fat depression

Diet-induced milk fat depression (MFD) is a condition marked by a reduction in milk fat yield experimentally achieved by increasing dietary unsaturated fatty acids and fermentable carbohydrates. 2-Hydroxy-4-(methylthio) butanoate (HMTBa) is a methionine analog observed to reduce diet-induced MFD in dairy cows. We hypothesize that the reduction in diet-induced MFD by HMTBa is due to changes in the rumen microbiota. To test this, 22 high-producing cannulated Holstein dairy cows were placed into 2 groups using a randomized block design and assigned to either control or HMTBa supplementation (0.1% of diet dry matter). All cows were then exposed to 3 different diets with a low risk (32% neutral detergent fiber, no added oil; fed d 1 to 7), a moderate risk (29% neutral detergent fiber and 0.75% soybean oil; fed d 8 to 24), or a high risk (29% neutral detergent fiber and 1.5% soybean oil; fed d 25 to 28) for diet-induced MFD. Rumen samples were collected on d 0, 14, 24, and 28, extracted for DNA, PCR-amplified for the V1-V2 region of the 16S rRNA gene, sequenced on an Illumina MiSeq (Illumina, San Diego, CA), and subjected to bacterial diversity analysis using the QIIME pipeline. The α diversity estimates (species richness and Shannon diversity) were decreased in the control group compared with the HMTBa group. Bacterial community composition also differed between control and HMTBa groups based on both weighted UniFrac (relative abundance of commonly detected bacteria) and unweighted UniFrac (presence/absence) distances. Within the HMTBa group, no differences were observed in bacterial community composition between d 0 and d 14, 24, and 28; however, in the control group, d 0 samples were different from d 14, 24, and 28. Certain bacterial genera including Dialister, Megasphaera, Lachnospira, and Sharpea were increased in the control group compared with the HMTBa group. Interestingly, these genera were positively correlated with milk fat trans-10,cis-12 conjugated linoleic acid and trans-10 C18:1, fatty acid isomers associated with biohydrogenation-induced MFD. It can be concluded that diet-induced MFD is accompanied by significant alterations in the rumen bacterial community and that HMTBa supplementation reduces these microbial perturbations.

Performance of finishing beef cattle fed diets containing maize silages inoculated with lactic-acid bacteria and Bacillus subtilis

Our objective was to evaluate the effect of lactic-acid bacteria and Bacillus subtilis as silage additives on feed intake and growth performance of finishing feedlot beef cattle. Whole-maize forage was ensiled either with distilled water (untreated), or inoculated with Lactobacillus buchneri and L. plantarum at a rate 1 × 105 cfu/g fresh forage for each bacteria (LBLP); or inoculated with B. subtilis and L. plantarum at a rate 1 × 105 cfu/g fresh forage for each bacteria (BSLP). Thirty-six young crossbreed bulls (316 ± 33.9 kg) were used in the feedlot program for 110 days, and they were assigned (n = 12) to one of three diets containing untreated, LBLP, or BSLP silages in a 40:60 forage:concentrate ratio. Dry matter (DM) intake, average daily gain, and carcass yield of bulls were unaffected by silage inoculation. Conversely, bulls fed the BSLP silage had lower DM, organic matter, and crude protein digestibility compared with bulls fed untreated silage. Bulls fed both inoculated silages had a reduction of ~12% in neutral detergent fibre and acid detergent fibre digestibility compared with that in bulls fed untreated silage. Bulls fed the LBLP silage spent more time chewing (496 min/day) than bulls fed untreated silage. There was little effect of silage inoculation on rumen fermentation, but bulls fed the inoculated silages had a lower concentration of ammonia-N. In conclusion, adding L. plantarum combined with L. buchneri or B. subtilis to maize silage do not improve the growth performance of finishing feedlot beef cattle.

Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows

In this study, differences in the ruminal bacterial community between high-yield and low-yield lactating dairy cows under the same dietary conditions were investigated. Sixteen lactating dairy cows with similar parity and days in milk were divided into high-yield (HY) and low-yield (LY) groups based on their milk yield. On day 21, rumen content samples were collected, and their microbiota compositions were determined using high-throughput sequencing of the 16S rRNA gene by the Illumina MiSeq platform. During the study period, dry matter intake (DMI) and milk yield were measured daily, and milk composition was assessed 3 times per week. The results showed that the milk of the LY group tended to have higher fat (P = 0.08), protein (P = 0.01) and total solid contents (P = 0.04) than that of the HY group, while the HY group had higher ruminal propionate (P = 0.08) proportion and volatile fatty acid (VFA) (P = 0.02) concentrations. Principal coordinate analysis indicated significant differences in ruminal bacterial community compositions and structures between the HY group and LY group. The abundances of Ruminococcus 2, Lachnospiraceae and Eubacterium coprostanoligenes were significantly higher in the HY group than in the LY group. In addition, Bacteroides, Ruminococcus 2 and Candidatus-Saccharimonas were positively correlated with ruminal propionate proportion (r>0.4, P<0.05). These findings enhance the understanding of bacterial synthesis within the rumen and reveal an important mechanism underlying differences in milk production in dairy cows.

Silage review: Silage feeding management: Silage characteristics and dairy cow feeding behavior

Feeding environment and feed accessibility influence the dairy cow's response to the ration and forage composition. Fiber content, physical form, and fermentability influence feeding behavior, feed intake, and overall cow metabolic and lactational responses to forage. It is possible to vary eating time of lactating dairy cattle by over 1 h/d by changing dietary silage fiber content, digestibility, and particle size. Optimizing silage particle size is important because excessively long particles increase the necessary chewing to swallow a bolus of feed, thereby increasing eating time. Under competitive feeding situations, excessively coarse or lower fiber digestibility silages may limit DMI of lactating dairy cows due to eating time requirements that exceed available time at the feed bunk. Additionally, greater silage particle size, especially the particles retained on the 19-mm sieve using the Penn State Particle Separator, are most likely to be sorted. Silage starch content and fermentability may influence ruminal propionate production and thereby exert substantial control over meal patterns and feed consumption. Compared with silage fiber characteristics, relatively little research has assessed how silage starch content and fermentability interact with the feeding environment to influence dairy cow feeding behavior. Finally, voluminous literature exists on the potential effects that silage fermentation end products have on feeding behavior and feed intake. However, the specific mechanisms of how these end products influence behavior and intake are poorly understood in some cases. The compounds shown to have the greatest effect on feeding behavior are lactate, acetate, propionate, butyrate, ammonia-N, and amines. Any limitation in the feeding environment will likely accentuate the negative response to poor silage fermentation. In the future, to optimize feeding behavior and dry matter intake of silage-based diets fed to dairy cattle, we will need to consider the chemical and physical properties of silage, end products of silage fermentation, and the social and physical components of the feeding environment.

Camelina Seed Supplementation at Two Dietary Fat Levels Change Ruminal Bacterial Community Composition in a Dual-Flow Continuous Culture System

This experiment aimed to determine the effects of camelina seed (CS) supplementation at different dietary fat levels on ruminal bacterial community composition and how it relates to changes in ruminal fermentation in a dual-flow continuous culture system. Diets were randomly assigned to 8 fermenters (1,200–1,250 mL) in a 2 × 2 factorial arrangement of treatments in a replicated 4 × 4 Latin square with four 10-day experimental periods that consisted of 7 days for diet adaptation and 3 days for sample collection. Treatments were: (1) no CS at 5% ether extract (EE, NCS5); (2) no CS at 8% EE (NCS8); (3) 7.7% CS at 5% EE (CS5); and (4) 17.7% CS at 8% EE (CS8). Megalac was used as a control to adjust EE levels. Diets contained 55% orchardgrass hay and 45% concentrate, and fermenters were equally fed a total of 72 g/day (DM basis) twice daily. The bacterial community was determined by sequencing the V4 region of the 16S rRNA gene using the Illumina MiSeq platform. Sequencing data were analyzed using mothur and statistical analyses were performed in R and SAS. The most abundant phyla across treatments were the Bacteroidetes and Firmicutes, accounting for 49 and 39% of the total sequences, respectively. The bacterial community composition in both liquid and solid fractions of the effluent digesta changed with CS supplementation but not by dietary EE. Including CS in the diets decreased the relative abundances of Ruminococcus spp., Fibrobacter spp., and Butyrivibrio spp. The most abundant genus across treatments, Prevotella, was reduced by high dietary EE levels, while Megasphaera and Succinivibrio were increased by CS supplementation in the liquid fraction. Correlatively, the concentration of acetate was decreased while propionate increased; C18:0 was decreased and polyunsaturated fatty acids, especially C18:2 n-6 and C18:3 n-3, were increased by CS supplementation. Based on the correlation analysis between genera and fermentation end products, this study revealed that CS supplementation could be energetically beneficial to dairy cows by increasing propionate-producing bacteria and suppressing ruminal bacteria associated with biohydrogenation. However, attention should be given to avoid the effects of CS supplementation on suppressing cellulolytic bacteria.

Transient changes in milk production efficiency and bacterial community composition resulting from near-total exchange of ruminal contents between high- and low-efficiency Holstein cows

The objectives of this study were to determine if milk production efficiency (MPE) is altered by near-total exchange of ruminal contents between high- (HE) and low-MPE (LE) cows and to characterize ruminal bacterial community composition (BCC) before exchange and over time postexchange. Three pairs of ruminally cannulated, third-lactation cows were selected whose MPE (energy-corrected milk per unit of dry matter intake) differed over their first 2 lactations. Approximately 95% of ruminal contents were exchanged between cows within each pair. Ruminal pH and volatile fatty acid (VFA) profiles, along with BCC (characterized by sequencing of the variable 4 region of 16S rRNA genes), were assessed just before feeding on d -8, -7, -5, -4, -1, 1, 2, 3, 7, 10, 14, 21, 28, 35, 42, and 56, relative to the exchange date. High-MPE cows had higher total ruminal VFA concentrations, higher molar percentages of propionate and valerate, and lower molar percentages of acetate and butyrate than did LE cows, and re-established these differences 1 d after contents exchange. Across all LE cows, MPE increased during 7 d postexchange but declined thereafter. Two of the 3 HE cows displayed decreases in MPE following introduction of the ruminal contents from the corresponding LE cow, but MPE increased in the third HE cow, which was determined to be an outlier. For all 6 cows, both liquid- and solids-associated BCC differed between individuals within a pair before contents exchange. Upon exchange, BCC of both phases in all 3 pairs was more similar to that of the donor inoculum than to preexchange host BCC. For 5 of 6 cows, the solids-associated community returned within 10 d to more resemble the preexchange community of that host than that of the donor community. Individual variability before the exchange was greater in liquids than in solids, as was the variability in response of bacterial communities to the exchange. Individual cows varied in their response, but generally moved toward re-establishment of their preexchange communities by 10 d after contents exchange. By contrast, ruminal pH and VFA profiles returned to preexchange levels within 1 d. Despite the small number of cows studied, the data suggest an apparent role for the ruminal bacterial community as a determinant of MPE.

Influence of Lactobacillus buchneri as silage additive and forage:concentrate ratio on the growth performance, fatty acid profile in longissimus muscle, and meat quality of beef cattle

Our objective was to investigate Lactobacillus buchneri as a silage additive and the forage:concentrate (F:C) ratio on growth performance and meat quality of finishing beef cattle. The trial was a 2 (corn silage untreated or inoculated with L. buchneri) × 2 (two F:C ratios, 60:40 or 40:60) factorial. Bulls fed a 40:60 F:C diet containing inoculated silage had greater dry matter (DM) intake (P < 0.01) and average daily gain (P = 0.029) compared with other treatments. DM (P = 0.02) and neutral detergent digestibility (P < 0.01) were depressed by inoculation of corn silage with L. buchneri. Thiobarbituric acid concentration in meat increased (P < 0.01) by 15% in bulls fed the 60:40 F:C diet compared with the 40:60 F:C diet. Inoculation of silage increased (P = 0.02) the ratio of unsaturated fatty acids to saturated fatty acids. Compared with the 60:40 F:C diet, the concentrations of polyunsaturated fatty acids (P = 0.03) and omega-6 fatty acids (P = 0.02) increased in longissimus muscle by 23% and 26%, respectively, in bulls fed the 40:60 F:C diet. Inoculation of corn silage with L. buchneri inconsistently improved the growth performance and meat traits of finishing bulls consuming diets differing in F:C.

Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters

The present study applied the PacBio single molecule, real-time sequencing technology (SMRT) in evaluating the quality of silage production. Specifically, we produced four types of Medicago sativa silages by using four different lactic acid bacteria-based additives (AD-I, AD-II, AD-III and AD-IV). We monitored the changes in pH, organic acids (including butyric acid, the ratio of acetic acid/lactic acid, γ-aminobutyric acid, 4-hyroxy benzoic acid and phenyl lactic acid), mycotoxins, and bacterial microbiota during silage fermentation. Our results showed that the use of the additives was beneficial to the silage fermentation by enhancing a general pH and mycotoxin reduction, while increasing the organic acids content. By SMRT analysis of the microbial composition in eight silage samples, we found that the bacterial species number and relative abundances shifted apparently after fermentation. Such changes were specific to the LAB species in the additives. Particularly, Bacillus megaterium was the initial dominant species in the raw materials; and after the fermentation process, Pediococcus acidilactici and Lactobacillus plantarum became the most prevalent species, both of which were intrinsically present in the LAB additives. Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage.

Effects of ruminal dosing of Holstein cows with Megasphaera elsdenii on milk fat production, ruminal chemistry, and bacterial strain persistence

Megasphaera elsdenii is a lactate-utilizing bacterium whose ruminal abundance has been shown to be greatly elevated during milk fat depression (MFD). To further examine this association, a total of 23 cannulated multiparous Holstein cows were examined in 3 experiments in which strains of M. elsdenii were directly dosed into the rumen (~2 × 10(12) cells/dose); control cows were dosed with sterile lactate-free culture medium. Cows were fed a total mixed ration (292 g of starch/kg of dry matter) that contained primarily corn silage, alfalfa silage, finely ground high-moisture corn, supplemental protein, and corn oil (3 g/kg of dry matter). Experiments differed in stage of lactation of the cows (early or late), dosing events (single dose, or 4 doses over a 5-d period), timing of dose (prefeed or 4 h postfeed), and M. elsdenii strain (laboratory strain YI9 or 3 strains isolated from cows in the same herd). Dry matter intake and milk yield and composition were measured from 5 to 0 d before dosing and 1 to 7d after first dosing, plus later time points that varied by experiment. Milk yield and composition were not affected by dosing. Megasphaera elsdenii was quantified in the liquid phase of ruminal contents by automated ribosomal intergenic spacer analysis, or by PCR with relative quantification (M. elsdenii 16S rRNA gene copy number as a percentage of total bacterial 16S rRNA gene copies). Neither the M. elsdenii-dosed or control cows displayed MFD after dosing, and in almost all cases M. elsdenii populations returned to low baseline levels (<0.02% of 16S rRNA gene copy number) within 24 h of dosing. This rapid decline in M. elsdenii also occurred in several cows that were dosed with a strain of M. elsdenii that had been isolated from that particular cow during a previous bout of MFD. Ruminal pH and total millimolar volatile fatty acids and lactate did not differ between dosed and control cows, although acetate-to-propionate ratio declined in both groups and butyrate increased after dosing with M. elsdenii. The results confirm that establishing exogenously added bacterial strains in the rumen is difficult, even for strains previously isolated from the recipient cow. The potential role of M. elsdenii as an agent of MFD remains unclear in the absence of successful establishment of the dosed strains.

Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations

The ruminal microbial community is remarkably diverse, containing 100s of different bacterial and archaeal species, plus many species of fungi and protozoa. Molecular studies have identified a “core microbiome” dominated by phyla Firmicutes and Bacteroidetes, but also containing many other taxa. The rumen provides an ideal laboratory for studies on microbial ecology and the demonstration of ecological principles. In particular, the microbial community demonstrates both redundancy (overlap of function among multiple species) and resilience (resistance to, and capacity to recover from, perturbation). These twin properties provide remarkable stability that maintains digestive function for the host across a range of feeding and management conditions, but they also provide a challenge to engineering the rumen for improved function (e.g., improved fiber utilization or decreased methane production). Direct ruminal dosing or feeding of probiotic strains often fails to establish the added strains, due to intensive competition and amensalism from the indigenous residents that are well-adapted to the historical conditions within each rumen. Known exceptions include introduced strains that can fill otherwise unoccupied niches, as in the case of specialist bacteria that degrade phytotoxins such as mimosine or fluoroacetate. An additional complicating factor in manipulating the ruminal fermentation is the individuality or host specificity of the microbiota, in which individual animals contain a particular community whose species composition is capable of reconstituting itself, even following a near-total exchange of ruminal contents from another herd mate maintained on the same diet. Elucidation of the interactions between the microbial community and the individual host that establish and maintain this specificity may provide insights into why individual hosts vary in production metrics (e.g., feed efficiency or milk fat synthesis), and how to improve herd performance.

Bacterial communities in the rumen of Holstein heifers differ when fed orchardgrass as pasture vs. hay

The rich and diverse microbiota of the rumen provides ruminant animals the capacity to utilize highly fibrous feedstuffs as their energy source, but there is surprisingly little information on the composition of the microbiome of ruminants fed all-forage diets, despite the importance of such agricultural production systems worldwide. In three 28-day periods, three ruminally-cannulated Holstein heifers sequentially grazed orchardgrass pasture (OP), then were fed orchardgrass hay (OH), then returned to OP. These heifers displayed greater shifts in ruminal bacterial community composition (determined by automated ribosomal intergenic spacer analysis and by pyrotag sequencing of 16S rRNA genes) than did two other heifers maintained 84 d on the same OP. Phyla Firmicutes and Bacteroidetes dominated all ruminal samples, and quantitative PCR indicated that members of the genus Prevotella averaged 23% of the 16S rRNA gene copies, well below levels previously reported with cows fed total mixed rations. Differences in bacterial community composition and ruminal volatile fatty acid (VFA) profiles were observed between the OP and OH despite similarities in gross chemical composition. Compared to OP, feeding OH increased the molar proportion of ruminal acetate (P = 0.02) and decreased the proportion of ruminal butyrate (P < 0.01), branched-chain VFA (P < 0.01) and the relative population size of the abundant genus Butyrivibrio (P < 0.001), as determined by pyrotag sequencing. Despite the low numbers of animals examined, the observed changes in VFA profile in the rumens of heifers on OP vs. OH are consistent with the shifts in Butyrivibrio abundance and its known physiology as a butyrate producer that ferments both carbohydrates and proteins.

Fiber degradability, chemical composition and conservation characteristics of alfalfa haylage ensiled with exogenous fibrolytic enzymes and a ferulic acid esterase-producing inoculant

Lynch, J. P., Prema, D., Van Hamme, J. D., Church, J. S. and Beauchemin, K. A. 2014. Fiber degradability, chemical composition and conservation characteristics of alfalfa haylage ensiled with exogenous fibrolytic enzymes and a ferulic acid esterase-producing inoculant. Can. J. Anim. Sci. 94: 697–704. This study investigated the effects of two fibrolytic enzyme products, applied at baling alone or in combination with a ferulic acid esterase-producing bacterial additive, on the ensilage dynamics, chemical composition and digestibility of alfalfa haylage. Five replicate wrapped bales were produced with one of five treatments, including an untreated control, and one of two fibrolytic enzyme products (EN1 and EN2) applied either alone or in combination with a ferulic-acid producing bacterial additive (FAEI). No effect of treatment was observed on the neutral detergent fiber (NDF) (P=0.889) or acid detergent fiber (ADF) (P=0.065) concentrations of haylage after ensilage, but haylage produced using fibrolytic enzyme products underwent greater (P<0.018) increases in temperature following exposure to aerobic conditions. Haylages produced with fibrolytic enzyme products had a greater (P<0.001) in vitro NDF degradability (NDFD) than untreated haylage. The use of fibrolytic enzymes applied to alfalfa haylage at ensiling increased the NDFD, despite minimal effects on the chemical composition of the herbage. However, the greater aerobic deterioration of fibrolytic enzyme-treated bales indicates higher dry matter losses during aerobic exposure. The use of FAEI with fibrolytic enzymes did not further enhance the effects of fibrolytic-enzyme treatments.

Special topics--Mitigation of methane and nitrous oxide emissions from animal operations: I. A review of enteric methane mitigation options

The goal of this review was to analyze published data related to mitigation of enteric methane (CH4) emissions from ruminant animals to document the most effective and sustainable strategies. Increasing forage digestibility and digestible forage intake was one of the major recommended CH4 mitigation practices. Although responses vary, CH4 emissions can be reduced when corn silage replaces grass silage in the diet. Feeding legume silages could also lower CH4 emissions compared to grass silage due to their lower fiber concentration. Dietary lipids can be effective in reducing CH4 emissions, but their applicability will depend on effects on feed intake, fiber digestibility, production, and milk composition. Inclusion of concentrate feeds in the diet of ruminants will likely decrease CH4 emission intensity (Ei; CH4 per unit animal product), particularly when inclusion is above 40% of dietary dry matter and rumen function is not impaired. Supplementation of diets containing medium to poor quality forages with small amounts of concentrate feed will typically decrease CH4 Ei. Nitrates show promise as CH4 mitigation agents, but more studies are needed to fully understand their impact on whole-farm greenhouse gas emissions, animal productivity, and animal health. Through their effect on feed efficiency and rumen stoichiometry, ionophores are likely to have a moderate CH4 mitigating effect in ruminants fed high-grain or mixed grain-forage diets. Tannins may also reduce CH4 emissions although in some situations intake and milk production may be compromised. Some direct-fed microbials, such as yeast-based products, might have a moderate CH4-mitigating effect through increasing animal productivity and feed efficiency, but the effect is likely to be inconsistent. Vaccines against rumen archaea may offer mitigation opportunities in the future although the extent of CH4 reduction is likely to be small and adaptation by ruminal microbes and persistence of the effect is unknown. Overall, improving forage quality and the overall efficiency of dietary nutrient use is an effective way of decreasing CH4 Ei. Several feed supplements have a potential to reduce CH4 emission from ruminants although their long-term effect has not been well established and some are toxic or may not be economically feasible.

Changes in rumen bacterial community composition in steers in response to dietary nitrate

The effect of dietary nitrate supplementation on rumen bacterial community composition was examined in beef steers fed either a nitrate-N diet or urea-N diet. An automated method of ribosomal intergenic spacer analysis was applied to solid and liquid fractions of ruminal contents to allow comparison of bacterial communities. Supplemental N source affected relative population size of four amplicon lengths (ALs) in the liquid fraction and three ALs in the solid fraction. Five ALs were more prevalent after adaptation to nitrate. Correspondence analysis indicated that feeding the steers the nitrate-N diet versus urea-N diet changed the bacterial community composition in the liquid but not in the solid fraction. This led to an investigation of the relative sizes of potential nitrate-reducing populations. Mannheimia succiniciproducens, Veillonella parvula, and Campylobacter fetus were obtained from nitrate enrichment culture and quantified by real-time PCR based on 16S rRNA sequence. Nitrate supplementation increased the percentage of C. fetus in the liquid and solid phases, and in solid phase, the percentage of M. succiniciproducens increased. No change in species prevalence was observed for V. parvula. However, even after adaptation to dietary nitrate, the relative population sizes for all three putative nitrate-reducing species were very low (<0.06 % of 16S rRNA gene copy number). The liquid-associated bacterial community composition changed due to nitrate supplementation, and at least part of this change reflects an increase in the species prevalence of C. fetus, a species which is not typically regarded as a ruminal inhabitant.