Rumen Microbial Population Research Articles

Enhancing Butyrate Production, Ruminal Fermentation and Microbial Population through Supplementation with Clostridium saccharobutylicum.

Butyrate is known to play a significant role in energy metabolism and regulating genomic activities that influence rumen nutrition utilization and function. Thus, this study investigated the effects of an isolated butyrate-producing bacteria, Clostridium saccharobutylicum, in rumen butyrate production, fermentation parameters and microbial population in Holstein-Friesian cow. An isolated butyrate-producing bacterium from the ruminal fluid of a Holstein-Friesian cow was identified and characterized as Clostridium saccharobutylicum RNAL841125 using 16S rRNA gene sequencing and phylogenetic analyses. The bacterium was evaluated on its effects as supplement on in vitro rumen fermentation and microbial population. Supplementation with 106 CFU/ml Clostridium saccharobutylicum increased (p < 0.05) microbial crude protein, butyrate and total volatile fatty acids concentration but had no significant effect on NH3-N at 24 h incubation. Butyrate and total VFA concentrations were higher (p < 0.05) in supplementation with 106 CFU/ml Clostridium saccharobutylicum compared with control, with no differences observed for total gas production, NH3-N and propionate concentration. However, as the inclusion rate (CFU/ml) of C. saccharobutylicum was increased, reduction of rumen fermentation values was observed. Furthermore, butyrate-producing bacteria and Fibrobacter succinogenes population in the rumen increased in response with supplementation of C. saccharobutylicum, while no differences in the population in total bacteria, protozoa and fungi were observed among treatments. Overall, our study suggests that supplementation with 106 CFU/ml C. saccharobutylicum has the potential to improve ruminal fermentation through increased concentrations of butyrate and total volatile fatty acid, and enhanced population of butyrate-producing bacteria and cellulolytic bacteria F. succinogenes.

Impact of Ecklonia stolonifera extract on in vitro ruminal fermentation characteristics, methanogenesis, and microbial populations.

ObjectiveThis study was conducted to evaluate the effects of Ecklonia stolonifera (E. stolonifera) extract addition on in vitro ruminal fermentation characteristics, methanogenesis and microbial populations.MethodsOne cannulated Holstein cow (450±30 kg) consuming timothy hay and a commercial concentrate (60:40, w/w) twice daily (09:00 and 17:00) at 2% of body weight with free access to water and mineral block were used as rumen fluid donors. In vitro fermentation experiment, with timothy hay as substrate, was conducted for up to 72 h, with E. stolonifera extract added to achieve final concentration 1%, 3%, and 5% on timothy hay basis.ResultsAdministration of E. stolonifera extract to a ruminant fluid-artificial saliva mixture in vitro increased the total gas production. Unexpectedly, E. stolonifera extracts appeared to increase both methane emissions and hydrogen production, which is contrasts with previous observations with brown algae extracts used under in vitro fermentation conditions. Interestingly, real-time polymerase chain reaction indicated that as compared with the untreated control the ciliate-associated methanogen and Fibrobacter succinogenes populations decreased, whereas the Ruminococcus flavefaciens population increased as a result of E. stolonifera extract supplementation.ConclusionE. stolonifera showed no detrimental effect on rumen fermentation characteristics and microbial population. Through these results E. stolonifera has potential as a viable feed supplement to ruminants.

Effects of oregano essential oil on the ruminal pH and microbial population of sheep.

Oregano essential oil (OEO), which has antimicrobial properties, may be used for altering the ruminal pH and microbial populations of sheep, as observed by the altered volatile fatty acid patterns. To further elucidate the effects of OEO on ruminal pH and microbial populations of sheep, 3 German merino sheep × local sheep crossbred rams with permanent ruminal fistulas were randomly assigned to a 3 × 3 Latin square design with 12-d periods. The treatments were as follows: control (CON); OEO4: OEO supplied at 4 g•d-1; and OEO7: OEO supplied at 7 g•d-1. Starting on day 11, rumen fluid was collected at 0 h, and at 4, 8, 12, 24 and 48 h after supplying OEO, and then pH values of rumen fluid were immediately measured. The abundance of microbial populations was determined by using qPCR. The ruminal pH values were similar among the sheep from all treatments. The abundance of ruminal fungi was higher for the sheep supplied OEO7 compared with the sheep supplied CON and OEO4, especially at 4 and 12 h. The abundance of ruminal protozoa decreased with supplied OEO, indicating that OEO could inhibit the protozoa. The abundance of the total ruminal bacteria was similar for the sheep from all treatments, but R. flavefaciens, R. albus and F. succinogenes increased in the sheep supplied OEO4 compared with those in the sheep supplied CON, however, the sheep supplied OEO7 had higher abundances of R. flavefaciens than the sheep supplied CON. These results demonstrated that supplying OEO to sheep did not affect the ruminal pH but could shift the rumen microbial population to one with less protozoa. Supplying OEO can preferentially enhance the growth of certain rumen microbial populations, but the shifts were influenced by the supply rate. Therefore, supplying low amount (i.e. 4 g•d-1) of OEO could have positive effects on ruminal microbial populations, whereas supplying elevated doses of OEO could be detrimental to those same ruminal microbial populations.

Metatranscriptomic Analysis of Sub-Acute Ruminal Acidosis in Beef Cattle.

Simple SummaryThis study evaluated the functional activity of rumen microbiota during sub-acute ruminal acidosis, a metabolic disease of ruminants characterized by low pH caused by feeding highly fermentable carbohydrate feeds. The abundance of rumen bacteria that degrade cellulose (Fibrobacter succinogenes, Ruminococcus albus, and R. bicirculans) were reduced by induced acidotic challenge. Genes mapped to carbohydrate, amino acid, energy, vitamin and co-factor metabolism pathways, and bacterial biofilm formation pathways were enriched in beef cattle challenged with sub-acute acidosis. This study enhances our understanding of the response of rumen microbiota to sub-acute ruminal acidosis by revealing transcriptionally active taxa and metabolic pathways of rumen microbiota.Subacute ruminal acidosis (SARA) is a metabolic disease of ruminants characterized by low pH, with significant impacts on rumen microbial activity, and animal productivity and health. Microbial changes during subacute ruminal acidosis have previously been analyzed using quantitative PCR and 16S rRNA sequencing, which do not reveal the actual activity of the rumen microbial population. Here, we report the functional activity of the rumen microbiota during subacute ruminal acidosis. Eight rumen-cannulated Holstein steers were assigned randomly to acidosis-inducing or control diet. Rumen fluid samples were taken at 0, 3, 6, and 9 h relative to feeding from both treatments on the challenge day. A metatranscriptome library was prepared from RNA extracted from the samples and the sequencing of the metatranscriptome library was performed on Illumina HiSeq4000 following a 2 × 150 bp index run. Cellulolytic ruminal bacteria including Fibrobacter succinogenes, Ruminococcus albus, and R. bicirculans were reduced by an induced acidotic challenge. Up to 68 functional genes were differentially expressed between the two treatments. Genes mapped to carbohydrate, amino acid, energy, vitamin and co-factor metabolism pathways, and bacterial biofilm formation pathways were enriched in beef cattle challenged with sub-acute acidosis. This study reveals transcriptionally active taxa and metabolic pathways of rumen microbiota during induced acidotic challenge.

Human perception and efficacy of Carassius auratus on maintaining water quality in equine water tanks

The rumen contains a great diversity of prokaryotic and eukaryotic microorganisms that allow the ruminant to utilize ligno-cellulose material and to convert non-protein nitrogen into microbial protein to obtain energy and amino acids. However, rumen fermentation also has potential deleterious consequences associated with the emissions of greenhouse gases, excessive nitrogen excreted in manure and may also adversely influence the nutritional value of ruminant products. While several strategies for optimizing the energy and nitrogen use by ruminants have been suggested, a better understanding of the key microorganisms involved and their activities is essential to manipulate rumen processes successfully. Diet is the most obvious factor influencing the rumen microbiome and fermentation. Among dietary interventions, the ban of antimicrobial growth promoters in animal production systems has led to an increasing interest in the use of plant extracts to manipulate the rumen. Plant extracts (e.g. saponins, polyphenol compounds, essential oils) have shown potential to decrease methane emissions and improve the efficiency of nitrogen utilization; however, there are limitations such as inconsistency, transient and adverse effects for their use as feed additives for ruminants. It has been proved that the host animal may also influence the rumen microbial population both as a heritable trait and through the effect of early-life nutrition on microbial population structure and function in adult ruminants. Recent developments have allowed phylogenetic information to be upscaled to metabolic information; however, research effort on cultivation of microorganisms for an in-depth study and characterization is needed. The introduction and integration of metagenomic, transcriptomic, proteomic and metabolomic techniques is offering the greatest potential of reaching a truly systems-level understanding of the rumen; studies have been focused on the prokaryotic population and a broader approach needs to be considered.

Microbial population and blood parameters of West African dwarf goats fed scent leaf (Ocimum gratissimum) as additive

A study was carried out to determine the rumen microbial population and blood parameters of 20 West African dwarf goats fed Ocimum gratissimum (scent leaf) as additive in a concentrate supplement. The goats were divided into four treatment groups (T1, T2, T3 andT4) with five replicates in a completely randomized design. Four concentrate supplements were formulated to contain scent leaf at levels 0,5,10, and 15g/kg DM. Panicum maximum was the basal diet. Chemical composition of scent leaf and the diets were determined. Rumen fluid and blood were collected from the goats before and after the experiment to determine microbial population and blood parameters. Results showed that scent leaf has moderate crude protein of 10.61% and rich in tannin, saponin and oxalate. At the end of the experiment, bacteria and protozoa counts were not significantly (p&gt;0.05) influenced by the experimental diets, however there was a reduction in their values. Fungi count was significantly (p&lt;0.05) affected by the diets and their values reduced as the level of scent leaf in the diets increased. The highest count (0.35×106 cfu/ml) was obtained at T1 (control) and the lowest value (0.05×106cfu/ml) obtained in goats fed 15g/kg DM scent leaf (T4). Red blood cell (RBC) count, packed cell volume (PCV) and haemoglobin values increased at the end of the study and were significantly (p&lt;0.05) highest (15.03×1012/l, 36.50% and 13.32g/dl respectively) in goats fed T3 (10g/kg DM of O. gratissimum). Serum urea and cholesterol levels were significantly lowest in goats fed T3 and T4. Alanine amino transferase (ALT) and aspartate aminotransferase (AST) values were reduced by the experimental diets. It can therefore be concluded that scent leaf can be included in the diet of West African dwarf goats up to 10g/kg DM for improved RBC, PCV and Hb, and regulation of serum enzymes, urea and cholesterol levels

Effects of long-term diet supplementation with Gliricidia sepium foliage mixed with Enterolobium cyclocarpum pods on enteric methane, apparent digestibility, and rumen microbial population in crossbred heifers1.

In the last decades, strategies have been evaluated to reduce rumen methane (CH4) production by supplementing tropical forages rich in secondary compounds; however, most of these beneficial effects need to be validated in terms of their persistence over time. The aim of this study was to assess CH4 emissions over time in heifers fed with and without Gliricidia sepium foliage (G) mixed with ground pods of Enterolobium cyclocarpum(E). Two groups of 4 crossbred (Bos taurus x Bos indicus) heifers (284 ±17 kg initial weight) were fed with 2 diets (0% and 15% of a mixture of the pods and foliage [E + G:0 and E + G:15, respectively]) over 80 d, plus 2 wk before the experiment, in which every animal was fed a legume and pod-free diet. Every 14 d, CH4 production, apparent digestibility, volatile fatty acids (VFA), and microbial population were quantified for each animal. The experiment was conducted with a repeated measurements design over time. Diets fed differed in terms of their crude protein (CP), condensed tannins, and saponins content supplied by E. cyclocarpum and G. sepium. For most of the experiment, dry matter intake (DMI) and digestible dry-matter intake (DDMI) were 6.3 kg DMI/d and 512 g DDMI/kg, respectively, for both diets (diet: P > 0.05). Apparent digestible crude protein (DCP) was reduced by 21 g DCP/kg DM when the diet was supplemented with E + G:15 (P = 0.040). Molar proportions of VFA's in the rumen did not differ between diets or in time (P > 0.05). Daily methane production, expressed in relation to DMI, was 23.95 vs. 23.32 g CH4/kg DMI for the diet E + G:0 and E + G:15, respectively (diet: P = 0.016; Time: P > 0.05). Percent gross energy loss as CH4 (Ym) with grass-only diets was above 8.1%, whereas when feeding heifers with the alternate supplementation, Ym values of 7.59% (P = 0.016) were observed. The relative abundance of total bacterial, protozoa, and methanogenic archaeal replicates was not affected by time nor by the incorporation of legume and pods into the diet (P > 0.05). Results suggest that addition of G. sepium mixed with E. cyclocarpum pods can reduce CH4 production in heifers and this response remains over time, without effect on microbial population and VFA concentration and a slight reduction in CPD digestibility.

Ruminal Microbial Populations and Fermentation Characteristics in Beef Cattle Grazing Tropical Forage in Dry Season and Supplemented with Different Protein Levels.

We tested the hypothesis that supplementation with protein improves fermentation parameters without damaging the rumen microbial populations of beef cattle grazing Urochloa brizantha cv. Marandu during the dry season. Four rumen-cannulated Nellore bulls (571 ± 31kg of body weight) were used in a 4 × 4 Latin square design. The treatments were not supplemented with concentrate (only free-choice mineral salt ad libitum) and supplemented (supplements with low-LPSU, medium-MPS, and high protein supplement-HPS), supplying 155, 515, and 875g/animal/day of crude protein (CP), respectively. The abundance of each target taxon was calculated as a fraction of the total 16S rRNA gene copies in the samples, using taxon-specific and domain bacteria primers. There was no difference (P > 0.05) across treatments for intakes of dry matter (DM), forage and neutral detergent fiber (NDF), digestibility of DM and NDF, and ruminal pH. Animals supplemented with concentrate had greater (P < 0.05) intakes and digestibility of CP, ether extract and non-fibrous carbohydrate contents of the substrates (EE + NFC), and ruminal ammonia nitrogen (RAN) compared to control. Bulls that received only mineral salt had lower proportions of Butyrivibrio fibrisolvens and had greater (P < 0.05) proportions of Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens, Methanogen archaea than bulls supplemented with concentrate. The MPS animals had greater (P < 0.05) intake and digestibility of CP, RAN concentration, and had lower (P < 0.05) proportions of Fibrobacter succinogenes, Ruminococcus flavefaciens, and Selenomonas ruminantium than LPSU animals. The HPS provided higher (P < 0.05) intake of CP, RAN and proportion of Ruminococcus albus when compared with MPS. In conclusion, supply of 515g/animal/day of protein via supplement provides better ruminal conditions for the growth of cellulolytic bacteria of bulls on pasture during dry season.

Effects of tannins and saponins contained in foliage of Gliricidia sepium and pods of Enterolobium cyclocarpum on fermentation, methane emissions and rumen microbial population in crossbred heifers

Incorporation of foliage and pods of tropical legumes in ruminant rations is an alternative to mitigate enteric methane emissions. The objective of this research was to evaluate the effect of adding increasing levels of ground pods of Enterolobium cyclocarpum (Jacq.) Griseb. mixed with foliage of Gliricidia sepium (Jacq.) Steud. on emissions of ruminal methane (CH4), volatile fatty acid proportions, rumen pH and microbial population in cattle. Four heifers (218 ± 18 kg LW) were fed (13 days) 0, 15, 30, and 45% of pods of E. cyclocarpum mixed with foliage of G. sepium, which were supplemented to a basal ration of Brachiaria brizantha (Hochst. ex A. Rich.) Stapf. Data were analyzed as a 4 × 4 Latin square. After three days of CH4 measurements in open-circuit respiration chambers, rumen fluid was collected to determine volatile fatty acid (VFA) molar proportions and quantify the microbial population. Samples of ration ingredients, refusals and feces were collected to evaluate nutrient composition. Foliage and pods of legumes provided crude protein (CP), condensed tannins (CT) and saponins, while grass was characterized by higher concentrations of neutral detergent fiber (NDF). Dry matter intake (DMI) was 5.35 kg/day on average (P = 0.272). Apparent fiber digestibility was reduced (81 g/kg) and digestible CP intake (13 g/kg) increased when E. cyclocarpum mixed with G. sepium in rations were given (P < 0.05). Incorporation of legume foliage and pods had a linear effect on molar proportions of butyric acid and acetic to propionic acid ratio (P < 0.05). Methane production, expressed on basis to digestible dry matter intake (DDMI), ranged between 43.22 and 49.94 g/kg DDMI (P = 0.131) and when CH4 was related to digestible CP (347 vs. 413 g CH4 /kg DCP) or annual weight gains (0.30 vs. 0.38 kg CH4/kg weight gain, P < 0.001) there were differences between the E. cyclocarpum mixed with G. sepium rations compared to the control treatment, respectively. Rumen population of total bacteria, methanogenic archaea, and total protozoa was not affected by the increasing levels of condensed tannins and saponins in rations (P > 0.05). Substitution of 15 and 30% of pods of E. cyclocarpum mixed with foliage of G. sepium in the ration, decreases annual methane emissions per unit product, without affecting dry matter intake or rumen microbial population, on the contrary, digestible CP intake and animal productivity increased due to supply of CP, CT and saponins.

Effect of bamboo grass (Tiliacora triandra, Diels) pellet supplementation on rumen fermentation characteristics and methane production in Thai native beef cattle.

ObjectiveThe objective of this study was to investigate the effect of bamboo grass (Tiliacora triandra, Diels) pellet (Bamboo-Cass) supplementation on feed intake, nutrient digestibility, rumen microbial population and methane production in Thai native beef cattle.MethodsFour Thai native beef cattle bulls (190±2 kg) were randomly allotted to four respective dietary treatments in a 4×4 Latin square design. Treatments were the varying levels of Bamboo-Cass supplementation at 0, 50, 100, and 150 g/head/d, respectively. Rice straw was fed ad libitum and the concentrate offered at 0.5% of body weight.ResultsUnder this experiment, the findings revealed that acetate and butyrate production were decreased (p<0.05), propionate increased (p<0.05), whilst ruminal NH3-N concentration was decreased (p<0.05) by supplementation of Bamboo-Cass at 150 g/head/d. Moreover, rice straw intake, and microbial population were linearly increased (p<0.05), while methane production was decreased (p<0.05).ConclusionThe results from the present study indicate that supplementation of Bamboo-Cass at 150 g/head/d significantly enhanced feed intake, decreased protozoa and increased bacterial population, rumen fermentation efficiency while decreased methane production. Therefore, Bamboo-Cass as a supplement is promising as a rumen enhancer in beef cattle fed on rice straw.

Effect of Graded Levels of Bromoethanesulfonic Acid Supplementation on Methane Production, Rumen Microbial Diversity and Fermentation Characteristics

Bromoethanesulfonic acid (BES) was examined as a methane inhibitor and its impact on rumen microbial populations in male cattle calves. Ten crossbred cattle calves (average body weight, 132±2 kg) were divided into two groups of five each and were fed on a diet containing 19.9% CP and 72.6% TDN. In the experimental group, BES was fed at the rate of 5 mg for first 10 days, 10 mg for next 10 days (11–20th day) and 15 mg/kg BW for another 10 days (21 to 30th days) of the experiment. Rumen liquor was collected by stomach tube from calves after feeding of each level of BES and was used for studying the microbial profile by real time PCR and as an inoculum for in vitro gas production test. The in vitro methane production (ml/g DDM) was reduced (P<0.05) by 35, 8.1 and 15 per cent on feeding BES at the levels of 5, 10 and 15 mg/kg BW (P<0.001, P=0.007 and P=0.009, respectively). The in vitro true digestibility of feed was not affected at lower levels but was significantly improved at 15 mg BES level (P=0.026). The population of protozoa, was significantly reduced at 5 mg BES (P=0.014) level but at 10 mg level, fungi and methanogens were reduced significantly (P=0.031, P=0.034) and at 15 mg BES level only fungal population was reduced (P=0.029). The results indicated that BES can reduce rumen methanogenesis but cannot eliminate methanogens completely from the rumen.

Climate Change and Goat Production: Enteric Methane Emission and Its Mitigation.

Simple SummaryGiven that goats are considered more climate resilient than other ruminant species, research efforts are therefore needed to understand goat productivity during exposure to high ambient temperatures. Heat stress can affect the digestion and rumen fermentation pattern of goats, which contributes to the reduction in production performance in goats. Diet composition, breed and environmental stresses are common factors which negatively influence rumen function and enteric methane (CH4) emission. There are three mechanisms by which enteric CH4 can be reduced: targeting end product of digestion to propionate, providing alternate hydrogen sink and selectively inactivating rumen methanogens. The various strategies that can be implemented to mitigate enteric CH4 include nutritional interventions, management strategies and application of advanced biotechnological tools.The ability of an animal to cope and adapt itself to the changing climate virtually depends on the function of rumen and rumen inhabitants such as bacteria, protozoa, fungi, virus and archaea. Elevated ambient temperature during the summer months can have a significant influence on the basic physiology of the rumen, thereby affecting the nutritional status of the animals. Rumen volatile fatty acid (VFA) production decreases under conditions of extreme heat. Growing recent evidence suggests there are genetic variations among breeds of goats in the impact of heat stress on rumen fermentation pattern and VFA production. Most of the effects of heat stress on rumen fermentation and enteric methane (CH4) emission are attributed to differences in the rumen microbial population. Heat stress-induced rumen function impairment is mainly associated with an increase in Streptococcus genus bacteria and with a decrease in the bacteria of Fibrobactor genus. Apart from its major role in global warming and greenhouse effect, enteric CH4 is also considered as a dietary energy loss in goats. These effects warrant mitigating against CH4 production to ensure optimum economic return from goat farming as well as to reduce the impact on global warming as CH4 is one of the more potent greenhouse gases (GHG). The various strategies that can be implemented to mitigate enteric CH4 emission include nutritional interventions, different management strategies and applying advanced biotechnological tools to find solution to reduce CH4 production. Through these advanced technologies, it is possible to identify genetically superior animals with less CH4 production per unit feed intake. These efforts can help the farming community to sustain goat production in the changing climate scenario.

Profiling of rumen fermentation, microbial population and digestibility in goats fed with dietary oils containing different fatty acids

BackgroundThe effects of the dietary oils with differing fatty acid profiles on rumen fermentation, microbial population, and digestibility in goats were investigated. In Experiment I, rumen microbial population and fermentation profiles were evaluated on 16 fistulated male goats that were randomly assigned to four treatment groups: i) control (CNT), ii) olive oil (OL), iii) palm olein oil (PO), and iv) sunflower oil (SF). In Experiment II, another group of 16 male goats was randomly assigned to the same dietary treatments for digestibility determination.ResultsRumen ammonia concentration was higher in CNT group compared to treatment groups receiving dietary oils. The total VFA and acetate concentration were higher in SF and OL groups, which showed that they were significantly affected by the dietary treatments. There were no differences in total microbial population. However, fibre degrading bacteria populations were affected by the interaction between treatment and day of sampling. Significant differences were observed in apparent digestibility of crude protein and ether extract of treatment groups containing dietary oils compared to the control group.ConclusionsThis study demonstrated that supplementation of different dietary oils containing different fatty acid profiles improved rumen fermentation by reducing ammonia concentration and increasing total VFA concentration, altering fibre degrading bacteria population, and improving apparent digestibility of crude protein and ether extract.

In vitro study of postbiotics from Lactobacillus plantarum RG14 on rumen fermentation and microbial population

ABSTRACT An in vitro study was carried out to identify the effects of different inclusion levels of postbiotics from Lactobacillus plantarum RG14 on rumen fermentation profiles, gas production kinetics, and microbial population in rumen fluid collected from goats. Postbiotics were added at different levels (0, 0.3, 0.6, 0.9, and 1.2%) and incubated for 72 h with 200 mg dry matter (DM) of a substrate containing 60% Guinea grass and 40% commercial concentrate. The experiment was conducted in triplicate on different [...]

Effects of commercial aldehydes from green leaf volatiles (green odour) on rumen microbial population and fermentation profile in an artificial rumen (Rusitec)

The effects of plant metabolites on rumen metabolism vary greatly depending on their antimicrobial spectrum and applied doses. In this study, the minimum inhibitory concentrations (MICs) of commercial aldehydes, trans-2-hexenal (T2H), cis-3-hexenal (C3H), trans-2-nonenal (T2N), and trans-2-decenal (T2D) from green leaf volatiles, were tested on rumen bacteria. These compounds were found more effective on Gram-positive rumen bacteria than the Gram-negatives, and C3H was the most effective compound. Then, for 14 days, the in vitro effects of C3H compared with monensin (5 mg/day) on the rumen microbial population and ruminal fermentation at 187.5, 375 and 750 mg/day doses were tested based on the MIC value (500 μg/mL) by using the rumen simulation technique (Rusitec). Supplementation with C3H at 375 mg/day increased the cell numbers of Butyrivibrio fibrisolvens significantly. The addition of C3H at 375 and 750 mg/day doses also increased Streptecoccus bovis cell counts. The use of monensin did not affect the cell numbers of these bacteria. On the other hand, C3H did not change the counts of total bacteria, methanogens, or hyper-ammonia-producing (HAP) bacteria like monensin. The numbers of Ruminococcus albus and Ruminococcus flavefaciens were also stable in the presence of C3H but decreased significantly with the addition of monensin (P < 0.05). Fibrobacter succinogenes, Megasphaera elsdenii, and Selenomonas ruminantium cell counts were not affected by either application. In addition, C3H increased the acetate and methane production along with the acetate-to-propionate ratio at all tested concentrations, unlike monensin. Supplementation with C3H decreased propionate production significantly, except at the 187.5 mg/day dose. Butyrate production increased (P < 0.05) only in the presence of 187.5 and 375 mg/day doses of C3H. Production of total volatile fatty acids (VFA) and dry matter digestibility (DMD) did not change in treatment groups. Also, the total protozoa numbers and ammonia-N concentrations significantly decreased (P < 0.05) in C3H-treated samples, similar to monensin. Although C3H did not have favorable effects on energy efficiency, it suppressed rumen protozoa and mitigated rumen ammonia without adversely effecting ruminal fermentation in all applied doses. Based on the result, C3H has the potential to improve protein utilization in the rumen.

Effects of red clover isoflavones on tall fescue seed fermentation and microbial populations in vitro.

Negative impacts of endophyte-infected Lolium arundinaceum (Darbyshire) (tall fescue) are responsible for over $2 billion in losses to livestock producers annually. While the influence of endophyte-infected tall fescue has been studied for decades, mitigation methods have not been clearly elucidated. Isoflavones found in Trifolium pratense (red clover) have been the subject of recent research regarding tall fescue toxicosis mitigation. Therefore, the aim of this study was to determine the effect of ergovaline and red clover isoflavones on rumen microbial populations, fiber degradation, and volatile fatty acids (VFA) in an in vitro system. Using a dose of 1.10 mg × L-1, endophyte-infected or endophyte-free tall fescue seed was added to ANKOM fiber bags with or without 2.19 mg of isoflavones in the form of a control, powder, or pulverized tablet, resulting in a 2 × 3 factorial arrangements of treatments. Measurements of pH, VFA, bacterial taxa, as well as the disappearance of neutral detergent fiber (aNDF), acid detergent fiber (ADF), and crude protein (CP) were taken after 48 h of incubation. aNDF disappearance values were significantly altered by seed type (P = 0.003) and isoflavone treatment (P = 0.005), and ADF disappearance values were significantly different in a seed × isoflavone treatment interaction (P ≤ 0.05). A seed × isoflavone treatment interaction was also observed with respect to CP disappearance (P ≤ 0.05). Eighteen bacterial taxa were significantly altered by seed × isoflavone treatment interaction groups (P ≤ 0.05), eight bacterial taxa were increased by isoflavones (P ≤ 0.05), and ten bacterial taxa were altered by seed type (P ≤ 0.05). Due to the beneficial effect of isoflavones on tall fescue seed fiber degradation, these compounds may be viable options for mitigating fescue toxicosis. Further research should be conducted to determine physiological implications as well as microbiological changes in vivo.

Correction: Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling.

[This corrects the article DOI: 10.1371/journal.pone.0182271.].

A metagenomic study of the rumen virome in domestic caprids.

This project sought to investigate the domestic caprid rumen virome by developing a robust viral DNA isolation and enrichment protocol (utilizing membrane filtration, ultra-centrifugation, overnight PEG treatment and nuclease treatment) and using RSD-PCR and high throughput sequencing (HTS) techniques. 3.53% of the reads obtained were analogous to those of viruses denoting Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, Microviridae, Poxviridae, Tectiviridae and Marseillevirus. Most of the sequenced reads from the rumen were similar to those of phages, which are critical in maintaining the rumen microbial populations under its carrying capacity. Though identified in the rumen, most of these viruses have been reported in other environments as well. Improvements in the viral DNA enrichment and isolation protocol are required to obtain data that are more representative of the rumen virome. The 102,130 unknown reads (92.31%) for the goat and 36,241 unknown reads (93.86%) for the sheep obtained may represent novel genomes that need further study.

16S rRNA Sequencing Reveals Relationship Between Potent Cellulolytic Genera and Feed Efficiency in the Rumen of Bulls.

The rumen microbial population dictates the host’s feed degradation capacity and subsequent nutrient supply. The rising global human population and intensifying demand for animal protein is creating environmental challenges. As a consequence, there is an increasing requirement for livestock with enhanced nutrient utilization capacity in order to more efficiently convert plant material to high quality edible muscle. In the current study, residual feed intake (RFI), a widely used and a highly accepted measure of feed efficiency in cattle, was calculated for a combination of three cohorts of Simmental bulls. All animals were managed similarly from birth and offered concentrate ad libitum in addition to 3 kg of grass silage daily during the finishing period. Solid and liquid rumen digesta samples collected at slaughter and were analyzed using amplicon sequencing targeting the 16S rRNA gene utilizing the Illumina MiSeq platform. Volatile fatty acid analysis was also conducted on the liquid digesta samples. Spearman’s correlation coefficient was utilized to determine the association between RFI and bacterial and archaeal taxa and inter-taxonomic relationships. The data indicate a tendency toward an increase in butyrate (P = 0.06), which corresponds with an increase in plasma β-hydroxybutyrate concentration in low RFI (LRFI) bulls in comparison to their high RFI (HRFI) contemporaries (P < 0.05). A decrease in propionate (P < 0.05) was also recorded in the rumen of LRFI in comparison to HRFI bulls. These results indicate alternate fermentation patterns in the rumen of LRFI bulls. The data also identified that OTUs within the phyla Tenericutes, Fibrobacteres, and Cyanobacteria may potentially influence RFI phenotype. In particular, a negative association between F. succinogenes and RFI was evident. The unique cellulolytic metabolism of F. succinogenes suggests it could contribute to host efficiency by providing substrate to the host ruminant and other microbial populations (e.g., Selenomonas ruminantium, Methanobrevibacter, and Methanomassiliicoccaceae) in the rumen. This study provides evidence that bacterial OTUs within common phyla could influence ruminant feed efficiency phenotype through their role in ruminal degradation of complex plant polysaccharides or increased capability to harvest nutrients from ingested feed.

Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria

The rumen is a complex ecosystem. It is the primary site for microbial fermentation of ingested feed allowing conversion of a low nutritional feed source into high quality meat and milk products. However, digestive inefficiencies lead to production of high amounts of environmental pollutants; methane and nitrogenous waste. These inefficiencies could be overcome by development of forages which better match the requirements of the rumen microbial population. Although challenging, the application of meta-proteomics has potential for a more complete understanding of the rumen ecosystem than sequencing approaches alone. Here, we have implemented a meta-proteomic approach to determine the association between taxonomies of microbial sources of the most abundant proteins in the rumens of forage-fed dairy cows, with taxonomic abundances typical of those previously described by metagenomics. Reproducible proteome profiles were generated from rumen samples. The most highly abundant taxonomic phyla in the proteome were Bacteriodetes, Firmicutes and Proteobacteria, which corresponded with the most abundant taxonomic phyla determined from 16S rRNA studies. Meta-proteome data indicated differentiation between metabolic pathways of the most abundant phyla, which is in agreement with the concept of diversified niches within the rumen microbiota.