Rumen microbial population dynamics in response to photoperiod

AIMS: This work was carried out to determine if there was a difference in the microbial population of the rumen associated with daylength at which sheep are housed. METHODS AND RESULTS: Denaturing gradient gel electrophoresis (DGGE) was used to study the ciliate and bacterial diversity in the rumen of Soay rams kept in long day (16 h light) or short day (8 h light) photoperiods. Bacterial diversity varied according to the daylength conditions where the host animal was housed, as did total volatile fatty acids (VFA) concentrations. No differences associated with daylength were detected in ciliate diversity, branched VFA concentrations or the ruminal ammonia concentrations. CONCLUSIONS: As diets had identical composition, yet voluntary intakes levels were higher during long days, it is proposed that the differences in bacterial populations arise because of the differences in amount of food consumed. SIGNIFICANCE AND IMPACT OF THE STUDY: The outcome of this study demonstrated that factors beyond dietary composition must be taken into account when trying to study microbial populations, even in what can be considered a fairly constant environment.     

The host species affects the microbial community in the goat rumen

AIMS: This study was carried out to determine whether bacterial and ciliate populations in goat rumen vary significantly between different goat species living in the same environment. METHODS AND RESULTS: Bacterial and ciliate communities in the rumen of three goat species were analysed at the molecular level using denaturing gradient gel electrophoresis. The microbial community varied considerably among goats living in the same environment. Interspecies variation in the bacterial population was noticeably greater than intraspecies variation. In contrast, there was considerable variation in the ciliate population among goats within the same species, and intraspecies similarities were no greater than those observed across species. CONCLUSIONS: Because environmental factors and diets were identical for all goats, differences in bacterial populations reflect species-specific differences in rumen microbes. SIGNIFICANCE AND IMPACT OF THE STUDY: Factors related to the host species have an important effect on determining the bacterial composition in the goat rumen.     

Changes to the rumen bacterial population of sheep with the addition of 2,4,6-trinitrotoluene to their diet

Previous work has shown that bacterial isolates from the sheep rumen are capable of detoxifying 2,4,6-trinitrotoluene (TNT) into polar constituents. In this study, the dietary effects of TNT on the sheep rumen microbial community were evaluated using molecular microbiology ecology tools. Rumen samples were collected from sheep fed with and without TNT added to their diet, genomic DNA was extracted, and the 16S rRNA-V3 gene marker was used to quantify changes in the microbial population in the rumen. Control and treatment samples yielded 533 sequences. Phylogenetic analyses were performed to determine the microbial changes between the two conditions. Results indicated the predominant bacterial populations present in the rumen were comprised of the phyla Firmicutes and Bacteroidetes, irrespective of presence/absence of TNT in the diet. Significant differences (P < 0.001) were found between the community structure of the bacteria under TNT (−) and TNT (+) diets. Examination of the TNT (+) diet showed an increase in the clones belonging to family Ruminococcaceae, which have previously been shown to degrade TNT in pure culture experiments.     

Effect of coconut oil and defaunation treatment on methanogenesis in sheep

The present study was conducted to evaluate in vivo the role of rumen ciliate protozoa with respect to the methane-suppressing effect of coconut oil. Three sheep were subjected to a 2 x 2 factorial design comprising two types of dietary lipids (50 g x kg(-1) coconut oil vs. 50 g x kg(-1) rumen-protected fat) and defaunation treatment (with vs. without). Due to the defaunation treatment, which reduced the rumen ciliate protozoa population by 94% on average, total tract fibre degradation was reduced but not the methane production. Feeding coconut oil significantly reduced daily methane release without negatively affecting the total tract nutrient digestion. Compared with the rumen-protected fat diet, coconut oil did not alter the energy retention of the animals. There was no interaction between coconut oil feeding and defaunation treatment in methane production. An interaction occurred in the concentration of methanogens in the rumen fluid, with the significantly highest values occurring when the animals received the coconut oil diet and were subjected to the defaunation treatment. Possible explanations for the apparent inconsistency between the amount of methane produced and the concentration of methane-producing microbes are discussed. Generally, the present data illustrate that a depression of the concentration of ciliate protozoa or methanogens in rumen fluid cannot be used as a reliable indicator for the success of a strategy to mitigate methane emission in vivo. The methane-suppressing effect of coconut oil seems to be mediated through a changed metabolic activity and/or composition of the rumen methanogenic population.     

Isolation and attempted introduction of sugar alcohol-utilizing bacteria in the sheep rumen

R.J. WALLACE AND N.D. WALKER. 1993. Bacteria that use sorbitol, xylitol, maltitol and dulcitol (galactitol) were isolated from the sheep rumen following enrichments in which bacteria were grown in rumen fluid medium where the sugar alcohol was the only added energy source. Only isolates obtained with sorbitol and maltitol grew sufficiently rapidly to be considered for enrichment by the sugar alcohol in vivo. Isolate SS2, a strain of Selenomonas ruminantium var. lactilytica which grew on sorbitol at 0.87 h^-1 was selected for further study and a rifampicin-resistant mutant, SS2/R5, was isolated to facilitate tracking in the mixed population. Despite an initial transient increase in numbers, a significant population of S. ruminantium SS2/R5 failed to establish in sheep which were dosed twice daily with 10 g of sorbitol. Continuous infusion of sorbitol increased numbers only slightly compared with twice-daily dosing. In vitro experiments indicated that strain SS2/R5 grew less well in the presence of other rumen organisms, particularly ciliate protozoa, than in pure culture. Furthermore, the concentration of sorbitol in vivo was lower than predicted from in vitro experiments, indicating that sorbitol was absorbed rapidly from the rumen. Similar observations were made with xylitol, dulcitol and maltitol. Proposed enrichment strategies that use sugar alcohols or other materials to support the growth of introduced bacteria will thus have to take account of the combined problems of microbe-microbe interactions and the loss of the compounds by absorption from the rumen.     

The importance of methanogens associated with ciliate protozoa in ruminal methane production in vitro

The importance of methanogenic bacteria associated with ciliate protozoa was estimated either by removing protozoa from whole rumen fluid (using defaunated rumen fluid to correct for the effects of centrifugation on bacteria) or by isolating the protozoa. Rumen fluid was withdrawn from sheep inoculated with either Polyplastron multivesiculatum , a co-culture of Isotricha prostoma plus Entodinium spp. or a mixed type B fauna of Entodinium, Eudiplodinium and Epidinium spp. Methanogenesis was highest in rumen fluid containing a mixed protozoal population of the following genera: Entodinium, Eudiplodinium and Epidinium , was lower in defaunated rumen fluid and lowest in rumen fluid containing either I. prostoma plus Entodinium or P. multivesiculatum . Methanogenic bacteria associated with rumen ciliates were apparently responsible for between 9 and 25% of methanogenesis in rumen fluid.     

现代分子生物学技术在瘤胃微生态系统研究中的应用

瘤胃中栖息着大量的微生物,由于这些微生物组成复杂且有些细菌在体外无法培养,目前对这些微生物的了解仍然很少。现代分子生物学技术的发展为研究瘤胃微生物提供了有效的方法,利用核酸探针、基因序列分析、遗传指纹技术、全细胞杂交和实时定量PCR等技术可以对瘤胃微生物的分类及进化关系、区系结构图、重要酶的表达以及目的微生物的准确定量进行更为深入和透彻的研究。发展和利用这些技术不仅可以研究微生物之间的关系以及微生物与饲料颗粒之间时间与空间的关系,还能直接在细菌自然生长的环境中对其各种特征进行研究。     

Effect of rumen ciliates on the digestive utilization of various carbohydrate-rich diets and on the end-products formed in the rumen. II. Utilization of inulin, saccharose and lactose

Three diets rich in inulin, saccharose and lactose, respectively, were given to 10 rumen-fistulated sheep. Two animals were defaunated, two were inoculated with either Polyplastron multivesibulatum or Entodinium sp., and two others were inoculated with both. The latter two were bred in conventional conditions. All animals ingested the same amounts of carbohydrates in the three diets (21-22 g/kg P0.75/day). Dietary nitrogen content was similar (table 1). The ciliate population was improved with the inulin diet (fig. 1; table 2). With a mixed population, the Entodinium improved with the inulin diet (fig 1; table 2). With a mixed population, the Entodinium sp. genus was always predominant. Holotrich protozoa (mainly Isotricha) in the rumen of the conventional sheep represented 15 to 30% of the total ciliate biomass, indicating that they were able to metabolize these soluble sugars. We also observed that P. multivesiculatum can ferment cellulose and all the soluble carbohydrates proposed in these diets. However, Entodinium sp. development occurred mainly in the presence of the sugard produced during carbohydrate hydrolysis by other ciliates or bacteria. The highest organic matter digestibility, noted in faunated animals (table 3) was confirmed by the VFA concentration in the rumen (table 4). This could be explained either by an activation of bacterial metabolism due to predation or by the direct effect of ciliates on fermentations, or both. Modifications in the VFA composition varied with ciliate inoculation, showing that ciliate metabolism may vary with the nature of the energy in the diet or that the observed results depended on various opposite effects in which the intensity of each component was influenced by the diet. In general, the acetic acid molar proportion increased and propionic acid decreased when there was a considerable Entodinium sp. population. The effect on butyric acid was low with these diets. Higher ammonia and lactic acid concentrations were observed in the rumen of faunated than defaunated sheep, irrespective of the ciliate inoculum.     

Effect of Absence of Ciliate Protozoa From the Rumen on Microbial Activity and Growth of Lambs

A survey of the components of the rumen ciliate population in a series of adult sheep, raised in the Faculty of Agriculture, University of Alexandria, has shown that a mixture of Entodinium, Isotricha, Ophryoscolex, Diplodinium, and Polyplastron species was found in the rumen contents of Egyptian sheep; no Epidinium and a negligible number of Dasytricha ruminantium were also observed. The microbial population, reducing sugars, ammonia, volatile fatty acids (VFA) production, and growth rate of 14 lambs inoculated with whole rumen contents from a mature sheep were compared over a 6-month period with those of 13 lambs maintained under the same conditions, except that they were strictly isolated from other ruminants. Certain large oval organisms and large numbers of flagellates and Oscillospira were frequently observed in the rumen contents of the isolated lambs. The reducing sugars, ammonia, and VFA levels, measured before and at intervals after feeding, in the inoculated lambs showed a pronounced rise above the values found in the ciliate-free animals. The propionic acid-acetic acid ratio in the rumen contents of the faunated lambs was considerably higher than in the nonfaunated controls. The inoculated lambs grew faster than the isolated lambs. Differences in weight gain which ranged from 15 to 17% were statistically significant. The inoculated animals impressed the observers by their good appearance which was superior to that of the ciliate-free lambs. It was, therefore, concluded that the rumen ciliate protozoa are essential for the metabolism and growth of young lambs.     

The effects of organic selenium supplementation on the rumen ciliate population in sheep

The effect of selenium supplementation on the rumen protozoan population of sheep was demonstrated. Both the total and generic counts of rumen ciliates in sheep fed a diet with basal Se content (70 microg/kg dry matter) were compared to those of animals given feed supplemented with inorganic (disodium selenite) or organic Se (selenized yeast) (310 microg/kg dry matter). The genera of Entodinium, Isotricha, Dasytricha, Ophryoscolex, Diploplastron and Polyplastron occurred in all sheep except for the control, in which Ophryoscolex was not observed. The population of Ophryoscolex caudatus f. tricoronatus was significantly higher in sheep supplemented with organic Se than in animals given inorganic Se (by 160 %). Supplementation of feed with selenized yeast induced significant growth in the Diploplastron population (by 63 %) while no change occurred in sheep given selenite. The populations of Dasytricha ruminantium and Polyplastron multivesiculatum were higher than control in both Se-supplemented groups. The ciliate population of Entodinium spp. was not influenced by Se supplements. Our results suggest a protective effect of Se feed supplementation on the development of some rumen ciliate species in young ruminants.     

Variation in Numbers and Mass of Ciliate Protozoa in the Rumens of Sheep Fed Chaffed Alfalfa (Medicago sativa)

Masses and numbers of rumen ciliate protozoa were markedly different in individual sheep fed chaffed alfalfa hay under different feeding regimens. Studies on the ciliate contribution to specific aspects of rumen fermentation should take into account the size of members of each genus in individual animals as well as the numbers present.     

Evaluation of a Method of Measuring Fermentation Rates and Net Growth of Rumen Microorganisms

The method of el-Shazly and Hungate for measuring gas production in rumen contents was slightly modified and used throughout this investigation. The variation in the fermentation rates due to samples collected separately from a sheep fed on hay was less than 2%. When samples obtained through a stomach tube were compared with samples collected through the rumen fistula, the variation was about 3%. The rates of gas and acid production were approximately similar in samples obtained from the rumen at the same time when no sodium bicarbonate was added. During in vitro incubation of whole ruminal contents, there was a highly significant correlation between the net growth rate values (obtained by using fermentation capacity as an index) and the change in concentration of viable rumen bacteria or total ciliate protozoa.     

Pros and Cons of Ion-Torrent Next Generation Sequencing versus Terminal Restriction Fragment Length Polymorphism T-RFLP for Studying the Rumen Bacterial Community

The development of next generation sequencing has challenged the use of other molecular fingerprinting methods used to study microbial diversity. We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP). Although absolute number differed, there was a high correlation between NGS and T-RFLP in terms of richness and diversity with R values of 0.836 and 0.781 for richness and Shannon-Wiener index, respectively. Dendrograms for both datasets were also highly correlated (Mantel test = 0.742). Eighteen OTUs and ten genera were significantly impacted by the addition of rumen protozoa, with an increase in the relative abundance of Prevotella, Bacteroides and Ruminobacter, related to an increase in free ammonia levels in the rumen. Our findings suggest that classic fingerprinting methods are still valuable tools to study microbial diversity and structure in complex environments but that NGS techniques now provide cost effect alternatives that provide a far greater level of information on the individual members of the microbial population.     

Rumen function in red deer, hill sheep and reindeer in the scottish highlands.

Red deer, sheep and reindeer grazing on their normal hill ranges were examined at intervals over a period of four years. Samples from the digestive tract were taken at different seasons and processed in the field. The Red deer and reindeer were killed before samples were taken; rumen samples from the sheep were taken by stomach tube, but a number of animals were also killed at different seasons to correlate stomach tube and whole rumen samples. The animals sampled were representative of the general condition of the herds. Examinations were made for parasites and any pathological conditions. In most instances parasitic infections were slight. Apparent seasonal changes were found in the compositions of the diets. The Red deer and sheep ate principally heather and grass, the proportion of heather increasing in the winter. The reindeer ate mainly grass in the summer, with lichens and grass forming the winter diet, and these animals seemed to have a higher nutritional status in the winter than did the other two species. The weights of the animals and of their rumen contents, the concentrations of rumen ammonia and volatile fatty acid, and the rates at which different dietary components were fermented are recorded. Rumen fermentation was low in winter and the diets were generally inadequate for the animals. A lack of nitrogen seemed to be a major factor. Some data on caecal contents are also given.     

Removal of anaerobic fungi from the rumen of sheep by chemical treatment and the effect on feed consumption and in vivo fibre digestion

The population of anaerobic fungi in the rumen of sheep was reduced by the addition of tetronasin (an ionophore antibiotic) to a herbage diet. Fungi were reduced to undetectable levels (< 1 fungal zoospore per ml rumen fluid) by the combined addition of tetronasin and cycloheximide (a protein synthesis inhibitor) and the absence of fungi was maintained with low levels of tetronasin. Sheep with fungi present in the rumen ate 40% more of a straw-based diet (with a fibre digestibility in vivo of 51%) than they ate when without fungi (47% fibre digestibility). Counts of total viable bacteria, cellulolytic bacteria and ciliate protozoa in the rumen were not significantly different when anaerobic fungi were either present or absent.     

Methanogen Colonisation Does Not Significantly Alter Acetogen Diversity in Lambs Isolated 17?h After Birth and Raised Aseptically

Reductive acetogenesis is not competitive with methanogenesis in adult ruminants, whereas acetogenic bacteria are the dominant hydrogenotrophs in the early rumen microbiota. The ecology of hydrogenotrophs in the developing rumen was investigated using young lambs, raised in sterile isolators, and conventional adult sheep. Two lambs were born naturally, left with their dams for 17?h and then placed into a sterile isolator and reared aseptically. They were inoculated with cellulolytic bacteria and later with Methanobrevibacter sp. 87.7 to investigate the effect of methanogen establishment on the rumen acetogen population since they lacked cultivable representatives of methanogens. Putative acetogens were investigated by acetyl-CoA synthase and formyltetrahydrofolate synthetase gene analysis and methanogens by methyl coenzyme reductase A gene analysis. Unexpectedly, a low abundant but diverse population of methanogens (predominantly Methanobrevibacter spp.) was identified in isolated lambs pre-inoculation with Mbb. sp 87.7, which was similar to the community structure in conventional sheep. In contrast, potential acetogen diversity in isolated lambs and conventional sheep was different. Potential acetogens affiliated between the Lachnospiraceae and Clostridiaceae in conventional sheep and with the Blautia genus and the Lachnospiraceae in isolated lambs. The establishment of Mbb. sp. 87.7 (1,000-fold increase in methanogens) did not substantially affect acetogen diversity.     

Detection and monitoring of anaerobic rumen fungi using an ARISA method

Aim: To develop an automated ribosomal intergenic spacer region analysis (ARISA) method for the detection of anaerobic rumen fungi and also to demonstrate utility of the technique to monitor colonization and persistence of fungi, and diet‐induced changes in community structure. Methods and Results: The method could discriminate between three genera of anaerobic rumen fungal isolates, representing Orpinomyces, Piromyces and Neocallimastix species. Changes in anaerobic fungal composition were observed between animals fed a high‐fibre diet compared with a grain‐based diet. ARISA analysis of rumen samples from animals on grain showed a decrease in fungal diversity with a dominance of Orpinomyces and Piromyces spp. Clustering analysis of ARISA profile patterns grouped animals based on diet. A single strain of Orpinomyces was dosed into a cow and was detectable within the rumen fungal population for several weeks afterwards. Conclusions: The ARISA technique was capable of discriminating between pure cultures at the genus level. Diet composition has a significant influence on the diversity of anaerobic fungi in the rumen and the method can be used to monitor introduced strains. Significance and Impact of the Study: Through the use of ARISA analysis, a better understanding of the effect of diets on rumen anaerobic fungi populations is provided.     

Effects of cross-inoculation from elk and feeding pine needles on the protozoan fauna of pregnant cows: occurrence of Parentodinium africanum in domestic U.S. cattle (Bos taurus)

Consumption of pine needles tends to cause abortion in domestic cattle but not in elk. The present study was undertaken to determine whether this difference was associated with the rumen microbial population. After emptying the rumen, pregnant cattle were inoculated with either elk or cattle rumen contents. For those cows fed the pine needle diet, there was no difference in abortion rate between those inoculated with rumen contents from either elk or cattle. Protozoal concentrations and number of genera were observed to decrease markedly in all cows fed the diet containing pine needles. The cycloposthiid ciliate Parentodinium africanum was observed in rumen contents from several of the domestic cattle (Bos taurus). Concentrations ranged from 1.4 to 130.6 x 10(4) per ml of rumen contents, which comprised 4.6 to 80.3% of the total ciliate population. Mean dimensions of this species were: length, 33.4 microns; width, 19.7 microns; length/width ratio, 1.70, which were similar to those previously reported for this species from Bos indicus in Brazil. This is the first observation of P. africanum, originally observed and described in stomach contents of the hippopotamus, either in Bos taurus or in any host in the northern hemisphere.     

Molecular diversity of rumen methanogens from sheep in Western Australia

The molecular diversity of rumen methanogens in sheep in Australia was investigated by using individual 16S rRNA gene libraries prepared from the rumen contents obtained from six merino sheep grazing pasture (326 clones), six sheep fed an oaten hay-based diet (275 clones), and five sheep fed a lucerne hay-based diet (132 clones). A total of 733 clones were examined, and the analysis revealed 65 phylotypes whose sequences (1,260 bp) were similar to those of cultivated methanogens belonging to the order Methanobrevibacter: Pasture-grazed sheep had more methanogen diversity than sheep fed either the oaten hay or lucerne hay diet. Methanobrevibacter strains SM9, M6, and NT7 accounted for over 90% of the total number of clones identified. M6 was more prevalent in grazing sheep, and SM9, despite being found in 16 of the 17 sheep, was more prevalent in sheep fed the lucerne-based diet. Five new species were identified. Two of these species exhibited very little sequence similarity to any cultivated methanogens and were found eight times in two of the six sheep that were grazing pasture. These unique sequences appear to represent a novel group of rumen archaea that are atypical for the rumen environment.     

Buccal Swabbing as a Noninvasive Method To Determine Bacterial,Archaeal, and Eukaryotic Microbial Community Structures in the Rumen

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants.