Phylogenetic diversity of gene sequences isolated from the rumen as analysed using a self‐organizing map (SOM)

Aims: To determine the origins of DNA sequences isolated from the rumen microbial ecosystem using a self‐organizing map (SOM). Methods and Results: DNA sequences other than 16S small subunit ribosomal RNA (SSU rRNA) gene sequences that were detected from the rumen were analysed by the SOM method reported by Abe et al. [2000, Self‐Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes. Gene 365, 27–34]. Because query sequences positioned by SOM were scattered on the master drawing of SOM, it was suggested that many DNA sequences isolated from the rumen were collected from a broad range of micro‐organisms. Although the results obtained by SOM were similar to those obtained by the neighbour‐joining (NJ) method, SOM was able to presume the phylotypes of the query sequences without information about the 16S SSU rRNA gene sequences and homology searches, and to reveal existence of novel micro‐organisms deduced to be cellulolytic bacteria, archaea and methanotrophic bacterium. Conclusions: As the SOM method defined phylotypes of unreported rumen micro‐organisms, it is presumed that these phylotypes would be involved in rumen fermentation in cooperation with known rumen micro‐organisms. Moreover, it is demonstrated that SOM is a useful tool for affiliating DNA sequences, which have no matches in databases. Significance and Impact of Study: Through SOM analysis, a better means of identifying rumen micro‐organisms and estimating their roles in rumen function was provided.     

Rumen chemical and bacterial changes during stepwise adaptation to a high-concentrate diet in goats

The correlation between rumen chemical and bacterial changes was investigated during a four periodical stepwise adaptation to a high-concentrate diet (concentrate level at 0%, 30%, 50% and 70% for diet I to IV, respectively) in goats. The results showed that ruminal pH decreased from 6.7 to 5.5 after switching from diet I to II, and was maintained at about 5.5 on diet III. Denaturing gradient gel electrophoresis results showed that the rumen bacterial community was relatively stable during the initial three feeding periods, except for the appearance of three bands when diet changed from I to II, suggesting that an appropriate concentrate level can promote the proliferation of some bacteria. After 12 days of feeding diet III, total volatile fatty acid (VFA) concentration and butyrate proportion decreased. At days 2 and 3 of feeding diet IV, ruminal pH declined sharply to 5.3 and 4.7, respectively, and total VFA concentration decreased further while lactic acid concentration increased markedly, suggesting a relation between lactic acid accumulation and ruminal pH decline. At the same time, many bacteria disappeared, including most fibrolytic-related bacteria while Streptococcus bovis and Prevotella-like species dominated. Interestingly, Succinivibrio dextrinosolvens-like species maintained throughout the experiment, suggesting its tolerance to low pH. In conclusion, rumen bacterial community was relatively stable feeding 0% to 50% concentrate diets, and it was observed that appropriate concentrate levels in the diet could increase the diversity of rumen bacteria. However, concentrate-rich diets caused lactic acid accumulation and low ruminal pH that caused the disappearance of most fibrolytic-related bacteria sensitive to low pH while S. bovis and genus Prevotella persisted.     

Biohydrogenation of C18 unsaturated fatty acids to stearic acid by a strain of Butyrivibrio hungatei from the bovine rumen

AIMS: To identify a ruminal isolate which transforms oleic, linoleic and linolenic acids to stearic acid and to identify transient intermediates formed during biohydrogenation. METHODS AND RESULTS: The stearic acid-forming bacterium, isolated from the rumen of a grazing cow, was a Gram-negative motile rod which utilized a range of growth substrates including starch and pectin but not cellulose or xylan. From its 16S rRNA gene sequence, the isolate was identified as a strain of Butyrivibrio hungatei. During conversion of linoleic acid, 9,11-conjugated linoleic acid formed as a transient intermediate before trans-vaccenic acid accumulated together with stearic acid. Unlike previously studied ruminal biohydrogenating bacteria, B. hungatei Su6 was able to convert alpha-linolenic acid to stearic acid. Linolenic acid was converted to stearic via conjugated linolenic acid, linoleic acid and trans-vaccenic acid as intermediates. Oleic acid and cis-vaccenic acid were converted to a series of trans monounsaturated isomers as well as stearic acid. An investigation of these isomers indicated that mixed trans positional isomers are intermediate in the biohydrogenation of cis monounsaturated fatty acids to stearic acid. CONCLUSION: This, the first rigorous identification and characterization of a ruminal bacterium which forms stearic acid, shows that B. hungatei plays an important role in unsaturated fatty acid transformations in the rumen. SIGNIFICANCE AND IMPACT OF THE STUDY: Biohydrogenating bacteria which convert C18 unsaturated fatty acids to stearic acid have not been available for study for many years. Access to B. hungatei Su6 now provides a fresh opportunity for understanding biohydrogenation mechanisms and rumen processes which lead to saturated fat in ruminant products.     

Rumen microbes and fermentation of wild sika deer on the Shiretoko peninsula of Hokkaido Island,Japan

A total of 32 wild Hokkaido sika deer (Cervus nippon yesoensis) were shot (13 in summer, nine in autumn and 10 in winter) in the Syari district, Shiretoko Peninsula of Hokkaido Island, Japan. The ingested foods, rumen fermentation parameters and microbes were determined to evaluate digestive strategy and food availability in each season. Ingested foods and ruminal characteristics greatly varied by season. Rumen digesta mainly comprised of graminoids in summer, graminoids and agricultural products in autumn, and bark and twigs in winter. Rumen pH showed seasonal differences (P<0.05) and was lowest in summer, highest in winter, and intermediate in autumn, reflecting the seasonal differences in ruminal concentration of total volatile fatty acids which were significantly lower (P<0.05) in winter than in summer and autumn. Acetate proportions were significantly higher in winter than in other seasons (P<0.05), while the opposite trend was seen in proportions of propionate and butyrate. Rumen ammonia levels showed significant seasonal differences (P<0.05), decreasing from summer to autumn to winter. Rumen protozoa levels in autumn and winter decreased to 28 and 10% of the levels observed in summer, respectively (P<0.05 for both). The rumen bacteria level in winter was lower (P<0.05) than that in autumn, but no difference was seen for the other seasonal comparisons. Gram negative cocci were present in significantly higher proportions in winter than in other seasons (P<0.05), while Gram negative curved rods were less frequently observed in winter (P<0.05). Based on these results, wild sika deer in this area are shown to survive with rumen microbial populations altered with the dietary conditions that vary greatly by season.     

Establishing populations of Megasphaera elsdenii YE 34 and Butyrivibrio fibrisolvens YE 44 in the rumen of cattle fed high grain diets

AIM: To determine whether Megasphaera elsdenii YE34 (lactic acid degrader) and Butyrivibrio fibrisolvens YE44 (alternative starch utilizer to Streptococcus bovis) establish viable populations in the rumen of beef cattle rapidly changed from a forage-based to a grain-based diet. METHODS AND RESULTS: Five steers were inoculated with the two bacterial strains (YE34 and YE44) and five served as uninoculated controls. With the exception of one animal in the control group, which developed acidosis, all steers rapidly adapted to the grain-based diet without signs of acidosis (pH decline and accumulation of lactic acid). Bacterial populations of S. bovis, B. fibrisolvens and M. elsdenii were enumerated using real-time Taq nuclease assays. Populations of S. bovis remained constant (except in the acidotic animal) at ca 10(7) cell equivalents (CE) ml-1 throughout the study. Megasphaera elsdenii YE34, was not detectable in animals without grain in the diet, but immediately established in inoculated animals, at 10(6) CE ml-1, and increased 100-fold in the first 4 days following inoculation. Butyrivibrio fibrisolvens, initially present at 10(8) CE ml-1, declined rapidly with the introduction of grain into the diet and was not detectable 8 days after grain introduction. CONCLUSION: Megasphaera elsdenii rapidly establishes a lactic acid-utilizing bacterial population in the rumen of grain-fed cattle 7-10 days earlier than in uninoculated cattle. SIGNIFICANCE AND IMPACT OF THE STUDY: The study has demonstrated that rumen bacterial populations, and in particular the establishment of bacteria inoculated into the rumen for probiotic use, can be monitored by real-time PCR.     

Establishment of a spinated type of Diplodinium rangiferi by transfaunation of the rumen ciliates of Japanese sika deer (Cervus nippon centralis) to the rumen of two Japanese shorthorn calves (Bos taurus taurus)

One liter of rumen fluid containing 4.7 x 10(4) ciliates/ml, representing four genera including nine species of ciliates from a Japanese sika deer was inoculated into two unfaunated Japanese shorthorn calves. Two weeks after inoculation, all species originally present in the inoculum were subsequently detected in the rumen fluid of one or both calves. Ciliate densities ranged from 10(5)-10(6) cells/ml over the remainder of the 33-wk experiment. The inoculum contained Diplodinium rangiferi. which lacks caudal appendages, as is characteristic for the species. However, three weeks later, the rumen fluid of both calves contained D. rangiferi, which possesses caudal appendages varying from a single spine to multiple spines with a complicated furcate appearance. The caudal spines of D. rangiferi did not disappear during the experiment, even when the diet of the calves was switched to the ration of sika deer from which the inoculum was obtained.     

Effects of Energy Substrates on Nitrate Reduction and Nitrate Reductase Activity in a Ruminal Bacterium, Selenomonas ruminantium

The factors affecting the rate of nitrate reduction and the nitrate reductase content in Selenomonas ruminantium were examined. The rate of nitrate reduction per cell mass was higher when S. ruminantium was grown on lactate than when grown on glucose, and the rate was further enhanced when grown on succinate. The nitrate reduction rate was parallel to the nitrate reductase content in cells, suggesting that the amount of nitrate reductase limits the rate of nitrate reduction. The amount of nitrate reductase was inversely related to growth rate. The growth rate was related to the level of intracellular ATP, which was inversely related to the levels of ADP and AMP. The ratio of NADH to NAD⁺was related to the rate of nitrate reduction and to the amount of nitrate reductase. From these results, it is conceivable that the synthesis of nitrate reductase is regulated in response to the sufficiency of energy and electron supply. Intracellular concentrations of adenine nucleotides and pyridine nucleotides may be the regulating factors. The amount of nitrate reductase was increased by the presence of nitrate, suggesting that the synthesis of nitrate reductase is enhanced by nitrate. In addition, nitrate reduction altered the fermentation pattern as a result of electron consumption.     

Hydrolysis of oligosaccharides of the β-(1→4)-linked d-xylose series by an endo(1→4)-β-d-xylanase from the anaerobic rumen fungus Neocallimastix frontalis

An endo-(14)--d-xylanase from Neocallimastix frontalis was purified by anion-exchange chromatography. The enzyme had an apparent molecular mass of 30 kDa on SDS-PAGE and exhibited maximum activity at 50°C and at pH values between 6.0 and 6.6. Kinetic studies on the hydrolysis of xylo-oligosaccharides, ranging from xylobiose to xylodecaose, showed that xylohexaose and xyloheptaose were the preferred substrates for the enzyme and that xylobiose, xylotriose and xylotetraose were not hydrolysed. Xylose was not a product of the hydrolysis of any of the xylo-oligosaccharide substrates tested. The enzyme appeared to have a strong preference for the hydrolysis of the internal glycosidic bonds of the oligosaccharides, which is typical of endo-(14)--d-xylanase activity, but it differed from other fungal endo-(14)--d-xylanases in that it had uniform action on the various internal linkages in the xylo-oligosaccharides.V. Garcia-Campayo, S.I. McCrae and T.M. Wood are with The Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB2 9SB, UK     

Influence of methylamine on anaerobic rumen bacterial growth and plant fiber digestion

Anaerobic rumen bacteria were screened for growth inhibition by methylamine. Under nitrogen-limited growth conditions only Ruminobacter amylophilus, Prevotella ruminicola and Megasphaera elsdenii were significantly inhibited. Ruminobacter amylophilus was inhibited more than any other species. Inhibition of R. amylophilus growth occured at all increments in methylamine for all NH₄Cl concentrations tested (0·2–1·8 m ). Dimethylamine was less inhibitory, while trimethyl-, ethyl- and diethylamine were not inhibitory. When methylamine was added to in vitro mixed culture, ruminal fermentations containing alfalfa, neutral detergent fiber disappearance and ammonia production were not affected. This suggests that although methylamine may inhibit specific rumen bacteria, it does not alter overall mixed ruminal microorganism activities with alfalfa as a substrate.