Prevotella Ruminicola Research Articles

Short communication: Comparison of pH, volatile fatty acids, and microbiome of rumen samples from preweaned calves obtained via cannula or stomach tube

The objective of this study was to compare rumen samples from young dairy calves obtained via a stomach tube (ST) or a ruminal cannula (RC). Five male Holstein calves (46±4.0kg of body weight and 11±4.9 d of age) were ruminally cannulated at 15 d of age. Calves received 4 L/d of a commercial milk replacer (25% crude protein and 19.2% fat) at 12.5% dry matter, and were provided concentrate and chopped oats hay ad libitum throughout the study (56 d). In total, 29 paired rumen samples were obtained weekly throughout the study in most of the calves by each extraction method. These samples were used to determine pH and volatile fatty acids (VFA) concentration, and to quantify Prevotella ruminicola and Streptococcus bovis by quantitative PCR. Furthermore, a denaturing gradient gel electrophoresis was performed on rumen samples harvested during wk 8 of the study to determine the degree of similarity between rumen bacteria communities. Rumen pH was 0.30 units greater in ST compared with RC samples. Furthermore, total VFA concentrations were greater in RC than in ST samples. However, when analyzing the proportion of each VFA by ANOVA, no differences were found between the sampling methods. The quantification of S. bovis and P. ruminicola was similar in both extraction methods, and values obtained using different methods were highly correlated (R2=0.89 and 0.98 for S. bovis and P. ruminicola, respectively). Fingerprinting analysis showed similar bacteria band profiles between samples obtained from the same calves using different extraction methods. In conclusion, when comparing rumen parameters obtained using different sampling techniques, it is recommended that VFA profiles be used rather than total VFA concentrations, as total VFA concentrations are more affected by the method of collection. Furthermore, although comparisons of pH across studies should be avoided when samples are not obtained using the same sampling method, the comparison of fingerprinting of a bacteria community or a specific rumen bacterium is valid.

Effects of vanillin, quillaja saponin, and essential oils on in vitro fermentation and protein-degrading microorganisms of the rumen

This study investigated the effects of vanillin on methanogenesis and rumen fermentation, and the responses of ruminal protein-degrading bacteria to vanillin (at concentrations of 0, 0.76 and 1.52g/L), essential oils (clove oil, 1g/L; origanum oil, 0.50g/L, and peppermint oil, 1g/L), and quillaja saponin (at concentration of 0 and 6g/L) in vitro. Methane production, degradabilities of feed substrate, and ammonia concentration decreased linearly with increasing doses of vanillin. Concentration of total volatile fatty acids also decreased, whereas proportion of butyrate tended to increase linearly with increasing doses of vanillin. Protozoa population decreased, but abundances of Ruminococcus flavefaciens, Prevotella bryantii, Butyrivibrio fibrisolvens, Prevotella ruminicola, Clostridium aminophilum, and Ruminobacter amylophilus increased with increasing doses of vanillin. Origanum and clove oils resulted in lower ammonia concentrations compared to control and peppermint oil. All the tested essential oils decreased abundances of protozoa, Selenomonas ruminantium, R. amylophilus, P. ruminicola and P. bryantii, with the largest decrease resulted from origanum oil followed by clove oil and peppermint oil. The abundances of Megasphaera elsdenii, C. aminophilum, and Clostridium sticklandii were deceased by origanum oil while that of B. fibrisolvens was lowered by both origanum and clove oils. Saponin decreased ammonia concentration and protozoal population, but increased the abundances of S. ruminantium, R. amylophilus, P. ruminicola, and P. bryantii, though the magnitude was small (less than one log unit). The results suggest that reduction of ammonia production by vanillin and saponin may not be caused by direct inhibition of major known proteolytic bacteria, and essential oils can have different inhibitory effects on different proteolytic bacteria, resulting in varying reduction in ammonia production.

Effects of soybean small peptides on rumen fermentation and on intestinal and total tract digestion of luxi yellow cattle.

Four Luxi beef cattle (400±10 kg) fitted with ruminal, duodenal and ileal cannulas were used in a 4×4 Latin square to assess the effects of soybean small peptide (SSP) infusion on rumen fermentation, diet digestion and flow of nutrient in the gastrointestinal tract. The ruminal infusion of SSP was 0 (control), 100, 200 and 300 g/d. Ruminal SSP infusion linearly (p<0.01) and quadratically (p<0.01) increased microbial protein synthesis and rumen ammonia-N concentration. Concentrations of total volatile fatty acid were linearly increased (p = 0.029) by infusion SSP. Rumen samples were obtained for analysis of microbial ecology by real-time PCR. Populations of rumen Butyrivibrio fibrisolvens, Streptococcus bovis, Ciliate protozoa, Ruminococcus flavefaciens, and Prevotella ruminicola were expressed as a proportion of total Rumen bacterial 16S ribosomal deoxyribonucleic acid (rDNA). Butyrivibrio fibrisolvens populations which related to total bacterial 16S rDNA were increased (p<0.05), while Streptococcus bovis populations were linearly (p = 0.049) and quadratically (p = 0.020) decreased by infusion of SSP. Apparent rumen digestibility of DM and NDF were (Q, p<0.05; L, p<0.05) increased with infusion SSP. Total tract digestion of DM, OM and NDF were linearly (p<0.01) and quadratically (p<0.01) increased by infusing SSP. The flow of total amino acids (AA), essential amino acids (EAA) and individual amino acids were linearly (p<0.01) and quadratically (p<0.01) increased with infusion SSP. The digestibility of Lysine was quadratically (p = 0.033) increased and apparent degradability of Arginine was linearly (p = 0.032) and quadratically (p = 0.042) increased with infusion SSP. The results indicated that infusion SSP could improve nutrient digestion, ruminal fermentation and AA availability.

Growth and fermentation of D-xylose by Saccharomyces cerevisiae expressing a novel D-xylose isomerase originating from the bacterium Prevotella ruminicola TC2-24

BackgroundSaccharomyces cerevisiae strains expressing D-xylose isomerase (XI) produce some of the highest reported ethanol yields from D-xylose. Unfortunately, most bacterial XIs that have been expressed in S. cerevisiae are either not functional, require additional strain modification, or have low affinity for D-xylose. This study analyzed several XIs from rumen and intestinal microorganisms to identify enzymes with improved properties for engineering S. cerevisiae for D-xylose fermentation.ResultsFour XIs originating from rumen and intestinal bacteria were isolated and expressed in a S. cerevisiae CEN.PK2-1C parental strain primed for D-xylose metabolism by over expression of its native D-xylulokinase. Three of the XIs were functional in S. cerevisiae, based on the strain’s ability to grow in D-xylose medium. The most promising strain, expressing the XI mined from Prevotella ruminicola TC2-24, was further adapted for aerobic and fermentative growth by serial transfers of D-xylose cultures under aerobic, and followed by microaerobic conditions. The evolved strain had a specific growth rate of 0.23 h-1 on D-xylose medium, which is comparable to the best reported results for analogous S. cerevisiae strains including those expressing the Piromyces sp. E2 XI. When used to ferment D-xylose, the adapted strain produced 13.6 g/L ethanol in 91 h with a metabolic yield of 83% of theoretical. From analysis of the P. ruminicola XI, it was determined the enzyme possessed a Vmax of 0.81 μmole/min/mg protein and a Km of 34 mM.ConclusionThis study identifies a new xylose isomerase from the rumen bacterium Prevotella ruminicola TC2-24 that has one of the highest affinities and specific activities compared to other bacterial and fungal D-xylose isomerases expressed in yeast. When expressed in S. cerevisiae and used to ferment D-xylose, very high ethanol yield was obtained. This new XI should be a promising resource for constructing other D-xylose fermenting strains, including industrial yeast genetic backgrounds.

Effect of non‐starch‐polysaccharide‐degrading enzymes as feed additive on the rumen bacterial population in non‐lactating cows quantified by real‐time PCR

The effects of non-starch-polysaccharide-degrading enzymes, added to a maize silage- and grass silage-based total mixed ration (TMR) at least 14 h before feeding, on the rumen bacterial population were investigated. Six non-lactating Holstein Friesian cows were allocated to three treatment groups using a duplicate 3 × 3 Latin square design with three 31-day periods (29 days of adaptation and 2 days of sampling). Treatments were control TMR [69% forage and 31% concentrates on a dry matter (DM) basis] or TMR with 13.8 or 27.7 ml/kg of feed DM of Roxazyme G2 liquid with activities (U/ml enzyme preparation) of xylanase 260 000, β-glucanase 180 000 and cellulase 8000 (DSM Nutritional Products, Basel, Switzerland). The concentrations of 16S rDNA of Anaerovibrio lipolytica, Fibrobacter succinogenes, Prevotella ruminicola, Ruminococcus flavefaciens, Selenomonas ruminantium and Treponema bryantii, and their relative percentage of total bacteria in rumen samples obtained before feeding and 3 and 7 h after feeding and from two rumen fractions were determined using real-time PCR. Sampling time had only little influence, but bacterial numbers and the composition of the population differed between the transition layer between rumen fluid and the fibre mat (fraction A) and the rumen fluid (fraction B) highlighting the importance to standardize sampling. The 16S rDNA copies of total bacteria and the six bacterial species as well as the population composition were mainly unaffected by the high levels of exogenous enzymes supplemented at all sampling times and in both rumen fractions. Occasionally, the percentages of the non-fibrolytic species P.ruminicola and A.lipolytica changed in response to enzyme supplementation. Some increases in the potential degradability of the diet and decreases in lag time which occurred collaterally indicate that other factors than changes in numbers of non-particle-associated bacteria are mainly responsible for the effects of exogenous enzymes.

Effects of plant tannin supplementation on animal responses and in vivo ruminal bacterial populations associated with bloat in heifers grazing wheat forage

<h2>ABSTRACT</h2> Two experiments were conducted to 1) enumerate the effect of tannin supplementation on ADG, bloat frequency, in vitro gas, and biofilm and foam production, and 2) quantify the influence of tannin supplementation on ruminal bacterial populations of heifers grazing wheat forage. Twenty-six heifers (286 ± 26 kg) were randomly allocated to 1 of 3 treatments that included a control (nontannin group) and 2 types of tannins (mimosa and chestnut tannins). Plant tannins (1.5% of DMI) were supplemented once daily mixed with a textured feed (500 g/animal). Heifers were visually monitored daily for bloat score (0 = no bloat, 3=severe bloat). In Exp. 1, supplementation of tannins reduced the rate of frothy foam and biofilm production with chestnut being more efficacious than mimosa tannins. There was no treatment × time interaction (P > 0.1) for ADG and bloat measurement. Chestnut tannin supplementation increased ADG (P < 0.05) with time (P < 0.01). Mean bloat score and bloat day were greater (P < 0.01) for the control diet than for tannin-supplemented treatment groups. In Exp. 2, Fibrobacter succinogenes, Streptococcus bovis, and Prevotella ruminicola strains were relatively stable with time (d 0, 10, and 25) in the rumen of animals not receiving tannin supplementation. However, with supplementation of chestnut and mimosa tannins, populations of P. ruminicola and strains of both F. succinogenes and Ruminococcus flavefaciens were increased, respectively. Results show that daily supplementing mimosa and chestnut tannins to heifers grazing wheat forage improved beef production and minimized bloat frequency with minimum impact to the microbial populations studied.

Anaerobic bioremediation of RDX by ovine whole rumen fluid and pure culture isolates

The ability of ruminal microbes to degrade the explosive compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in ovine whole rumen fluid (WRF) and as 24 bacterial isolates was examined under anaerobic conditions. Compound degradation was monitored by high-performance liquid chromatography analysis, followed by liquid chromatography-tandem mass spectrometry identification of metabolites. Organisms in WRF microcosms degraded 180 μM RDX within 4 h. Nitroso-intermediates hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX), hexahydro-1,3-dinitroso-5-nitro-1,3,5-triazine (DNX), and hexahydro-1,3,5-trinitroso-1,3,5-triazine (TNX) were present as early as 0.25 h and were detected throughout the 24-h incubation period, representing one reductive pathway of ring cleavage. Following reduction to MNX, peaks consistent with m/z 193 and 174 were also produced, which were unstable and resulted in rapid ring cleavage to a common metabolite consistent with an m/z of 149. These represent two additional reductive pathways for RDX degradation in ovine WRF, which have not been previously reported. The 24 ruminal isolates degraded RDX with varying efficiencies (0-96 %) over 120 h. Of the most efficient degraders identified, Clostridium polysaccharolyticum and Desulfovibrio desulfuricans subsp. desulfuricans degraded RDX when medium was supplemented with both nitrogen and carbon, while Anaerovibrio lipolyticus, Prevotella ruminicola, and Streptococcus bovis IFO utilized RDX as a sole source of nitrogen. This study showed that organisms in whole rumen fluid, as well as several ruminal isolates, have the ability to degrade RDX in vitro and, for the first time, delineated the metabolic pathway for its biodegradation.

Effect of Triticale Dried Distillers Grains with Solubles on Ruminal Bacterial Populations as Revealed by Real Time Polymerase Chain Reaction

Real time PCR was used in this study to determine the effect of triticale dried distillers grains with solubles (TDDGS) as a replacement for grain or barley silage in finishing diets on the presence of six classical ruminal bacterial species (Succinivibrio dextrinosolvens, Selenomonas ruminantium, Streptococcus bovis, Megasphaera elsdenii, Prevotella ruminicola and Fibrobacter succinogenes) within the rumen contents of feedlot cattle. This study was divided into a step-wise adaptation experiment (112 days) that examined the effects of adaptation to diets containing increasing levels of TDDGS up to 30% (n = 4), a short-term experiment comparing animals (n = 16) fed control, 20%, 25% or 30% TDDGS diets over 28 days, and a rapid transition experiment (56 days) where animals (n = 4) were rapidly switched from a diet containing 30% TDDGS to a barley-based diet with no TDDGS. It was found that feeding TDDGS as replacement for barley grain (control vs. 20% TDDGS) decreased 16S rRNA copy numbers of starch-fermenting S. ruminantium and S. bovis (p<0.001 and p = 0.04, respectively), but did not alter 16S rRNA copy numbers of the other rumen bacteria. Furthermore, feeding TDDGS as a replacement barley silage (20% vs. 25% and 30% TDDGS) increased 16S rRNA copy numbers of S. ruminantium, M. elsdenii and F. succinogenes (p<0.001; p = 0.03 and p<0.001, respectively), but decreased (p<0.001) the 16S rRNA copy number of P. ruminicola . Upon removal of 30% TDDGS and return to the control diet, 16S rRNA copy numbers of S. ruminantium, M. elsdenii and F. succinogenes decreased (p = 0.01; p = 0.03 and p = 0.01, respectively), but S. dextrinosolvens and S. bovis increased (p = 0.04 and p = 0.009, respectively). The results suggest that replacement of TDDGS for grain reduces 16S rRNA copy numbers of starch-fermenting bacteria, whereas substitution for barley silage increases 16S rRNA copy numbers of bacteria involved in fibre digestion and the metabolism of lactic acid. This outcome supports the contention that the fibre in TDDGS is highly

Purification, characterization, and expression of multiple glutamine synthetases from Prevotella ruminicola 23.

The Prevotella ruminicola 23 genome encodes three different glutamine synthetase (GS) enzymes: glutamine synthetase I (GSI) (ORF02151), GSIII-1 (ORF01459), and GSIII-2 (ORF02034). GSI, GSIII-1, and GSIII-2 have each been heterologously expressed in and purified from Escherichia coli. The subunit molecular mass of GSI was 56 kDa, while GSIII-1 and GSIII-2 were both 83 kDa. Optimal conditions for γ-glutamyl transferase activity were found to be 35°C at pH 5.6 with 0.25 mM Mn(2+) ions (GSI) or 37°C at pH 6.0 (GSIII-1 and GSIII-2) with 0.50 to 1.00 mM Mn(2+) ions. GSIII biosynthetic activity was found to be optimal at 50 to 60°C and pH 6.8 to 7.0 with 10 mM Mn(2+) ions, while GSI displayed no GS biosynthetic activity. Kinetic analysis revealed K(m) values for glutamate and ammonium as well as for hydrolysis of ATP to be 8.58, 0.48, and 1.91 mM, respectively, for GSIII-1 and 1.72, 0.43, and 2.65 mM, respectively, for GSIII-2. A quantitative reverse transcriptase PCR assay (qRT-PCR) revealed GSIII-2 to be significantly induced by high concentrations of ammonia, and this corresponded with increases in measured GS activity. Collectively, these results show that both GSIII enzymes in P. ruminicola 23 are functional and indicate that GSIII-2, flanked by GOGAT (gltB and gltD genes), plays an important role in the acquisition and metabolism of ammonia, particularly under nonlimiting ammonia growth conditions.

Rumen Microbial Population in the In vitro Fermentation of Different Ratios of Forage and Concentrate in the Presence of Whole Lerak (Sapindus rarak) Fruit Extract

This experiment was designed to investigate the effect of lerak extract on the dynamic of rumen microbes in the in vitro fermentation of diet with different ratios of forage and concentrate. In vitro fermentation was conducted according to the method of Tilley and Terry (1963). The design of experiment was a factorial block design with 2 factors. The first factor was the ratio of forage and concentrate (90:10, 80:20, and 70:30 w/w) and the second factor was the level of lerak extract (0, 0.6, and 0.8 mg/ml). Total volatile fatty acid (VFA) concentration, proportional VFA and NH3 concentration were measured at 4 h incubation. Protozoal numbers in the buffered rumen fluid after 4 and 24 h of incubation were counted under a microscope. Bacterial DNAs of buffered rumen fluid were isolated from incubated samples after 24 h of incubation using a QiaAmp kit. Total bacteria, Fibrobacter succinogenes, Ruminococcus albus, and Prevotella ruminicola were quantified using real time polymerase chain reaction (PCR). Lerak extract markedly reduced protozoal numbers in buffered rumen fluid of all diets after 24 h of incubation. Total bacteria did not change with lerak extract addition. While no difference in F. succinogenes was found, there was a slight increase in R. albus number and a significant enhancement in P. ruminicola number by increasing the level of lerak extract in all diets. Propionate concentration significantly increased in the presence of lerak extract at level 0.8 mg/ml. It was concluded that the addition of lerak extract could modify rumen fermentation and had positive

Molecular diversity of bacteria in Yunnan yellow cattle (Bos taurs) from Nujiang region, China

The rumen content of four Yunnan Yellow Cattle (Bos taurs) were collected to determine the bacteria diversity by using 16S rRNA gene sequence analysis. A total of 129 sequences were examined and the sequences were referred as 107 OTU (Operational Taxonomy Unit) according to the similarity level of 97% in gene sequence. Similarity analysis revealed that Yunnan Yellow Cattle had 12 sequences (10 OTU) shared 97% or greater similarity with cultured rumen bacteria Butyrivibrio fibrisolvens, Succiniclasticum ruminis, Ruminococcus bromii, Clostridium proteoclasticum, Ruminococcus flavefaciens, Pseudobutyrivibrio ruminis, Jeotgalicoccus psychrophilus, and Prevotella ruminicola, which accounting for 9.3% of the total clones (9.2% of the total OTU). The further 12 sequences (9 OTU) shared 90-97% similarity with cultured bacteria Clostridium aminobutyricum, butyrate-producing bacterium, Schwartzia succinivorans, Prevotella ruminicola, Eubacterium ruminantium, Ruminococcus albus, and Clostridium termitidis, also accounting for 9.3% of the total sequences (8.3% of the total OTU). The remaining 105 sequences (90 OTU) shared less than 90% similarity with cultured bacteria, accounting for 81.4% of the total sequences (82.5% of the total OTU). According to the phylogenetic analysis, all sequences were phylogenetically placed within phyla of low G+C subdivision (accounting for 72.1 and 72.5% of the total clones and OTU, respectively) and CFB subdivision (Cytophaga-Flexibacter-Bacteroides; accounting for 27.9 and 27.5% of the total clones and OTU, respectively). Among the examined clones, rare bacteria Jeotgalicoccus psychrophilus was detected in the rumen of cattle.

Identification and characterisation of the predominant lactic acid-producing and lactic acid-utilising bacteria in the foregut of the feral camel (Camelus dromedarius) in Australia

The camel is emerging as a new and important animal in the Australian livestock industry. However, little is known regarding the microbial ecosystem of the gastrointestinal tract of this ruminant-like animal. This study was carried out to determine the diversity of lactic acid-producing and lactic acid-utilising bacteria in the foregut of the feral camel (Camelus dromedarius) in Australia. Putative lactic acid bacteria were isolated from the foregut contents of camels by culturing on De Man, Rogosa, Sharpe and lactic acid media. Identification of representative isolates was based on the analysis of 16S rRNA gene sequences. Fermentation end products of glucose (i.e. volatile fatty acids and lactate) were also measured in vitro. The key predominant bacteria identified in this study were closely related to Streptococcus bovis, Selenomonas ruminantium, Butyrivibrio fibrisolvens, Lachnospira pectinoschiza and Prevotella ruminicola. The main L-lactate producers were those isolates closely related to S. bovis, S. ruminantium and Lactococcus garvieae, while the efficient lactate utilisers were S. ruminantium-related isolates. D-lactate was produced by isolates closely related to either L. pectinoschiza or S. ruminantium. The predominant bacteria isolated and characterised in this study are identical and/or closely related to those typically found in true ruminants (e.g. S. ruminantium, B. fibrisolvens, S. bovis). In addition, some of the bacteria isolated represent novel species of Lachnospira and Clostridium in the context of lactic acid bacteria from a large herbivorous host. The results from this study have contributed to our understanding and provide opportunities to reduce foregut acidosis in the camel.

ORIGINAL ARTICLE: Description of development of rumen ecosystem by PCR assay in milk-fed, weaned and finished lambs in an intensive fattening system

This study examined the reticulo-rumen characteristics of the microbial community and its fermentative characteristics in milk-fed, at weaning and finished lambs in a conventional fattening system. Five lambs were assigned to each of three groups: milk-fed lambs slaughtered at 30 days (T30), weaned lambs slaughtered at 45 days (T45) and 'finished lambs' slaughtered at 90 days (T90). At slaughter, rumen size, fermentation parameters (pH, volatile fatty acids and microbial enzyme activity) and protozoal counts were recorded. Quantitative PCR was used to quantify the genes encoding 16S and 18S ribosomal DNA of the rumen bacterial and protozoal populations, respectively, and the sequential colonization of the rumen by cellulolytic (Ruminococcus albus, Ruminococcus flavefaciens) and amylolytic (Prevotella ruminicola, Streptococcus bovis) bacteria, and protozoa (Entodinium sp.). Denaturing gradient gel electrophoresis was used to study the development of rumen microbiota biodiversity. Intake of solid food before weaning caused a significant increase in rumen weight (p < 0.0001) and bacterial DNA (p < 0.05) and volatile fatty acid analysis concentration (p < 0.01), whereas pH declined. In milk-fed lambs, cellulolytic bacteria were evident after 30 days. Thereafter, in the 45-day and 90-day groups, the proportions of R. flavefaciens decreased and R. albus increased. Amylolytic bacteria were present in milk-fed lambs; the proportion of P. ruminicola increased in fattening lambs and S. bovis was the least abundant species. Protozoal concentrations were irregular; milk-fed lambs had a significant number of protozoa species from Entodinium and subfamily Isotrichiidae, but they disappeared at weaning. Lamb rumen were refaunated in some individuals at 90 days (Entodinium and subfamily Diplodiniinae spp.), although individual concentrations were variable.

Evaluation of the microbial population in ruminal fluid using real time PCR in steers treated with virginiamycin

The objective of the present study was to investigate the effects of virginiamycin (VM ) supplementation on ruminal fermentation and microbial populations in steers. Four ruminally cannulated Chinese Luxi steers (BW 559.4 &amp;plusmn; 30.1 kg) were used in a crossover design experiment with an experimental period of 28 days. The forage to concentrate ratio of the basal diet was 35:65 on dry matter basis. The experiment consisted of control treatment and treatment with control diet plus VM at a dose of 30 mg/kg concentrate (DM basis). Rumen fluid was collected at 07:30 prefeeding, at 11:30 and 17:30 postfeeding on day 27 and 28. A part of the pooled sample from rumen fluid was transferred to anaerobic culture by a roll-tube technique and analysed for species-specific real-time PCR quantification. The remaining pooled rumen fluid sample was analyzed for pH, VFA, ammonia N and l-lactic acid. The results showed that VM increased the ruminal pH (6.70 vs. 6.63; P &amp;lt; 0.05), but it decreased ammonia nitrogen (4.94 vs. 6.19 mg/100 ml; P &amp;lt; 0.01) and mean counts of amylolytic bacteria and proteolytic bacteria (P &amp;lt; 0.01) as compared to the control. The additive VM did not affect the l-lactic acid concentration (1.39 vs. 1.26 mmol/l) in rumen fluid. Compared to the control, the steers receiving VM have altered a trend of quantification of Selenomonas ruminantium, Anaerovibrio lipolytica, Ruminococcus albus and Streptococcus bovis in rumen fluid (0.05&amp;lt;p&amp;lt;0.1) as compared to the control. However, VM had no significant effect on Lactobacillus spp. (P = 0.41), Butyrivibrio fibrisolvens (P = 0.35), on the genus Ruminococcus (P = 0.25), Ruminococcus flavefaciens (P = 0.52), Prevotella ruminicola (P = 0.54), on the genus Prevotella (P = 0.67) and Megasphaera elsdenii (P = 0.97). In this study, we found that VM had selective effects on ruminal bacteria and influenced ruminal fermentation by changing a part of the specific ruminal bacteria populations.

Comparative Genome Analysis of Prevotella ruminicola and Prevotella bryantii: Insights into Their Environmental Niche

The Prevotellas comprise a diverse group of bacteria that has received surprisingly limited attention at the whole genome-sequencing level. In this communication, we present the comparative analysis of the genomes of Prevotella ruminicola 23 (GenBank: CP002006) and Prevotella bryantii B(1)4 (GenBank: ADWO00000000), two gastrointestinal isolates. Both P. ruminicola and P. bryantii have acquired an extensive repertoire of glycoside hydrolases that are targeted towards non-cellulosic polysaccharides, especially GH43 bifunctional enzymes. Our analysis demonstrates the diversity of this genus. The results from these analyses highlight their role in the gastrointestinal tract, and provide a template for additional work on genetic characterization of these species.

Diversity and abundance of the bacterial 16S rRNA gene sequences in forestomach of alpacas ( Lama pacos) and sheep ( Ovis aries)

Two bacterial 16S rRNA gene clone libraries were constructed from the forestomach of alpacas and sheep fed alfalfa. After the amplification using the universal 16S rRNA gene primers, equal quantities of PCR products from the same species were mixed and used to construct the two libraries. Sequence analysis showed that the 60 clones from alpacas were divided into 27 phylotypes with 25% clones affiliated with Eubacterium sp. F1. The 60 clones from sheep were divided into 21 phylotypes with 7 phylotypes affiliated with Prevotella ruminicola (40% clones). Clones closely related to Clostridium proteoclasticum, Eubacterium sp. F1, Clostridium cellobioparum, Mogibacterium neglectum, Eubacterium ventriosum, Clostridiaceae bacterium WN011, Clostridium coccoides, Clostridium orbiscindens, Eubacterium sp. F1, Cytophaga sp. Dex80-37, Treponema bryantii and Pelotomaculum sp. FP were only found in the forestomach of alpacas, and those to Anaerovorax odorimutans, Treponema zioleckii, Bifidobacterium indicum, Paludibacter propionicigenes, Paraprevotella clara, Eubacterium siraeum, Desulfotomaculum sp. CYP1, Clostridium bolteae, Clostridium termitidis and Clostridiaceae bacterium DJF_LS40 only in the rumen of sheep. Quantitative real-time PCR revealed that the forestomach of alpacas had significantly lower density of bacteria, with bacterial 16S rRNA gene copies (6.89 [Log10 (copies per gram of wet weight)]), than that of sheep (7.71, P < 0.01). The two clone libraries also appeared different in Shannon index (library from alpacas 3.30 and from sheep 3.04). Our results showed that there were apparent differences in the bacterial diversity and abundance in the forestomach between alpacas and sheep.

Detection and identification of rumen bacteria constituting a fibrolytic consortium dominated by Fibrobacter succinogenes

A fibrolytic consortium, dominated by the rumen cellulolytic bacterium Fibrobacter succinogenes, was artificially constructed on hay stems to detect and identify rumen bacteria that can potentially interact with F. succinogenes. Consortium-bacterial members were determined by DGGE and sequencing analysis targeted bacterial 16S rDNA. An artificial consortium was formed in a 2-step incubation of hay stems; the first step with group 1, 2 or 3 F. succinogenes strains, the second step with rumen fluid. After consortium formation, morphologically different bacteria were observed in association with F. succinogenes. DGGE exhibited more than 30 bands, the pattern of which depended on the F. succinogenes group. Sequencing suggested that Butyrivibrio fibrisolvens, Pseudobutyrivibrio ruminis, Clostridium sp., F. succinogenes group 2, Prevotella ruminicola and unclassified Bacteroides were prominent in the group 1 consortium and that Treponema bryantii, B. fibrisolvens, Acinetobacter sp, and Wolinella succinogenes were prominent in the group 2 consortium. However, in the group 3 consortium, F. succinogenes-like bacteria were microscopically undetectable, whereas cellulolytic Ruminococcus albus and F. succinogenes group 1 were prominent, suggesting that the group 3 cannot be a core member of this consortium. This study is the first attempt to identify bacterial members of a fibrolytic consortium dominated by a specific bacterium.

Isolation and use of Prevotella ruminicola TC18 plasmid pTC18 in Escherichia coli-P. ruminicola shuttle vector construction

A cryptic plasmid of approximately 3 kilobases named pTC18 was discovered in a ruminal Prevotella ruminicola TC18 strain and cloned into Escherichia coli. Based on pTC18, several shuttle vectors, containing Prevotella/Bacteroides tetQ selection marker and E. coli vector pUC19 inserted at two different positions in pTC18 were constructed. The shuttle vectors, protected with HaeIII methylase against the P. ruminicola 23 restriction were electroporated into P. ruminicola. Despite numerous attempts a tetracycline resistant recombinant strain 23 was not obtained. The possible causes for electroporation failure are discussed.

Phylogenetic analysis of 16S rRNA gene sequences reveals rumen bacterial diversity in Yaks (Bos grunniens)

Six matured male Yaks (Bos grunniens) with a mean live weight of 450 +/- 23 kg (mean +/- SD), were housed indoors in metabolism cages and fed pelleted lucerne (Medicago sativum). After an adjustment period of 24 days of feeding the diet, samples of rumen content were obtained for analysis of the bacteria in the liquor. The diversity of rumen bacteria was investigated by constructing a 16S rRNA gene clone library using the general bacterial primers F27 and R1492. A total of 130 clones, comprising nearly full length sequences (approx. 1.5 kb) were sequenced and submitted to BLAST and phylogenetic analysis. Using the criterion that similarity of 97% or greater with the sequences of cultivated bacteria, 16 clones were identified as Butyrivibrio fibrisolvens, Pseudobutyrivibrio ruminis, Ruminococcus flavefaciens, Succiniclasticum ruminis, Selenomonas ruminantium and Prevotella ruminicola, respectively. A further 10 clones shared similarity ranging from 90 to 97% with cultivated bacteria but the similarity in sequences for the remaining 104 clones were less than 90% of those of cultivated bacteria. Using a phylogenetic analysis it was found that the majority of the clones identified (63.8%) were located in the Low G + C Subdivision, with most of the remainder (35.4% of clones) located in the Cytophaga-Flexibacter-Bacteroides phylum and one clone (0.8%) was identified as a Proteobacteria. It was apparent that Yaks have a large and diverse range of bacteria in the rumen content which differ from those of cattle and other ruminants.

Isolation and characterization of novel cellulase genes from uncultured microorganisms in different environmental niches

Four different environmental DNA libraries were prepared from microbial consortium collected from forest soil, dung of elephant, cow rumen and rotted tree. Seven independent clones specifying cellulase activities (five endo-beta-1,4-glucanases and two beta-glucosidases) were isolated and identified. Sequence analysis of the retrieved genes revealed that the encoded products of these cellulase genes shared less than 50% identities and 70% similarities to cellulases in the databases. Domain analysis predicted that four endo-beta-1,4-glucanases conform to glycolsyl hydrolase family 5 (GHF 5) and one endo-beta-1,4-glucanase to glycolsyl hydrolase family 9 (GHF 9), while both beta-glucosidases belong to glycolsyl hydrolase family 3 (GHF 3). Further sequence analysis indicated that although a solid affiliation could be made for the two endo-beta-1,4-glucanases to the typical ruminal microbe Prevotella ruminicola, the rest formed deep-branched lineages with no close relatives. The revelation of the phylogenetic novelty provided a snapshot on the great diversity of cellulases in these natural environments.