Microbial protein and peptide metabolism in rumen fluid from faunated and ciliate-free sheep

Rumen microbes, enzymes, metabolisms, and application in lignocellulosic waste conversion - A comprehensive review

The rumen of ruminants is a natural anaerobic fermentation system that efficiently degrades lignocellulosic biomass and mainly depends on synergistic interactions between multiple microbes and their secreted enzymes. Ruminal microbes have been employed as biomass waste converters and are receiving increasing attention because of their degradation performance. To explore the application of ruminal microbes and their secreted enzymes in biomass waste, a comprehensive understanding of these processes is required. Based on the degradation capacity and mechanism of ruminal microbes and their secreted lignocellulose enzymes, this review concentrates on elucidating the main enzymatic strategies that ruminal microbes use for lignocellulose degradation, focusing mainly on polysaccharide metabolism-related gene loci and cellulosomes. Hydrolysis, acidification, methanogenesis, interspecific H2 transfer, and urea cycling in ruminal metabolism are also discussed. Finally, we review the research progress on the conversion of biomass waste into biofuels (bioethanol, biohydrogen, and biomethane) and value-added chemicals (organic acids) by ruminal microbes. This review aims to provide new ideas and methods for ruminal microbe and enzyme applications, biomass waste conversion, and global energy shortage alleviation.

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

BACKGROUND

The 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.

RESULTS

Rumen 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.

CONCLUSIONS

This 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.

The effects of high dose of two manganese supplements (organic and inorganic) on the rumen microbial ecosystem

Little is known about the effects of the high dose and types of manganese supplements on rumen environment at manganese intake level close above the limit of 150 mg/kg of dry feed matter. The effects of high dose of two manganese supplements (organic and inorganic) on rumen microbial ecosystem after four months of treatment of 18 lambs divided into three treatment groups were studied. We examined the enzyme activities (α-amylase, xylanase, and carboxymethyl cellulase), total and differential microscopic counts of rumen ciliates, total microscopic counts of bacteria, and fingerprinting pattern of the eubacterial and ciliates population analyzed by PCR-DGGE. Lambs were fed a basal diet with a basal Mn content (34.3 mg/kg dry matter; control) and supplemented either with inorganic manganous sulfate or organic Mn-chelate hydrate (daily 182.7, 184 mg/kg dry matter of feed, respectively). Basal diet, offered twice daily, consisted of ground barley and hay (268 and 732 g/kg dry matter per animal and day). The rumens of the lambs harbored ciliates of the genera of Entodinium, Epidinium, Diplodinium, Eudiplodinium, Dasytricha, and Isotricha. No significant differences between treatment groups were observed in the total ciliate number, the number of ciliates at the genus level, as well as the total number of bacteria. Organic Mn did decrease the species richness and diversity of the eubacterial population examined by PCR-DGGE. No effects of type of Mn supplement on the enzyme activities were observed. In comparison to the control, α-amylase specific activities were decreased and carboxymethyl-cellulase specific activities were increased by the Mn supplements. Xylanase activities were not influenced. In conclusion, our results suggested that the intake of tested inorganic and organic manganese supplements in excess may affect the specific groups of eubacteria. More studies on intake of Mn supplements at a level close to the limit can reveal if the changes in microbial population impact remarkably the other rumen enzymatic activities.

Effect of dried distillers’ grains with solubles on enteric methane emissions and nitrogen excretion from finishing beef cattle

Hünerberg, M., McGinn, S. M., Beauchemin, K. A., Okine, E. K., Harstad, O. M. and McAllister, T. A. 2013. Effect of dried distillers’ grains with solubles on enteric methane emissions and nitrogen excretion from finishing beef cattle. Can. J. Anim. Sci. 93: 373–385. The objective of this study was to examine the impact of corn- or wheat-based dried distillers’ grains with solubles (CDDGS, WDDGS) on enteric methane (CH4) emissions from finishing beef cattle, and to determine if any observed reductions were a result of the fat content of CDDGS. A second objective was to compare the effect of CDDGS or WDDGS on N excretion. The experiment was designed as replicated 4×4 Latin square with 28-d periods using 16 ruminally fistulated crossbred heifers. The control diet contained 87% barley grain, 8% barley silage and 5% supplement (dry matter; DM basis). Treatment diets were formulated by replacing 40% DM of barley grain with CDDGS, WDDGS, or corn oil supplemented WDDGS (WDDGS+oil). For the WDDGS+oil diet 6.5% corn oil was added to WDDGS (3.4% fat DM) to achieve a similar fat level as in CDDGS (9.7% DM). All diets were fed as total mixed rations once daily ad libitum. Total collection of urine and faeces was conducted between days 18 and 21. Methane was measured between days 25 and 28 using four identical open circuit respiratory chambers. Compared with WDDGS, feeding CDDGS and WDDGS+oil reduced (P<0.05) CH4emissions as a percentage of gross energy intake (GEI) from 5.5 to 4.0 and 4.2%, respectively. Feeding CDDGS also reduced (P<0.05) CH4emissions compared with the control (5.0% of GEI), while WDDGS+oil tended (P=0.08) to elicit a similar response. Methane (% of GEI) between WDDGS and the control did not differ (P=0.29). Excretion of total N was greater (P<0.001) for CDDGS, WDDGS and WDDGS+oil (220, 253, and 265 g d−1) compared with the control (143 g d−1). Although oil appears to be responsible for reducing CH4emissions when DDGS is included in the diet, increased N excretion requires that a complete life cycle assessment be conducted to assess the full impact of DDGS on greenhouse gas emissions from finishing cattle.

Ammonia production by human faecal bacteria, and the enumeration, isolation and characterization of bacteria capable of growth on peptides and amino acids

Background

The products of protein breakdown in the human colon are considered to be detrimental to gut health. Amino acid catabolism leads to the formation of sulfides, phenolic compounds and amines, which are inflammatory and/or precursors to the formation of carcinogens, including N-nitroso compounds. The aim of this study was to investigate the kinetics of protein breakdown and the bacterial species involved.

Results

Casein, pancreatic casein hydrolysate (mainly short-chain peptides) or amino acids were incubated in vitro with suspensions of faecal bacteria from 3 omnivorous and 3 vegetarian human donors. Results from the two donor groups were similar. Ammonia production was highest from peptides, followed by casein and amino acids, which were similar. The amino acids metabolized most extensively were Asp, Ser, Lys and Glu. Monensin inhibited the rate of ammonia production from amino acids by 60% (P = 0.001), indicating the involvement of Gram-positive bacteria. Enrichment cultures were carried out to investigate if, by analogy with the rumen, there was a significant population of asaccharolytic, obligately amino acid-fermenting bacteria (‘hyper-ammonia-producing’ bacteria; HAP) in the colon. Numbers of bacteria capable of growth on peptides or amino acids alone averaged 3.5% of the total viable count, somewhat higher than the rumen. None of these were HAP, however. The species enriched included Clostridium spp., one of which was C. perfringens, Enterococcus, Shigella and Escherichia coli.

Conclusions

Protein fermentation by human faecal bacteria in the absence of sugars not only leads to the formation of hazardous metabolic products, but also to the possible proliferation of harmful bacteria. The kinetics of protein metabolism were similar to the rumen, but HAP bacteria were not found.

Effects of lauric acid on ruminal protozoal numbers and fermentation pattern and milk production in lactating dairy cows

The objectives of this study were to evaluate lauric acid (LA) as a practical ruminal protozoa-suppressing agent and assess effects of protozoal suppression on fermentation patterns and milk production in dairy cows. In a pilot study, 6 lactating Holstein cows fitted with ruminal cannulae were used in a randomized complete-block design trial. Cows were fed a basal total mixed ration (TMR) containing (DM basis) 15% alfalfa silage, 40% corn silage, 30% rolled high moisture shelled corn, and 14% solvent soybean meal, and assigned to 1 of 3 treatments: 1) control, 2) 160 g/d of LA, or 3) 222 g/d of sodium laurate, which is equimolar to 160 g/d of LA, all given as a single dose into the rumen via cannulae before feeding. Both agents showed high antiprotozoal activity when pulse dosed at these amounts via ruminal cannulae, reducing protozoa by 90% (P<0.01) within 2 d of treatment. Lauric acid reduced ruminal ammonia concentration by 60% (P<0.01) without altering DMI. Both agents reduced ruminal total free AA concentration (P<0.01) and LA did not affect ruminal pH or total VFA concentration. In a large follow-up feeding trial, 52 Holstein cows (8 with ruminal cannulae) were used in a randomized complete-block design trial. Cows were assigned to 1 of 4 diets and fed only that diet throughout the study. The TMR contained (DM basis) 29% alfalfa silage, 36% corn silage, 14% rolled high moisture shelled corn, and 8% solvent soybean meal. The 4 experimental diets were similar, except part of the finely ground dry corn was replaced with LA in stepwise increments from 0 to 0.97% of dietary DM, which provided (as consumed) 0, 83, 164, and 243 g/d of LA. Adding these amounts of LA to the TMR did not affect DMI, ruminal pH, or other ruminal traits, and milk production. However, LA consumed at 164 and 243 g/d in the TMR reduced the protozoal population by only 25% and 30% (P=0.05), respectively, showing that these levels, when added to the TMR, were not sufficient to achieve a concentration within the rumen that promoted the antiprotozoal effect of LA.

Effect of grain processing and silage on microbial protein synthesis and nutrient digestibility in beef cattle fed barley-based diets

Effects of the extent of grain processing and the percentage of silage in barley-based feedlot diets on microbial protein synthesis and nutrient digestibility were evaluated using four steers (initial BW of 442 +/- 15 kg) with ruminal and duodenal cannulas. The experiment was a 4 x 4 Latin square with four periods of 21 d each. Dietary treatments were arranged as a 2 x 2 factorial with two levels of barley silage (20 and 5% DM basis) and two degrees of barley grain processing (coarsely and flatly steamrolled to a processing index [PI] of 86 and 61%, respectively). The PI was quantified as the volume weight of the barley grain after processing, expressed as a percentage of the volume weight prior to processing. Digest a flow (Yb) and microbial (15N) markers were continuously infused into the rumen for a period of 13 d. Ruminal, duodenal, and fecal samples were collected at various times over the last 6 d of marker infusion. Diurnal ruminal pH was measured for 48 h. Intake of DM averaged 1.8% of BW, and was not different among the dietary treatments (P > 0.10). Ruminal starch digestibility was higher (P < 0.05) for the more extensively processed grain and tended (P < 0.10) to be highest when the more extensively processed grain was combined with 5% barley silage. In contrast, ruminal fiber digestibility for the 5% silage diets was reduced (P < 0.05) when the grain was more extensively processed. There was, however, no effect of grain processing on ruminal OM digestibility (P > 0.10), and hence, no inhibitory effect on microbial N flow to the intestine (P > 0.10). There was also no effect of the level of silage on microbial N flow (P > 0.10), but there was a tendency for improved efficiency of microbial protein synthesis for the 20% silage diets (P = 0.072). Ruminal escape of nonmicrobial N (P = 0.003) was greater, and thus, protein flow to the intestine was greater for the 5% silage diets. Diurnal ruminal pH was lower (P < 0.05) for 11 of the 24 hourly time points in steers fed the 5% silage diets than those fed the 20% silage diets. In conclusion, barley grain rolled to a PI of 86 to 61% and combined with 20 and 5% barley silage had little effect on microbial protein supply. Microbial protein supply was not inhibited when the barley grain was extensively processed (PI of 61%) and the silage was limited to only 5% of the diet DM, but feed intake of steers in this study was lower than would be expected in the feedlot.

Ammonia production by ruminal microorganisms and enumeration, isolation, and characterization of bacteria capable of growth on peptides and amino acids from the sheep rumen

Excessive NH(3) production in the rumen is a major nutritional inefficiency in ruminant animals. Experiments were undertaken to compare the rates of NH(3) production from different substrates in ruminal fluid in vitro and to assess the role of asaccharolytic bacteria in NH(3) production. Ruminal fluid was taken from four rumen-fistulated sheep receiving a mixed hay-concentrate diet. The calculated rate of NH(3) production from Trypticase varied from 1.8 to 19.7 nmol mg of protein(-1) min(-1) depending on the substrate, its concentration, and the method used. Monensin (5 micro M) inhibited NH(3) production from proteins, peptides, and amino acids by an average of 28% with substrate at 2 mg/ml, compared to 48% with substrate at 20 mg/ml (P = 0.011). Of the total bacterial population, 1.4% grew on Trypticase alone, of which 93% was eliminated by 5 micro M monensin. Many fewer bacteria (0.002% of the total) grew on amino acids alone. Nineteen isolates capable of growth on Trypticase were obtained from four sheep. 16S ribosomal DNA and traditional identification methods indicated the bacteria fell into six groups. All were sensitive to monensin, and all except one group (group III, similar to Atopobium minutum), produced NH(3) at >250 nmol min(-1) mg of protein(-1), depending on the medium, as determined by a batch culture method. All isolates had exopeptidase activity, but only group III had an apparent dipeptidyl peptidase I activity. Groups I, II, and IV were most closely related to asaccharolytic ruminal and oral Clostridium and Eubacterium spp. Group V comprised one isolate, similar to Desulfomonas piger (formerly Desulfovibrio pigra). Group VI was 95% similar to Acidaminococcus fermentans. Growth of the Atopobium- and Desulfomonas-like isolates was enhanced by sugars, while growth of groups I, II, and V was significantly depressed by sugars. This study therefore demonstrates that different methodologies and different substrate concentrations provide an explanation for different apparent rates of ruminal NH(3) production reported in different studies and identifies a diverse range of hyper-ammonia-producing bacteria in the rumen of sheep.

Influence of 1-[(E)-2-(2-methyl-4-nitrophenyl)diaz-1-enyl]pyrrolidine-2-carboxylic acid and diphenyliodonium chloride on ruminal protein metabolism and ruminal microorganisms

The effects of 1-[(E)-2-(2-methyl-4-nitrophenyl)diaz-1-enyl]pyrrolidine-2-carboxy lic acid (LY29) and diphenyliodonium chloride (DIC) on the degradation of protein to ammonia were determined in a mixed rumen microbial population taken from sheep on a grass hay-concentrate diet. Both compounds decreased NH3 production by inhibiting deamination of amino acids. LY29, but not DIC, inhibited growth of the high-activity ammonia-producing species, Clostridium aminophilum and Clostridium sticklandii.

Inhibition by 1,10-phenanthroline of the breakdown of peptides by rumen bacteria and protozoa

The rate of peptide breakdown in the rumen frequently exceeds the rate at which the amino acids released can be used for microbial growth. The final step in this often wasteful process involves the cleavage of dipeptides. The main rumen bacterial species with high dipeptidase activity, Prevotella ruminicola, Fibrobacter succinogenes, Lachnospira multipara and Megasphaera elsdenii, had activities which were inhibited > 95% by 1,10-phenanthroline, a chelator of divalent metal ions and metalloprotease inhibitor. Dipeptidase activity in digesta taken from the rumen of sheep decreased by 33% in the presence of 1,10-phenanthroline, while mixed bacteria from the same samples were inhibited by 80% and the activity of mixed protozoa decreased by only 15%. Thus a substantial amount of dipeptide breakdown appears to be due to ciliate protozoa in the mixed population. Extensive washing of the protozoa increased the sensitivity of protozoal dipeptidase activity to 1,10-phenanthroline, suggesting that protozoa too have a metallo-dipeptidase activity but that it is normally protected from inhibition by 1,10-phenanthroline. Breakdown of the pentapeptide, Ala5, was also inhibited 27% by 1,10-phenanthroline in the mixed population, and when Trypticase, a pancreatic casein hydrolysate containing a mixture of oligopeptides, dipeptides and amino acids, was incubated with rumen fluid, the production of ammonia and free amino groups was inhibited 71% by 1,10-phenanthroline. It was concluded that metal ion chelation inhibits oligopeptidase and dipeptidase activities of rumen micro-organisms and may be a means of controlling ammonia production from peptides in the rumen.

Breakdown of different peptides by Prevotella (Bacteroides) ruminicola and mixed microorganisms from the sheep rumen

Several di-, tri-, and oligopeptides were incubated individually in vitro with rumen fluid from two sheep receiving a mixed grass hay/concentrate diet and with washed cells of Prevotella (formerly Bacteroides) ruminicola M384 and P. ruminicola B(1)4. The rates of breakdown of most peptides were similar in the rumen fluid from the two sheep. Acidic and proline-containing peptides tended to be more slowly degraded than neutral or basic peptides. The dipeptide at the N-terminus of higher peptides was observed as an early product of hydrolysis, confirming that a dipeptidyl aminopeptidase type of activity was present. The relative rates of breakdown of dipeptides by P. ruminicola were different from that of rumen fluid, but the hydrolysis of higher peptides followed a similar pattern, and dipeptides from the N-terminus were detected as early products.

Recent developments in gastrointestinal absorption and tissue utilization of peptides: a review

Considerable evidence has been accumulated regarding the absorption of dipeptides and tripeptides, yet, even with the growing body of knowledge, the nutritional and metabolic significance of peptide absorption is not fully understood, especially in ruminants. Muscle, mammary gland, liver, kidney, intestinal mucosa, and other tissues either have been shown to have, or are suspected to have, the ability to utilize peptides as a source of AA to meet cellular demands. Investigations suggest that ruminal microbes have the ability to produce substantial amounts of small peptides as a consequence of their hydrolysis of dietary proteins. The extent to which intact peptides may be absorbed into the blood is controversial. Some of the inconsistency in reported observations may be because of limitations of analytical procedures, species differences, or both. Peptide absorption appears to be an important physiological process in ruminants and may constitute the primary source of absorbed AA. The recent observation that the stomach region of the gastrointestinal tract may be an important site of peptide absorption is highly significant. Emerging evidence for the contribution that peptide absorption makes to AA provisioning of ruminants may change some of the currently held views about protein utilization in these unique animals.

Balancing carbohydrates and proteins for optimum rumen microbial yield

Establishing conditions under which rumen fermentation will be optimized requires an understanding of the nutrient requirements of the mixed microbial population. The major nutrients required by rumen microbes are carbohydrates and proteins, but the most suitable sources and quantities needed to support maximum growth have not been determined. Digestion of proteins results in the production of peptides, which can accumulate in the rumen. Peptides are further hydrolyzed to amino acids, some of which are deaminated, producing ammonia. Although peptides, amino acids, and ammonia all may individually serve as sources of N for various microbes, the total population achieves the highest growth rate on mixtures of all three sources. In a somewhat analogous manner, carbohydrates are digested by exoenzymes to oligosaccharides that are available for crossfeeding by the mixed microbial population. Based on data from both in vitro and in vivo studies, there is general agreement that rate of digestion of carbohydrates is the major factor controlling the energy available for microbial growth; in addition, rate of digestion of total carbohydrate is directly related to proportion of starches, pectins, and sugars. Proteins affect both total fermentation and production of microbial DM per unit of carbohydrate fermented. It appears that the quantity of ruminally available protein needed to optimize microbial growth may, under some conditions, be as high as 14 to 15% of diet DM.

Total protozoa counts and ammonia in the rumen of mature dry Friesian cows on hay-based rations

The present work was an attempt to determine whether the variations in ruminal ammonia concentrations could be directly correlated to corresponding changes in total protozoa numbers of cattle. Four dry Friesian cows fed with hay-based rations were used through several experiments in which the twice daily feeding (6.15-15.30 h) as well as a 30 h-fasting period were studied. Simultaneously to a continuous or a regular collection of rumen liquor (for NH3), samples of rumen contents (for total protozoa numbers) were regularly withdrawn from the ventral sac. Any definite nycthemeral cycle of the protozoa numbers could not be related to feeding time. Moreover, no significant relationship could be found between the ruminal ammonia and the corresponding total protozoa numbers measured in the nocturnal interprandial period or during starvation. The data suggest that the nycthemeral ammonia profiles recorded in cattle are not directly related to protozoal activity.

[The effect of different centrifugation conditions in the isolation of mixed rumen bacteria on their content of nitrogen and diaminopimelic acid: use of duodenal content as raw material]

The objective of the present study was, to investigate the effect of varying conditions of differential centrifugation of duodenal content on the isolation of bacteria (B-fraction) and feed particles + protozoa (FP-fraction). The treatments at low-speed centrifugation were as follows: 100 x g/5 min, 400 x g/10 min, 1000 x g/10 min and 2000 x g/10 min, high speed conditions were 30,000 x g/30 min/4 degrees C. The results of three experiments are given. Analytical examination gave similar results for N-contents for all treatments, the mean values being 7.90 +/- 0.27% (n = 12) for B-fractions and 6.53 +/- 0.73% (n = 12) for FP-fractions. Increasing the low-speed from 100 x g to 2000 x g lead to increasing DAP-contents and decreasing N:DAP-ratios of the bacterial isolates, the values being 2.43, 3.02, 3.22 and 3.39 mg DAP/g DM and 32.0, 27.4, 25.0 and 23.0 N:DAP-ratio. Decreased isolation of bacterial material in the B-fraction in conjunction with increased incorporation in the FP-fraction resulted in rising the speed of the low speed centrifugation. The rates of loss of DAP, measured by comparison with the total amount were 10, 32, 48 and 70% respectively. It was concluded to prefer the isolation of bacteria from rumen fluid.

Factors affecting the rate of breakdown of bacterial protein in rumen fluid

1. The cellular proteins of Butyrivibrio fibrisolvens, Lactobacillus casei, Megasphaera elsdenii, Selenomonas ruminantium and Streptococcus bovis were labelled by growth in the presence of L-[14C]leucine, and the breakdown of labelled protein was measured in incubations of these bacteria with rumen fluid to which unlabelled 5 mM-L-leucine was added. The rate of protein breakdown was estimated from the rate of release of radioactivity into acid-soluble material. 2. Protein breakdown occurred at different rates in different species. The mean rates for B. fibrisolvens, L. casei, M. elsdenii, Sel. ruminantium and Str. bovis were 28.6, 18.1, 17.7, 10.5 and 5.3%/h respectively in samples of strained rumen fluid (SRF) with different protozoal populations. Rates of 3%/h or less were found in SRF from ciliate-free sheep or in faunated SRF from which protozoa had been removed by centrifugation. Further removal of mixed rumen bacteria had little effect. Suspensions of washed protozoa degraded bacterial protein at rates which were of the same order as those found in SRF. 3. The rate of breakdown of bacterial protein in different samples of SRF tended to increase as the numbers of small entodiniomorphid protozoa increased. The numbers of larger entodiniomorphs and holotrichs had no obvious influence on this rate. 4. Autoclaved and u.v.-treated bacteria were generally no different from live bacteria in their susceptibility to breakdown in SRF from faunated sheep, indicating that endogenous protein turnover was not a significant cause of bacterial protein catabolism. 5. The rate of bacterial protein breakdown was unrelated to the proteolytic activity of SRF. 6. It was concluded that predation by small protozoa is by far the most important cause of bacterial protein turnover in the rumen, with autolysis, other lytic factors and endogenous proteolysis being of minor importance.