Degradation of protein and utilization of the hydrolytic products by a predominant ruminal bacterium, Prevotella ruminicola B1(4)

Linkage of in situ ruminal degradation of crude protein with ruminal degradation of amino acids and phytate from different soybean meals in dairy cows

The objectives of this study were to determine the range in ruminal degradability of crude protein (CP) and intestinal digestibility of rumen undegradable protein in commercial soybean meal (SBM) and to investigate the range in in situ ruminal AA and phytate (InsP6) degradation and their relationship to CP degradation. An in situ study was conducted using 3 lactating Jersey cows with permanent rumen cannulas. Seventeen SBM variants from Europe, Brazil, Argentina, North America, and India were tested for ruminal CP and AA degradation, and in vitro intestinal digestibility of rumen undegradable protein. Nine variants were used to investigate the ruminal degradation of InsP6. The estimated rapidly degradable fraction (a) of CP showed an average value of 4.5% (range: 0.0%-9.0%), the slowly degradable fraction (b) averaged 95% (91%-100%), and the potential degradation was complete for all 17 SBM variants. The degradation of fraction b started after a mean lag phase of 1.7 h (1.1-2.0 h) at an average rate (c) of 10% per hour, but with a high range from 4.5% to 14% per hour. Differences in the degradation parameters induced a considerable range in CP effective degradation at a rumen passage rate of 6% per hour (CPED6) from 38% to 67%; hence, the concentration of rumen undegradable protein varied widely from 33% to 62%. The range in AA degradation between the SBM variants was high, with Ser showing the widest range, from 28% to 96%, and similar for the other AA. The regression equations showed close relationships between CP and AA degradation after 16 h of in situ incubation. However, the slopes of the linear regressions were significantly different between AA, suggesting that degradation among individual AA differs upon a change in CP degradation. The concentrations of InsP6 and myo-inositol pentakisphosphate in bag residues in the in situ study decreased constantly with longer ruminal incubation times. The ruminal degradation parameters of InsP6 ranged from 11% to 37% for fraction a, 63% to 89% for fraction b, and from 7.7% to 21% per hour for degradation rate c, with average values of 21%, 79%, and 16% per hour, respectively. The calculated InsP6 effective degradation at a rumen passage rate of 6% per hour (InsP6ED6) varied from 61% to 84% among the SBM variants. Significant correlations were detected between InsP6ED6 and CPED6 and between InsP6ED6 and chemical protein fractions A, B1, B2, B3, and C. Linear regression equations were developed to predict ruminal InsP6 degradation using CPED6 and chemical protein fractions B3 and C chosen by a stepwise selection procedure. We concluded that a high range in CP, AA, and InsP6 degradation exists among commercial SBM, suggesting that general degradability values may not be precise enough for diet formulation for dairy cows. Degradation of CP in SBM may be used to predict rumen degradation of AA and InsP6 using linear regression equations. Degradation of CP and InsP6 could also be predicted from the chemical protein fractions.

Prevotella: A Key Player in Ruminal Metabolism

Ruminants are foregut fermenters that have the remarkable ability of converting plant polymers that are indigestible to humans into assimilable comestibles like meat and milk, which are cornerstones of human nutrition. Ruminants establish a symbiotic relationship with their microbiome, and the latter is the workhorse of carbohydrate fermentation. On the other hand, during carbohydrate fermentation, synthesis of propionate sequesters H, thus reducing its availability for the ultimate production of methane (CH4) by methanogenic archaea. Biochemically, methane is the simplest alkane and represents a downturn in energetic efficiency in ruminants; environmentally, it constitutes a potent greenhouse gas that negatively affects climate change. Prevotella is a very versatile microbe capable of processing a wide range of proteins and polysaccharides, and one of its fermentation products is propionate, a trait that appears conspicuous in P. ruminicola strain 23. Since propionate, but not acetate or butyrate, constitutes an H sink, propionate-producing microbes have the potential to reduce methane production. Accordingly, numerous studies suggest that members of the genus Prevotella have the ability to divert the hydrogen flow in glycolysis away from methanogenesis and in favor of propionic acid production. Intended for a broad audience in microbiology, our review summarizes the biochemistry of carbohydrate fermentation and subsequently discusses the evidence supporting the essential role of Prevotella in lignocellulose processing and its association with reduced methane emissions. We hope this article will serve as an introduction to novice Prevotella researchers and as an update to others more conversant with the topic.

Biochemical characterization of an engineered bifunctional xylanase/feruloyl esterase and its synergistic effects with cellulase on lignocellulose hydrolysis

Herein, the xylanase and feruloyl esterase domains of the xylanase/feruloyl esterase bifunctional enzyme (Xyn-Fae) from Prevotella ruminicola 23 were identified using N- and C-terminal truncation mutagenesis. In addition, a novel and more efficient xylanase/feruloyl esterase bifunctional enzyme XynII-Fae was constructed, and its synergistic action with a commercial cellulase for lignocellulose hydrolysis was studied. When 40% cellulase was replaced by XynII-Fae, the production of reducing sugars increased by 65% than that with the cellulase alone, and the conversions of xylan and glucan were increased by 125.1% and 54.3%, respectively. When 80% cellulase was substituted by XynII-Fae, up to 43.5 μg/mL ferulic acid and 418.7 μg/mL acetic acid were obtained. The XynII-Fae could also accelerate the hydrolysis of wheat straw and sugarcane bagasse with commercial cellulase. These results indicated that the synergistic action of XynII-Fae with cellulase could dramatically improve the hydrolysis efficiency of lignocellulose, showing the great potential for industrial applications.

Gastrointestinal biotransformation and tissue distribution of pterostilbene after long-term dietary administration in mice

The metabolic fate of dietary compounds is closely related to their biological functions. Pterostilbene (PT) is a methylated stilbene found in many plant foods. Herein, we investigated gastrointestinal biotransformation and tissue distribution of PT in mice fed with 0.05% PT (w/w) for 5 weeks. PT and its major metabolites i.e. PT sulfate (PT-S), pinostilbene, pinostilbene sulfate, hydroxylated PT and hydroxylated PT sulfate were identified and quantified in the mucosa and content of the digestive tissues, blood, urine and vital organs. The results showed PT underwent demethylation, hydroxylation and conjugation in the small intestine, while the conjugated metabolites were largely deconjugated in the colon. Anaerobic fermentation with mouse cecal bacteria demonstrated the microbiota mediated deconjugation and demethylation of PT-S and PT, respectively. In conclusion, oral consumption of PT led to extensive biotransformation in mouse gastrointestinal tract and the metabolites of PT might play important roles in the bioactivity of PT.

Fermented soybean meal affects the ruminal fermentation and the abundance of selected bacterial species in Holstein calves: a multilevel analysis

The effect of soybean meal (SBM) replacement with fermented SBM (FSBM) on ruminal fermentation and bacterial abundance in Holstein calves was investigated in this study. Thirty nine calves were randomized to: (1) control: 27% SBM + 0% FSBM (FSBM0, n = 13); (2) 18% SBM + 9% FSBM (FSBM9, n = 13); and (3) 13.5% SBM + 13.5% FSBM (FSBM13, n = 13). SBM contained a greater amount of large peptides containing 3 to 10 amino acids (AAs), while FSBM had a greater amount of ammonia nitrogen (NH3-N), free AAs, and small peptides containing 2 to 3 AAs. The calves fed FSBM13 had the lowest acetic acid, NH3-N, and the ratio of acetate to propionate, with the greatest concentration of caproic acid, valeric acid and isovaleric acid in ruminal fluid. Compared to those fed FSBM9 or FSBM13, the calves fed FSBM0 had the greatest proportion of Butyrivibrio fibrisolvens and Ruminococcus albus in rumen fluid. However, the ruminal abundance of Prevotella ruminicola in calves fed FSBM13 was greater than in calves fed FSBM0. Network analysis showed that the abundance of the Ruminococcus albus was associated with large peptides, and butyric acid was correlated with small peptide. Taken together, our findings suggest that FSBM may have the potential to boost calf performance by changing the fermentation products and the relative abundance of some members of the bacterial community in the rumen.

Calcium propionate supplementation alters the ruminal bacterial and archaeal communities in pre- and postweaning calves

The aim of this study was to determine the effect of calcium propionate (CaP) on rumen microbiota, fermentation indicators, and weight gain in calves both pre- and postweaning. Twenty-four newborn calves were randomly divided into 4 groups (2 × 2 factorial treatment arrangement): either pre- (90 d) or postweaning (160 d), and either without or with dietary CaP supplementation (5% dry matter). The CaP supplementation increased the body weight and rumen weight of the calves and lowered NH₃-N concentration in the rumen. Microbiota composition was characterized by sequencing the amplicons of the bacterial and archaeal 16S rRNA genes. The CaP supplementation decreased the relative abundance of the phylum Bacteroidetes but tended to increase that of Proteobacteria. In addition, CaP supplementation decreased the diversity of bacteria and archaea in the rumen compared with the calves fed the control diet. Linear discriminant analysis of the rumen microbiota revealed that Succinivibrionaceae and Methanobrevibacter were enriched in the CaP group postweaning. A correlation was also present between the acetate to propionate ratio and the species that acted as co-occurrence network hubs, including Succiniclasticum, Treponema, and Megasphaera. In conclusion, CaP supplementation can improve body weight gain and rumen growth and alter the ruminal microbiota in calves both pre- and postweaning.

Identification of Uncultured Bacterial Species from Firmicutes, Bacteroidetes and CANDIDATUS Saccharibacteria as Candidate Cellulose Utilizers from the Rumen of Beef Cows

The ability of ruminants to utilize cellulosic biomass is a result of the metabolic activities of symbiotic microbial communities that reside in the rumen. To gain further insight into this complex microbial ecosystem, a selection-based batch culturing approach was used to identify candidate cellulose-utilizing bacterial consortia. Prior to culturing with cellulose, rumen contents sampled from three beef cows maintained on a forage diet shared 252 Operational Taxonomic Units (OTUs), accounting for 41.6-50.0% of bacterial 16S rRNA gene sequences in their respective samples. Despite this high level of overlap, only one OTU was enriched in cellulose-supplemented cultures from all rumen samples. Otherwise, each set of replicate cellulose supplemented cultures originating from a sampled rumen environment was found to have a distinct bacterial composition. Two of the seven most enriched OTUs were closely matched to well-established rumen cellulose utilizers (Ruminococcusflavefaciens and Fibrobactersuccinogenes), while the others did not show high nucleotide sequence identity to currently defined bacterial species. The latter were affiliated to Prevotella (1 OTU), Ruminococcaceae (3 OTUs), and the candidate phylum Saccharibacteria (1 OTU), respectively. While further investigations will be necessary to elucidate the metabolic function(s) of each enriched OTU, these results together further support cellulose utilization as a ruminal metabolic trait shared across vast phylogenetic distances, and that the rumen is an environment conducive to the selection of a broad range of microbial adaptations for the digestion of plant structural polysaccharides.

Metabolic networks for nitrogen utilization in Prevotella ruminicola 23

Nitrogen metabolism in gut systems remains poorly studied in spite of its importance for microbial growth and its implications for the metabolism of the host. Prevotella spp. are the most predominant bacteria detected in the rumen, but their presence has also been related to health and disease states in the human gut and oral cavity. To explore the metabolic networks for nitrogen assimilation in this bacterium, changes in gene expression profiles in response to variations in the available nitrogen source and to different concentrations of ammonium were analyzed by microarray and reverse transcription quantitative PCR, and linked with function by further proteomic analysis. The observed patterns of transcript abundances for genes involved in ammonium assimilation differed from the classical “enteric paradigm” for nitrogen utilization. Expression of genes encoding high substrate affinity nitrogen assimilation enzymes (GS-GOGAT system) was similar in growth-limiting and non-limiting nitrogen concentrations in P. ruminicola 23, whereas E. coli and Salmonella spp. responses to excess nitrogen involve only low substrate affinity enzymes. This versatile behavior might be a key feature for ecological success in habitats such as the rumen and human colon where nitrogen is rarely limiting for growth, and might be linked to previously reported Prevotella spp. population imbalances relative to other bacterial species in gut systems.

Isolation and characterization of a novel glycosyl hydrolase family 74 (GH74) cellulase from the black goat rumen metagenomic library

This study aimed to isolate and characterize a novel cellulolytic enzyme from black goat rumen by using a culture-independent approach. A metagenomic fosmid library was constructed from black goat rumen contents and screened for a novel cellulase. The KG37 gene encoding a protein of 858 amino acid residues (92.7 kDa) was isolated. The deduced protein contained a glycosyl hydrolase family 74 (GH74) domain and showed 77% sequence identity to two endo-1,4-β-glucanases from Fibrobacter succinogenes. The novel GH74 cellulase gene was overexpressed in Escherichia coli, and its protein product was functionally characterized. The recombinant GH74 cellulase showed a broad substrate spectrum. The enzyme exhibited its optimum activity at pH 5.0 and temperature range of 20-50 °C. The enzyme was thermally stable at pH 5.0 and at a temperature of 20-40 °C. The novel GH74 cellulase can be practically exploited to convert lignocellulosic biomass to value-added products in various industrial applications in future.

Nitrogen utilization and metabolism in Ruminococcus albus 8

The model rumen Firmicutes organism Ruminococcus albus 8 was grown using ammonia, urea, or peptides as the sole nitrogen source; growth was not observed with amino acids as the sole nitrogen source. Growth of R. albus 8 on ammonia and urea showed the same growth rate (0.08 h(-1)) and similar maximum cell densities (for ammonia, the optical density at 600 nm [OD600] was 1.01; and for urea, the OD600 was 0.99); however, growth on peptides resulted in a nearly identical growth rate (0.09 h(-1)) and a lower maximum cell density (OD600 = 0.58). To identify differences in gene expression and enzyme activities, the transcript abundances of 10 different genes involved in nitrogen metabolism and specific enzyme activities were analyzed by harvesting mRNA and crude protein from cells at the mid- and late exponential phases of growth on the different N sources. Transcript abundances and enzyme activities varied according to nitrogen source, ammonia concentration, and growth phase. Growth of R. albus 8 on ammonia and urea was similar, with the only observed difference being an increase in urease transcript abundance and enzyme activity in urea-grown cultures. Growth of R. albus 8 on peptides showed a different nitrogen metabolism pattern, with higher gene transcript abundance levels of gdhA, glnA, gltB, amtB, glnK, and ureC, as well as higher activities of glutamate dehydrogenase and urease. These results demonstrate that ammonia, urea, and peptides can all serve as nitrogen sources for R. albus and that nitrogen metabolism genes and enzyme activities of R. albus 8 are regulated by nitrogen source and the level of ammonia in the growth medium.

Functional diversity of four glycoside hydrolase family 3 enzymes from the rumen bacterium Prevotella bryantii B14

Prevotella bryantii B(1)4 is a member of the phylum Bacteroidetes and contributes to the degradation of hemicellulose in the rumen. The genome of P. bryantii harbors four genes predicted to encode glycoside hydrolase (GH) family 3 (GH3) enzymes. To evaluate whether these genes encode enzymes with redundant biological functions, each gene was cloned and expressed in Escherichia coli. Biochemical analysis of the recombinant proteins revealed that the enzymes exhibit different substrate specificities. One gene encoded a cellodextrinase (CdxA), and three genes encoded beta-xylosidase enzymes (Xyl3A, Xyl3B, and Xyl3C) with different specificities for either para-nitrophenyl (pNP)-linked substrates or substituted xylooligosaccharides. To identify the amino acid residues that contribute to catalysis and substrate specificity within this family of enzymes, the roles of conserved residues (R177, K214, H215, M251, and D286) in Xyl3B were probed by site-directed mutagenesis. Each mutation led to a severely decreased catalytic efficiency without a change in the overall structure of the mutant enzymes. Through amino acid sequence alignments, an amino acid residue (E115) that, when mutated to aspartic acid, resulted in a 14-fold decrease in the k(cat)/K(m) for pNP-beta-d-xylopyranoside (pNPX) with a concurrent 1.1-fold increase in the k(cat)/K(m) for pNP-beta-d-glucopyranoside (pNPG) was identified. Amino acid residue E115 may therefore contribute to the discrimination between beta-xylosides and beta-glucosides. Our results demonstrate that each of the four GH3 enzymes has evolved to perform a specific role in lignopolysaccharide hydrolysis and provide insight into the role of active-site residues in catalysis and substrate specificity for GH3 enzymes.

Biochemical analysis of a beta-D-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23

Prevotella ruminicola 23 is an obligate anaerobic bacterium in the phylum Bacteroidetes that contributes to hemicellulose utilization within the bovine rumen. To gain insight into the cellular machinery that this organism elaborates to degrade the hemicellulosic polymer xylan, we identified and cloned a gene predicted to encode a bifunctional xylanase-ferulic acid esterase (xyn10D-fae1A) and expressed the recombinant protein in Escherichia coli. Biochemical analysis of purified Xyn10D-Fae1A revealed that this protein possesses both endo-beta-1,4-xylanase and ferulic acid esterase activities. A putative glycoside hydrolase (GH) family 3 beta-D-glucosidase gene, with a novel PA14-like insertion sequence, was identified two genes downstream of xyn10D-fae1A. Biochemical analyses of the purified recombinant protein revealed that the putative beta-D-glucosidase has activity for pNP-beta-D-xylopyranoside, pNP-alpha-L-arabinofuranoside, and xylo-oligosaccharides; thus, the gene was designated xyl3A. When incubated in combination with Xyn10D-Fae1A, Xyl3A improved the release of xylose monomers from a hemicellulosic xylan substrate, suggesting that these two enzymes function synergistically to depolymerize xylan. Directed mutagenesis studies of Xyn10D-Fae1A mapped the catalytic sites for the two enzymatic functionalities to distinct regions within the polypeptide sequence. When a mutation was introduced into the putative catalytic site for the xylanase domain (E280S), the ferulic acid esterase activity increased threefold, which suggests that the two catalytic domains for Xyn10D-Fae1A are functionally coupled. Directed mutagenesis of conserved residues for Xyl3A resulted in attenuation of activity, which supports the assignment of Xyl3A as a GH family 3 beta-D-xylosidase.

Optimal protease production condition for Prevotella ruminicola 23 and characterization of its extracellular crude protease

In this study, Prevotella ruminicola 23 (ATCC 19189), a ruminal proteolytic bacterium, was used as protease producer to examine the optimal condition for protease production. The best carbon and nitrogen sources for the maximum growth were glucose with peptone. Both sucrose and glucose could stimulate high protease production. Casein and peptone are better nitrogen sources for protease production than other choice in this study. The best enzyme production condition was 18-20 h incubation which was at late log phase in the broth of 5% glucose or sucrose as carbon source with 0.1% ammonium chloride and 0.2% peptone as nitrogen sources. Most of the protease activity was secreted into broth (65%) and on cell surface (18%). The optimal temperature and pH for protease reaction were 40 degrees C and pH 6.8, respectively. After incubation for 6h, the crude extract maintained 50% of original protease activity at 30 and 50 degrees C, and protease activity was stable between pH 6 and 8. The protease inhibitor test showed that serine, aspartic acid and metallo-protease inhibitors could cause inhibition of proteolysis. Protein feedstuff degradation experiments suggested that protease in crude extract had higher degradation ability on fish meal, whey, and feather meal (2.39, 2.60 and 1.76 micromol aminoacid/mg enzyme/h) in comparison to soybean meal and blood meal (1.11 and 1.09 micromol aminoacid/mg enzyme/h). The protease in the crude extract should have application potential in term of improving utilization of fish meal and feather meal for monogastric animals.

Applications of the ninhydrin reaction for analysis of amino acids, peptides, and proteins to agricultural and biomedical sciences

The reaction of ninhydrin with primary amino groups to form the purple dye now called Ruhemann's purple (RP) was discovered by Siegfried Ruhemann in 1910. In addition, imines such as pipecolic acid and proline, the guanidino group of arginine, the amide groups of asparagine, the indole ring of tryptophan, the sulfhydryl group of cysteine, amino groups of cytosine and guanine, and cyanide ions also react with ninhydrin to form various chromophores of analytical interest. Since its discovery, extensive efforts have been made to apply manual and automated ninhydrin reactions as well as ninhydrin spray reagents to the detection, isolation, and analysis of numerous compounds of interest across a broad spectrum of disciplines. These include agricultural, biochemical, clinical, environmental, food, forensic, histochemical, microbiological, medical, nutritional, plant, and protein sciences. This reaction is unique among chromogenic reactions in that at pH 5.5 it results in the formation of the same soluble chromophore by all primary amines which react, be they amines, amino acids, peptides, proteins, and even ammonia. Because the chromophore is not chemically bound to the protein or other insoluble material, it is not lost when the insoluble substrate is removed by centrifugation or filtration after the reaction is completed. The visible color of the chromophore is distinctive and is generally not affected by the yellow colors present in many food, plant, and tissue extracts. Adaptations of the classical ninhydrin reaction to specialized needs in analytical chemistry and biochemistry include the use of acid, alkaline, and fluorogenic ninhydrin reagents. To cross-fertilize information among several disciplines wherein an interest in the ninhydrin reaction has developed, and to enhance its utility, this review attempts to integrate and correlate the widely scattered literature on ninhydrin reactions of a variety of structurally different compounds. Specifically covered are the following aspects: historical perspective, chemistry and mechanisms, applications, and research needs. A better understanding of these multifaceted ninhydrin reactions provide a scientific basis for further improvements of this important analytical technique.

Glutamine synthetase and protease enzyme activities and growth response of ruminal bacterium Prevotella ruminicola strain B(1)4 to nitrogen source and concentration

The objective of this study was to determine the effects of varying nitrogen sources and concentrations upon glutamine synthetase and protease activities in Prevotella ruminicola strain B(1)4. Based on growth response it appears that ammonium chloride or pepticase limited P. ruminicola becomes nitrogen limited when nitrogen concentration is at 0.5 mM. However, when casein was provided as the sole source of nitrogen P. ruminicola becomes nitrogen limited at 2.5 mM. Glutamine synthetase activity was measured from mid-log phase cells grown in either nitrogen-limited or non-limited conditions. No activity was detectable in the non-limited treatments. However, in the N-limited treatments, pepticase had the highest activity (20.76 units), followed by ammonium chloride (18.72 units) and casein (14.42 units). Protease activity assays indicated that nitrogen-limited cultures had higher proteolytic activity than non-limited cultures. Moreover, these activities appeared to follow the same response pattern as the previously observed glutamine synthetase activities. The results of this study indicate that P. ruminicola strain B(1)4 protease activity may be influenced by nitrogen concentration such that activity increases when nitrogen availability decreases.

Continuous culture selection of bifidobacteria and lactobacilli from human faecal samples using fructooligosaccharide as selective substrate

The human large intestine contains a large and diverse population of bacteria. Certain genera, namely Bifidobacterium and Lactobacillus, are thought to exert health-promoting effects. Prebiotics such as fructooligosaccharides (FOS) have been shown to stimulate the growth of endogenous bifidobacteria. In this study, changes of lactic acid producing bacteria in continuous culture fermentors (semi-defined, anaerobic medium containing 5 g 1(-1) FOS, dilution rate of 0.1 h-1, pH 5.5) were followed over a 21 d period after inoculation with blended human faeces from four healthy adults. Samples were also taken every 3 d for influent/effluent FOS, short chain fatty acid (SCFA), lactate and microbiological analyses. Results showed that SCFA concentrations decreased abruptly 1 d after inoculation while lactate concentrations increased. Classical methods of enumeration using selective media showed that the proportion of total culturable count represented by bifidobacteria and lactobacilli increased from 11.9% on day 1 to 98.1% on day 21. However, molecular methods using genus-specific 16S rRNA oligonucleotide probes indicated that the bifidobacterial population maintained a level between 10 and 20% of total 16S rRNA during the first 6 d and disappeared rapidly when the maximum concentration of lactate was reached. Lactobacilli, which were initially present in low numbers, increased until day 9 and remained at high levels (20-42% of total 16S rRNA) to day 21, with the exception of day 18. Although FOS has usually been regarded as a selective substrate for bifidobacteria, these observations suggest that: (1) lactobacilli are also able to use FOS, (2) lactobacilli can out-compete bifidobacteria in continuous culture at pH 5.2-5.4 when FOS is the primary carbon and energy source, and (3) bifidobacteria can grow faster on FOS than lactobacilli under controlled conditions.