Reducing microbial ureolytic activity in the rumen by immunization against urease therein

Climate change and dairy farming sustainability; a causal loop paradox and its mitigation scenario

It is arguable at this time whether climate change is a cause or effect of the disruption in dairy farming. Climate change drastically affects the productive performance of livestock, including milk and meat production, and this could be attributed to the deviation of energy resources towards adaptive mechanisms. However, livestock farming also contributes substantially to the existing greenhouse gas pool, which is the causal of the climate change. We gathered relevant information from the recent publication and reviewed it to elaborate on sustainable dairy farming management in a changing climatic scenario, and efforts are needed to gather this material to develop methods that could help to overcome the adversities associated with livestock industries. We summarize the intervention points to reverse these adversities, such as application of genetic technology, nutrition intervention, utilization of chemical inhibitors, immunization, and application of metagenomics, which may help to sustain farm animal production in the changing climate scenario.

Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle

BACKGROUND

Ruminants can utilize urea as a dietary nitrogen source owing to their ability to recycle urea-N back to the rumen where numerous ureolytic bacteria hydrolyze urea into ammonia, which is used by numerous bacteria as their nitrogen source. Rumen ureolytic bacteria are the key microbes making ruminants the only type of animals independent of pre-formed amino acids for survival, thus having attracted much research interest. Sequencing-based studies have helped gain new insights into ruminal ureolytic bacterial diversity, but only a limited number of ureolytic bacteria have been isolated into pure cultures or studied, hindering the understanding of ureolytic bacteria with respect to their metabolism, physiology, and ecology, all of which are required to effectively improve urea-N utilization efficiency.

RESULTS

We established and used an integrated approach, which include urease gene (ureC) guided enrichment plus in situ agarose microsphere embedding and cultivation under rumen-simulating conditions, to isolate ureolytic bacteria from the rumen microbiome. We optimized the dilutions of the rumen microbiome during the enrichment, single-cell embedding, and then in situ cultivation of microsphere-embedded bacteria using dialysis bags placed in rumen fluid. Metabonomic analysis revealed that the dialysis bags had a fermentation profile very similar to the simulated rumen fermentation. In total, we isolated 404 unique strains of bacteria, of which 52 strains were selected for genomic sequencing. Genomic analyses revealed that 28 strains, which were classified into 12 species, contained urease genes. All these ureolytic bacteria represent new species ever identified in the rumen and represented the most abundant ureolytic species. Compared to all the previously isolated ruminal ureolytic species combined, the newly isolated ureolytic bacteria increased the number of genotypically and phenotypically characterized ureolytic species by 34.38% and 45.83%, respectively. These isolated strains have unique genes compared to the known ureolytic strains of the same species indicating their new metabolic functions, especially in energy and nitrogen metabolism. All the ureolytic species were ubiquitous in the rumen of six different species of ruminants and were correlated to dietary urea metabolism in the rumen and milk protein production. We discovered five different organizations of urease gene clusters among the new isolates, and they had varied approaches to hydrolyze urea. The key amino acid residues of the UreC protein that potentially plays critical regulatory roles in urease activation were also identified.

CONCLUSIONS

We established an integrated methodology for the efficient isolation of ureolytic bacteria, which expanded the biological resource of crucial ureolytic bacteria from the rumen. These isolates play a vital role in the incorporation of dietary nitrogen into bacterial biomass and hence contribute to ruminant growth and productivity. Moreover, this methodology can enable efficient isolation and cultivation of other bacteria of interest in the environment and help bridge the knowledge gap between genotypes and phenotypes of uncultured bacteria. Video abstract.

Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods

In silico prediction of epitopes is a potentially time-saving alternative to experimental epitope identification but is often subject to misidentification of epitopes and may not be useful for proteins from archaeal microorganisms. In this study, we mapped B- and T-cell epitopes of a model antigen from the methanogen Methanobrevibacter ruminantium M1, the Big_1 domain (AdLP-D1, amino acids 19-198) of an adhesin-like protein. A series of 17 overlapping 20-mer peptides was selected to cover the Big_1 domain. Peptide-specific antibodies were produced in mice and measured by ELISA, while an in vitro splenocyte re-stimulation assay determined specific T-cell responses. Overall, five peptides of the 17 peptides were shown to be major immunogenic epitopes of AdLP-D1. These immunogenic regions were examined for their localization in a homology-based model of AdLP-D1. Validated epitopes were found in the outside region of the protein, with loop like secondary structures reflecting their flexibility. The empirical data were compared with epitope predictions made by programmes based on a range of algorithms. In general, the epitopes identified by in silico predictions were not comparable to those determined empirically.

Current knowledge on urease and nitrification inhibitors technology and their safety

OBJECTIVE

Urea is one of the most widely used commercial fertilisers worldwide due to its high N density and cost effectiveness. However, it can be lost in the form of gaseous ammonia and other greenhouse gas (GHG) emissions which can potentially lead to environmental pollution. Farmers are compelled to apply more urea to account for those losses, thereby increasing their expenditure on fertilization. The objective of this paper is to present a literature review on current knowledge regarding inhibitor technologies such as urease inhibitor; n-(N-butyl) thiophosphoric triamide (NBPT), and nitrification inhibitor; dicyandiamide (DCD).

METHODS

A thorough review of all the scientific literature was carried out and a proposed risk assessment framework developed.

RESULTS

The study showed that the urease inhibitor NBPT significantly reduced NH3 loss from urea. However, concerns about NBPT safety to human health had been raised when the nitrification inhibitor DCD appeared as a residue in milk. This article presents a risk assessment framework for evaluating human exposure to chemicals like NBPT or DCD, following the consumption of foods of animal origin (e.g. milk) from cows grazing on inhibitor-treated pasture.

CONCLUSION

The EU's target of a 40% reduction of greenhouse gas emissions by 2030 can be aided by using NBPT as part of an overall suite of solutions. A comprehensive risk assessment is advised for effective evaluation of potential risks from exposure to these inhibitors.

Urea transport and hydrolysis in the rumen: A review

Inefficient dietary nitrogen (N) conversion to microbial proteins, and the subsequent use by ruminants, is a major research focus across different fields. Excess bacterial ammonia (NH3) produced due to degradation or hydrolyses of N containing compounds, such as urea, leads to an inefficiency in a host's ability to utilize nitrogen. Urea is a non-protein N containing compound used by ruminants as an ammonia source, obtained from feed and endogenous sources. It is hydrolyzed by ureases from rumen bacteria to produce NH3 which is used for microbial protein synthesis. However, lack of information exists regarding urea hydrolysis in ruminal bacteria, and how urea gets to hydrolysis sites. Therefore, this review describes research on sites of urea hydrolysis, urea transport routes towards these sites, the role and structure of urea transporters in rumen epithelium and bacteria, the composition of ruminal ureolytic bacteria, mechanisms behind urea hydrolysis by bacterial ureases, and factors influencing urea hydrolysis. This review explores the current knowledge on the structure and physiological role of urea transport and ureolytic bacteria, for the regulation of urea hydrolysis and recycling in ruminants. Lastly, underlying mechanisms of urea transportation in rumen bacteria and their physiological importance are currently unknown, and therefore future research should be directed to this subject.

DHA content in milk and biohydrogenation pathway in rumen: a review

Docosahexaenoic acid (DHA) is an essential human nutrient that may promote neural health and development. DHA occurs naturally in milk in concentrations that are influenced by many factors, including the dietary intake of the cow and the rumen microbiome. We reviewed the literature of milk DHA content and the biohydrogenation pathway in rumen of dairy cows aim to enhance the DHA content. DHA in milk is mainly derived from two sources: α-linolenic acid (ALA) occurring in the liver and consumed as part of the diet, and overall dietary intake. Rumen biohydrogenation, the lymphatic system, and blood circulation influence the movement of dietary intake of DHA into the milk supply. Rumen biohydrogenation reduces DHA in ruminal environmental and limits DHA incorporation into milk. The fat-1 gene may increase DHA uptake into the body but this lacks experimental confirmation. Additional studies are needed to define the mechanisms by which different dietary sources of DHA are associated with variations of DHA in milk, the pathway of DHA biohydrogenation in the rumen, and the function of the fat-1 gene on DHA supply in dairy cows.

Exploring the Diversity of Active Ureolytic Bacteria in the Rumen by Comparison of cDNA and gDNA

Simple Summary

Ureolytic bacteria produce urease that hydrolyzes dietary or recycled urea to ammonia, which can then be converted into microbial proteins. The diversity of ruminal ureolytic bacteria benefits N utilization efficiency in ruminants. However, there is no information at the complementary DNA (cDNA) level to reflect the active status of ureolytic bacteria. To reveal the diversity of active ureolytic bacteria in the rumen, we compared ureC amplicons between genomic DNA (gDNA) and cDNA. These results revealed distinct ureolytic bacterial community profiles based on gDNA and cDNA. The dominant ureolytic bacterial had high transcriptional activity, and the differential were mainly distributed in the genus of low abundance.

Abstract

In this study we revealed the diversity of active ureolytic bacteria in the rumen by compared ureC amplicons between gDNA and cDNA. Rumen fluid was collected from four Holstein dairy cows with rumen fistulas at 0, 2, and 6 h after morning feeding. Total microbial gDNA and RNA were isolated, and the RNA was reverse-transcribed into cDNA. The ureC gene amplicons of gDNA and cDNA were produced and sequenced by MiSeq. These results revealed that the sampling time had no significant difference on the alphssa and beta diversity indices of the ureolytic bacteria. The Shannon diversity of the ureC gene for cDNA was greater than that for gDNA (p < 0.05). There were significant difference in the beta diversity of ureolytic bacteria between gDNA and cDNA (p < 0.01), which indicates a shift in the community of active ureolytic bacteria. Approximately 67% of ureC sequences from cDNA could not be confidently classified at the genus level. The active ureolytic bacteria were mainly from Helicobacter, Herbaspirillum, Clostridium, Paenibacillus, Synechococcus, and Sphingobacterium sp. Changes in the operational taxonomic units revealed that the top abundant ureC genes were mostly consistent between gDNA and cDNA, and most differences occurred in the ureC genes with lower abundances. These results revealed distinct ureolytic bacteria community profiles based on gDNA and cDNA. The dominant ureolytic bacteria had high transcriptional activity, and the differential were mainly distributed in the genus of low abundance.

Are Vaccines the Solution for Methane Emissions from Ruminants? A Systematic Review

Ruminants produce considerable amounts of methane during their digestive process, which makes the livestock industry as one of the largest sources of anthropogenic greenhouse gases. To tackle this situation, several solutions have been proposed, including vaccination of ruminants against microorganisms responsible for methane synthesis in the rumen. In this review, we summarize the research done on this topic and describe the state of the art of this strategy. The different steps implied in this approach are described: experimental design, animal model (species, age), antigen (whole cells, cell parts, recombinant proteins, peptides), adjuvant (Freund's, Montanide, saponin, among others), vaccination schedule (booster intervals and numbers) and measurements of treatment success (immunoglobulin titers and/or effects on methanogens and methane production). Highlighting both the advances made and knowledge gaps in the use of vaccines to inhibit ruminant methanogen activity, this research review opens the door to future studies. This will enable improvements in the methodology and systemic approaches so as to ensure the success of this proposal for the sustainable mitigation of methane emission.

Recent advances in design of new urease inhibitors: A review

Urease is a nickel-dependent metalloenzyme found in plants, some bacteria, and fungi. Bacterial enzyme is of special importance since it has been demonstrated as a potent virulence factor for some species. Especially it is central to Helicobacter pylori metabolism and virulence being necessary for its colonization of the gastric mucosa, and is a potent immunogen that elicits a vigorous immune response. Therefore, it is not surprising that efforts to design, synthesize and evaluate of new inhibitors of urease are and active field of medicinal chemistry. In this paper recent advances on this field are reviewed.

Does intra-ruminal nitrogen recycling waste valuable resources? A review of major players and their manipulation

Nitrogenous emissions from ruminant livestock production are of increasing public concern and, together with methane, contribute to environmental pollution. The main cause of nitrogen-(N)-containing emissions is the inadequate provision of N to ruminants, leading to an excess of ammonia in the rumen, which is subsequently excreted. Depending on the size and molecular structure, various bacterial, protozoal and fungal species are involved in the ruminal breakdown of nitrogenous compounds (NC). Decelerating ruminal NC degradation by controlling the abundance and activity of proteolytic and deaminating microorganisms, but without reducing cellulolytic processes, is a promising strategy to decrease N emissions along with increasing N utilization by ruminants. Different dietary options, including among others the treatment of feedstuffs with heat or the application of diverse feed additives, as well as vaccination against rumen microorganisms or their enzymes have been evaluated. Thereby, reduced productions of microbial metabolites, e.g. ammonia, and increased microbial N flows give evidence for an improved N retention. However, linkage between these findings and alterations in the rumen microbiota composition, particularly NC-degrading microbes, remains sparse and contradictory findings confound the exact evaluation of these manipulating strategies, thus emphasizing the need for comprehensive research. The demand for increased sustainability in ruminant livestock production requests to apply attention to microbial N utilization efficiency and this will require a better understanding of underlying metabolic processes as well as composition and interactions of ruminal NC-degrading microorganisms.

Steam explosion enhances digestibility and fermentation of corn stover by facilitating ruminal microbial colonization

The purpose of this study was to evaluate steam explosion as a pretreatment to enhance degradation of corn stover by ruminal microbiome. The steam explosion conditions were first optimized, and then the efficacy of steam explosion was evaluated both in vitro and in vivo. Steam explosion altered the physical and chemical structure of corn stover as revealed by scanning electron microscopy (SEM) and Fourier-transform infrared (FTIR) spectroscopy, respectively, and increased its cellulose content while decreasing hemicellulose content. Steam-exploded corn stover also increased release of reducing sugars, rate of fermentation, and production of volatile fatty acids (VFAs) in vitro. The steam explosion treatment increased microbial colonization and in situ degradation of cellulose and hemicellulose of corn stover in the rumen of dairy cows. Steam explosion may be a useful pretreatment of corn stover to improve its nutritional value as forage for cattle, or as feedstock for biofuel production.

Ureases in the gastrointestinal tracts of ruminant and monogastric animals and their implication in urea-N/ammonia metabolism: A review

Urea in diets of ruminants has been investigated to substitute expensive animal and vegetable protein sources for more than a century, and has been widely incorporated in diets of ruminants for many years. Urea is also recycled to the fermentative parts of the gastrointestinal (GI) tracts through saliva or direct secretory flux from blood depending upon the dietary situations. Within the GI tracts, urea is hydrolyzed to ammonia by urease enzymes produced by GI microorganisms and subsequent ammonia utilization serves the synthesis of microbial protein. In ruminants, excessive urease activity in the rumen may lead to urea/ammonia toxicity when high amounts of urea are fed to animals; and in non-ruminants, ammonia concentrations in the GI content and milieu may cause damage to the GI mucosa, resulting in impaired nutrient absorption, futile energy and protein spillage and decreased growth performance. Relatively little attention has been directed to this area by researchers. Therefore, the present review intends to discuss current knowledge in ureolytic bacterial populations, urease activities and factors affecting them, urea metabolism by microorganisms, and the application of inhibitors of urease activity in livestock animals. The information related to the ureolytic bacteria and urease activity could be useful for improving protein utilization efficiency in ruminants and for the reduction of the ammonia concentration in GI tracts of monogastric animals. Application of recent molecular methods can be expected to provide rationales for improved strategies to modulate urease and urea dynamics in the GI tract. This would lead to improved GI health, production performance and environmental compatibility of livestock production.

A cold-adapted endoglucanase from camel rumen with high catalytic activity at moderate and low temperatures: an anomaly of truly cold-adapted evolution in a mesophilic environment

Endoglucanases are important enzymes in plant biomass degradation. They have current and potential applications in various industrial sectors including human and animal food processing, textile, paper, and renewable biofuel production. It is assumed that the cold-active endoglucanases, with high catalytic rates in moderate and cold temperatures, can improve the cost-effectiveness of industrial processes by lowering the need for heating and, thus, energy consumption. In this study, the endoglucanase CelCM3 was procured from a camel rumen metagenome via gene cloning and expression in Escherichia coli BL21 (DE3). The maximum activity of the enzyme on carboxymethyl cellulose (CMC) was obtained at pH 5 and 30 °C with a V_max and K_m of 339 U/mg and 2.57 mg/ml, respectively. The enzyme with an estimated low melting temperature of 45 °C and about 50% activity at 4 °C was identified to be cold-adapted. A thermodynamic analysis corroborated that CelCM3 with an activation energy (E_a), enthalpy of activation (ΔH), and Gibb's free energy (ΔG) of, respectively, 18.47 kJ mol^-1, 16.12 kJ mol^-1, and 56.09 kJ mol^-1 is a cold-active endoglucanase. In addition, CelCM3 was tolerant of metal ions, non-ionic detergents, urea, and organic solvents. Given these interesting characteristics, CelCM3 shows promise to meet the requirements of industrial applications.

Differences in Ureolytic Bacterial Composition between the Rumen Digesta and Rumen Wall Based on ureC Gene Classification

Ureolytic bacteria are key organisms in the rumen producing urease enzymes to catalyze the breakdown of urea to ammonia for the synthesis of microbial protein. However, little is known about the diversity and distribution of rumen ureolytic microorganisms. The urease gene (ureC) has been the target gene of choice for analysis of the urea-degrading microorganisms in various environments. In this study, we investigated the predominant ureC genes of the ureolytic bacteria in the rumen of dairy cows using high-throughput sequencing. Six dairy cows with rumen fistulas were assigned to a two-period cross-over trial. A control group (n = 3) were fed a total mixed ration without urea and the treatment group (n = 3) were fed rations plus 180 g urea per cow per day at three separate times. Rumen bacterial samples from liquid and solid digesta and rumen wall fractions were collected for ureC gene amplification and sequencing using Miseq. The wall-adherent bacteria (WAB) had a distinct ureolytic bacterial profile compared to the solid-adherent bacteria (SAB) and liquid-associated bacteria (LAB) but more than 55% of the ureC sequences did not affiliate with any known taxonomically assigned urease genes. Diversity analysis of the ureC genes showed that the Shannon and Chao1 indices for the rumen WAB was lower than those observed for the SAB and LAB (P < 0.01). The most abundant ureC genes were affiliated with Methylococcaceae, Clostridiaceae, Paenibacillaceae, Helicobacteraceae, and Methylophilaceae families. Compared with the rumen LAB and SAB, relative abundance of the OTUs affiliated with Methylophilus and Marinobacter genera were significantly higher (P < 0.05) in the WAB. Supplementation with urea did not alter the composition of the detected ureolytic bacteria. This study has identified significant populations of ureolytic WAB representing genera that have not been recognized or studied previously in the rumen. The taxonomic classification of rumen ureC genes in the dairy cow indicates that the majority of ureolytic bacteria are yet to be identified. This survey has expanded our knowledge of ureC gene information relating to the rumen ureolytic microbial community, and provides a basis for obtaining regulatory targets of ureolytic bacteria to moderate urea hydrolysis in the rumen.

Vaccination of Sheep with a Methanogen Protein Provides Insight into Levels of Antibody in Saliva Needed to Target Ruminal Methanogens

Methane is produced in the rumen of ruminant livestock by methanogens and is a major contributor to agricultural greenhouse gases. Vaccination against ruminal methanogens could reduce methane emissions by inducing antibodies in saliva which enter the rumen and impair ability of methanogens to produce methane. Presently, it is not known if vaccination can induce sufficient amounts of antibody in the saliva to target methanogen populations in the rumen and little is known about how long antibody in the rumen remains active. In the current study, sheep were vaccinated twice at a 3-week interval with a model methanogen antigen, recombinant glycosyl transferase protein (rGT2) formulated with one of four adjuvants: saponin, Montanide ISA61, a chitosan thermogel, or a lipid nanoparticle/cationic liposome adjuvant (n = 6/formulation). A control group of sheep (n = 6) was not vaccinated. The highest antigen-specific IgA and IgG responses in both saliva and serum were observed with Montanide ISA61, which promoted levels of salivary antibodies that were five-fold higher than the second most potent adjuvant, saponin. A rGT2-specific IgG standard was used to determine the level of rGT2-specific IgG in serum and saliva. Vaccination with GT2/Montanide ISA61 produced a peak antibody concentration of 7 × 10¹⁶ molecules of antigen-specific IgG per litre of saliva, and it was estimated that in the rumen there would be more than 10⁴ molecules of antigen-specific IgG for each methanogen cell. Both IgG and IgA in saliva were shown to be relatively stable in the rumen. Salivary antibody exposed for 1–2 hours to an in vitro simulated rumen environment retained approximately 50% of antigen-binding activity. Collectively, the results from measuring antibody levels and stablility suggest a vaccination-based mitigation strategy for livestock generated methane is in theory feasible.

Insights into Abundant Rumen Ureolytic Bacterial Community Using Rumen Simulation System

Urea, a non-protein nitrogen for dairy cows, is rapidly hydrolyzed to ammonia by urease produced by ureolytic bacteria in the rumen, and the ammonia is used as nitrogen for rumen bacterial growth. However, there is limited knowledge with regard to the ureolytic bacteria community in the rumen. To explore the ruminal ureolytic bacterial community, urea, or acetohydroxamic acid (AHA, an inhibitor of urea hydrolysis) were supplemented into the rumen simulation systems. The bacterial 16S rRNA genes were sequenced by Miseq high-throughput sequencing and used to reveal the ureoltyic bacteria by comparing different treatments. The results revealed that urea supplementation significantly increased the ammonia concentration, and AHA addition inhibited urea hydrolysis. Urea supplementation significantly increased the richness of bacterial community and the proportion of ureC genes. The composition of bacterial community following urea or AHA supplementation showed no significant difference compared to the groups without supplementation. The abundance of Bacillus and unclassified Succinivibrionaceae increased significantly following urea supplementation. Pseudomonas, Haemophilus, Neisseria, Streptococcus, and Actinomyces exhibited a positive response to urea supplementation and a negative response to AHA addition. Results retrieved from the NCBI protein database and publications confirmed that the representative bacteria in these genera mentioned above had urease genes or urease activities. Therefore, the rumen ureolytic bacteria were abundant in the genera of Pseudomonas, Haemophilus, Neisseria, Streptococcus, Actinomyces, Bacillus, and unclassified Succinivibrionaceae. Insights into abundant rumen ureolytic bacteria provide the regulation targets to mitigate urea hydrolysis and increase efficiency of urea nitrogen utilization in ruminants.