Physiological study of an obligately anaerobic ureolytic bacterium

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.

Isolation and pan-genome analysis of Enterobacter hormaechei Z129, a ureolytic bacterium, from the rumen of dairy cow

Introduction

Urea is an important non-protein nitrogen source for ruminants. In the rumen, ureolytic bacteria play critical roles in urea-nitrogen metabolism, however, a few ureolytic strains have been isolated and genomically sequenced. The purpose of this study was to isolate a novel ureolytic bacterial strain from cattle rumen and characterize its genome and function.

Methods

The ureolytic bacterium was isolated using an anaerobic medium with urea and phenol red as a screening indicator from the rumen fluid of dairy cattle. The genome of isolates was sequenced, assembled, annotated, and comparatively analyzed. The pan-genome analysis was performed using IPGA and the biochemical activity was also analyzed by test kits.

Results

A gram-positive ureolytic strain was isolated. Its genome had a length of 4.52 Mbp and predicted genes of 4223. The 16S rRNA gene and genome GTDB-Tk taxonomic annotation showed that it was a novel strain of Enterobacter hormaechei, and it was named E. hormaechei Z129. The pan-genome analysis showed that Z129 had the highest identity to E. hormaechei ATCC 49162 with a genome average nucleotide identity of 98.69% and possessed 238 unique genes. Strain Z129 was the first E. hormaechei strain isolated from the rumen as we know. The functional annotation of the Z129 genome showed genes related to urea metabolism, including urea transport (urtA-urtE), nickel ion transport (ureJ, tonB, nixA, exbB, exbD, and rcnA), urease activation (ureA-ureG) and ammonia assimilation (gdhA, glnA, glnB, glnE, glnL, glsA, gltB, and gltD) were present. Genes involved in carbohydrate metabolism were also present, including starch hydrolysis (amyE), cellulose hydrolysis (celB and bglX), xylose transport (xylF-xylH) and glycolysis (pgi, pgk, fbaA, eno, pfkA, gap, pyk, gpmL). Biochemical activity analysis showed that Z129 was positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-glucosidase, β-glucosidase, and pyrrolidone arylaminase, and had the ability to use D-ribose, L-arabinose, and D-lactose. Urea-nitrogen hydrolysis rate of Z129 reached 55.37% at 48 h of incubation.

Discussion

Therefore, the isolated novel ureolytic strain E. hormaechei Z129 had diverse nitrogen and carbon metabolisms, and is a preferred model to study the urea hydrolysis mechanism in the rumen.

Rumen bacterial diversity in relation to nitrogen retention in beef cattle

This study aimed to characterize the rumen bacterial diversity of beef steers differing in the efficiency of nitrogen retention (ENR). Eight castrated steers and fitted with ruminal silicone - and duodenal T-type cannulas were used in a cross-over design with three consecutive periods and three diets. During each experimental period, nitrogen balance was measured, and based on the efficiency of N utilization data, steers were split into three ENR groups: high (HNR, 56.6% ± 3.3%, n = 10), medium (MNR, 45.8% ± 2.2%, n = 6), and low (LNR, 37.7% ± 1.9%, n = 8) using the NbClust package version 2.0.4 in R. Prevotellaceae, Lactobacillaceae, Leuconostocaceae, Clostridiales_Incertae_Sedis_XIII, Lachnospiraceae, and Peptostreptococcaceae were more abundant in LNR (P < 0.05) compared to HNR or MNR. Negative correlations were found between N retention and Mogibacterium, Anaerofustis, Butyrivibrio, Coprococcus, Hespellia, Lactonifactor and Lachnospiraceae (r ≤ -0.61; P ≤ 0.05). Prevotella, Hespellia, Lactonifactor, Lachnospiraceae_other, and Anaerobiospirillum were positively correlated between urinary N excretion (r > 0.55; P < 0.01), and negative correlations were found with Elusimicrobia, Victivallis and Treponema (r < -0.41; P < 0.05). The adjustment of the rumen bacterial community differed significantly between the N use retention groups. The high N retention in beef cattle was associated with less abundant bacteria in the rumen; however, N fixation capacity and uncharacterized rumen microorganisms need to be elucidated in future studies. In contrast, lower N utilization was associated with high abundance of bacteria that promote greater urinary N excretion through ruminal protein degradation.

Substitution of residues in UreG to investigate UreE interactions and nickel binding in a predominant urease gene cluster from the ruminal metagenome

Microbial ureases catalyze the hydrolysis of urea to ammonia, and inhibition of these enzymes in rumen has the potential to improve urea utilization efficiency and reduce urinary nitrogen excretion. Urease activity is catalyzed by a protein complex encoded by a gene cluster, and its accessory proteins (especially UreE and UreG) play important roles in transferring nickel to the active site for urease maturation. In this study, a predominant urease gene cluster (5290 bp) from the ruminal microbial metagenome was identified. Isothermal titration calorimetry (ITC) and analytical ultracentrifugation (AUC) analyses showed that the reaction of identified UreE with UreG was endothermic, and was dominated by a hydrophobic interaction, in which each UreE dimer bound 2 M equivalents of UreG monomer to form a UreE₂-2UreG complex. Mutagenesis analyses showed that the UreG residues Glu-23, Asp-41, Glu-46, Glu-66, Cys-70, His-72, Asp-78, and Asp-118 were involved in the GTPase activity of UreG. Furthermore, variants of Cys-70 and His-72 involved in CPH motif of UreG, as well as the nearby Glu-66 and Asp-78, not only prevented interactions with UreE, but also prevented nickel binding. These data provide additional information regarding UreG residues that may be targeted for the design of new urease inhibitors.

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.

Some nutritional characteristics of predominant culturable ruminal bacteria

Bryant, M. P. (U.S. Department of Agriculture, Beltsville, Md.) and I. M. Robinson. Some nutritional characteristics of predominant culturable ruminal bacteria. J. Bacteriol. 84:605-614. 1962.-The effect of enzymatic hydrolysate of casein, NH(4) (+), a mixture of volatile fatty acids (acetic, n-valeric, isovaleric, 2-methylbutyric, and isobutyric), hemin, and ruminal fluid on growth of 89 freshly isolated strains of predominant culturable ruminal bacteria was studied, using basal media containing glucose, cellobiose, or maltose as energy source, minerals, cysteine, and S(=) as reducing agents, and H(2)CO(3)-HCO(3) (-) buffer. Of these strains, 13% (four morphological groups) grew poorly or not at all in defined medium plus casein hydrolysate; 6% (one morphological group) required casein hydrolysate; 56% (four morphological groups) grew with either NH(4) (+) or casein hydrolysate as the main source of nitrogen; and NH(4) (+), but not casein hydrolysate, was essential for 25% of the strains (five morphological groups). The volatile fatty acid mixture excluding acetate was essential for 19% of the strains (five morphological groups), and this mixture and acetate were necessary for good growth of 23% of the strains (one morphological group) when casein hydrolysate was excluded from the medium; 30% of the strains (one morphological group) required hemin. Similar studies are reported on 35 old laboratory strains of ruminal bacteria, most of which were previously identified. The results indicate that most strains of ruminal bacteria can be grown in defined media, and suggest the relative importance of NH(4) (+) and volatile fatty acids and the relative lack of importance of organic nitrogen compounds such as amino acids in the nutrition of these bacteria.

Carbon dioxide formation and elimination in man. Recent theories and possible consequences

Systemic metabolism results in a production of not only carbon dioxide, water and urea but also bicarbonate ions. Most of these bicarbonate ions are generated during the catabolism of glutamine. In order to be eliminated as carbon dioxide in the lungs bicarbonate ions must be protonised. This protonisation of the bicarbonate ion seems to take place in a number of tissue compartments in which acid-base balance is maintained. One of the most important processes for protonisation of the bicarbonate ion is the hepatic ureagenesis from ammonia/ammonium ions. A substantial part of the ammonia/ammonium ions are generated during the catabolism of amino acids. Terminal oxidation of glutamine in the gut seems to be of great significance for this process. In certain conditions the enteric generation of ammonium ions seems so important that an ATP-driven enterohepatic recirculation of ammonium ions/urea constituting an amplifying mechanism for the protonisation of the bicarbonate ion is motivated.

Bioavailability of urea nitrogen for the low birthweight infant

Previous studies have demonstrated increased retention (40%) of dietary urea nitrogen by term infants recovering from infection compared to healthy infants (13%), possibly due to a higher requirement for nitrogen. Since low birthweight infants also have a high requirement for nitrogen, the bioavailability of urea nitrogen was investigated in low birthweight infants using 15N,15N-urea. Four low birthweight infants (gestational age = 30 +/- 2.2 weeks [mean +/- SD], birthweight = 1.4 +/- 0.3 kg) were fed formula enriched with 15N,15N-urea. Metabolic balance studies (72 hours) were performed with urine and fecal collections. Nitrogen was quantitated by Kjeldahl analysis and 15N,15N-urea by gas chromatography/mass spectrometry. Mean nitrogen intake was 489 +/- 32 mg/kg/d, with 75% nitrogen absorption and 62% nitrogen retention. Maximum urinary enrichment was 8%. Cumulative 15N,15N-urea excretion was 72%, resulting in 28% retention. Thus the bioavailability of urea nitrogen for low birthweight infants appears to be intermediate between compromised and normal term infants.

Microbial ecology and activities in the rumen: part 1

This review describes the progress which has been made during the last 10 to 15 years in the field of rumen microbiology. It is basically an account of new discoveries in the bacteriology, protozoology, biochemistry, and ecology of the rumen microbial population. As such it covers a wide range of subjects including the isolation and properties of methanogenic bacteria, the role of rumen phycomycete fungi, anaerobic energy conservation, and general metabolic aspects of rumen microorganisms. It also attempts, however, to describe and develop new concepts in rumen microbiology. These consist principally of interactions of the microbemicrobe, microbe-food and microbe-host types, and represent the main areas of recent advance in our understanding of the rumen ecosystem. The development of experimental techniques such as chemostat culture and scanning electron microscopy are shown to have been instrumental in progress in these areas. The paper is concluded with an assessment of our present knowledge of the rumen fermentation, based on the degree of success of experiments with gnotobiotic ruminants inoculated with defined flora and in mathematical modeling of the fermentation. The efficacy of chemical manipulation of the fermentation in ruminant is also discussed in this light.

Urease assay and urease-producing species of anaerobes in the bovine rumen and human feces

A growth medium and test were developed for rapid detection of urease in fermentative anaerobic bacteria. Using nonselective rumen fluid roll-tube agar medium and the new test, it was confirmed that Peptostreptococcus productus is often the most numerous urease-forming species in human feces. Also, some fecal strains of Ruminococcus albus, Clostridium innocuum, and Clostridium beijerinckii produced urease. Single strains of Fusobacterium prausnitzii, Coprococcus catus, and Streptococcus mitis that were strongly ureolytic on isolation later lost this ability. Urease activity was also detected in many strains of nonselectively isolated rumen species. They include Succinivibrio dextrinosolvens, Treponema sp., Ruminococcus bromii (not previously known to be present in the rumen), Butyrivibrio sp., Bifidobacterium sp., Bacteroides ruminicola, and P. productus. Most P. productus strains contain urease; however, the uniformity of this feature in the other species noted above is not known. The urease in many of these species was not detected if the growth medium contained 0.2% or more (each) yeast extract and Trypticase.

Isolation of ureolytic Peptostreptococcus productus from feces using defined medium; failure of common urease tests

Colony counts of fecal samples from three persons, obtained by using a chemically defined anaerobic roll-tube medium (containing glucose, maltose, glycerol, minerals, hemin, B-vitamins, methionine, volatile fatty acids, sulfide, bicarbonate, agar, carbon dioxide (gas phase), and 1 mM NH(4) (+) as main nitrogen source), averaged 60% of the 8.8 x 10(10) bacteria per g obtained when 0.2% Trypticase and 0.05% yeast extract were added to the otherwise identical medium. When 0.2% vitamin-free Casitone replaced Trypticase and yeast extract, counts were 94% those of the more complex medium. When urea-nitrogen was added to the defined medium as the main nitrogen source in place of NH(4) (+), counts of relatively large colonies averaged 1.0 x 10(9) per g of feces from five persons-1.1% of counts on the medium containing Trypticase and yeast extract. All of the organisms from the large colonies in the urea roll tubes were morphologically similar, and all six representative strains isolated were identified as urease-forming Peptostreptococcus productus, a species not previously known to produce urease. Ureolytic strains of Selenomonas ruminantium and P. productus were negative for urease activity in three assay media when inocula were from media containing complex nitrogen sources. The study documents that P. productus is the most numerous ureolytic species so far found in human feces and suggests that NH(4) (+) and more complex organic nitrogen sources strongly repress its production of urease. The study also indicates the efficacy of chemically defined media for direct selective isolation of nutritional groups of bacteria from feces.