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PubMed2026

Maternal contact and age-dependent succession influence the assembly of the calf rumen microbiome and virome.

Early-life colonization of the rumen is particularly important; however, the processes by which microbial and viral communities are transmitted and developed remain poorly understood. Here, we present a genome-resolved investigation of the effects of maternal contact and age-dependent succession on the calf rumen microbiome and DNA virome by comparing calves raised with or without maternal contact across early life using the metagenome-assembled genomes (MAGs) and viral operational taxonomic units (vOTUs) reconstructed from whole- and virus-like particle metagenomes. Across longitudinal samples from calves and their mothers, we identified 694 MAGs and 30,479 vOTUs, substantially expanding current genome databases and revealing extensive microbial and viral novelty. Our analyses demonstrated that both prokaryotes and DNA viruses are shared between dams and calves, with greater sharing observed in calves raised with maternal contact than in calves raised without maternal contact. Notably, viral sharing between cow-calf pairs was markedly lower compared to prokaryotes, suggesting high turnover and rapid viral diversification. Age-associated analyses further revealed coordinated shifts in prokaryotes and their viruses, with dominant genera such as Prevotella, Ruminococcus, and Fibrobacter, and their corresponding viruses increasing after day 40. These findings indicate that the early-life rumen microbiome and DNA virome undergo substantial age-dependent succession and are associated with maternal contact, providing new insights into host-microbe-virus interactions during rumen development.IMPORTANCEThis study provides one of the first genome-resolved views of DNA viral community development during early rumen colonization in calves (from 1 week to 70 days of age) and reveals how maternal contact and age influence the establishment of the calf rumen microbiome and virome. By analyzing longitudinal samples from calves raised with or without their mothers, we show that prokaryotes and their viruses undergo coordinated, age-dependent succession. Our results demonstrate that maternal separation alters the assembly of the calf rumen microbiome, highlighting the influence of maternal contact during early-life rumen development. These findings underscore the high plasticity of the early-life rumen ecosystem and suggest that early management practices, such as maternal separation, can have lasting effects on rumen development. This work provides fundamental insights into the establishment and succession of the calf rumen microbiome and DNA virome during early life and may contribute to future microbiome manipulation studies.

Animals↗

PubMed1975

Changes in the rumen metabolism of sheep given increasing amounts of linseed oil in their diet.

1. Linseed oil was incorporated gradually into the diet of four sheep until the animals received 90 g additional fat/d. Attempts were made to measure changes in concentration of substances and rates of synthesis in the rumen directly, and by incubation of rumen contents in vitro (zero-time technique). 2. The high-fat diet increased the dilution rate and the volume of rumen contents and decreased the synthesis of diaminopimelic acid in the rumen. The number of protozoa decreased and the number of bacteria increased in the rumen of animals receiving the high-fat diet. 3. The concentration of volatile fatty acids (VFA) in the rumen decreased for sheep given the high-fat diet, but the capacity of rumen contents to produce VFA in vitro increased. 4. The incorporation of radioactivity from [14C]acetate into lipids during incubation of rumen contents vitro increased with the amount of linseed oil in the diet. The greatest proportional increase was with the bacterial fraction of rumen contents. 5. In the group of four animals used, one animal showed consistent differences in the magnitude of the measured varibles. This animal appeared to have a smaller rumen, a lower dilution rate and larger concentrations of some substances in the rumen. A higher proportion of fatty acids appeared to be synthsized by the micro-organisms from this animal.

Animal Nutritional Physiological Phenomena↗

PubMed2026

Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities.

BACKGROUND: The rumen functions as an anaerobic fermentation chamber, housing microorganisms with cellulolytic and proteolytic capabilities that facilitate feed utilization. Fiber-degrading bacteria possess the capability to enhance the productivity of cellulolytic feed. The application of omics technologies has greatly improved our understanding of the rumen microbiome. Determining microbial composition and functional patterns in the rumen does not equate to a comprehensive exploration of rumen microbial resources and their mechanisms of action. This study seeks to integrate high throughput 16S rRNA data with information on culturomics, cellulolytic activities, nutrition, and synthetic microbial communities (SynCom) engineering. The objective is to evaluate the relationship between rumen microbial activity and fiber utilization efficiency in cattle, ultimately aiming to develop a more powerful intervention strategy for the ruminant industry. RESULTS: The enrichment culture with various carbon sources led to significant alterations in the composition and structure of rumen microbiota, particularly enhancing those associated with carbohydrate metabolism. Employing the culturomics methodology, 896 strains from 78 species (including 8 novel species) were isolated, resulting in a 10.1% isolation rate relative to the rumen bacterial community. Among them, 35 strains demonstrated boosted cellulose-degrading capability on plates, while 25 exhibited the ability to degrade hemicellulose as well. SynComs of these candidates were prepared based on the ratio observed in rumen microbiota exhibiting high cellulolytic performance. SynCom 3 improved the neutral detergent fiber degradation (NDFD) by 20.39% averagely. Additionally, both in vitro and in situ assessments indicated that the optimization of dose/strain in SynCom 3 significantly improved the in vitro NDFD by 20.56% and increased the in situ NDFD by 7.81%, along with the acidic detergent fiber (ADF, + 11.47%). Genomic analysis revealed that the SynCom 3 functioned well in fiber degradation through the synergistic action of key carbohydrate-active enzymes. CONCLUSIONS: This study strengthens rumen microbiome research by integrating omics and SynCom engineering within a microbiota-bacteria-enzymes-genes framework, revealing the significance of enzymatic synergy in carbohydrate metabolism. The findings establish a framework for utilizing low-abundance microbes and engineering functional consortia, which are crucial for improving ruminant feed utilization and biomass conversion. Future research should investigate the transcriptomic profiles and the metabolic cross-feeding mechanisms of fiber-degrading strains in the rumen. Video Abstract.

Animals↗

PubMed2026

Rumen DNA virome plasticity and viral metabolic potential are associated with seasonal adaptation in grazing yak and cattle on the Qinghai-Tibet Plateau.

BACKGROUND: As a diverse and abundant component of the rumen ecosystem, viruses interact with other microorganisms and are thought to influence microbial metabolism and host productivity. However, how the rumen virome responds to seasonal fluctuations in extreme environments remains poorly understood. Here, metagenomic analyses were used to investigate temporal dynamics of viral diversity, functional potential, and virus-host associations in the rumen virome of yak and cattle on the Qinghai-Tibet Plateau across warm and cold seasons. RESULTS: Rumen viral communities exhibited pronounced seasonal variation in both yaks and cattle, with higher alpha diversity observed during the cold season than in the warm season. Across seasons, the yak rumen virome showed greater alpha diversity and community stability than that of cattle. In total, 27,353 temperate and 31,976 virulent viral operational taxonomic units (vOTUs) were identified, predominantly belonging to the class Caudoviricetes. These viruses were linked to microbial hosts spanning 24 bacterial and 8 archaeal phyla, with Bacteroidota and Bacillota representing the dominant lineages. Virus-host associations were more numerous in the cold season and showed distinct host-specific patterns between yaks and cattle. Cold-season virome exhibited reduced diversity of anti-defense genes and enrichment of auxiliary metabolic genes (AMGs) associated with fatty acid metabolism and hemicellulose degradation. Notably, greater divergence between yaks and cattle was observed during the cold season: the yak rumen virome was enriched in pathways related to amino acid, lipid, and energy metabolism, as well as cellulose-degrading CAZyme families, whereas the cattle rumen virome showed enrichment in general carbohydrate metabolism and replication and repair processes. CONCLUSION: Seasonal plasticity of rumen DNA virome and pronounced interspecific divergence between yaks and cattle provide insight into their distinct microbial processes in the harsh environment of the Qinghai-Tibet Plateau. These findings suggest that the rumen DNA virome exhibits complex ecological and functional responses to seasonal variation and may be associated with host-microbiome interactions and nutrient utilization under environmental stress. This study highlights the ecological relevance of rumen viral genomes in understanding virus-microbiome interactions, microbial adaptation, and nutrient utilization in high-altitude ruminants.

Auxiliary metabolic genes↗

PubMed1975

Rumen bypass and protection of proteins and amino acids.

Potent rumen microbial proteases and deaminases rapidly degrade protein and amino acids which are soluble in the rumen liquid phase. Because protein sources vary in their solubility, the degree of degradation in the rumen is variable. Methods of decreasing protein and amino acid degradation in the rumen include heat treatment, chemical treatment, encapsulation, use of amino acid analogs, selective manipulation of balances of rumen metabolic pathways, and esophageal groove closure. It is important that procedures do not interfere with ruminal metabolism or post-ruminal digestion. Bypassing the rumen changes sites in the digestive tract of nutrient digestion and absorption and provides a mechanism for supplementing outflow of nutrients from the rumen. A feasible approach to production of animal protein from ruminants would be utilization of nonprotein nitrogen for rumen protein production, maximization of rumen bypass of dietary protein, and supplementation with rumen nondegradable amino acids.

Amino Acids↗

PubMed1976

Effect of sampling location, time, and method of concentration of ammonia nitrogen in rumen fluid.

In experiment 1, rumen fluid samples were obtained from dorsal, midpoint, and ventral regions of the rumen of rumenfistulated dairy cows at hourly intervals for 24 h. Dorsal, midpoint, and ventral rumen fluid samples contained 16.1, 14.2, and 12.1 mg/100 ml of ammonia nitrogen. Time after feeding resulted in differences in the concentration of ammonia in rumen fluid with the greatest concentration 30 to 90 min postfeeding. The concentration of ammonia nitrogen was greater for cows fed a high-concentrate diet (14.7% crude protein, 86% concentrate) than for cows receiving a normal diet (15.1% crude protein, 42% concentrate), 15.2 versus 13.1 mg/100 ml. In a second experiment, rumen fluid samples were obtained immediately before feeding and at 1 and 6 h postfeeding by stomach tube and from dorsal, midpoint, ventral, and mixed rumen contents via a rumen cannula. Concentrations of ammonia nitrogen (mg/100 ml) in the respective rumen fluid samples were 14.3, 23.0, 18.3, 17.2, and 19.6. Location of sampling, method of sampling, time of sampling, type of diet, and rumen fluid volume are factors that affect the concentration of ammonia nitrogen in rumen fluid.

Ammonia↗

PubMed2026

Genome-resolved multi-omics provide new insights into microbial nitrogen utilization by the rumen microbiota.

BACKGROUND: Optimizing nitrogen (N) utilization in ruminant production systems holds both economic and environmental significance. However, traditional paradigms of N metabolism, derived primarily from well-studied model rumen bacteria, do not fully reflect the diverse and complex N metabolism in the rumen ecosystem. RESULTS: To address this gap, we utilized comparative genomics and genome-resolved multi-omics analyses using a curated set of microbial genomes to investigate N assimilation and regulation in rumen microbes. We discovered that well-established mechanisms of ammonia assimilation and regulation, such as the glutamine synthetase (GS)/glutamate synthase (GOGAT) pathways and their regulatory proteins, are absent in many of the predominant rumen microbes, which likely utilize alternative pathways for ammonia assimilation. These findings challenge the applicability of E. coli-based N regulation models to rumen bacteria in response to ammonia availability. We further linked polysaccharide utilization and ammonia assimilation across hundreds of rumen microbial species. Furthermore, we identified specific microbial species involved in ureolysis and denitrification, as well as phages carrying auxiliary metabolic genes involved in N assimilation. Using an animal trial involving 11 pairs of lamb twins in a crossover design, we demonstrated that dietary crude protein (CP) at 10% and 13% had minimal impact on rumen microbiome composition and expression of N assimilation genes. Instead, changes in concentrate levels altered N assimilation, notably increasing expression of amino acid biosynthesis pathways. CONCLUSION: These findings indicate a nuanced, species-specific microbial response to dietary interventions, highlighting the limitations of traditional N metabolism models applied to rumen microbes and the need for more granular studies of rumen microbial ecosystems.

Multiomics↗

PubMed1977

[The passage of nitrogenous compounds through the wall of perfused sheep rumen (author's transl)].

Experiments were performed by the method of the extracorporeal perfusion of sheep rumen lasting 150 minutes. After 60 minutes of perfusion, 20 g of enzymatic casein hydrolyzate were applied to the rumen. Ammonia, urea, and total nitrogen were determined in the samples of perfusate, and ammonia and pH were determined in the rumen content. Considerable amounts of ammonia accumulated in the perfusate in the course of the experiment. At the end of perfusion, the concentration of NH3-N reached an average value of up to 12 mg per 100 ml. The level of urea in the perfusate decreased only in the first phase of perfusion (before the application of casein hydrolyzate to the rumen) and remained unchanged in the subsequent phase. It is assumed that part of urea-N from the perfusate after urea hydrolysis, taking place already in the rumen wall, returned to the perfusate in the form of ammonia. In the first phase of perfusion the passage of nitrogen from the blood into the rumen took place, in the second phase its absorption from the rumen into the blood was observed. The urea-N ratio from the passage of total nitrogen into the rumen ranged between 4.63% and 13.84%, but the concentration of total nitrogen in the perfusate decreased by 7-15% and that of urea nitrogen by 37-42%. It follows from the results that a major part of endogenous nitrogen passing from perfusate to the rumen was represented by proteins and/or their peptidic splits.

Ammonia↗

PubMed2025

The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media.

Ruminants play an important part in global food security, but also emit methane, which contributes to global warming. Rumen microbes strongly influence the energy retention efficiency from the host's plant-based diet and produce methane as a by-product. While thousands of novel microbial genomes have been assembled from metagenomic sequence data, their culturability is ill-defined. Here, different media (Med10, Med2, and MedTC) were used to isolate co-cultures of microbes from rumen fluid. Thirty-four OTUs were identified belonging to the phyla Bacillota (75.28 ± 6.34%), Bacteroidota (19.99 ± 4.85%), Pseudomonadota (2.46 ± 2.01%), and Actinomycetota (2.09 ± 1.07%). The most abundant genera were Selenomonas (28.08 ± 11.71%), Streptococcus (22.67 ± 6.06%), Prevotella (18.71 ± 4.02%), and unclassified Lachnospiraceae (11.50 ± 2.54%), and 31 significantly enriched on at least one medium, with each medium successfully culturing a distinct range of microbes. The composition of the source rumen fluid was vastly different from those cultured. Bacteroidota (52.53 ± 5.10%) predominated, with Bacillota (41.00 ± 3.96%), Methanobacteriota (5.12 ± 1.94%), Pseudomonadota (1.22 ± 0.78%), and Actinomycetota (0.12 ± 0.08%) comprising the rest. The most abundant genera were Prevotella (29.13 ± 4.16%), Butyrivibrio (18.21 ± 2.08%), Succiniclasticum (15.57 ± 5.03%), unclassified Bacteroidetes (13.91 ± 1.67%), and unclassified Prevotellaceae (9.50 ± 2.01%). These data further emphasize the importance of using defined media to select for different microbial taxa. This is essential to understand the complex workings of the rumen microbes to enhance digestion efficiency and reduce the loss of energy that could potentially be utilized by the host.IMPORTANCEThis research demonstrates that using a range of culture media, containing a wide variety of substrates, can lead to the culture of key rumen microbes. The knowledge of which of these microbes is selectively enriched on each medium is essential to understand how to grow these microbes in co-culture and isolate them in pure culture for further investigation. In addition, this research shows the stark disparity between the population of rumen microbes grown in co-culture and those found in the rumen itself. This further demonstrates the need for a targeted approach to growing and isolating these microbes. Learning how these microbes respond to culture media with different nutritional compositions will lead to a better understanding of the rumen microbiota, and this research provides a valuable insight into how selective media can target the enrichment of different microbes. This knowledge will contribute to increasing ruminant digestion efficiency and reducing methane production.

Rumen↗

PubMed1976

Urease activity in the rumen of sheep and the isolation of ureolytic bacteria.

Urease activity in the sheep rumen varied with the diet of the sheep, but appeared to be largely or entirely present in the small bacterial fraction. Screening of over 1000 strains of rumen bacteria isolated on different media showed that urease activity was apparently confined to species of Staphylococcus, Lactobacillus casei var. casei and Klebsiella aerogenes. Consideration of the numbers in which these occurred and their activities suggested that the bacteria could not be responsible for the total rumen urease activity. By enrichment culture a ureolytic strain of Streptococcus faecium was isolated. This had a higher urease activity than the other bacteria and occurred in higher numbers in the rumen. It could live with other bacteria in the rumen of a gnotobiotic lamb in numbers, and with a urease activity, comparable with those in the normal sheep rumen. The other properties of the bacterium also suggested that it would grow and produce urease in the rumen, but was unlikely to retain its urease activity after isolation. It was concluded that this bacterium was the main source of rumen urease in roughage-fed, and probably other, sheep.

Acetates↗

PubMed1975

Effect of 1,2-propanediol on the rumen mucosal growth of kids.

Intra-abomasally administered 1,2-propanediol, 150 to 160 g per Japanese meat-type kid in 3 to 4 wk, increased the ratio of rumen to body weight, of rumen to total stomach, and of rumen mucosa to muscle over the control which received only water. Intra-abomasal administration of glycerol, glucose, fructose, 1.3-butanediol, xylitol, lactic acid, sodium propionate, or sodium butyrate showed no increases over the control. Only propanediol chemically stimulated rumen mucosal growth. Intraruminal administration of propanediol showed the same stimulation as intra-abomasal. Intraruminal administration of minerals or of polyethylene glycol (Carbowax 4,000) and intraruminal insertion of plastic cubes were not effective, but the latter showed a cooperative effect to accelerate rumen growth with propanediol stimulation. Average fresh tissue weights of rumen mucosa in kids of 2.7 kg body weight of control, of propanediol-treatment, and of plastic cube plus propanediol-treatment were 6.4, 10.4, and 14.8 g, and those of rumen muscle were 7.9, 8.3, and 11.1 g. Propanediol may be involved directly in the local control of rumen epithelial growth.

Abomasum↗

PubMed1978

Effect of succulent and nonsucculent diets on rumen motility and pressure before, during, and after eating.

Rumen motility was measured in cattle by recording changes in rumen pressure through a rumen cannula. Irrespective of diet, eating increased rumen motility and amplitude of primary rumen contractions. Succulent, readily fermentable, and nonscabrous alfalfa tops fed alone or with oat hay produced a greater frequency of primary and secondary rumen contractions than oat hay fed alone. The intrarumen pressure was also greater when alfalfa tops were fed. Oat hay in the diet caused primary rumen contractions of a greater amplitude than when alfalfa tops were fed alone. Correlations were positive between frequency of primary and secondary rumen contractions and intrarumen pressure.

Animal Feed↗

PubMed1977

[Significance of ruminal juice examination in the diagnosis of subclinical rumen dysfunction].

The suitability of the metabolic test of rumen liquor for the diagnosis of subclinical rumen dysfunction was tested. The test for the assessment of the metabolic profile of the rumen included: the determination of pH, total titration acidity in clinical units, lactic acid in mg%, fatty acids in mmol 1-1, ammonia N in mg%, urea N in mg% and the number of infusorians in 1 ml of rumen liquor. This test enabled, on the basis of the examination of rumen liquor, to determine not only the kind and form of the disease but also its cause, with an incomplete clinical syndrome. Therapeutic measures, either direct (in the rumen liquor) or indirect (adjusted monodiet) improved the health condition and provided optimum rumen fermentation of permanent character. The resuption of rumen fermentation also enabled an increased production of fatty acids which favourably influenced the content of butterfat in milk.

Animals↗

PubMed1978

Transfer of urea from the blood to the rumen of sheep.

1. The rate of transfer of plasma urea-nitrogen to rumen ammonia was measured by infusion of 15NH4Cl and [15N]urea into sheep given brome grass (Bromus inermis) or lucerne (Medicago sativa) pellets. Urea was infused into the rumen or abomasum of two sheep given brome grass in order to increase the concentration of rumen ammonia. 2. From 6.2 to 9.8 g/d of plasma urea-N were transferred to the rumen of sheep given brome grass pellets and a measurement of 1.3 g nitrogen/d was obtained for a sheep given lucerne pellets. When urea was infused into the rumen of sheep given brome grass pellets the transfer was only 2.8--3.7 g N/d. 3. There was a significant negative correlation between the rate of transfer of plasma urea-N to the rumen and the concentration of rumen ammonia.

Ammonia↗

PubMed1979

[Motility of the rumen after feeding sheep pelleted rations].

In an experiment with wethers the effect of the feeding with pelleted feed rations and the partial replacement of coarse fodder by non-treated beech sawdust on the motorial activity of the rumen was observed. The rumen motility was measured through a rumen fistula by means of the balloon method with the help of a capacitator primary unit, an electric manometer and a recording instrument. Over a period of 24 weeks the animals consumed 1.3 kg dry matter per day. It consisted of 41.8% meadow hay, 25.3% barley, 15.4% sawdust, 15.0% molasses, 1.3% urea, 0.76% mixed minerals and 0.48% hexametaphosphate in the form of pellets (test group) or the traditional classical form (control group). The feeding of pellets diminished the frequency (P less than 0.001) and the intensity of rumen contractions before and 1, 3 and 5 hours after feeding. Maximal frequency values were registered one hour after the food intake. During this time the number of secondary contractions of the rumen increased; differences of the frequency were, however, not registered, which means that the different physical form of the diet had no influence on the motorial activity of the rumen and that the food intake as such is the decisive factor. The diminished rumen motility in further hours after feeding was effected by treating the feed (grinding and pelleting).

Animal Feed↗

PubMed1975

Ureolytic bacteria in sheep rumen.

Estimates were made of the numbers of viable bacteria in the rumens of sheep receiving different rations. Representative colonies were isolated and tested for urease production. Some urease-positive isolates were characterized and identified. The ureolytic activities of the urease-producing isolates were determined and compared with the activity of rumen fluid. The rations fed to the sheep did not exert a significant influence on the relative numbers of the urease-producting organisms in the rumen. No obligately anaerobic ureolytic bacteria were found. All urease-positive isolates were facultatively anaerobic, Gram-positive, catalase-positive cocci. Out of ten isolates, nine were identified as Staphylococcus saprophyticus and one as Micrococcus varians. The total urease activity of the different isolates based on the lowest numbers in which they were present in the rumen, compared favourably with the urease activity of rumen fluid. The facultatively anaerobic Gram-positive cocci were probably responsible for a large proportion of the urease activity of the rumen fluid. Conditions prevailing in the rumen were found to be conducive to urease production by the isolates tested.

Anaerobiosis↗

PubMed1976

Variation in colony counts of total viable anaerobic rumen bacteria as influenced by media and cultural methods.

Volume and type of medium, carbohydrate concentration, carbohydrate ratios, and inoculum level were investigated as possible factors influencing total colony counts of anaerobic rumen bacteria obtained in roll tubes (18 by 150 mm). Colony counts were lower when the rumen fluid was clarified by centrifugation before inclusion in the medium; however, decreasing the volume of 40% rumen fluid glucose-cellobiose-starch-agar medium (RGCSA medium with 0.025% each of glucose and cellobiose and 0.05% starch, 4 ml per tube) was compared to the clarified rumen fluid medium and non-rumen fluid medium (medium 10) of Caldwell and Bryant (1966), 9 ml of each per tube. Total counts of rumen contents from sheep consuming four different types of rations were higher with the 4 ml of RGCSA medium than with the other two media. Dilution of the basal medium as a result of inoculum volume, as much as 1.5 ml per 4 ml of medium, did not appear to affect total counts. Colony counts and the simplicity of medium preparation and inoculation would favor the present method for routine use in estimating numbers of total viable anaerobic rumen bacteria, especially when large numbers of samples are involved.

Agar↗

PubMed1979

Enumeration and selective isolation of rumen spirochetes.

Enumeration by means of light microscopy showed that from 0.4 x 10(8) to 2.0 x 10(8) spirochetes were present per ml of bovine rumen fluid. Viable cell counts yielded slightly lower values, ranging from 0.1 x 10(8) to 1.2 x 10(8) spirochetes per ml of rumen fluid. The antibiotic rifampin, which served as a selective agent for rumen spirochetes, was added to agar media used in the estimation of viable spirochete numbers in rumen fluid. Morphologically diverse spirochetes were isolated from rumen fluid by means of a procedure involving the use of rifampin as a selective agent in agar media. The strains isolated represented seven morphological types of spirochetes differing in cell size, cell coiling pattern, and number of periplasmic fibrils per cell. Electron microscopy showed that the number of periplasmic fibrils present in the different morphological types of rumen spirochetes ranged from 2 to more than 20 per cell. The results of this study indicate that the bovine rumen is a highly favorable environment for a number of morphologically diverse spirochetes.

Agar↗