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Feedlot cattle may be subjected to digestive disorders, including ruminal acidosis, due to high concentration of grain in their diet. Therefore, novel feeding strategies are required to maximize animal performance and mitigate economic losses in the operation. This study employed a two-period crossover design to assess the effect of direct ruminal administration of native rumen microorganisms (NRM) inoculation on cattle that underwent a high-grain challenge. The NRM inoculation consisted of six microorganisms (1.70 M CFU /day/animal) isolated from the rumen of healthy feedlot cattle: Succinivibrio dextrinosolvens ASCUSBF53, Prevotella albensis ASCUSBF41, Chordicoccus furentiruminis ASCUSBF65, Bacteroides xylanisolvens ASCUSBF52, Clostridium beijerinckii ASCUSBF26, and Syntrophococcus sp. ASCUSBF60. The trial consisted of 16 Angus heifers receiving NRM ( n  = 8) or a CON (CON = Carrier Buffer; n  = 8) inoculation daily for 14-days as pre-challenge while on a high-grain diet and continued daily for a 21-day treatment period. The combined 35 days of microbial supplementation resulted in an improved average daily gain (ADG) of 29% ( P  = 0.037) and a tendency toward a 19% decrease in the feed efficiency metric, gain to feed ratio (G: F) ( P  = 0.055). Additionally, administration of NRM to animals on a high-grain diet, improved ruminal microbiome stability ( P  < 0.001), potentially encouraging the conversion of rumen lactate to propionate over time via the succinate pathway and alleviating metabolic stress.

Recently, returning straw to the fields has been proved as a direct and effective method to tackle soil nutrient loss and agricultural pollution. Meanwhile, the slow decomposition of straw may harm the growth of the next crop. This study aimed to determine the effects of rumen microorganisms (RMs) on straw decomposition, bacterial microbial community structure, soil properties, and soil enzyme activity. The results showed that RMs significantly enhanced the degradation rate of straw in the soil, reaching 39.52%, which was 41.37% higher than that of the control on the 30th day after straw return. After 30 d, straw degradation showed a significant slower trend in both the control and the experimental groups. According to the soil physicochemical parameters, the application of rumen fluid expedited soil matter transformation and nutrient buildup, and increased the urease, sucrase, and cellulase activity by 10%–20%. The qualitative analysis of straw showed that the hydroxyl functional group structure of cellulose in straw was greatly damaged after the application of rumen fluid. The analysis of soil microbial community structure revealed that the addition of rumen fluid led to the proliferation of Actinobacteria with strong cellulose degradation ability, which was the main reason for the accelerated straw decomposition. Our study highlights that returning rice straw to the fields with rumen fluid inoculation can be used as an effective measure to enhance the biological value of recycled rice straw, proposing a viable solution to the problem of sluggish straw decomposition.

Nitrate is used as a methane inhibitor while cysteamine is considered as a growth promoter in ruminants. The present study evaluated the effect of sodium nitrate and cysteamine on methane (CH4) production, rumen fermentation, amino acid (AA) metabolism, and rumen microbiota in a low protein diet. Four treatments containing a 0.5 g of substrate were supplemented with 1 mg/mL sodium nitrate (SN), 100 ppm cysteamine hydrochloride (CS), and a combination of SN 1 mg/mL and CS 100 ppm (CS+SN), and a control (no additive) were applied in a completely randomized design. Each treatment group had five replicates. Two experimental runs using in vitro batch culture technique were performed for two consecutive weeks. Total gas and CH4 production were measured in each fermentation bottle at 3, 6, 9, 12, 24, 48, and 72 h of incubation. The results showed that SN and CS+SN reduced the production of total gas and CH4, increased the rumen pH, acetate, acetate to propionate ratio (A/P), and microbial protein (MCP) contents (p < 0.05), but decreased other volatile fatty acids (VFA) and total VFA (p = 0.001). The CS had no effect on CH4 production and rumen fermentation parameters except for increasing A/P. The CSN increased the populations of total bacteria, fungi, and methanogens but decreased the diversity and richness of rumen microorganisms. In conclusion, CS+SN exhibited a positive effect on rumen fermentation by increasing the number of fiber degrading and hydrogen-utilizing bacteria, with a desirable impact on rumen fermentation while reducing total gas and CH4 production.

The aim of this experiment was to investigate the effects of intravenous infusion of lipopolysaccharide (LPS) and feeding different ratios of lysine (Lys) and methionine (Met) on feed intake, apparent digestibility, rumen fermentation and microorganisms in young Holstein bulls. Five seven-month-old Holstein bulls with similar body weights (279 ± 42 kg) were selected and subjected to a 5 × 5 Latin square experiment. The control group (CON) was fed with basal diet and the ratio of Lys to Met in the diet was adjusted to 3.0: 1. The experimental groups were received LPS infusion while being fed the basal diet (TRT1), along with LPS infusion and the addition of rumen-protected lysine (RPL) and rumen-protected methionine (RPM) to make the ratio of Lys to Met to 2.5:1 (TRT2), 3.0:1 (TRT3) and 3.5: 1 (TRT4), respectively. The LPS jugular infusion dose was set at 0.01 μg/kg body weight on days 1–3 and 0.05 μg/kg body weight on days 4–7. The trial was conducted over five periods, consisting of a 7-day trial period and a 6-day interval. The results indicated that there were no significant effects of LPS infusion on feed intake and apparent digestibility in young Holstein bulls fed different ratios of Lys and Met ( p  > 0.05). The treatment had no significant effects on the pH and total volatile fatty acids ( p  > 0.05). Compared with CON, the acetate content in the experimental groups exhibited an increasing trend ( p  = 0.066), while the content of NH 3 -N decreased significantly ( p  < 0.05). LPS infusion had no significant effect on rumen microorganisms at either the species or phylum level ( p  > 0.05). However, feeding different ratios of Lys and Met could significantly increasing the abundance of Oribacterium ( p  < 0.05) and tended to increase the abundance of norank_f__norank_o__RF_39 at the genus level ( p  = 0.087). These findings suggest that adding RPL and RPM into the diet may enhance the rumen environment in young Holstein bulls. Under the conditions of this experiment, adding RPL and RPM can mitigate the negative effects associated with LPS infusion, with an optimal ratio of Lys and Met is 3.0:1.

Ruminants have the remarkable ability to convert human-indigestible plant biomass into human-digestible food products, due to a complex microbiome residing in the rumen compartment of their upper digestive tract. Here we report the discovery that rumen microbiome components are tightly linked to cows' ability to extract energy from their feed, termed feed efficiency. Feed efficiency was measured in 146 milking cows and analyses of the taxonomic composition, gene content, microbial activity and metabolomic composition was performed on the rumen microbiomes from the 78 most extreme animals. Lower richness of microbiome gene content and taxa was tightly linked to higher feed efficiency. Microbiome genes and species accurately predicted the animals' feed efficiency phenotype. Specific enrichment of microbes and metabolic pathways in each of these microbiome groups resulted in better energy and carbon channeling to the animal, while lowering methane emissions to the atmosphere. This ecological and mechanistic understanding of the rumen microbiome could lead to an increase in available food resources and environmentally friendly livestock agriculture.

Farmed ruminants are the largest source of anthropogenic methane emissions globally. The methanogenic archaea responsible for these emissions use molecular hydrogen (H 2 ), produced during bacterial and eukaryotic carbohydrate fermentation, as their primary energy source. In this work, we used comparative genomic, metatranscriptomic and co-culture-based approaches to gain a system-wide understanding of the organisms and pathways responsible for ruminal H 2 metabolism. Two-thirds of sequenced rumen bacterial and archaeal genomes encode enzymes that catalyse H 2 production or consumption, including 26 distinct hydrogenase subgroups. Metatranscriptomic analysis confirmed that these hydrogenases are differentially expressed in sheep rumen. Electron-bifurcating [FeFe]-hydrogenases from carbohydrate-fermenting Clostridia (e.g., Ruminococcus ) accounted for half of all hydrogenase transcripts. Various H 2 uptake pathways were also expressed, including methanogenesis ( Methanobrevibacter ), fumarate and nitrite reduction ( Selenomonas ), and acetogenesis ( Blautia ). Whereas methanogenesis-related transcripts predominated in high methane yield sheep, alternative uptake pathways were significantly upregulated in low methane yield sheep. Complementing these findings, we observed significant differential expression and activity of the hydrogenases of the hydrogenogenic cellulose fermenter Ruminococcus albus and the hydrogenotrophic fumarate reducer Wolinella succinogenes in co-culture compared with pure culture. We conclude that H 2 metabolism is a more complex and widespread trait among rumen microorganisms than previously recognised. There is evidence that alternative hydrogenotrophs, including acetogenic and respiratory bacteria, can prosper in the rumen and effectively compete with methanogens for H 2 . These findings may help to inform ongoing strategies to mitigate methane emissions by increasing flux through alternative H 2 uptake pathways, including through animal selection, dietary supplementation and methanogenesis inhibitors.

Ruminants are important for global food security but emit the greenhouse gas methane. Rumen microorganisms break down complex carbohydrates to produce volatile fatty acids and molecular hydrogen. This hydrogen is mainly converted into methane by archaea, but can also be used by hydrogenotrophic acetogenic and respiratory bacteria to produce useful metabolites. A better mechanistic understanding is needed on how dietary carbohydrates influence hydrogen metabolism and methanogenesis. We profiled the composition, metabolic pathways, and activities of rumen microbiota in 24 beef cattle adapted to either fiber-rich or starch-rich diets. The fiber-rich diet selected for fibrolytic bacteria and methanogens resulting in increased fiber utilization, while the starch-rich diet selected for amylolytic bacteria and lactate utilizers, allowing the maintenance of a healthy rumen and decreasing methane production ( p  < 0.05). Furthermore, the fiber-rich diet enriched for hydrogenotrophic methanogens and acetogens leading to increased electron-bifurcating [FeFe]-hydrogenases, methanogenic [NiFe]- and [Fe]-hydrogenases and acetyl-CoA synthase, with lower dissolved hydrogen (42%, p  < 0.001). In contrast, the starch-rich diet enriched for respiratory hydrogenotrophs with greater hydrogen-producing group B [FeFe]-hydrogenases and respiratory group 1d [NiFe]-hydrogenases. Parallel in vitro experiments showed that the fiber-rich selected microbiome enhanced acetate and butyrate production while decreasing methane production ( p  < 0.05), suggesting that the enriched hydrogenotrophic acetogens converted some hydrogen that would otherwise be used by methanogenesis. These insights into hydrogen metabolism and methanogenesis improve understanding of energy harvesting strategies, healthy rumen maintenance, and methane mitigation in ruminants.

ABSTRACT The bovine gastrointestinal (GI) tract microbiota has important influences on animal health and production. Presently, a large number of studies have used high-throughput sequencing of the archaeal and bacteria 16S rRNA gene to characterize these microbiota under various experimental parameters. By aggregating publically available archaeal and bacterial 16S rRNA gene datasets from 52 studies we were able to determine taxa that are common to nearly all microbiota samples from the bovine GI tract as well as taxa that are strongly linked to either the rumen or feces. The methanogenic genera Methanobrevibacter and Methanosphaera were identified in nearly all fecal and rumen samples (> 99.1%), as were the bacterial genera Prevotella and Ruminococcus (≥ 92.9%). Bacterial genera such as Alistipes, Bacteroides, Clostridium, Faecalibacterium and Escherichia/Shigella were associated with feces and Fibrobacter, Prevotella, Ruminococcus and Succiniclasticum with the rumen. As expected, individual study strongly affected the bacterial community structure, however, fecal and rumen samples did appear separated from each other. This meta-analysis provides the first comparison of high-throughput sequencing 16S rRNA gene datasets generated from the bovine GI tract by multiple studies and may serve as a foundation for improving future microbial community research with cattle. All publicly available cattle gut microbiota datasets were collected and re-analyzed together to identify shared and differentially abundant archaeal and bacterial groups, as well factors influencing the gut microbiota.

Background The rumen microbiome plays an essential role in maintaining ruminants’ growth and performance even under extreme environmental conditions, however, which factors influence rumen microbiome stability when ruminants are reared in such habitats throughout the year is unclear. Hence, the rumen microbiome of yak (less domesticated) and cattle (domesticated) reared on the Qinghai-Tibetan Plateau through the year were assessed to evaluate temporal changes in their composition, function, and stability. Results Rumen fermentation characteristics and pH significantly shifted across seasons in both cattle and yak, but the patterns differed between the two ruminant species. Ruminal enzyme activity varied with season, and production of xylanase and cellulase was greater in yak compared to cattle in both fall and winter. The rumen bacterial community varied with season in both yak and cattle, with higher alpha diversity and similarity (beta diversity) in yak than cattle. The diversity indices of eukaryotic community did not change with season in both ruminant species, but higher similarity was observed in yak. In addition, the similarity of rumen microbiome functional community was higher in yak than cattle across seasons. Moreover, yak rumen microbiome encoded more genes (GH2 and GH3) related to cellulose and hemicellulose degradation compared to cattle, and a new enzyme family (GH160) gene involved in oligosaccharides was uniquely detected in yak rumen. The season affected microbiome attenuation and buffering values (stability), with higher buffering value in yak rumen microbiome than cattle. Positive correlations between antimicrobial resistance gene ( dfrF ) and CAZyme family (GH113) and microbiome stability were identified in yak, but such relationship was negatively correlated in cattle. Conclusions The findings of the potential of cellulose degradation, the relationship between rumen microbial stability and the abundance of functional genes varied differently across seasons and between yak and cattle provide insight into the mechanisms that may underpin their divergent adaptation patterns to the harsh climate of the Qinghai-Tibetan Plateau. These results lay a solid foundation for developing strategies to maintain and improve rumen microbiome stability and dig out the potential candidates for manufacturing lignocellulolytic enzymes in the yak rumen to enhance ruminants’ performance under extreme environmental conditions.

The paucity of enzymes that efficiently deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels. Cow rumen microbes specialize in degradation of cellulosic plant material, but most members of this complex community resist cultivation. To characterize biomass-degrading genes and genomes, we sequenced and analyzed 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen. From these data, we identified 27,755 putative carbohydrate-active genes and expressed 90 candidate proteins, of which 57% were enzymatically active against cellulosic substrates. We also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome sequencing. These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass.