Integrating 16S rRNA Sequencing and LC⁻MS-Based Metabolomics to Evaluate the Effects of Live Yeast on Rumen Function in Beef Cattle

Pediococcus pentosaceus ZZ61 enhances growth performance and pathogenic resistance of silkworm Bombyx mori by regulating gut microbiota and metabolites

Probiotics have attracted considerable attention in animal husbandry due to their positive effect on animal growth and health. This study aimed to screen candidate probiotic strain promoting the growth and health of silkworm and reveal the potential mechanisms. A novel probiotic Pediococcus pentosaceus strain (ZZ61) substantially promoted body weight gain, feed efficiency, and silk yield. These effects were likely mediated by changes in the intestinal digestive enzyme activity and nutrient provisioning (e.g., B vitamins) of the host, improving nutrient digestion and assimilation. Additionally, P. pentosaceus produced antimicrobial compounds and increased the antioxidant capacity to protect the host against pathogenic infection. Furthermore, P. pentosaceus affected the gut microbiome and altered the levels of gut metabolites (e.g., glycine and glycerophospholipids), which in turn promotes host nutrition and health. This study contributes to an improved understanding of the interactions between probiotic and host and promotes probiotic utilization in sericulture.

Effects of dietary supplementation with alkaline mineral complex on in vitro ruminal fermentation and bacterial composition

Introduction

Dairy industry growth faces challenges in China due to inadequate forage, leading to high-concentrate diets and potential rumen issues. Buffering agents, like sodium bicarbonate, play a crucial role in stabilizing rumen pH. Alkaline Mineral Complex (AMC), a liquid additive with a pH of 14, shows promise in supporting dairy cow health and mitigating heat stress through ionization.

Methods

This experiment was aimed to study the effect of adding AMC to total mixed ration (TMR) on in vitro ruminal fermentation and bacterial composition. AMCat 1, 2, 4, and 8 mL/kg was added to the substrate (0.5 g TMR). Nutrient digestibility was measured after 48 h fermentation, and fermentation parameters and microbial composition were measured after 48 h fermentation.

Results and discussion

The results of the experiment indicated that: The different concentrations of AMC showed a significant impact on time taken for gas production to reach 1/2 of the total gas production (HT) parameters (p < 0.05). Linear pH increase occurs at 6 and 24 h with rising AMC concentration (p < 0.05), showing a quadratic trend at 12 h (p < 0.05). The optimal buffering effect on rumen acid-base balance was observed at a 2 mL/kg concentration of AMC. Microbial diversity analysis indicated that there was no significant change in α-diversity with different AMC concentrations (p > 0.05). The microbial level demonstrated no significant difference in species diversity of rumen fluid bacteria among the various AMC concentration treatment groups compared to the control group, further supporting that the advantage of adding AMC in stabilizing the rumen environment without altering the structure of the rumen microbiota. Besides, the addition of AMC significantly increased the concentrations of acetate, propionate, total fatty acids (TVFA), and NH3-N, suggesting that AMC contributed to enhancing the energy and nitrogen utilization efficiency in ruminants. Based on the above detection indicators, we recommend that the most favorable concentration is 2 mL/kg.

The effect of anaerobic digestate as an organic soil fertilizer on the diversity and structure of the indigenous soil microbial and nematode communities

Anaerobic digestate is a popular soil additive which can promote sustainability and transition toward a circular economy. This study addresses how anaerobic digestate modifies soil health when combined with a common chemical fertilizer. Attention was given to soil microbes and, a neglected but of paramount importance soil taxonomic group, soil nematodes. A mesocosm experiment was set up in order to assess the soil's microbial and nematode community. The results demonstrated that the microbial diversity was not affected by the different fertilization regimes, although species richness increased after digestate and mixed fertilization. The composition and abundance of nematode community did not respond to any treatment. Mixed fertilization notably increased potassium (K) and boron (B) levels, while nitrate (NO3-) levels were uniformly elevated across fertilized soils, despite variations in nitrogen input. Network analysis revealed that chemical fertilization led to a densely interconnected network with mainly mutualistic relationships which could cause ecosystem disruption, while digestate application formed a more complex community based on bacterial interactions. However, the combination of both orchestrated a more balanced and less complex community structure, which is more resilient to random disturbances, but on the downside, it is more likely to collapse under targeted perturbations.

Effects of Caragana korshinskii tannin on fermentation, methane emission, community of methanogens, and metabolome of rumen in sheep

The purpose of this research was to investigate the impact of dietary supplementation of Caragana korshinskii tannin (CKT) on rumen fermentation, methane emission, methanogen community and metabolome in rumen of sheep. A total of 15 crossbred sheep of the Dumont breed with similar body conditions, were divided into three groups (n = 5), which were fed with CKT addition at 0, 2 and 4%/kg DM. The study spanned a total of 74 days, with a 14-day period dedicated to adaptation and a subsequent 60-day period for conducting treatments. The results indicated that the levels of ammonia nitrogen (NH3-N) and acetate were reduced (p < 0.05) in rumen sheep fed with 2 and 4% CKT; The crude protein (CP) digestibility of sheep in 2 and 4% CKT groups was decreased(p < 0.05); while the neutral detergent fiber (NDF) digestibility was increased (p < 0.05) in 4% CKT group. Furthermore, the supplementation of CKT resulted in a decrease (p < 0.05) in daily CH4 emissions from sheep by reducing the richness and diversity of ruminal methanogens community, meanwhile decreasing (p < 0.05) concentrations of tyramine that contribute to methane synthesis and increasing (p < 0.05) concentrations of N-methy-L-glutamic acid that do not contribute to CH4 synthesis. However, CH4 production of DMI, OMI, NDFI and metabolic weight did not differ significantly across the various treatments. To sum up, the addition of 4% CKT appeared to be a viable approach for reducing CH4 emissions from sheep without no negative effects. These findings suggest that CKT hold promise in mitigating methane emissions of ruminant. Further investigation is required to evaluate it effectiveness in practical feeding strategies for livestock.

Polystyrene microplastics induce size-dependent multi-organ damage in mice: Insights into gut microbiota and fecal metabolites

Particle size is one of the most important factors in determining the biological toxicity of microplastics (MPs). In this study, we attempted to examine the systemic toxicity of polystyrene MPs of different sizes (0.5 µm MP1 and 5 µm MP2) in C57BL/6 J mice. After the mice were given oral gavage of MPs for 8 consecutive weeks, histopathology and molecular biology assays, 16 S rRNA sequencing of the gut microbiota, and untargeted metabolomics were performed. The results showed that MPs were distributed in the organs in a size-dependent manner, with smaller particles demonstrating greater biodistribution. Further analysis indicated that exposure to MPs caused multi-organ damage through distinct toxicity pathways. Specifically, exposure to 0.5 µm MP1 led to excessive accumulation and induced more serious inflammation and mechanical damage in the spleen, kidney, heart, lung, and liver. However, 5 µm MP2 led to more severe intestinal barrier dysfunction, as well as gut dysbiosis and metabolic disorder in association with neuroinflammation. These results are helpful in expanding our knowledge of the toxicity of MPs of different sizes in mammalian models.

Effects of feed additives on rumen function and bacterial and archaeal communities during a starch and fructose challenge

The objective of this study was to improve understandings of the rumen microbial ecosystem during ruminal acidosis and responses to feed additives to improve prudent use strategies for ruminal acidosis control. Rumen bacterial and archaeal community composition (BCC) and its associations with rumen fermentation measures were examined in Holstein heifers fed feed additives and challenged with starch and fructose. Heifers (n = 40) were randomly allocated to 5 treatment groups: (1) control (no additives); (2) virginiamycin (VM; 200 mg/d); (3) monensin (MT; 200 mg/d) + tylosin (110 mg/d); (4) monensin (MLY; 220 mg/d) + live yeast (5.0 × 1012 cfu/d); (5) sodium bicarbonate (BUF; 200 g/d) + magnesium oxide (30 g/d). Heifers were fed twice daily a 62% forage:38% concentrate total mixed ration at 1.25% of body weight (BW) dry matter (DM)/d for a 20-d adaptation period with their additive(s). Fructose (0.1% of BW/d) was added to the ration for the last 10 d of adaptation. On d 21 heifers were challenged once with a ration consisting of 1.0% of BW DM wheat and 0.2% of BW fructose plus their additive(s). A rumen sample was collected from each heifer via stomach tube weekly (d 0, 7, 14) and 5 times over a 3.6 h period at 5, 65, 115, 165, and 215 min after consumption of the challenge ration (d 21) and analyzed for pH, and ammonia, d- and l-lactate, volatile fatty acids (VFA), and histamine concentrations and total bacteria and archaea. The 16S rRNA gene spanning the V4 region was PCR amplified and sequenced. Alpha and β diversity and associations of relative abundances of taxa with rumen fermentation measures were evaluated. Rumen BCC shifted among treatment groups in the adaptation period and across the challenge sampling period, indicating the feed additives had different modes of action. The monensin-containing treatment groups, MT and MLY often had similar relative abundances of rumen bacterial phyla and families. The MLY treatment group was characterized in the challenge period by increased relative abundances of the lactate utilizing genera Anaerovibrio and Megasphaera. The MLY treatment group also had increased diversity of ruminal bacteria which may provide resilience to changes in substrates. The control and BUF treatment groups were most similar in BCC. A redundancy analysis showed the MLY treatment group differed from all other treatment groups and concentrations of histamine and valerate in the rumen were associated with the most variation in the microbiota, 5.3% and 4.8%, respectively. It was evident from the taxa common to all treatment groups that cattle have a core microbiota. Functional redundancy of rumen bacteria which was reflected in the greater sensitivity for the rumen BCC than rumen fermentation measures likely provide resilience to changes in substrate. This functional redundancy of microbes in cattle suggests that there is no single optimal ruminal microbial population and no universally superior feed additive(s). In summary, differences in modes of action suggest the potential for more targeted and improved prudent use of feed additives with no single feed additive(s) providing an optimal BCC in all heifers.

Yeast culture repairs rumen epithelial injury by regulating microbial communities and metabolites in sheep

This study delves into the impact of yeast culture (YC) on rumen epithelial development, microbiota, and metabolome, with the aim of investigating YC's mechanism in regulating rumen fermentation. Thirty male lambs of Hu sheep with similar age and body weight were selected and randomly divided into three groups with 10 lambs in each group. Lambs were fed a total mixed ration [TMR; rough: concentrate (R:C) ratio ≈ 30:70] to meet their nutritional needs. The experiment adopted completely randomized design (CRD). The control group (CON) was fed the basal diet with high concentrate, to which 20 g/d of YC was added in the low dose YC group (LYC) and 40 g/d of YC in the high dose YC group (HYC). The pretrial period was 14 days, and the experimental trial period was 60 days. At the end of a 60-day trial, ruminal epithelial tissues were collected for histomorphological analysis, and rumen microorganisms were analyzed by 16S rDNA sequencing and rumen metabolites by untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics techniques. The results showed that YC improved rumen papilla development and increased rumen papilla length (p < 0.05), while decreased cuticle thickness (p < 0.05). The 16S rDNA sequencing results showed that YC reduced the relative abundance of Prevotella_1 (p < 0.05), while significantly increased the relative abundance of Ruminococcaceae_UCG-005, uncultured_bacterium_f_Lachnospiraceae, and Ruminococcus_1 genus (p < 0.05). Metabolomics analysis showed that YC changed the abundance of metabolites related to amino acid metabolism, lipid metabolism and vitamin metabolism pathways in the rumen. In summary, YC might maintain rumen health under high-concentrate diet conditions by changing rumen microbiota structure and fermentation patterns, thereby affecting rumen metabolic profiles and repairing rumen epithelial injury.

Multi-omics revealed the long-term effect of ruminal keystone bacteria and the microbial metabolome on lactation performance in adult dairy goats

BACKGROUND

The increased growth rate of young animals can lead to higher lactation performance in adult goats; however, the effects of the ruminal microbiome on the growth of young goats, and the contribution of the early-life rumen microbiome to lifelong growth and lactation performance in goats has not yet been well defined. Hence, this study assessed the rumen microbiome in young goats with different average daily gains (ADG) and evaluated its contribution to growth and lactation performance during the first lactation period.

RESULTS

Based on monitoring of a cohort of 99 goats from youth to first lactation, the 15 highest ADG (HADG) goats and 15 lowest ADG (LADG) goats were subjected to rumen fluid microbiome and metabolome profiling. The comparison of the rumen metagenome of HADG and LADG goats revealed that ruminal carbohydrate metabolism and amino acid metabolism function were enhanced in HADG goats, suggesting that the rumen fluid microbiome of HADG goats has higher feed fermentation ability. Co-occurrence network and correlation analysis revealed that Streptococcus, Candidatus Saccharimonans, and Succinivibrionaceae UCG-001 were significantly positively correlated with young goats' growth rates and some HADG-enriched carbohydrate and protein metabolites, such as propionate, butyrate, maltoriose, and amino acids, while several genera and species of Prevotella and Methanogens exhibited a negative relationship with young goats' growth rates and correlated with LADG-enriched metabolites, such as rumen acetate as well as methane. Additionally, some functional keystone bacterial taxa, such as Prevotella, in the rumen of young goats were significantly correlated with the same taxa in the rumen of adult lactation goats. Prevotella also enriched the rumen of LADG lactating goats and had a negative effect on rumen fermentation efficiency in lactating goats. Additional analysis using random forest machine learning showed that rumen fluid microbiota and their metabolites of young goats, such as Prevotellaceae UCG-003, acetate to propionate ratio could be potential microbial markers that can potentially classify high or low ADG goats with an accuracy of prediction of > 81.3%. Similarly, the abundance of Streptococcus in the rumen of young goats could be predictive of milk yield in adult goats with high accuracy (area under the curve 91.7%).

CONCLUSIONS

This study identified the keystone bacterial taxa that influence carbohydrate and amino acid metabolic functions and shape the rumen fluid microbiota in the rumen of adult animals. Keystone bacteria and their effects on rumen fluid microbiota and metabolome composition during early life can lead to higher lactation performance in adult ruminants. These findings suggest that the rumen microbiome together with their metabolites in young ruminants have long-term effect on feed efficiency and animal performance. The fundamental knowledge may allow us to develop advanced methods to manipulate the rumen microbiome and improve production efficiency of ruminants. Video Abstract.

Feeding an unsalable carrot total-mixed ration altered bacterial amino acid degradation in the rumen of lambs

The objective of this study was to determine the influence of a total-mixed ration including unsalable carrots at 45% DM on the rumen microbiome; and the plasma, rumen and liver metabolomes. Carrots discarded at processing were investigated as an energy-dense substitute for barley grain in a conventional feedlot diet, and improved feed conversion efficiency by 25%. Here, rumen fluid was collected from 34 Merino lambs at slaughter (n = 16 control; n = 18 carrot) after a feeding period of 11-weeks. The V4 region of the 16S rRNA gene was sequenced to profile archaeal and bacterial microbe communities. Further, a comprehensive, targeted profile of known metabolites was constructed for blood plasma, rumen fluid and biopsied liver metabolites using a gas chromatography mass spectrometry (GC-MS) metabolomics approach. An in vitro batch culture was used to characterise ruminal fermentation including gas and methane (CH₄) production. In vivo rumen microbial community structure of carrot fed lambs was dissimilar (P < 0.01; PERMANOVA), and all measures of alpha diversity were greater (P < 0.01), compared to those fed the control diet. Unclassified genera in Bacteroidales (15.9 ± 6.74% relative abundance; RA) were more abundant (P < 0.01) in the rumen fluid of carrot-fed lambs, while unclassified taxa in the Succinivibrionaceae family (11.1 ± 3.85% RA) were greater (P < 0.01) in the control. The carrot diet improved in vitro ruminal fermentation evidenced as an 8% increase (P < 0.01) in DM digestibility and a 13.8% reduction (P = 0.01) in CH₄ on a mg/ g DM basis, while the control diet increased (P = 0.04) percentage of propionate within total VFA by 20%. Fourteen rumen fluid metabolites and 27 liver metabolites were influenced (P ≤ 0.05) by diet, while no effect (P ≥ 0.05) was observed in plasma metabolites. The carrot diet enriched (impact value = 0.13; P = 0.01) the tyrosine metabolism pathway (acetoacetic acid, dopamine and pyruvate), while the control diet enriched (impact value = 0.42; P ≤ 0.02) starch and sucrose metabolism (trehalose and glucose) in rumen fluid. This study demonstrated that feeding 45% DM unsalable carrots diversified bacterial communities in the rumen. These dietary changes influenced pathways of tyrosine degradation, such that previous improvements in feed conversion efficiency in lambs could be explained.

Flavonoids in Amomum tsaoko Crevost et Lemarie Ameliorate Loperamide-Induced Constipation in Mice by Regulating Gut Microbiota and Related Metabolites

Amomum tsaoko (AT) is a dietary botanical with laxative properties; however, the active ingredients and mechanisms are still unclear. The active fraction of AT aqueous extract (ATAE) for promoting defecation in slow transit constipation mice is the ethanol-soluble part (ATES). The total flavonoids of ATES (ATTF) were the main active component. ATTF significantly increased the abundance of Lactobacillus and Bacillus and reduced the dominant commensals, such as Lachnospiraceae, thereby changing the gut microbiota structure and composition. Meanwhile, ATTF changed the gut metabolites mainly enriched in pathways such as the serotonergic synapse. In addition, ATTF increased the serum serotonin (5-HT) content and mRNA expression of 5-hydroxytryptamine receptor 2A (5-HT_2A), Phospholipase A2 (PLA2), and Cyclooxygenase-2 (COX2), which are involved in the serotonergic synaptic pathway. ATTF increased Transient receptor potential A1 (TRPA1), which promotes the release of 5-HT, and Myosin light chain 3(MLC3), which promotes smooth muscle motility. Notably, we established a network between gut microbiota, gut metabolites, and host parameters. The dominant gut microbiota Lactobacillus and Bacillus, prostaglandin J2 (PGJ2) and laxative phenotypes showed the most significant associations. The above results suggest that ATTF may relieve constipation by regulating the gut microbiota and serotonergic synaptic pathway and has great potential for laxative drug development in the future.

Potential roles of the rectum keystone microbiota in modulating the microbial community and growth performance in goat model

BACKGROUND

Ruminal microbiota in early life plays critical roles in the life-time health and productivity of ruminant animals. However, understanding of the relationship between gut microbiota and ruminant phenotypes is very limited. Here, the relationship between the rectum microbiota, their primary metabolites, and growth rate of a total of 76 young dairy goats (6-month-old) were analyzed, and then 10 goats with the highest or lowest growth rates respectively were further compared for the differences in the rectum microbiota, metabolites, and animal's immune parameters, to investigate the potential mechanisms by which the rectum microbiota contributes to the health and growth rate.

RESULTS

The analysis of Spearman correlation and microbial co-occurrence network indicated that some keystone rectum microbiota, including unclassified Prevotellaceae, Faecalibacterium and Succinivibrio, were the key modulators to shape the rectum microbiota and closely correlated with the rectum SCFA production and serum IgG, which contribute to the health and growth rate of young goats. In addition, random forest machine learning analysis suggested that six bacterial taxa in feces could be used as potential biomarkers for differentiating high or low growth rate goats, with 98.3% accuracy of prediction. Moreover, the rectum microbiota played more important roles in gut fermentation in early life (6-month-old) than in adulthood stage (19-month-old) of goats.

CONCLUSION

We concluded that the rectum microbiota was associated with the health and growth rate of young goats, and can be a focus on the design of the early-life gut microbial intervention.

In Vitro Modulation of Rumen Fermentation by Microbiota from the Recombination of Rumen Fluid and Solid Phases

Rumen microbiota transplantation (RMT) can improve rumen fermentation and ruminant performance. However, due to the microbial distinction in the fluid and solid phases, the current understanding of their specific roles in RMT is insufficient. Thus, this study was conducted to determine the effects of the microbiota from the recombination of the rumen fluid and solid phases on in vitro fermentation. The rumen fresh fluid (FF) and fresh solid (FS) phases were collected, and FS was washed for the fresh solid washing solution (FW). The fractions of FF, FS, and FW were autoclaved to obtain autoclaved fluid (AF), solid (AS), and washing solution (AW). Then, these phases were recombined to form eight treatments: FFFS, FFAS, FFFW, FFAW, AFFS, AFAS, AFFW, and AFAW. After 24 h of fermentation, the gas production in AFFS, FFFS, and FFAS was significantly higher than that of other groups. AFAS and AFAW had significantly lower alpha diversity than did other groups. The solid phase was enriched with fiber-degrading bacteria, including Treponema, Succinivibrio, and Ruminococcus. The fluid phase was dominated by Prevotella, Christensenellaceae R-7 group, and Rikenellaceae RC9 gut group. The washing solution had more Ruminobacter, Lachnospiraceae, and Fibrobacter. Moreover, the double-autoclaved phases displayed increased abundances of harmful bacteria, as AFAS and AFAW had higher Streptococcus and Prevotellaceae YAB2003 group abundances. A network analysis showed that the signature microbiota in AFAS and AFAW were negatively associated with the keystone microbiota in the other groups. In summary, the recombination of the solid phase and the autoclaved fluid phase had the best in vitro fermentation result, which provided certain references for RMT. IMPORTANCE This is the first study to systematically evaluate the in vitro fermentation efficiency of diets by bacteria harvested and recombined from the fluid and solid phases of rumen contents, and it took into account the effect of washing the rumen solid phase. Using "reconstituted rumen content", this study confirmed that bacteria from different fractions of the rumen digesta resulted in different fermentation production of diets and found the characteristic bacteria in each phase of rumen contents. Our data reveal that the bacteria in the solid phase have more positive effects on the in vitro fermentation parameters, that the combination of the autoclaved fluid phase and the fresh solid phase have the most ideal fermentation effect, and that the autoclave process significantly influenced the microbial composition and increased the abundance of harmful bacteria. This study provides a landmark reference for the future use of rumen microbiota transplantation to improve animal feed utilization and growth performance.

Comparison of rectum fecal bacterial community of finishing bulls fed high-concentrate diets with active dry yeast and yeast culture supplementation

OBJECTIVE

The objective of this study was to investigate the effects of feeding active dry yeast (ADY) and yeast culture (YC) on fecal bacterial community in finishing bulls fed high-concentrate diets in the same experimental environment.

METHODS

Forty-five healthy finishing cattle (Simmental×Chinese Luxi yellow bulls; 24 months; 505±29 kg) were randomly divided into three groups: i) CON group (control group, only fed basal diet), ii) ADY group (fed basal diet + active dry yeast), and iii) YC group (fed basal diet + yeast culture). At the end of the trial, nine rectum fecal samples were randomly selected from each group for bacterial DNA sequencing.

RESULTS

There was no difference among groups about alpha diversity indices (all p>0.05), including ACE, Chao 1, Shannon, and Simpson indices. Principal component analysis and non-metric multidimensional scaling analysis showed a high similarity among three groups. Compared with CON group, ADY and YC groups had greater relative abundance of c_Clostridia, o_Oscillospirales, and f_Oscillospiraceae, but lesser relative abundance of g_Megasphaera, and s_Megasphaera_elsdenii (all p<0.01). And, the relative abundances of p_Firmicutes (p = 0.03), s_Prevotella_sp (p = 0.03), o_Clostridiales (p<0.01), g_Clostridium (p<0.01), f_Caloramatoraceae (p<0.01), and f_Ruminococcaceae (p = 0.04) were increased in the ADY group. The PICRUSt2 prediction results showed that the metabolic pathways had no significant differences among groups (p>0.05). Besides, the relative abundance of c_Clostridia (r = 0.42), and f_Oscillospiraceae (r = 0.40) were positively correlated to average daily gain of finishing bulls (p<0.05).

CONCLUSION

Both of ADY and YC had no effect on diversity of fecal bacteria in finishing bulls, but the supplementation of ADY and YC can improve the large intestinal function in finishing bulls by increasing the abundance of cellulolytic bacteria and altering the abundance of lactic acid-utilizing bacteria.

Alterations in the rumen bacterial communities and metabolites of finishing bulls fed high-concentrate diets supplemented with active dry yeast and yeast culture

This study investigated the effects of active dry yeast (ADY) and yeast culture (YC) supplementation on rumen bacteria and metabolites in finishing bulls fed high-concentrate diets using the full-length 16S rDNA gene sequencing and liquid chromatography-mass spectrometry. Supplementation with ADY improved the alpha diversity and relative abundance of rumen bacteria, while YC only affected relative abundance of rumen bacteria at the genus level. Sixty-three differential metabolites were identified in rumen fluid after ADY supplementation, and 17 after YC. PICRUSt2 functional prediction showed that ADY supplementation improved the capacity of amino acid metabolism, lipid metabolism, carbohydrate metabolism, metabolism of terpenoids and polyketides, and energy metabolism in rumen bacteria (all P < 0.05). Correlation analysis showed that the rumen differential metabolites following ADY supplementation were mainly related to Oligosphaera, Verruc, Mycoplasma, and Anaeroplasma. Supplementation with ADY was more effective than YC in remodeling the rumen bacterial flora structure and metabolite composition under high-concentrate diets.

Rumen bacteria and epithelial metabolism contribute to improving N utilization efficiency of calves

The purpose of this study was to investigate the role of urea-N recycling, rumen bacterial community, and rumen epithelial gene expression in nitrogen utilization of calves. Here, 12 Holstein calves were divided into two dietary treatments: a high-protein diet (HP, 173 g/kg), and a low-protein diet (LP, 125 g/kg). Urea-N kinetics was evaluated using urea-¹⁵N¹⁵N isotope labeling method. Gene expression in rumen epithelium and liver, bacterial diversity, and metabolites in rumen were characterized using transcriptomic, Illumina HiSeq-based 16S rRNA, and LC/QTOF-MS-based metabolomics, respectively. We demonstrated that the bone weight, dressing percentage, and nitrogen utilization efficiency (NUE) increased in calves fed HP compared with LP. The urea synthesized, eliminated in urine, and return to ornithine cycle were higher in calves fed HP than LP, while the urea-N reused for anabolism were the opposite. Differentially expressed genes participated in amino acid metabolism and molecular transport in rumen epithelium. The increased abundance of bacteria and metabolites involved in protein and/or amino acid metabolism reflected the larger protein utilization in rumen of calves fed HP. In conclusion, the urea-N recycling could not fully compensate for the reduced NUE caused by N deficiency. Rumen bacteria and rumen epithelial metabolism contribute to improving NUE of calves.

Dietary Nutritional Level Affects Intestinal Microbiota and Health of Goats

The intestine is a complex micro-ecosystem, and its stability determines the health of animals. Different dietary nutritional levels affect the intestinal microbiota and health. In this study, the nutritional levels of energy and protein in the diet of goats were changed, and the body weight was measured every 15 days. In the late feeding period, 16 S rRNA sequencing technology was used to detect the content of microorganisms. A meteorological chromatograph was used to detect volatile fatty acids in the cecum and colon of goats. In the feeding stage, reducing the nutritional level of the diet significantly reduced the weight of the lamb (p < 0.05). In the cecum, the abundance of potentially harmful bacteria, such as Sphingomonas, Marvinbryantia, and Eisenbergiella, were significantly enriched in goats fed with the standard nutritional level diets (p < 0.05). Additionally, the contents of acetate (p = 0.037) and total VFAs (p = 0.041) increased. In the colon, the abundance of SCFAs-producing bacteria, such as Ruminococcaceae, Christensenellaceae, and Papillibacter, decreased as the nutritional level in the diet increased (p < 0.05). In conclusion, the increase in nutritional level could affect the growth performance and composition of intestinal microbiota.

Yeast Products Mediated Ruminal Subenvironmental Microbiota, and Abnormal Metabolites and Digestive Enzymes Regulated Rumen Fermentation Function in Sheep

Yeast products (YP) are commonly used as rumen regulators, but their mechanisms of action are still unclear. Based on our previous studies, we questioned whether yeast products would have an impact on rumen solid-associated (SA) and liquid-associated (LA) microorganisms and alter rumen fermentation patterns. Thirty 3-month-old male sheep weighing 19.27 ± 0.45 kg were selected and randomized into three groups for 60 days: (1) basal diet group (CON group), (2) basal diet add 20 g YP per day (low YP, LYP group) and (3) basal diet add 40 g YP per day (high YP, HYP group). The results demonstrated that the addition of YP increased rumen cellulase activity, butyrate and total volatile fatty acid (TVFA) concentrations (p < 0.05), while it decreased rumen amylase activity and abnormal metabolites, such as lactate, lipopolysaccharides (LPS) and histamine (HIS) (p < 0.05). Metagenomic analysis of rumen microorganisms in three groups revealed that YP mainly influenced the microbial profiles of the SA system. YP increased the relative abundance of R. flavefaciens and decreased methanogens in the SA system (p < 0.05). With the addition of YP, the abundance of only a few lactate-producing bacteria increased in the SA system, including Streptococcus and Lactobacillus (p < 0.05). However, almost all lactate-utilizing bacteria increased in the LA system, including Megasphaera, Selenomonas, Fusobacterium and Veillonella (p < 0.05). In addition, YP increased the abundance of certain GHs family members, including GH43 and GH98 (p < 0.05), but decreased the abundance of some KEGG metabolic pathways involved in starch and sucrose metabolism, biosynthesis of antibiotics and purine metabolism, among others. In conclusion, the addition of YP to high-concentrate diets can change the abundance of major functional microbiota in the rumen, especially in the solid fraction, which in turn affects rumen fermentation patterns and improves rumen digestibility.

Cysteamine-supplemented diet for cashmere goats: A potential strategy to inhibit rumen biohydrogenation and enhance plasma antioxidant capacity

Cysteamine (CS), as a feed supplement, can increase the level of growth hormone (GH) in the blood, promote animal growth. However, little attention has been paid to the effects of CS on the rumen microbiome and metabolic profile in cashmere goats. This study aimed to assess the effects of rumen microbiota, metabolites, and plasma antioxidative capacity induced by CS supplementation in cashmere goats. We selected 30 Inner Mongolia white cashmere goat ewes (aged 18 months), and randomly separate the goats into three groups (n = 10 per group) to experiment for 40 days. Oral 0 (control group, CON), 60 (low CS, LCS), or 120 mg/kg BW^-1 (high CS, HCS) coated CS hydrochloride every day. Using 16S and internal transcribed spacer (ITS) rRNA gene amplicon sequencing, we identified 12 bacterial and 3 fungal genera with significant changes among the groups, respectively. We found a significant increase in rumen NH₃-N and total volatile fatty acid (TVFA) concentrations in the LCS and HCS groups compared with the CON. With untargeted LC-MS/MS metabolomics, we screened 59 rumen differential metabolites. Among the screened metabolites, many unsaturated and saturated fatty acids increased and decreased with CS treatment, respectively. CS supplementation increased the levels of plasma total antioxidant capacity (T-AOC), glutathione peroxidase (GSH-Px), superoxide dismutase (SOD), GH, and insulin-like growth factor-1(IGF-1). Spearman correlation analysis revealed that the abundance of U29-B03, Lactococcus, and Brochothrix were positively associated with the levels of δ2-THA, TVFA and antioxidant capacity. In conclusion, CS significantly affected rumen microbiota and fermentation parameters, and ultimately inhibited the biohydrogenation of rumen metabolites, enhanced plasma antioxidant capacity, and regulated some hormones of the GH-IGF-1 axis. This study provides an overall view into the CS application as a strategy to improve health production in cashmere goats.

First Steps into Ruminal Microbiota Robustness

Despite its central role in ruminant nutrition, little is known about ruminal microbiota robustness, which is understood as the ability of the microbiota to cope with disturbances. The aim of the present review is to offer a comprehensive description of microbial robustness, as well as its potential drivers, with special focus on ruminal microbiota. First, we provide a briefing on the current knowledge about ruminal microbiota. Second, we define the concept of disturbance (any discrete event that disrupts the structure of a community and changes either the resource availability or the physical environment). Third, we discuss community resistance (the ability to remain unchanged in the face of a disturbance), resilience (the ability to return to the initial structure following a disturbance) and functional redundancy (the ability to maintain or recover initial function despite compositional changes), all of which are considered to be key properties of robust microbial communities. Then, we provide an overview of the currently available methodologies to assess community robustness, as well as its drivers (microbial diversity and network complexity) and its potential modulation through diet. Finally, we propose future lines of research on ruminal microbiota robustness.

Rumen fermentative metabolomic and blood insights into the effect of yeast culture supplement on growing bulls under heat stress conditions

This study was conducted to investigate the effects of yeast culture supplements on the physiological state and growth performance of growing bulls under heat stress conditions and the underlying mechanism. A total of 14 (6.0 ± 1.0 months old) growing bulls with similar body weight were randomly assigned into the control group (YC_0g/d) and yeast culture supplement group (YC_40g/d). YC_0g/d contained three replicates, with two bulls in each replicate, which were fed a basal diet. Meanwhile, the YC_40g/d treatment contained four replicates, with two bulls in each replicate, which were fed a basal diet supplemented with 40 g/day of yeast culture per cattle. Growth performance, nutrient digestibility, rumen fermentable metabolites, serum immunity, serum hormones, and serum antioxidant parameters were measured. Results showed that the average daily gain significantly increased (P < 0.05), while the feed-to-gain ratio significantly decreased (P < 0.01) after YC supplementation compared with the YC_0g/d. The digestibility of neutral detergent fiber (P < 0.05) was higher in YC_40g/d. There were no significant differences in ruminal pH, NH₃-N, butyrate, or acetate/propionate (P > 0.05). Besides, the rumen MCP, acetate, propionate, and total VFA content remarkably increased with the supplement of YC (P < 0.05). Yeast culture supplementation increased the concentration of nicotinamide riboside, neuromedin B, peptides, and formyl-5-hydroxykynurenamine. The YC_40g/d group had a significantly (P < 0.05) higher serum triiodothyronine level, serum glutathione peroxidase levels, and total antioxidant capacity while having a lower serum malondialdehyde level than the YC_0g/d group. In conclusion, the addition of yeast culture in the diet improves the growth performance of growing bulls under heat stress by increasing nutrient digestibility, rumen fermentation function, antioxidant capacity, and rumen metabolites.

Evaluating Starter Feeding on Ruminal Function in Yak Calves: Combined 16S rRNA Sequencing and Metabolomics

For young ruminants, starter feeding can effectively facilitate the growth and development of rumen in ruminants, but the development of rumen is an important physiological challenge as it remains unclear for the mechanism of starter feeding stimulating. In this study, we performed an analysis of ruminal microbiota and their metabolites in yak calves to explore how the ruminal microbiota and their metabolites stimulate the ruminal function. This study associated 16S rRNA sequencing with liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to evaluate the effects of starter feeding on ruminal microbiota diversity and metabolites in yak calves. We designed the experiment using 20 yak calves that were assigned equally into 2 groups, based on feeding milk replacer; the control (RA) group was fed with alfalfa hay while the treatment (RAS) group was fed with alfalfa hay and starter. After the experiment, we investigated the ruminal microbiota and metabolites through 16S rRNA sequencing and LC-MS-based metabolomics. During the preweaning period, the RAS group significantly promoted the growth performance and ruminal development in yak calves, including increases in body weight, chest girth, and development of rumen (P &lt; 0.05). The RAS group increased the relative abundance of Bacteroidota, Proteobacteria, Chloroflexi, Synergistota, and Spirochaetota and decreased the abundance of Firmicutes, Desulfobacterota, Actinobacteriota, and Actinobacteriota at the phylum level (P &lt; 0.05). At the genus level, the ruminal content of the RAS group was significantly enriched for Rikenellaceae_RC9_gut_group and Ruminococcus, while depleted for Prevotella, Christensenellaceae_R-7_group, and NK4A214_group (P &lt; 0.05). A total of 37 metabolites were identified between the RA group and the RAS group, of which 15 metabolites were upregulated and 22 metabolites were downregulated compared with the RA group. Metabolic pathway analyses indicated that upregulated the metabolites of the RAS group yak calves were related to carbohydrate metabolism, ubiquinone, and other terpenoid-quinone biosynthesis, while the downregulated metabolic pathway was relevant to xenobiotic biodegradation, metabolism, and nucleotide metabolism. In summary, starter feeding before weaning significantly increased the dry matter intake and body weight of yak calves, changed the diversity and abundance of ruminal microbiota, and positively regulated the good development of ruminal morphology and function, providing an important basis for high-quality cultivation and the nutritional level of nutrition of yak calves in the Qinghai Tibet plateau. This study is based on the availability of 16S rRNA sequencing and LC-MS-based metabolomics in clarifying the function of starter feeding in the yak calves.

Improved tenderness of beef from bulls supplemented with active dry yeast is related to matrix metalloproteinases and reduced oxidative stress

Supplementing diets with active dry yeast (ADY, Saccharomyces cerevisiae) improves the carcass quality grade of beef cattle and the tenderness of beef. The relevant mechanisms have not been fully elucidated, but may be related to the effect of ADY on oxidative stress and the activity of matrix metalloproteinases (MMPs). To provide further insight into these mechanisms, this study evaluated the influence of ADY supplementation on growth performance, carcass traits, meat quality, concentrations of MMPs in serum (MMP-2, MMP-9 and MMP-13), oxidative stress indices and antioxidant capacity indices in beef cattle. Forty-six crossbred Simmental × Yanbian bulls (∼18 months of age, BW 436 ± 35 kg) participated in a 145-day finishing trial. ADY supplementation significantly improved marbling deposition, intramuscular fat content, and beef tenderness (P < 0.05); altered individual fatty acid proportions in the beef and increased saturated fatty acids while decreasing polyunsaturated fatty acids (P < 0.05); significantly decreased the abundance of reactive oxygen species in serum and meat; significantly increased the level of superoxide dismutase in meat (P < 0.05); tended to increase the level of catalase (P = 0.075) in serum and glutathione reductase (P = 0.066) in meat; and increased the secretion of MMPs. The improvement of beef tenderness following ADY supplementation of finishing bulls is related to the effects of ADY on the secretion of MMPs and the lowering of oxidative stress.

Integration of Multiplied Omics, a Step Forward in Systematic Dairy Research

Due to their unique multi-gastric digestion system highly adapted for rumination, dairy livestock has complicated physiology different from monogastric animals. However, the microbiome-based mechanism of the digestion system is congenial for biology approaches. Different omics and their integration have been widely applied in the dairy sciences since the previous decade for investigating their physiology, pathology, and the development of feed and management protocols. The rumen microbiome can digest dietary components into utilizable sugars, proteins, and volatile fatty acids, contributing to the energy intake and feed efficiency of dairy animals, which has become one target of the basis for omics applications in dairy science. Rumen, liver, and mammary gland are also frequently targeted in omics because of their crucial impact on dairy animals’ energy metabolism, production performance, and health status. The application of omics has made outstanding contributions to a more profound understanding of the physiology, etiology, and optimizing the management strategy of dairy animals, while the multi-omics method could draw information of different levels and organs together, providing an unprecedented broad scope on traits of dairy animals. This article reviewed recent omics and multi-omics researches on physiology, feeding, and pathology on dairy animals and also performed the potential of multi-omics on systematic dairy research.

Effects of Saccharomyces Cerevisiae Cultures on Performance and Immune Performance of Dairy Cows During Heat Stress

The dairy farming industry is facing massive economic losses as heat stress continues to rise. The purpose of this study was to see how feeding Saccharomyces cerevisiae culture (SC) influences productive performance, lactation performance, serum biochemical indexes, hormonal level, antioxidant capacity, and immune function in mid-lactating cows during heat stress. Forty-five healthy mid-lactation dairy cows with comparable milk yield, lactation days, and parity were randomly divided into 3 groups (15 cows in each group). The control group (CON) was fed the basal diet, while the treatment groups were fed the basal diet + first Saccharomyces cerevisiae culture 100 g/d (SC-1) and the basal diet + second Saccharomyces cerevisiae culture 30 g/d (SC-2), respectively. The SC-1 and SC-2 groups with SC added in the treatment groups reduced rectal temperature and respiratory rate in heat-stressed cows (P &lt; 0.05). The milk yield of SC-1 and SC-2 treatment groups was significantly higher than that of CON (P &lt; 0.05). Except for somatic cell count, which was significantly lower in SC-1 and SC-2 than in CON (P &lt; 0.05), there were no significant differences in the milk components. The addition of SC: (i) increased serum urea levels (P &lt; 0.05), but there was no significant difference in glucose, total cholesterol, alanine transaminase, aspartate aminotransferase, total protein, albumin and alkaline phosphatase levels (P &gt; 0.05); (ii) increased serum levels of immunoglobulin-A, immunoglobulin-G, immunoglobulin M, interleukin-4, interleukin-10 and heat shock protein-70 (P &lt; 0.05), while decreasing serum levels of interleukin-1β, interleukin-6, interleukin-2, interferon-γ and tumor necrosis factor-α (P &lt; 0.05); (iii) increased total antioxidant capacity, glutathione peroxidase and superoxide dismutase in serum (P &lt; 0.05), while decreasing malondialdehyde; (iv) increased serum levels of glucocorticoids, insulin, cortisol and prolactin (P &lt; 0.05), while decreasing the serum levels of triiodothyronine and thyroxine (P &lt; 0.05). In conclusion, under the current experimental conditions, the addition of SC can reduce rectal temperature and respiratory rate in heat-stressed mid-lactation cows, reduce the number of somatic cells in milk and improve the mid-lactation cow performance. In addition, SC addition to the diet can raise serum urea levels, regulate serum hormone levels, boost antioxidant capacity in mid-lactation cows, and boost overall immunity.

Metabolomics-Guided Analysis of the Biocatalytic Conversion of Sclareol to Ambradiol by Hyphozyma roseoniger

The biocatalytic conversion of sclareol to ambradiol, a valuable component in the fragrance industry, using whole-cell biotransformation by the dimorphic yeast Hyphozyma roseoniger, was investigated using metabolomics tools. An integrated approach was used to identify and quantify the participating intermediates in this bioconversion using both nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography coupled to mass spectrometry (LC–MS). This study entailed growth stage-dependent analysis of H. roseoniger suspensions grown in batch culture over a 14-day period, beginning with a three-day induction period using 20 mg/200 mL sclareol, followed by a further 1 g/200 mL sclareol dose to enable ambradiol production. The progress of the bioconversion and the resulting dynamic changes to the metabolome were monitored using NMR analysis and semi-targeted LC–MS metabolomics. This outlined the molecular conversions occurring within the matrix and no novel intermediates participating in the sclareol to ambradiol conversion could be identified. This study presents new findings about the transformative capabilities of H. roseoniger as a whole cell biocatalyst, highlighting its potential utility in similar applications.

Seasonal diets supersede host species in shaping the distal gut microbiota of Yaks and Tibetan sheep

Yaks and Tibetan sheep are important and renowned livestock of the Qinghai-Tibetan Plateau (QTP). Both host genetics and environmental factors can shape the composition of gut microbiota, however, there is still no consensus on which is the more dominant factor. To investigate the influence of hosts and seasons on the gut microbiome diversity component, we collected fecal samples from yaks and Tibetan sheep across different seasons (summer and winter), during which they consumed different diets. Using 16S rRNA sequencing, principal component analysis (PCoA) data showed that PCo1 explained 57.4% of the observed variance (P = 0.001) and clearly divided winter samples from summer ones, while PCo2 explained 7.1% of observed variance (P = 0.001) and mainly highlighted differences in host species. Cluster analysis data revealed that the gut microbiota composition displayed a convergence caused by season and not by genetics. Further, we profiled the gut microbial community and found that the more dominant genera in yak and Tibetan sheep microbiota were influenced by seasonal diets factors rather than genetics. This study therefore indicated that seasonal diet can trump host genetics even at higher taxonomic levels, thus providing a cautionary note for the breeding and management of these two species.

Dietary supplementation with inulin improves lactation performance and serum lipids by regulating the rumen microbiome and metabolome in dairy cows

This study investigated the effects of inulin on rumen fermentation parameters, ruminal microbiome and metabolites, as well as lactation performance and serum indexes in dairy cows. Sixteen Holstein dairy cows with similar body conditions were randomly divided into 2 groups (n = 8 per group), with inulin addition at 0 and 200 g/d per cow. The experiment lasted for 6 weeks, including a 1-week adaptation period and a 5-week treatment period. At the end of the experimental period, the milk, serum and rumen fluid were sampled and analyzed. The microbiome and metabolome in the rumen fluid were analyzed via 16S rRNA sequencing and untargeted metabolomics, respectively. The results showed that supplementation with inulin (200 g/d per cow) increased the milk yield (P = 0.001), milk protein (P = 0.032), lactose rate (P = 0.004) and proportion of saturated fatty acids (SFA) in milk (P < 0.001), but decreased the proportion of unsaturated fatty acids (USFA) (P = 0.041). Rumen pH (P = 0.040) and the concentration of NH₃–N (P = 0.024) were decreased; however, acetate (P < 0.001), propionate (P = 0.003), butyrate (P < 0.001) and lactic acid (LA) (P = 0.043) were increased. The total cholesterol (TC) (P = 0.008) and triglycerides (TG) (P = 0.01) in serum were also reduced. Additionally, inulin addition elevated the relative abundance of several beneficial symbiotic and short-chain fatty acid (SCFA)-producing bacteria, such as Muribaculaceae (false discovery rate [FDR]-adjusted P < 0.01), Acetitomaculum (FDR-adjusted P = 0.043), and Butyrivibrio (FDR-adjusted P = 0.036), while elevating the levels of L-lysine (FDR-adjusted P = 4.24 × 10⁻³), L-proline (FDR-adjusted P = 0.0158), and L-phenylalanine (FDR-adjusted P = 0.027). In contrast, several pathogens and ruminal bacteria abundant in high-fat diets, such as Escherichia-Shigella (FDR-adjusted P = 0.022), Erysipelotrichaceae__UCG-004 (FDR-adjusted P < 0.01) and RF39 (FDR-adjusted P = 0.042) were decreased along with the reduction of lysophosphatidylcholine (LysoPC) (18:1 (9Z)) (FDR-adjusted P = 1.03 × 10⁻³), LysoPC (16:0) (FDR-adjusted P = 0.0108), LysoPC (18:2 (9Z, 12Z)) (FDR-adjusted P = 1.65 × 10⁻³) and 8-methylnonenoate. In conclusion, dietary inulin supplementation could increase the relative abundance of commensal microbiota and SCFA-producing bacteria, upregulate amino acidmetabolism and downregulate lipid metabolism in the rumen of dairy cows, which might further improve lactation performance and the level of serum lipids.

Oscillating dietary crude protein concentrations increase N retention of calves by affecting urea-N recycling and nitrogen metabolism of rumen bacteria and epithelium

The purpose of this study was to investigate the effects of oscillating crude protein (CP) concentration diet on the nitrogen utilization efficiency (NUE) of calves and determine its mechanism. Twelve Holstein calves were assigned randomly into static protein diet (SP, 149 g/kg CP) and oscillating protein diet (OP, 125 and 173 g/kg CP diets oscillated at 2-d intervals) groups. After 60 days of feeding, the weights of total stomach, rumen and omasum tended to increase in calves fed OP. The apparent crude fat digestibility, NUE and energy metabolism also increased. In terms of urea-N kinetics evaluated by urea-¹⁵N¹⁵N isotope labeling method, the urea-N production and that entry to gastrointestinal tended to increase, and urea-N reused for anabolism increased significantly in calves fed OP during the low protein phase. These data indicate that urea-N recycling contributed to improving NUE when dietary protein concentration was low. In addition, the differentially expressed genes in rumen epithelium and the rumen bacteria involved in protein and energy metabolism promoted the utilization of dietary protein in calves fed OP.

Changes in rumen fermentation and bacterial community in lactating dairy cows with subacute rumen acidosis following rumen content transplantation

Rumen microbiota intervention has long been used to cure ruminal indigestion in production and has recently become a research hotspot. However, how it controls the remodeling of rumen bacterial homeostasis and the restoration of rumen fermentation in cows of subacute ruminal acidosis (SARA) remains poorly understood. This study explored changes in rumen fermentation and bacterial communities in SARA cows following rumen content transplantation (RCT). The entire experiment comprised 2 periods: the SARA induction period and the RCT period. During the SARA induction period, 12 ruminally cannulated lactating Holstein cows were selected and allocated into 2 groups at random, fed either a conventional diet [CON; n = 4; 40% concentrate, dry matter (DM) basis] or a high-grain diet (HG; n = 8; 60% concentrate, DM basis). After the SARA induction period, the RCT period began. The HG cows were randomly divided into 2 groups: the donor-recipient (DR) group and the self-recipient (SR) group, and their rumen contents were removed completely before RCT. For the DR group, cows received 70% rumen content from the CON cows, paired based on comparable body weight; for the SR group, each cow received 70% rumen content, self-derived. The results showed that nearly all rumen fermentation parameters returned to the normal levels that the cows had before SARA induction after 6 d of transplantation, regardless of RCT. The concentrations of acetate, valerate, and total volatile fatty acids (VFA) were not recovered in the SR cows, whereas all of them were recovered in the DR cows. The amplicon sequencing results indicated that both the SR and DR cows rebuild their rumen bacterial homeostasis quickly within 4 d after RCT, and the DR group showed a higher level of bacterial community diversity. At the genus level, the DR cows displayed an improved proportion of unclassified Ruminococcaceae and Saccharofermentans compared with the SR cows. Correlation analysis between the rumen bacteria and rumen fermentation suggested some potential relationships between the predominant transplantation-sensitive operational taxonomic units and VFA. Co-occurrence network analysis revealed that RCT affected only those rumen bacterial taxa that showed weak interactions with other taxa and did not affect the pivotal rumen bacteria with high levels of co-occurrence. Our findings indicate that RCT contributes to the restoration of rumen bacterial homeostasis and rumen fermentation in cows suffering from SARA without affecting the core microbiome.

Effects of supplementation of nonforage fiber source in diets with different starch levels on growth performance, rumen fermentation, nutrient digestion, and microbial flora of Hu lambs

The objectives were to evaluate the effects of fiber source and dietary starch level on growth performance, nutrient digestion, rumen parameters, and rumen bacteria in fattening Hu lambs. A total of 360 Hu lambs (BW = 24.72 ± 0.14 kg, 2 months old) were subjected to a 2 × 3 factorial arrangement. Lambs randomly assigned 6 treatments with 6 repetitions (10 lambs per repetition) of each treatment. Six treatments were formulated to include the fiber sources with three starch levels. The experiment lasted a 63 d. The amount of feed, orts, and total feces were sampled on the 42nd day of the experiment. Rumen fluid samples were collected after 2 h of morning feeding on day 56. Rumen contents were collected last day after the selected lambs were slaughtered. Increasing the starch content decreased the digestibility of neutral detergent fiber (NDF, P = 0.005). Increasing the starch level increased the proportions of propionate (P = 0.002) and valerate (P = 0.001) and decreased the proportion of acetate (P < 0.001) and the ratio of acetate to propionate (P = 0.005). The abundance of Fibrobacter succinogenes was affected by an interaction between the fiber source and the starch level (P < 0.001). Fibrobacter succinogenes tended to be greater in lambs fed SH than in lambs fed BP (P = 0.091), which was greater in lambs fed high starch levels than in lambs fed low starch levels (P = 0.014). Increasing the starch level increased Streptococcus bovis abundance (P = 0.029) and decreased total bacteria (P = 0.025). At the genus level, increasing the starch level reduced the abundance of Butyrivibrio_2 (P = 0.020). Nevertheless, the final body weight (BW) and acid detergent fiber (ADF) digestibility were greater (P < 0.01) in lambs fed soybean hull (SH) than in lambs fed BP. The proportion of butyrate was greater (P = 0.005), while the rumen pH was lower (P = 0.001) in lambs fed beet pulp (BP) than in those fed SH. The abundances of Succiniclasticum, Candidatus_Saccharimonas, Ruminococcus_1, and Christensenellaceae_R-7 were greater in lambs fed SH than in those fed BP (P < 0.050), whereas the abundance of Fibrobacter was lower (P = 0.011). The predominant microbial phyla in all of the groups were Firmicutes, Bacteroidetes, and Fibrobacteres. Changing the starch level for fiber sources mainly changed the rumen community in terms of the phylum and genus abundances. Lambs fed SH with low starch level increased the final BW without affecting total volatile fatty acids (TVFA) concentrations.

Effects of a blend of mannan and glucan on growth performance, apparent nutrient digestibility, energy status, and whole-blood immune gene expression of beef steers during a 42-d receiving period

We examined the effects of dietary supplementation of a blend of mannan and glucan on the growth performance, energy status, and whole-blood immune gene expression of newly weaned beef steers during a 42-d receiving period. Forty-eight newly weaned Angus crossbred steers (2-d post-weaning; 199 ± 13 kg of initial body weight [BW]) from a single source were stratified by BW and randomly assigned to one of the two treatments: basal diet with no additive (CON; n = 24) or a basal diet top-dressed with 5 g of a blend of mannan and glucan (MANGLU; n = 24). Average daily gain (ADG) and feed efficiency (FE) from days 1 to 14, 15 to 42, and 1 to 42 were calculated from daily dry matter intake (DMI) and weekly BW. Blood samples were collected on days 0, 14, and 42 for measurement of plasma glucose and nonesterified fatty acids (NEFA). Blood samples collected on days 14 and 42 were composited for each steer for untargeted carbonyl-metabolome analysis (measurement of carbonyl-containing metabolites). Expression of 84 immune-related genes was analyzed on blood samples collected on day 42. Beginning on days 37 to 42, total mixed ration, refusals, and fecal samples were collected once daily to determine apparent total tract digestibility of DM, CP, NDF, and ADF using indigestible NDF as an internal marker. Over the 42-d feeding trial, supplemental MANGLU tended to increase final BW (P = 0.07) and ADG (P = 0.06). Compared to CON, beef steers fed supplemental MANGLU had greater (P = 0.01) DMI during the first 14 d, greater DM digestibility (P = 0.03), and tended to have greater NDF digestibility (P = 0.09). No treatment effects (P > 0.10) on plasma glucose and NEFA on days 14 and 42 were detected; however, carbonyl-metabolome analysis revealed increased (FDR ≤ 0.05) plasma concentrations of galactose and glyceraldehydes, and altered (FDR ≤ 0.05) concentrations of some microbiome-derived metabolites in beef steers fed MANGLU. Compared with CON, MANGLU increased (P ≤ 0.05) the expression of five immune-related genes involved in recognition of and mounting immune defense against microbial pathogens. In conclusion, the results of this study demonstrated that supplemental MANGLU enhances beef cattle immunocompetence and productivity during feedlot receiving period.

Effects of dry yeast supplementation on growth performance, rumen fermentation characteristics, slaughter performance and microbial communities in beef cattle

This study aimed to investigate the effects of active dry yeast (ADY) on growth performance, rumen microbial composition and carcass performance of beef cattle. Thirty-two finishing beef cattle (yak ♂ × cattle-yaks ♀), with an average body weight of 110 ± 12.85 kg, were randomly assigned to one of four treatments: the low plane of nutrition group (control), low plane of nutrition group + ADY 2 g/head daily (ADY2), low plane of nutrition group + ADY 4 g/head daily (ADY4) and the high plane of nutrition group (HPN). Supplementation of ADY increased average daily gain compared to the control group. The neutral detergent fiber and acid detergent fiber apparent digestibility in HPN group was greater than that in control group. The propionic acid concentration in the rumen in ADY2, ADY4, and HPN groups was greater than that in control group. The Simpson and Shannon indexes in control and HPN groups were higher than that in ADY4 group. At the phylum level, the relative abundance of Firmicutes in the HPN group was higher than that in ADY4 group. The relative abundance of Ruminococcaceae UCG-002 in ADY4 group was higher than that in control and HPN groups. In conclusion, supplementation ADY 4 g/head daily shift the rumen microbial composition of beef cattle fed low plane of nutrition to a more similar composition with cattle fed with HPN diet and produce the similar carcass weight with HPN diet.HighlightsThe ADY can improve the utilization of nitrogen and decrease the negative impact on the environment in beef cattle.Cattle fed low plane of nutrition diet supplemented with ADY 4 g/head daily increased growth performance.Supplementation ADY 4 g/head daily in low plane of nutrition diet might be produced comparable carcass weight to HPN diet.

Effects of Multi-Species Direct-Fed Microbial Products on Ruminal Metatranscriptome and Carboxyl-Metabolome of Beef Steers

We examined the effects of two direct-fed microbial (DFM) products containing multiple microbial species and their fermentation products on ruminal metatranscriptome and carboxyl-metabolome of beef steers. Nine ruminally-cannulated Holstein steers were assigned to 3 treatments arranged in a 3 × 3 Latin square design with three 21-d periods. Dietary treatments were (1) Control (CON; basal diet without additive), (2) Commence (PROB; basal diet plus 19 g/d of Commence), and (3) RX3 (SYNB; basal diet plus 28 g/d of RX3). Commence and RX3 are both S. cerevisiae-based DFM products containing several microbial species and their fermentation products. Mixed ruminal contents collected multiple times after feeding on day 21 were used for metatranscriptome and carboxyl-metabolome analysis. Partial least squares discriminant analysis revealed a distinct transcriptionally active taxonomy profiles between CON and each of the PROB and SYNB samples. Compared to CON, the steers fed supplemental PROB had 3 differential (LDA ≥ 2.0; p ≤ 0.05) transcriptionally active taxa, none of which were at the species level, and those fed SYNB had eight differential (LDA > 2.0, p ≤ 0.05) transcriptionally active taxa, but there was no difference (p > 0.05) between PROB and SYNB. No functional microbial genes were differentially expressed among the treatments. Compared with CON, 3 metabolites (hydroxylpropionic acid and 2 isomers of propionic acid) were increased (FC ≥ 1.2, FDR ≤ 0.05), whereas 15 metabolites, including succinic acid and fatty acid peroxidation and amino acid degradation products were reduced (FC ≤ 0.83, FDR ≤ 0.05) by supplemental PROB. Compared with CON, 2 metabolites (2 isomers of propionic acid) were increased (FC ≥ 1.2, FDR ≤ 0.05), whereas 2 metabolites (succinic acid and pimelate) were reduced (FC ≤ 0.83, FDR ≤ 0.05) by supplemental SYNB. Compared to SYNB, supplemental PROB reduced (FC ≤ 0.83, FDR ≤ 0.05) the relative abundance of four fatty acid peroxidation products in the rumen. This study demonstrated that dietary supplementation with either PROB or SYNB altered the ruminal fermentation pattern. In addition, supplemental PROB reduced concentrations of metabolic products of fatty acid peroxidation and amino acid degradation. Future studies are needed to evaluate the significance of these alterations to ruminal fatty acid and amino acid metabolisms, and their influence on beef cattle performance.

Comparative effects of two multispecies direct-fed microbial products on energy status, nutrient digestibility, and ruminal fermentation, bacterial community, and metabolome of beef steers

We examined the effects of two direct-fed microbials (DFM) containing multiple microbial species and their fermentation products on energy status, nutrient digestibility, and ruminal fermentation, bacterial community, and metabolome of beef steers. Nine ruminally cannulated Holstein steers (mean ± SD body weight: 243 ± 12.4 kg) were assigned to three treatments arranged in a triplicated 3 × 3 Latin square design with three 21-d periods. Dietary treatments were 1) control (CON; basal diet), 2) Commence (PROB; basal diet plus 19 g/d of Commence), and 3) RX3 (SYNB; basal diet plus 28 g/d of RX3). Commence and RX3 are both multispecies DFM products. From day 16 to 20 of each period, feed and fecal samples were collected daily to determine the apparent total tract digestibilities of nutrients using indigestible neutral detergent fiber method. On day 21 of each period, blood samples were collected for analysis of plasma glucose and nonesterified fatty acid. Ruminal contents were collected at approximately 1, 3, 6, 9, 12, and 18 h after feeding on day 21 for analysis of volatile fatty acids (VFA), lactate, ammonia-N concentrations, bacterial community, and metabolome profile. Total tract digestibilities of nutrients did not differ (P > 0.05) among treatments. Compared with CON, steers fed either supplemental PROB or SYNB had greater (P = 0.04) plasma glucose concentrations. Compared with CON, total ruminal VFA, propionate, isovalerate, and valerate concentrations increased (P ≤ 0.05) or tended to increase (P ≤ 0.10) with either supplemental PROB or SYNB, but were not different (P > 0.05) between PROB and SYNB. Compared with CON, PROB reduced (P ≤ 0.05) the relative abundance of Prevotella 1 and Prevotellaceae UCG-001 but increased (P ≤ 0.05) the relative abundance of Rikenellaceae RC9, Succinivibrionaceae UCG-001, Succiniclasticum, and Ruminococcaceae UCG-002. Supplemental SYNB decreased (P ≤ 0.05) the relative abundance of Prevotella 1 and Prevotellaceae UCG-001 but increased (P ≤ 0.05) the relative abundance of Prevotella 7, Succinivibrio, Succiniclasticum, and Ruminococcaceae UCG-014. Compared with CON, metabolome analysis revealed that some amino acids were increased (P ≤ 0.05) in steers fed PROB. This study demonstrated that, compared with CON, supplementation of either PROB or SYNB altered the ruminal bacterial community and metabolome differently; however, their effects on the ruminal VFA profile and energy status of the steers were not different from each other.

Integrating RNA-sequencing and untargeted LC-MS metabolomics to evaluate the effect of lysine deficiency on hepatic functions in Holstein calves

Lysine (Lys) is majorly metabolized in the liver. The liver functional consequences of a dietary Lys deficiency in young Holstein calves are unknown. This study aimed to investigate the effects of Lys deficiency in Holstein calf livers using RNA-sequencing and untargeted LC-MS metabolomics. Calves (n = 36; initial body weight 101.2 ± 10.8 kg; 90-day-old) were fed restricted diets, for 90 days, containing 19.2% crude protein that varied in Lys content (PC group 1.21%; PC-Lys group 0.85%; dry matter basis) for 90 days. Body weight, average daily gain, gain/feed, and Lys intake were significantly decreased in response to Lys deficiency (P < 0.05). Dry matter intake was not altered (P > 0.05). Network and pathway analyses revealed that noradrenaline, adenosine 5'-monophosphate, acetyl-CoA, and coenzyme A were significantly decreased. Regulating of lipolysis in adipocytes pathway and fatty acid degradation pathway were downregulated. We also identified eight significantly differentially expressed genes (SDEGs), among which adrenoceptor beta 2 (ADRB2), WAP four-disulfide core domain 2 (WFDC2), and claudin-4 (CLDN4) were associated with inhibition of lipolysis, and carbon catabolite repression 4-like (CCRN4L), FOS like 2 (FOSL2), and arginase 2 (ARG2) were associated with inhibiting lipid synthesis. Correlation tests showed that coenzyme A was strongly correlated with SDEGs (0.82 ≤|r|≤ 0.96). Acetyl-CoA and adenosine 5'-monophosphate were strongly correlated with CCRN4L (0.90 ≤|r|≤ 0.92), indicating a strong correlation between the changes in SDEGs and these metabolites. In conclusion, Lys deficiency caused dysplasia and affected lipid metabolism in the liver by inhibiting lipolysis and lipid synthesis in calves.

Effects of a blend of Saccharomyces cerevisiae-based direct-fed microbial and fermentation products on plasma carbonyl-metabolome and fecal bacterial community of beef steers

BACKGROUND

Previous studies have evaluated the metabolic status of animals fed direct-fed microbial (DFM) using enzyme-based assays which are time-consuming and limited to a few metabolites. In addition, little emphasis has been placed on investigating the effects of DFM on hindgut microbiota. We examined the effects of dietary supplementation of a blend of Saccharomyces cerevisiae-based DFM and fermentation products on the plasma concentrations of carbonyl-containing metabolites via a metabolomics approach, and fecal bacterial community, via 16S rRNA gene sequencing, of beef steers during a 42-day receiving period. Forty newly weaned steers were randomly assigned to receive a basal diet with no additive (CON; n = 20) or a basal diet supplemented with 19 g of Commence™ (PROB; n = 20) for a 42-day period. Commence™ (PMI, Arden Hills, MN) is a blend of 6.2 × 1011 cfu/g of S. cerevisiae, 3.5 × 1010 cfu/g of a mixture of Enterococcus lactis, Bacillus subtilis, Enterococcus faecium, and Lactobacillus casei, and the fermentation products of these aforementioned microorganisms and those of Aspergillus oryzae and Aspergillus niger. On d 0 and 40, rectal fecal samples were collected randomly from 10 steers from each treatment group. On d 42, blood was collected for plasma preparation.

RESULTS

A total number of 812 plasma metabolites were detected. Up to 305 metabolites [fold change (FC) ≥ 1.5, FDR ≤ 0.01] including glucose, hippuric acid, and 5-hydroxykynurenamine were increased by PROB supplementation, whereas 199 metabolites (FC ≤ 0.63, FDR ≤ 0.01) including acetoacetate were reduced. Supplementation of PROB increased (P ≤ 0.05) the relative abundance of Prevotellaceae UCG-003, Megasphaera, Dorea, Acetitomaculum, and Blautia. In contrast, the relative abundance of Elusimicrobium, Moheibacter, Stenotrophomonas, Comamonas, and uncultured bacterium belonging to family p-2534-18B5 gut group (phylum Bacteroidetes) were reduced (P ≤ 0.05).

CONCLUSIONS

The results of this study demonstrated that supplementation of PROB altered both the plasma carbonyl metabolome towards increased glucose concentration suggesting an improved energy status, and fecal bacterial community, suggesting an increased hindgut fermentation of the beef steers.

Effects of live yeast on differential genetic and functional attributes of rumen microbiota in beef cattle

Several studies have evaluated the effects of live yeast supplementation on rumen microbial population; however, its effect on differential microbial genes and their functional potential has not been described. Thus, this study applied shotgun metagenomic sequencing to evaluate the effects of live yeast supplementation on genetic and functional potential of the rumen microbiota in beef cattle. Eight rumen-cannulated Holstein steers were randomly assigned to two treatments in a cross-over design with two 25-day experimental periods and a 10-day wash-out between the two periods. The steers were housed in individual pens and fed 50% concentrate-mix and 50% red clover/orchard hay ad libitum. Treatments were (1) control (CON; basal diet without additive) and (2) yeast (YEA; basal diet plus 15 g/d of live yeast product). Rumen fluid samples were collected at 3, 6, and 9 h after feeding on the last d of each period. Sequencing was done on an Illumina HiSeq 2500 platform. Dietary yeast supplementation increased the relative abundance of carbohydrate-fermenting bacteria (such as Ruminococcus albus, R. champanellensis, R. bromii, and R. obeum) and lactate-utilizing bacteria (such as Megasphaera elsdenii, Desulfovibrio desulfuricans, and D. vulgaris). A total of 154 differentially abundant genes (DEGs) were obtained (false discovery rate < 0.01). Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis of the DEGs revealed that 10 pathways, including amino sugar and nucleotide sugar metabolism, oxidative phosphorylation, lipopolysaccharide biosynthesis, pantothenate and coenzyme A biosynthesis, glutathione metabolism, beta-alanine metabolism, polyketide sugar unit biosynthesis, protein export, ribosome, and bacterial secretory system, were enriched in steers fed YEA. Annotation analysis of the DEGs in the carbohydrate-active enzymes (CAZy) database revealed that the abundance of genes coding for enzymes belonging to glycoside hydrolases, glycosyltransferases, and carbohydrate binding modules were enriched in steers fed YEA. These results confirm the effectiveness of a live S. cerevisiae product for improving rumen function in beef steers by increasing the abundance of cellulolytic bacteria, lactic acid-utilizing bacteria, and carbohydrate-active enzymes in the rumen.

Could probiotics be the panacea alternative to the use of antimicrobials in livestock diets?

Probiotics are most frequently derived from the natural microbiota of healthy animals. These bacteria and their metabolic products are viewed as nutritional tools for promoting animal health and productivity, disease prevention and therapy, and food safety in an era defined by increasingly widespread antimicrobial resistance in bacterial pathogens. In contemporary livestock production, antimicrobial usage is indispensable for animal welfare, and employed to enhance growth and feed efficiency. Given the importance of antimicrobials in both human and veterinary medicine, their effective replacement with direct-fed microbials or probiotics could help reduce antimicrobial use, perhaps restoring or extending the usefulness of these precious drugs against serious infections. Thus, probiotic research in livestock is rapidly evolving, aspiring to produce local and systemic health benefits on par with antimicrobials. Although many studies have clearly demonstrated the potential of probiotics to positively affect animal health and inhibit pathogens, experimental evidence suggests that probiotics' successes are modest, conditional, strain-dependent, and transient. Here, we explore current understanding, trends, and emerging applications of probiotic research and usage in major livestock species, and highlight successes in animal health and performance.