Dietary Concentrate-to-Forage Ratio Affects Rumen Bacterial Community Composition and Metabolome of Yaks

Gut microbiome reveals the trophic variation and significant adaption of three sympatric forest-dwelling ungulates on the eastern Qinghai-Xizang Plateau

BACKGROUND

The gut microbiome of herbivorous mammals regulates numerous physiological processes, including digestion and energy metabolism. The complex stomach architecture of ruminants, in conjunction with the metabolic capabilities of their microbiota, confers a considerable adaptive advantage to these animals. Nevertheless, a significant gap persists in comparative studies on the variations in the gut microbiome among sympatric ruminants and their potential adaptive implications. Accordingly, in this study, 16S rRNA gene sequencing and metagenomic approaches were used to analyse the composition and functional attributes of the gut microbiome of sympatric Moschus chrysogaster, Capricornis sumatraensis, and Cervus albirostris inhabiting the eastern periphery of the Qinghai-Xizang Plateau.

RESULTS

The gut microbiome of C. albirostris exhibited a higher diversity than that of M. chrysogaster and C. sumatraensis, whereas those of M. chrysogaster and C. sumatraensis were similar. Although species-specific variations existed among the three mammalian microbiomes, the microbiomes of C. albirostris and C. sumatraensis were more similar, whereas that of M. chrysogaster was markedly distinct. Metagenomic analysis revealed a pattern of functional convergence in the gut microbiome of the three species, with the gut microbiome of C. albirostris exhibiting a pronounced emphasis on carbohydrate metabolism, significantly surpassing that of M. chrysogaster and C. sumatraensis. Compared to the other two species, the gut microbiome of C. sumatraensis presented significantly elevated levels of amino acids and energy metabolism, whereas that of M. chrysogaster presented an increased capacity for 3-hydroxyacyl- [acyl carrier protein]-dehydratase production.

CONCLUSION

These findings suggest that the gut microbiome of sympatric M. chrysogaster, C. sumatraensis, and C. albirostris tend to converge. Metabolic variations within their gut microbiome may result in differential food resource utilisation, potentially indicating significant nutritional and ecological trait characteristics for stable coexistence.

No rumen fermentation profiles and associated microbial diversities difference were found between Hu sheep and Karakul sheep fed a cottonseed hull diet

BACKGROUND

This research aimed to investigate differences in rumen fermentation characteristics between Karakul sheep and Hu sheep reared under identical conditions. The test subjects included newborn Hu and Karakul sheep, which were monitored across three stages: stage I (Weaning period: 15 ~ 30 days), stage II (Supplementary feeding period: 31 ~ 90 days), and stage III (Complete feeding period: 91 ~ 150 days). During the supplementary feeding period, cottonseed hulls were the main roughage source. To analyze the dynamics of rumen fermentation, 16S rRNA sequencing and metabolomics methods were employed, alongside measurements of rumen fermentation parameters and cellulase activity. This comprehensive approach aimed to investigate the potential impact of breed on rumen fermentation indicators, microbial community structure, and metabolites in Hu and Karakul sheep.

RESULTS

The 16S rRNA sequencing analysis revealed no significant differences in the relative abundance or dominant bacterial communities in the rumen across all stages. In stage II, rumen bacteria in both Hu and Karakul sheep were relatively stable. However, the Simpson index of Hu sheep in stage II was substantially greater than that of Karakul sheep, demonstrating similarities in the rumen microbial structure between stages II and III. Dynamic variations in fermentation parameters and cellulase activity in the rumen revealed that the indicators in both sheep breeds stabilized at 150 days. Metabolomic results revealed that the metabolic pathways in stage I were mainly concentrated in purine metabolism and lipid metabolism, while stage II was dominated by amino acid metabolism. Stage III involved mainly in pyrimidine and purine metabolism. An exploration of the relationships among rumen microbial biomarkers, key differentially abundant metabolites and rumen characteristics indicated that Karakul sheep exhibited superior lipid metabolism compared to Hu sheep.

CONCLUSION

These findings reveal that there were no interbreed differences in the rumen characteristics of Hu and Karakul sheep when fed the same cottonseed hull diet, despite differences in their metabolic pathways. The findings also indicate that the first 20 days represent the initial stage of rumen bacteria in Hu sheep, followed by a transition phase between 20 and 90 days, and a relatively stable stage from 90 to 150 days. These results provide a scientific basis for further understanding the rumen function of sheep and for optimizing their feeding strategies. Video Abstract.

Studies on fatty acids and microbiota characterization of the gastrointestinal tract of Tianzhu white yaks

Introduction

The gut microbiota significantly influences the host's production performance and health status, with different gastrointestinal tissues exhibiting functional diversity reflected in their microbial diversity.

Methods

In this study, five adult male Tianzhu white yaks (4.5 years old) were selected and fed under the same nutritional conditions. After the feeding experiment, the yaks were slaughtered, and chyme samples were collected from the rumen, abomasum, jejunum, and colon for 16S rRNA full-length sequencing and volatile fatty acid analysis.

Results

The results showed that the microbial composition and diversity of the rumen and abomasum were similar, with close genetic distances and functional projections. In contrast, the jejunum and colon had distinct microbial compositions and diversity compared to the rumen and abomasum. At the phylum level, the dominant phyla in the rumen, abomasum, and colon were Firmicutes and Bacteroidetes, while in the jejunum, the dominant phyla were Firmicutes and Proteobacteria. The abundance of Firmicutes differed significantly between the jejunum (87.24%) and the rumen (54.67%), abomasum (67.70%), and colon (65.77%). Similarly, Bacteroidetes showed significant differences between the jejunum (2.21%) and the rumen (36.54%), abomasum (23.81%), and colon (28.12%). At the genus level, Rikenellaceae_RC9_gut_group and Christensenellaceae_R-7_group were dominant in both the rumen and abomasum. In the jejunum, Romboutsia and Paeniclostridium were dominant, while Rikenellaceae_RC9_gut_group and UCG-005 were the dominant genera in the colon. At the species level, rumen_bacterium_g_Rikenellaceae_RC9_gut_group and rumen_bacterium_g_Christensenellaceae_R-7_group were dominant in both the rumen and abomasum, while Clostridium_sp._g_Romboutsia and bacterium_g_Paeniclostridium were unique to the jejunum. Ruminococcaceae_bacterium_g_UCG-005 and bacterium_g_Rikenellaceae_RC9_gut_group were unique to the colon. KEGG functional prediction of the microbiota indicated that the dominant functions in the rumen, abomasum, colon, and jejunum were amino acid metabolism, glycan biosynthesis and metabolism, carbohydrate metabolism, and membrane transport, respectively, reflecting the digestive functions of these organs. Volatile fatty acid analysis showed that the concentrations of acetic acid, propionic acid, and butyric acid in the rumen were significantly higher than those in the abomasum, jejunum, and colon (p < 0.05). Among these, the propionic acid concentration in the jejunum was significantly lower than in the abomasum and colon. Additionally, correlation analysis results indicated that acetic acid and butyric acid were significantly positively correlated with the ruminal bacterial community (p < 0.05). The total volatile fatty acid concentration was highest in the rumen, decreased to less than one-fifth of the rumen's total volatile fatty acid concentration in the abomasum and jejunum, and then reached a second peak in the colon.

Conclusion

This study explored the microbial composition and differential bacterial genera in the rumen and intestines of Tianzhu white yak, comparing the differences in volatile fatty acid levels and microbial composition and function across different regions. This is important for understanding their gastrointestinal microbiota's spatial heterogeneity.

Comprehensive omics analysis of the fecal microbiome and serum metabolome in Dezhou donkey foals at the end of weaning and after weaning

Weaning is essential for foal growth and development. We determined the intestinal flora structure of donkey foals at the end of weaning (PreW_4d) and three stages after weaning (PostW_4d, PostW_8d, and PostW_15d) to explore the effects of weaning on intestinal development of donkey foals. The results showed that the main microbial flora in the gut of the donkey foal were Firmicutes and Bacteroides, and the proportion of Firmicutes gradually increased with weaning, which was an important reflection of the donkey foal's adaptability to the transition from lactose liquid feed to plant fiber solid feed. We also identified important microorganisms that maintain intestinal stability and boost immune, such as oscillospiraceae, Firmicutes, and lachnospiraceae. The metabolome showed that serum metabolites were mainly enriched in arachidonic acid metabolism and the tricarboxylic acid cycle (TCA cycle), which can influence energy metabolism, growth, and immunity in weaned donkey foals. We also found that the metabolite resveratrol was positively correlated with g_NK4A214_group and lactobacillus, which may have important implications for the prevention of diseases such as colon-inflammation in donkey foals. In summary, we provide a theoretical basis for studying the mechanism of intestinal microbiome and serum metabolite changes in weaning and postweaning donkey foals.

Effects of High-Concentrate Diets on Growth Performance, Serum Biochemical Indexes, and Rumen Microbiota in House-Fed Yaks

The aim of this study is to determine the effects of a high-concentrate diet on growth performance, serum biochemical indexes, and rumen microbiota in house-fed yaks. Sixteen male yaks (body weight, 151.73 ± 14.11 kg; 18 months) were randomly allocated into two dietary treatments: a group with a low level of concentrate (n = 8, LC, concentrate-forage = 40:60) and a group with a high level of concentrate (n = 8, HC, concentrate-forage = 60:40). We found that compared with the LC group, the average daily feed intake (ADFI), the average daily gain (ADG), and the serum albumin (ALB) concentration in the HC group were significantly increased (p < 0.05). The rumen bacterial compositions also differed significantly between the groups, as indicated by principal coordinate analysis (p < 0.05). Firmicutes and Bacteroidota were the main dominant phyla of rumen bacteria in yaks. Compared with the LC group, the relative abundance of Firmicutes in the HC group was significantly increased (p < 0.05) and the relative abundance of Bacteroidota was significantly decreased (p < 0.05). At the genus level, Rikenellaceae_RC9_gut_group, Succiniclasticum, Prevotella, Christensenellaceae_R-7_group, and NK4A214_group had the highest relative abundance. The relative abundance of Christensenellaceae_R-7_group in the HC group was significantly higher than that in the LC group (p < 0.05). The PICRUSt 2 results showed a significant enrichment in glycosaminoglycan degradation, apoptosis, and ECM-receptor interaction in HC relative to LC (p < 0.05). In conclusion, high-concentrate diets can enhance growth performance and alter the compositions and functions of ruminal bacterial communities in yaks.

Interactions between rumen epithelium-associated microbiota and host immunological and metabolic adaptations in response to different milk replacer feeding intensities in dairy calves

The milk replacer feeding regime in dairy calves has a great impact on metabolic and immunological functioning and affects animal welfare and lifetime performance. The feeding regime influences the rumen microbial composition, and epithelium-associated microbes may interact with the immune system of the host. We examined the correlations between blood leukocyte counts and the rumen epithelium-associated microbiome in dairy calves fed 2 different milk replacer feeding intensities and if these factors related to metabolic traits. Fourteen newborn female dairy calves were allocated to a group receiving either 10% (n = 7) or 20% (n = 7) milk replacer of their body weight (on average 41 kg) and provided ad libitum access to grass hay and concentrate pellets. At 3 weeks of life, all calves were fitted with a rumen cannula. Calves were weaned at 12 weeks of life and received a total mixed ration for ad libitum intake. Pre- (8-10 weeks of life) and post-weaning (21-23 weeks of life), methane production was measured in respiration chambers, and rumen epithelium and blood were sampled for 16S rRNA sequencing and leukocyte analyses, respectively. Pre-weaning, the reduced milk replacer feeding intensity was accompanied with higher concentrate intake but lower growth performance (P < 0.001), a higher abundance of amylolytic and lower abundance of cellulolytic epimural microbes. The group fed a low milk replacer intensity had also greater portions of monocytes (P = 0.031), CD8+ (P < 0.001), and CD14+ (P = 0.044) leukocytes, suggesting elevated inflammatory conditions. Correlations between CD8+ T cells and rumen methanogens, Ruminococcaceae, and Lachnospiraceae were recorded, but these were not consistent throughout maturation. Post-weaning, differences in feed intake and rumen microbial composition converged among milk replacer groups, while differences in growth performance (P = 0.040) and CD8+ cells (P < 0.001) were still present. In conclusion, a reduced milk replacer feeding intensity in dairy calves compromised growth performance and immunity and this effect persisted in the long-term. Significant correlations between the proportion of leukocytes and distinct epimural microbe taxa indicated an interplay between rumen epimural colonization and immune functioning of the host. However, further research is required addressing this interplay between rumen epimural microbes and immune functioning in dairy calves.

Effect of Dietary Concentrate-to-Forage Ratios During the Cold Season on Slaughter Performance, Meat Quality, Rumen Fermentation and Gut Microbiota of Tibetan Sheep

This study aimed to investigate the effects of different dietary concentrate-to-forage ratios on slaughter performance, meat quality, rumen fermentation, rumen microbiota and fecal microbiota in Tibetan sheep. A total of sixty male Tibetan sheep were equally allocated into three dietary groups based on concentrate-to-forage ratios, i.e., 30:70 (C30), 50:50 (C50), and 70:30 (C70). Compared with the C30 group, sheep fed the C70 diet resulted in a higher (p < 0.05) slaughter live weight (SLW), hot carcass weight (HCW), dressing percentage (DP), eye muscle area, average daily gain (ADG), and ruminal total volatile fatty acids concentration and propionate molar proportion and lower (p < 0.05) shear force and cooking loss of meat, and ruminal acetate molar proportion and acetate:propionate ratio. Sheep in the C50 group exhibited a higher (p < 0.05) SLW, HCW, ADG, and ruminal propionate molar proportion and lower (p < 0.05) shear force and cooking loss of meat, and ruminal acetate molar proportion and acetate: propionate ratio compared with the C30 group. In rumen fluid, the relative abundance of Butyrivibrio was lower (p = 0.031) in the C30 group, and that of Ruminococcus was higher (p = 0.003) in the C70 group compared with the C50 group. In feces, genus Monoglobus and UCG_002 were the most abundant in the C30 group (p < 0.05), and the relative abundance of Prevotella was significantly higher in the C70 group than in other groups (p = 0.013). Correlation analysis revealed possible links between slaughter performance and meat quality and altered microbiota composition in the rumen and feces of Tibetan sheep. Overall, feeding a C70 diet resulted in superior carcass characteristics and meat quality in Tibetan sheep, thus laying a theoretical basis for the application of short-term remote feeding during the cold season.

Diurnal shifts of rumen fermentation and microbial profiles revealed circadian rhythms of rumen bacteria, methanogens, and protozoa under high-grain and high-forage diets

In this study, we investigated how the composition and population of rumen microbiota shifted in response to diurnal oscillations under 2 different diets (high grain vs. high forage). Five multiparous Holstein dairy cows with similar BW, DIM, and parity were enrolled in this study. The cows were fed high-grain (HG) diet for 21 d and then shifted to high-forage (HF) diet in the next 21 d (7-d washout and 14-d experimental period). During the experimental period, DMI and rumination activity were recorded, and rumen fluid was collected 8 times postfeeding every 6 h during the last 2 d of each dietary feeding period. The rumen microbial (bacterial, archaeal, and protozoal) population and composition were assessed using quantitative PCR and amplicon sequencing, respectively. The daily dynamic of measurements was assessed using the cosinor model. The associations between microbial taxa and rumen fermentation profiles were assessed using the linear mixed model, in which the cows were termed as random intercept effects. Daily rhythmicity was observed for DMI, rumination activity, and rumen fermentation profiles under both diets. Additionally, rumination time, rumen pH, and acetate/propionate ratio had a higher mesor (the average level of diurnal fluctuations) under HF diet than in HG diet. The amplitude (the distance between the peak and mesor) of DMI, rumen pH, ammonia nitrogen, and total volatile acid concentration were higher under the HG diet than in the HF diet. Although no significant diurnal oscillation was observed for the rumen microbial population, the relative abundance of 14 bacterial genera, 1 protozoal genus, and 2 archaeal species had significant diurnal oscillations under both HF and HG diets. Among them, the bacterial genera Ruminococcus and Colidextribacter had time at peak of rhythm within 0 to 12 h after feeding, which were also negatively associated with the rumen acetate/propionate ratio. The bacterial genus Rikenellaceae_RC9_gut_group had time at peak of rhythm within 12 to 24 h after feeding, which was also positively associated with the ruminal acetate/propionate ratio. Our study illustrated the daily dynamic on the rumen microbiota population and composition under different diets, and also identified the feeding-responsive rumen microbiota, highlighting that a more targeted approach is needed to manipulate rumen microbiota.

Investigation of guanidino acetic acid and rumen-protected methionine induced improvements in longissimus lumborum muscle quality in beef cattle

This study examined the impact of dietary guanidino acetic acid (GAA) and rumen-protected methionine (RPM) on beef quality in Simmental bulls. For 140 days, forty-five bulls (453.43 ± 29.05 kg) were randomly divided into control (CON), 0.1% GAA (GAA), and 0.1% GAA + 0.1% RPM (GAM) groups with 15 bulls in each group and containing 3 pen with 5 bulls in each pen. Significant improvements in eye muscle area, pH48h, redness (a*) value, and crude protein (CP) content of longissimus lumborum (LL) muscles were observed in the GAA and GAM groups (P < 0.05). Conversely, the lightness (L*) value, drip loss, cooking loss, and moisture contents decreased (P < 0.05). Additionally, glutathione (GSH) and glutathione peroxidase (GSH-PX) concentrations of LL muscles in GAM were higher (P < 0.05), while malondialdehyde (MDA) content of LL muscles in GAA and GAM groups were lower (P < 0.05). Polyunsaturated fatty acids (PUFA) profiles were enriched in beef from GAM group (P < 0.05). The addition of GAA and RPM affected the expression of genes in LL muscle, such as HMOX1, EIF4E, SCD5, and NOS2, which are related to hypoxia metabolism, protein synthesis, and unsaturated fatty acid synthesis-related signaling pathways. In addition, GAA and RPM also affected the content of a series of metabolites such as L-tyrosine, L-tryptophan, and PC (O-16:0/0:0) involved in amino acid and lipid metabolism-related signaling pathways. In summary, GAA and RPM can improve the beef quality and its nutritional composition. These changes may be related to changes in gene expression and metabolic pathways related to protein metabolism and lipid metabolism in beef.

Fermented Palm Kernel Cake Improves the Rumen Microbiota and Metabolome of Beef Cattle

In this study, we utilised palm kernel cake as a substrate and fermented it with a composite of bacteria (Pediococcus pentosaceus CGMCC No. 27203 and Lactobacillus plantarum CGMCC No. 27202) and enzymes. We conducted a trial with twenty-four cattle, randomly divided into two groups of twelve cattle each. The control group (CON) was fed the standard farm diet, whereas the treatment group (PKC) received a diet with 3% of soyabean replaced by fermented palm kernel cake. The trial lasted for six weeks. The results showed no significant differences in growth performance between the PKC and CON groups. The abundance of Firmicutes, Bacteroidetes, Proteobacteria, and Spirochaetes was significantly higher in the PKC group than in the CON group. At the genus level, the abundances of Anaeroplasma, norank_f__Bacteroidales_UCG-001, norank_f__Absconditabacteriales_SR1, norank_f__p-251-o5, Prevotellaceae_NK3B31_group, Prevotellaceae_UCG-001, Prevotellaceae_UCG-004, and Treponema significantly increased in the PKC group. Lipid digestion and absorption pathways were significantly enriched in the PKC group. The results indicate that adding fermented palm kernel cake to the diet can increase the abundance of Bacteroidetes and Fibrobacteres in the rumen of beef cattle, enhancing the ability of the PKC group to degrade protein, carbohydrates, and fibrous materials in the feed, thereby improving the feed utilisation efficiency in beef cattle. Adding fermented palm kernel cake to the diet improved carbohydrate metabolism, metabolism of cofactors and vitamins, and nucleotide metabolism. Correlation analysis between the rumen microbiota and metabolic pathways showed that Prevotellaceae_UCG-001 and Prevotellaceae_UCG-003 were positively correlated with amino acid metabolism, Rikenellaceae_RC9_gut_group and Succiniclasticum were positively correlated with metabolism of cofactors and vitamins, and Prevotella and Ruminococcus were positively correlated with nucleotide metabolism. These findings elucidate the differences in rumen microbiota when fermented palm kernel cake is added to the diet, providing a theoretical basis for the application of fermented palm kernel cake in the diet of beef cattle.

Different sources of alfalfa hay alter the composition of rumen microbiota in mid-lactation Holstein cows without affecting production performance

Alfalfa hay is a commonly used and important feed ingredient in dairy production. To better expand the alfalfa supply market, it is of great significance to explore the impact of alfalfa hay from different sources on dairy cow production performance. This study compared the effects of imported alfalfa hay from America (AAH) and Spain (SAH) on lactation performance and rumen microbiota of cows. Three hundred and sixty healthy mid-lactation Holstein cows with similar body weight, milk yield, and parity were randomly divided into two groups fed diets based on AAH or SAH for a 70-day experimental period. Each group was composed of four pens, with 45 cows in each pen. Daily records were kept for MY per cow and dry matter intake per pen. Twelve randomly selected cows per group were sampled to collect milk, feces, rumen fluid, and blood. The findings revealed no significant differences between the two groups in terms of production performance, nutrient apparent digestibility, serum biochemical indices, or rumen fermentation parameters. However, rumen microbial composition differed significantly between the two groups of cows based on β-diversity. On the genus level, the relative abundance of Prevotella, Succinivibrionaceae_UCG-002 increased while that of NK4A214_group, Ruminococcus, norank_f_F082 and Lachnospiraceae_NK3A20_group decreased in the SAH group compared with AAH group. There was no significant correlation between these core differential bacteria and the molar proportions of acetate and propionate, the concentration of total volatile fatty acids, and milk yield. In conclusion, the feeding effects of SAH were similar to those of AAH. These findings provided a reference for the application of alfalfa hay from different sources and for the improvement of the economic benefit of dairy farms.

GnRH Immunocastration in Male Xizang Sheep: Impacts on Rumen Microbiome and Metabolite Profiles for Enhanced Health and Productivity

Castration is a prevalent and indispensable practice in sheep husbandry, aiding in enhancing meat quality, mitigating aggressive behavior, and managing unwanted reproduction. Nevertheless, the conventional surgical castration procedure poses several challenges, including heightened stress and pain, detrimental impacts on animal welfare, and diminished economic efficacy in farming operations. Consequently, immunocastration methods, serving as substitutes for surgical castration, are progressively finding application in livestock. The rumen, an essential and distinctive digestive and absorptive organ in ruminants, has been associated with enhanced meat quality and productive performance following castration in previous research studies, albeit fewer investigations have explored the potential impacts of GnRH immunization on the rumen's internal milieu in sheep post-de-escalation. Hence, the present study delved into evaluating the impact of GnRH immunocastration on the rumen microbiome and metabolomics in male Xizang sheep. This was achieved through the establishment of a GnRH immunocastration animal model and the collection of rumen fluid for microbiological and comprehensive metabolomics investigations. The outcomes of this investigation unveiled that the impact of GnRH immunocastration on body weight gain was more pronounced during the achievement of the castration objective. In addition, the Firmicutes-to-Bacteroidota ratio in the immune male (IM) group exceeded that of the control group (EM), suggesting that GnRH immunodeficiency may enhance the digestion and absorption of feed in male Xizang sheep. At the taxonomic level, the elevated presence of Prevotella and Quinella bacteria in the IM group compared to the EM group indicated that castration influenced a segment of the rumen microbiota in male Xizang sheep, thereby bolstering the digestive and metabolic efficacy of the rumen concerning nutrient utilization, particularly in the breakdown and absorption of proteins, carbohydrates, and lipids, ultimately expediting the fattening process and weight gain in male Xizang sheep following castration. Moreover, analysis of ruminal fluid metabolomics revealed that GnRH immunization had notable impacts on certain metabolites in the ruminal fluid of male Xizang sheep, with metabolites like 5-hydroxyindole acetic acid and 3-hydroxyindole acetic acid showing significant downregulation in the IM group compared to the EM group, while niacin and tyramine exhibited significant upregulation. These findings indicate a profound influence of GnRH immunization on the maintenance of ruminal equilibrium and ruminal health (including the health of ruminal epithelial cells). This study validates that GnRH immunocastration not only achieves the objectives of castration but also enhances ruminal health in male Xizang sheep, thus laying a foundational theoretical basis for the application and dissemination of GnRH immunocastration technology.

A Comparison of Growth Performance, Blood Parameters, Rumen Fermentation, and Bacterial Community of Tibetan Sheep When Fattened by Pasture Grazing versus Stall Feeding

Traditionally, Tibetan sheep only graze pastures without any supplementary feed. However, in recent years, feedlots are being used for fattening Tibetan sheep. The present study compared the growth rates, blood parameters, rumen fermentation, and bacterial communities in Tibetan sheep fattened by pasture grazing (PG) versus those fattened by stall feeding (SF). Twenty 18-month-old Tibetan sheep wethers (42.6 ± 2.11 kg) were divided randomly into PG (n = 10) and SF (n = 10) groups. The PG sheep grazed the grasslands without any supplementary feed, while the SF sheep were offered a commercial total mixed ration (TMR) at a crude protein content of 16.2% DM and an ME of 10.59 MJ/kg. The sheep were on their treatments for 70 days, which included 10 days for adaptation and 60 days for measurements. The average daily gain, white blood cell and lymphocyte counts were greater (p < 0.05), while the platelet count was lower (p < 0.05) in the SF group than in the PG group. The serum glutathione peroxidase activity, and concentrations of total proteins and albumin were greater (p < 0.05), while glucose was lower (p < 0.01) in the PG group compared to the SF group. The concentrations of ruminal ammonia-N and total volatile fatty acids (VFAs) were greater (p < 0.05), while the pH was lower (p < 0.05) in the SF group compared to the PG group. The molar proportion of acetate and the ratio of acetate to propionate were greater (p < 0.01) in the PG sheep than in the SF sheep, but the molar proportion of propionate and iso-VFAs did not differ (p > 0.05) between the groups. Based on the PCoA, the ruminal bacterial communities were distinct between groups, and the alpha diversity was greater (p < 0.001) in the PG sheep than in the SF sheep. The dominant phyla of the rumen bacteria were Firmicutes and Bacteroidetes, while the Firmicutes to Bacteroidetes ratio was greater (p < 0.001) in the SF group than in the PG group. At the genus level, the relative abundance of Ruminococcus was greater (p < 0.05) in the SF group, while the abundances of Prevotella, the Rikenellaceae_RC9_gut_group, Butyrivibrio, and unclassified_f_Lachnospiraceae were greater (p < 0.05) in the PG group. It was concluded that the Tibetan sheep adopted a short-term intensive fattening strategy when stall fed which altered the rumen bacterial community and blood parameters, enhanced rumen fermentation, and, ultimately, improved their average daily gain.

Multi-omics analysis reveals the effects of host-rumen microbiota interactions on growth performance in a goat model

The growth rate of young ruminants has been associated with production performance in later life, with recent studies highlighting the importance of rumen microbes in supporting the health and growth of ruminants. However, the specific role of rumen epithelium bacteria and microbiota-host interactions in influencing the early life growth rate of ruminants remains poorly understood. In this study, we investigated the rumen fermentation pattern, microbiota characteristics, and global gene expression profiles of the rumen epithelium in 6-month-old goats with varying growth rates. Our results showed that goats with high average daily gain (HADG) exhibited higher rumen propionate concentrations. Goats with low average daily gain (LADG) had the higher relative abundances of rumen epithelium bacteria genera U29-B03 and Quinella, while exhibiting a lower relative abundance of Lachnospiraceae UCG-009. In the rumen fluid, the relative abundances of bacteria genus Alloprevotella were lower and Desulfovibrio were higher in LADG goats compared to HADG goats. Additionally, the relative abundance of fungal genus Symmetrospora was lower in LADG goats compared to HADG goats. Transcriptome analysis showed that 415 genes were differentially expressed between LADG and HADG goats, which were enriched in functions related to cell junction and cell adhesion, etc. Correlation analysis revealed that rumen epithelium bacteria genera UCG-005 and Candidatus Saccharimonas were negatively associated, while Lachnospiraceae NK3A20 group and Oscillospiraceae NK4A214 group were positively associated with average daily gain (ADG) and genes related to barrier function. The rumen fluid bacteria genus Alloprevotella was positively correlated, while Desulfovibrio was negatively correlated with rumen propionate and ammoniacal nitrogen (NH3-N) concentrations, as well as genes related to barrier function and short chain fatty acids (SCFAs) transport. In summary, our study reveals that the higher ruminal fermentation efficiency, improved rumen epithelial barrier functions, and enhanced SCFAs transport in HADG goats could be attributed to the rumen microbiota, particularly the rumen epithelium bacteria, such as Lachnospiraceae and Oscillospiraceae NK4A214 group.

Targeted and untargeted metabolomics reveals meat quality in grazing yak during different phenology periods on the Qinghai-Tibetan Plateau

Yak meat is more popular among consumers because of its high nutritional value, but little attention has been paid to its meat quality, which is affected by different phenology periods grass. We hypothesized that seasonal variations in grass composition influenced the ruminal bacteria community, and eventually affected the meat quality of yaks. This study aims to investigate the relationship of meat quality in grazing yak as well as the key rumen bacteria using targeted and untargeted metabolomics and 16S rRNA during different phenology periods. The main three altered metabolic pathways in grazing yak, including amino acids biosynthesis, glutathione metabolism, and fatty acids biosynthesis, were found in the grass period (GP) group compared to the regreen period (RP) and hay period (HP) groups. The GP group had higher concentrations of flavor amino acids (FAA), polyunsaturated fatty acids (PUFA), and a lower ratio of n-6/n-3 compared with the RP group. Correlation analysis results showed that Rikenellaceae_RC9_gut_group was positively correlated with fatty acids and lipid metabolites, which might be involved in lipid metabolism. Pediococcus had a positive correlation with biological peptides, which could be involved in the metabolism of bioactive compounds. In conclusion, grass in different phenology periods was associated with modified amino acids and fatty acids composition of yak meat as well as altered regulation of biological pathways, which was correlated with changes in rumen bacterial communities.

Effects of atrazine on movement, metabolism and gene expression in Pelophylax nigromaculatus larvae under global warming

Global warming and environmental pollutants both pose a threat to the behavior and physiology of animals, but research on the combined effects of the two is limited. Atrazine, a widely used herbicide, has toxic effects on organisms. In this study, the effects of environmental concentrations of atrazine exposure (100 μg/L) for seven days on the movement, metabolism and gene expression related to motility of Pelophylax nigromaculatus larvae (GS8) were investigated under global warming. The results showed that compared to the optimal growth temperature (18 °C), atrazine treatment under global warming (21 °C) significantly increased the average speed (about 11.2 times) and maximum acceleration (about 1.98 times) of P. nigromaculatus larvae, altered the relative abundance of 539 metabolites, including Formyl-5-hydroxykynurenamine, 2,4-Dihydroxybenzophenone, and FAPy-adenine, and changed the nucleotide metabolism, pyrimidine metabolism, glycerophospholipid metabolism, and purine metabolism, as well as increased the gene expression of SPLA2 (about 6.46 times) and CHK (about 3.25 times). In summary, atrazine treatment under global warming caused metabolic disorders in amphibian larvae and increased the expression of some movement-related genes in the brain, resulting in abnormally active.

The Changes in Fecal Bacterial Communities in Goats Offered Rumen-Protected Fat

Leizhou goats are famous for their delicious meat but have inferior growth performance. There is little information on rumen-protected fat (RPF) from the Leizhou goat. Hence, we observed the effects of RPF on growth, fecal short-chain fatty acids, and bacteria community with respect to Leizhou goats. Twelve goats (13.34 ± 0.024 kg) were selected and assigned randomly to one of two treatments: (1) a control diet (CON) and (2) 2.4% RPF with a control diet (RPF). The final body weight and average daily gain (ADG) were greater (p < 0.05), and the dry matter intake (DMI): ADG was lower (p < 0.05) in the RPF group than in the CON group. There were no differences in DMI between the CON and RPF groups. The concentrations of total short-chain fatty acids, acetate, propionate, and butyrate were lower (p < 0.05) in the RPF group than in the CON group. The relative abundances of Ruminococcus, Rikenellaceae_RC9_gut_group, Treponema, norank_f__norank_o__RF39, Eubacterium_siraeum_group, and Ruminococcus_torques_group were lower (p < 0.05) in the RPF group than in the CON group. The relative abundances of Bacteroides, norank_f__norank_o__Clostridia_UCG-014, norank_f__Eubacterium_coprostanoligenes_group, Eubacterium_ruminantium_group, norank_f__Oscillospirale-UCG-010, Oscillospiraceae_UCG-002, and Family_XIII_AD3011_group were greater (p < 0.05) in the RPF group than in the CON group. It was concluded that RPF could improve the goats' growth performance by regulating their fecal bacteria communities.

Intensive feeding alters the rumen microbiota and its fermentation parameters in natural grazing yaks

Introduction

Amidst the challenging environmental conditions characterized by low oxygen levels and cold temperatures on the plateau, alterations in nutrient supply emerge as pivotal factors influencing the survival and reproduction of yaks. Intensive feeding stands out as a substantial mechanism for nutrient provision, initiating discernible changes in the host's rumen flora. Within the extreme natural conditions prevailing in the plateau area of northwest Yunnan, China, there exists a con-strained comprehension of the variations in rumen microflora, fermentation parameters, and growth responses exhibited by yaks subjected to intensive feeding.

Methods

This study employs 16S rRNA and ITS sequencing methods to scrutinize the rumen flora of yaks engaged in both natural grazing (G) and intensive feeding (F) on the plateau.

Results

The outcomes unveil that, during the severe winter season, yaks adeptly modulate the abundance and diversity of rumen flora in response to dietary modifications under intensive feeding, aiming to optimize the efficient utilization of dietary fiber and energy. Principal Coordinate Analysis (PCoA) illustrates a substantial alteration in the rumen microbial community of naturally grazing yaks when exposed to intensive feeding. The natural grazing group manifests a higher prevalence of Firmicutes and Bacteroidetes, while the intensive feeding group exhibits heightened levels of Prevotella in the rumen. The Rikenellaceae _ RC9 _ gut_ group, associated with mycobacteria, prevails more abundantly in the natural grazing setting. PICRUSt2 analysis indicates that intensive feeding induces bacterial gene overexpression linked to protein metabolism. Rumen fungi showcase heightened diversity under intensification. Intensive feeding results in an augmented abundance of non-fiber-degrading bacteria and semi-fiber-degrading bacteria, accompanied by elevated concentrations of Volatile Fatty Acids (VFA).

Discussion

These findings yield novel insights into the shifts in the rumen microflora of yaks acclimated to intensive feeding in high-altitude environments, provide an important reference for the nutritional regulation of supplemental feeding of natural grazing yaks in the cold season, ultimately contributing to their enhanced growth.

Maintaining the native gut microbiota of bharal (Pseudois nayaur) is crucial in ex situ conservation

As wildlife protection continue to strengthen, research on the gut microbiota of wildlife is increasing. Carrying out conservation and research on endangered species in the Qinghai Tibet Plateau plays an important role in global biodiversity conservation. This study utilized 16S rRNA sequencing of fecal samples to investigate the composition, function, and changes of the gut microbiota of bharal in different environments, seasons, and genders. The results showed that Firmicutes and Bacteroidota were the dominant phyla and UCG-005, Bacteroides, UCG-010 were the dominant genera of bharal. In the wild, the abundance of Firmicutes increased which was conducive to the decomposition and utilization of cellulose, hemicellulose, and carbohydrate. Due to the variety of food types and nutrition in different seasons, the composition and function of gut microbiota were obviously different between genders. Compared with zoo, higher alpha diversity, a more complex gut microbiota network structure, and stronger metabolic function were conducive bharal to adapting to the wild environment. In the zoo, captive bharals were fed foods rich in high fat and protein, which increased the abundance of Bacteroidota and reduced the alpha diversity of gut microbiota. A fixed diet unified the gut microbiota between genders of bharal. It is very important to pay attention to the impact of captive environments and maintain the native gut microbiota of wildlife.

Effects of type of substrate and dilution rate on fermentation in serial rumen mixed cultures

Forages and concentrates have consistently distinct patterns of fermentation in the rumen, with forages producing more methane (CH4) per unit of digested organic matter (OM) and higher acetate to propionate ratio than concentrates. A mechanism based on the Monod function of microbial growth has been proposed to explain the distinct fermentation pattern of forages and concentrates, where greater dilution rates and lower pH associated with concentrate feeding increase dihydrogen (H2) concentration through increasing methanogens growth rate and decreasing methanogens theoretically maximal growth rate, respectively. Increased H2 concentration would in turn inhibit H2 production, decreasing methanogenesis, inhibit H2-producing pathways such as acetate production via pyruvate oxidative decarboxylation, and stimulate H2-incorporating pathways such as propionate production. We examined the hypothesis that equalizing dilution rates in serial rumen cultures would result in a similar fermentation profile of a high forage and a high concentrate substrate. Under a 2 × 3 factorial arrangement, a high forage and a high concentrate substrate were incubated at dilution rates of 0.14, 0.28, or 0.56 h-1 in eight transfers of serial rumen cultures. Each treatment was replicated thrice, and the experiment repeated in two different months. The high concentrate substrate accumulated considerably more H2 and formate and produced less CH4 than the high forage substrate. Methanogens were nearly washed-out with high concentrate and increased their initial numbers with high forage. The effect of dilution rate was minor in comparison to the effect of the type of substrate. Accumulation of H2 and formate with high concentrate inhibited acetate and probably H2 and formate production, and stimulated butyrate, rather than propionate, as an electron sink alternative to CH4. All three dilution rates are considered high and selected for rapidly growing bacteria. The archaeal community composition varied widely and inconsistently. Lactate accumulated with both substrates, likely favored by microbial growth kinetics rather than by H2 accumulation thermodynamically stimulating electron disposal from NADH into pyruvate reduction. In this study, the type of substrate had a major effect on rumen fermentation largely independent of dilution rate and pH.

Effect of Garlic Straw with Silage Corn Stalks on Hu Sheep Rumen Fermentation and Microbial Community In Vitro

Garlic, an important economic crop, provides nutrient-rich straw. When appropriately balanced with silage corn stalks, it is a high-quality forage resource. However, studies on the impact of garlic straw with silage corn stalks on Hu sheep's digestive metabolism and rumen microbiota are scarce. In this study, different addition ratios of garlic straw and silage corn stalks were utilized for in vitro experiments. We designed six experimental groups (CON, G0, G20, G40, G60, G80, and G100) based on varying ratios of garlic straw to silage corn stalks. Rumen microbiota was analyzed through 16S rRNA sequencing. Nutrient composition analysis indicated that garlic straw's relative feeding value (RFV) closely resembled that of silage corn stalks. After 24 h of fermentation, dry matter digestibility and in vitro gas production significantly increased, reaching peak values at a 60% addition ratio. Furthermore, volatile fatty acids (VFAs) such as acetic, propionic, and butyric acid exhibited elevated contents, with the highest yields observed at 60% inclusion. At the genus level, Prevotella, Rikenellaceae RC9 gut group, and Succiniclasticum were identified as the dominant bacterial groups. The gas production test showed a significant decrease in the G80 group compared to others. Microbial analysis revealed a higher abundance of Prevotella in G80 compared to G20, offering valuable insights for reducing greenhouse gas emissions from ruminant animals. Finally, this study predicted the impact of garlic straw with silage corn stalks' addition on Hu sheep's metabolic pathways and biological functions of the rumen microbiota. This research highlights the potential for effectively utilizing garlic straw as a feed resource for Hu sheep and proposes a rational proportion for combining garlic straw with silage corn stalks.

Probiotic-Fermented Distillers Grain Alters the Rumen Microbiome, Metabolome, and Enzyme Activity, Enhancing the Immune Status of Finishing Cattle

A total of 30 Simmental crossbred cattle (6.50 months old, 265.0 ± 22.48 kg) were randomly divided into three groups, with 10 heads per group, and fed for 45 days. The diet treatments consisted of the Control group without PFDG supplementation, the PFDG-15% group with 15% PFDG substituting for 15% concentrate, and PFDG-30% group with 30% PFDG substituting for 30% concentrate. The results showed that compared with the Control group, the average daily gain (ADG) of the cattle in the PFDG-30% group decreased significantly (0.890 vs. 0.768 kg/d, p = 0.005). The serum malondialdehyde content of cattle in the PFDG-15% and PFDG-30% groups decreased significantly (p = 0.047) compared to that of the Control group. However, the serum superoxide dismutase activity of cattle in the PFDG-30% group was significantly higher than that of the Control group (p = 0.047). Meanwhile, both the PFDG-15% and PFDG-30% groups (1758.47 vs. 2061.30 μg/mL) showed higher serum levels of immunoglobulin G, while the interleukin-10 concentration was lower in the PFDG-30% group (p = 0.027). In addition, the PFDG-15% and PFDG-30% groups shifted the rumen microbiota by improving the abundances of F082 (related to propionic acid production) and fiber-degrading bacteria (Lachnospiraceae_UGG-009 and Prevotellaceae_UCG-001) and reducing the abundance of the disease-associated bacteria Selenomonas. A Kyoto encyclopedia of genes and genomes (KEGG) analysis illustrated that three key metabolic pathways, including phenylalanine metabolism, pyrimidine metabolism, and tryptophan metabolism, were enriched in the PFDG-15% group, but eight key metabolic pathways, including arachidonic acid metabolism, were enriched in the PFDG-30% group. Importantly, both the PFDG-15% and PFDG-30% groups increased (p < 0.01) the activities of cellulase, lipase, and protease in the rumen. Finally, the different bacterial abundance in the rumen was associated with changes in the ADG, serum antioxidant capacity, immune status, rumen enzyme activity, and metabolites. These results suggest that PFDG alters rumen microbiome abundance, metabolome, and enzyme activity for enhancing serum antioxidant capacity and the immune status, but when the supplemental level reaches 30%, it has a negative effect on ADG and the anti-inflammatory factors in finishing cattle.

N-carbamylglutamate supplementation regulates hindgut microbiota composition and short-chain fatty acid contents in Charollais and Small Tail Han crossbred sheep

Introduction

The objective of this study was to investigate the effects of N-carbamylglutamate (NCG) supplementation on the growth performance, hindgut microbiota composition, and short-chain fatty acid (SCFA) contents in Charollais and Small Tail Han crossbred sheep.

Methods

A total of 16 female crossbred mutton sheep (Charollais × Small Tail Han), aged 4 months, with an initial body weight of 30.03 ± 0.08 kg, were utilized in a 60 days experiment. The sheep were divided into two groups based on their initial body weight. Each group consisted of 8 replicates, with each individual sheep considered as a replicate. The dietary treatments comprised a basal diet supplemented with either 0.00% or 0.12% NCG.

Results and discussion

Our findings indicate that NCG supplementation did not have a significant effect on the growth performance of mutton sheep. However, it did lead to changes in hindgut SCFA contents. Specifically, NCG supplementation increased the content of propanoic acid while decreasing acetic acid and hexanoic acid in the hindgut. Through microbiota analysis using the 16S rRNA technique, we identified Lachnospiraceae_NK3A20_group and Parasutterella as biomarkers for the hindgut microbiota in mutton sheep fed a diet containing NCG. Further analysis of the microbiota composition revealed that NCG supplementation significantly increased the abundance of Lachnospiraceae_NK3A20_group and Parasutterella, while decreasing unclassified_f_Lachnospiraceae and Lachnoclostridium. Correlation analysis between hindgut SCFA contents and microbiota composition revealed that the abundance of Lachnoclostridium was positively correlated with the contents of acetic acid and hexanoic acid, but negatively correlated with propanoic acid. Additionally, the abundance of Lachnospiraceae_NK3A20_group and Parasutterella was positively correlated with the content of propanoic acid, while being negatively correlated with acetic acid and hexanoic acid. Based on these findings, we conclude that dietary supplementation of 0.12% NCG can modulate hindgut SCFA contents in mutton sheep by regulating the composition of the hindgut microbiota.

Effects of Phlorotannins from Sargassum on In Vitro Rumen Fermentation, Microbiota and Fatty Acid Profile

The fatty acid profiles of ruminant-derived products are closely associated with human health. Ruminal microbiota play a vital role in modulating rumen biohydrogenation (BH). The aim of this study was to assess the influence of dietary supplementation with phlorotannins (PTs) extracted from Sargassum on rumen fermentation, fatty acid composition and bacterial communities by an in vitro culture study. The inclusion of PTs in the diet increased dry matter digestibility and gas production, and reduced ammonia-N concentration and pH. PT extract inhibited rumen BH, increasing the content of trans-9 C18:1, cis-9 C18:1, trans-9 and trans-12 C18:2 and reducing C18:0 concentration. 16S rRNA sequencing revealed that PTs caused an obvious change in rumen bacterial communities. The presence of Prevotella decreased while carbohydrate-utilizing bacteria such as Prevotellaceae_UCG-001, Ruminococcus, Selenomonas, Ruminobacter and Fibrobacter increased. Correlation analysis between rumen FA composition and the bacterial microbiome revealed that Prevotellaceae_UCG-001, Anaerovorax, Ruminococcus, Ruminobacter, Fibrobacter, Lachnospiraceae_AC2044_group and Clostridia_UCG-014 might have been involved in the BH process. In conclusion, the results suggest that the inclusion of PTs in the diet improved rumen fermentation and FA composition through modulating the rumen bacterial community.

Effects of Heated Drinking Water during the Cold Season on Serum Biochemistry, Ruminal Fermentation, Bacterial Community, and Metabolome of Beef Cattle

This study explored the effects of drinking heated water in the cold seasons on the serum metabolism, rumen microbial fermentation, and metabolome of beef cattle. Twelve fattening cattle (642 ± 14.6 kg) aged 21 to 22 months were randomly and equally divided into two groups based on body weight: one receiving room-temperature water (RTW; average 4.39 ± 2.55 °C) and the other heated water (HW; average 26.3 ± 1.70 °C). The HW group displayed a significant decrease in serum glucose (p < 0.01) and non-esterified fatty acid (p < 0.01), but increases in insulin (p = 0.04) and high-density lipoprotein (p = 0.03). The rumen fermentation parameters of the HW group showed substantial elevations in acetate (p = 0.04), propionate (p < 0.01), isobutyrate (p = 0.02), and total volatile fatty acids (p < 0.01). Distinct bacterial composition differences were found between RTW and HW at the operational taxonomic unit (OTU) level (R = 0.20, p = 0.01). Compared to RTW, the HW mainly had a higher relative abundance of Firmicutes (p = 0.07) at the phylum level and had a lower abundance of Prevotella (p < 0.01), norank_f_p-215-o5 (p = 0.03), and a higher abundance of NK4A214_group (p = 0.01) and Lachnospiraceae_NK3A20_group (p = 0.05) at the genus level. In addition, NK4A214_group and Lachnospiraceae_NK3A20_group were significantly positively correlated with the rumen propionate and isovalerate (r > 0.63, p < 0.05). Prevotella was negatively correlated with rumen propionate and total volatile fatty acids (r = -0.61, p < 0.05). In terms of the main differential metabolites, compared to the RTW group, the expression of Cynaroside A, N-acetyl-L-glutamic acid, N-acetyl-L-glutamate-5-semialdehyde, and Pantothenic acid was significantly upregulated in HW. The differentially regulated metabolic pathways were primarily enriched in nitrogen metabolism, arginine biosynthesis, and linoleic acid metabolism. Prevotella was significantly positively correlated with suberic acid and [6]-Gingerdiol 3,5-diacetate (r > 0.59, p < 0.05) and was negatively correlated with Pantothenic acid and isoleucyl-aspartate (r < -0.65, p < 0.05). NK4A214_group was positively correlated with L-Methionine and glycylproline (r > 0.57, p < 0.05). Overall, our research demonstrates the important relationship between drinking water temperature and metabolic and physiological responses in beef cattle. Heating drinking water during cold seasons plays a pivotal role in modulating internal energy processes. These findings underscore the potential benefits of using heated water as a strategic approach to optimize energy utilization in beef cattle during the cold seasons.

Concentrate supplementation improves cold-season environmental fitness of grazing yaks: responsive changes in the rumen microbiota and metabolome

Yak (Bos grunniens) is an important economic animal species on the Qinghai-Tibet Plateau. Yaks grazed in the cold season often suffer from nutritional stress, resulting in low production performance. This situation can be improved by properly feeding the grazing yaks in the cold season; however, there is still little information about the effect of different feeding levels on the intestinal microflora and metabolites of yaks. Therefore, this study aimed to explore the effect of feeding different doses of concentrate supplements on rumen bacterial communities and metabolites in grazing yaks during the cold season. Feed concentrate supplementation significantly improved the production performance and rumen fermentation status of grazing yaks during the cold season, and switched the type of ruminal fermentation from acetic acid fermentation to propionic acid fermentation. Ruminal fermentation parameters and ruminal bacterial abundance correlated strongly. At the phylum level, the abundance of Firmicutes increased with increasing concentrate supplementation, while the opposite was true for Bacteroidota. At the genus level, the abundance of Christensenellaceae_R-7_group, NK4A214_group, Ruminococcus, norank_f__Eubacterium_coprostanoligenes_group, norank_f__norank_o__ Clostridia_UCG-014, Lachnospiraceae_NK3A20_group, Acetitomaculum, and Family_XIII_AD3011_group increased with increasing concentrate supplementation, while the abundance of Rikenellaceae_RC9_gut_ group decreased. Dietary concentrate supplementation altered the concentration and metabolic mode of metabolites in the rumen, significantly affecting the concentration of metabolites involved in amino acid and derivative metabolism (e.g., L-aspartic acid, L-glutamate, and L-histidine), purine metabolism (e.g., guanine, guanosine, and hypoxanthine), and glycerophospholipid metabolism (e.g., phosphatidate, phosphatidylcholine, and phosphocholine), and other metabolic pathways. The strong correlation between yak rumen microorganisms and metabolites provided a more comprehensive understanding of microbial community composition and function. This study showed significant changes in the composition and abundance of bacteria and metabolites in the rumen of cool season grazing yaks fed with concentrate supplements. Changes in ruminal fermentation parameters and metabolite concentration also showed a strong correlation with ruminal bacterial communities. These findings will be helpful to formulate supplementary feeding strategies for grazing yaks in the cold season from the perspective of intestinal microorganisms.

Responses of rumen microorganisms and metabolites to different roughage of domesticated Tibetan sheep

Tibetan sheep can utilize high fiber feeds well. However, the mechanisms of rumen microbiota and metabolites in response to different roughage in a housed environment are still unclear. We fed Tibetan sheep with three different roughage diets: 50% whole corn silage (TS), 50% wheatgrass group (TW), and 25% each of whole corn silage and wheatgrass (TM). Subsequently, meat traits, rumen contents 16S rRNA and metabolomics were studied. The results showed that feeding wheat straw to Tibetan sheep significantly increased the abundance of bacteria such as Ruminococcus and Succiniclasticum in the rumen. These microorganisms significantly increased metabolites such as beta-alanyl-L-lysine, butanoic acid and prostaglandin E2. Eventually, production performance, such as carcass weight and intramuscular fat and meat quality characteristics, such as color and tenderness were improved by altering the rumen's amino acid, lipid and carbohydrate metabolism. This study demonstrated that including 25% wheatgrass and 25% whole corn silage in the diet improved the performance of Tibetan sheep, revealing the effect of the diet on the performance of Tibetan sheep through rumen microorganisms and metabolites.

Isoacids supplementation improves growth performance and feed fiber digestibility associated with ruminal bacterial community in yaks

Introduction

This study was conducted to assess the effect of mixed isoacid (MI) supplementation on fermentation characteristics, nutrient apparent digestibility, growth performance, and rumen bacterial community in yaks.

Methods

A 72-h in vitro fermentation experiment was performed on an ANKOM RF gas production system. MI was added to five treatments at doses of 0, 0.1%, 0.2%, 0.3%, 0.4%, and 0.5% on the dry matter (DM) basis of substrates using a total of 26 bottles (4 bottles per treatment and 2 bottles as the blank). Cumulative gas production was measured at 4, 8, 16, 24, 36, 48, and 72 h. Fermentation characteristics including pH, the concentration of volatile fatty acids (VFAs), ammonia nitrogen (NH3-N), microbial proteins (MCP), and the disappearance rate of dry matter (DMD), neutral detergent fiber (NDFD), and acid detergent fiber (ADFD) were measured after a 72-h in vitro fermentation to determine an optimal MI dose. Fourteen Maiwa male yaks (180-220 kg, 3-4 years old of age) were randomly assigned to the control group (without MI, n = 7) and the supplemented MI group (n = 7, supplemented with 0.3% MI on DM basis) for the 85-d animal experiment. Growth performance, nutrient apparent digestibility, rumen fermentation parameters, and rumen bacterial diversity were measured.

Results

Supplementation with 0.3% MI achieved the greatest propionate and butyrate content, NDFD and ADFD compared with other groups (P < 0.05). Therefore, 0.3% was used for the animal experiment. Supplementation with 0.3% MI significantly increased the apparent digestibility of NDF and ADF (P < 0.05), and the average daily weight gain of yaks (P < 0.05) without affecting the ruminal concentration of NH3-N, MCP, and VFAs. 0.3% MI induced rumen bacteria to form significantly different communities when compared to the control group (P < 0.05). g__norank_f__Bacteroidales_BS11_gut_group, g__norank_f__Muribaculaceae, g__Veillonellaceae_UCG-001, g__Ruminococcus_gauvreauii_group, g__norank_f__norank_o__RF39 and g__Flexilinea were identified as the biomarker taxa in responding to supplementation with 0.3% MI. Meanwhile, the abundance of g__Flexilinea and g__norank_f__norank_o__RF39 were significantly positively correlated with the NDF digestibility (P < 0.05).

Conclusion

In conclusion, supplementation with 0.3% MI improved the in vitro rumen fermentation characteristics, feed fiber digestibility, and growth performance in yaks, which was associated with changes of the abundance of g__Flexilinea and g__norank_f__norank_o__RF39.

Exploring the rumen microbiota of Hu lambs in response to diet with paper mulberry

Paper mulberry (Broussonetia papyrifera), as a new woody forage with high-protein characteristic, is being widely used in ruminant feeding. However, little is known about the comprehensive microbiota picture of whole ruminal niches (liquid, solid, and epithelium) under paper mulberry diet. To gain a better understanding of feeding paper mulberry on the rumen microbiota, the effects of fresh paper mulberry, paper mulberry silage, or a conventional high-protein alfalfa silage on rumen fermentation products and microbiota in rumen niches of Hu lambs were studied. Forty-five Hu lambs were randomly divided into 3 treatments with 15 replicates in each treatment. No significant difference was observed among treatments in the average daily gain (ADG). The fresh paper mulberry treatment had lower (P < 0.05) pH and higher (P < 0.05) total volatile fatty acids (TVFA) compared with silage treatments, but the fermentation parameters did not show significant differences between paper mulberry silage and alfalfa silage treatments. The Shannon index did not show a significant difference (P < 0.05) among treatments except between fresh paper mulberry and alfalfa silage treatment in rumen epithelial niches. Butyrivibrio and Treponema were the predominant genera in the rumen epithelial fraction, while Prevotella and Rikenellaceae_RC9 dominated in both rumen liquid and solid fractions. These results indicated the paper mulberry supplement did not have distinct impact on the microbial diversity and growth performance compared with alfalfa silage, especially for paper mulberry silage, which might help us develop an alternative animal feeding strategy of replacing alfalfa with paper mulberry. KEY POINTS: • Feeding paper mulberry silage did not show significant impact on the growth performance compared with alfalfa silage treatment. • Feeding fresh paper mulberry reduced rumen pH value and increased total volatile fatty acid. • The microbial diversity did not show significant difference among treatments.

High-Grain Diet Feeding Altered Blood Metabolites, Rumen Microbiome, and Metabolomics of Yaks

Currently, information available on the comprehensive changes in the rumen bacteria and metabolites of yaks fed high-grain diets is limited. This study aimed to investigate the effects of high-grain diet feeding on the blood metabolites, rumen microbiome, and metabolomics of yaks by using 16S rDNA gene sequencing and liquid chromatography–mass spectrometry (LC/MS). Here, fourteen healthy male yaks (body weight, 249.61 ± 8.13 kg) were randomly assigned to two different diets: a hay diet (0% grain, CON, n = 7), or a high-grain diet (70% grain, HG, n = 7). At the 74th day of treatment, blood and ruminal fluid samples were collected for the blood metabolites, rumen microbiome, and metabolomics analyses. The HG diet increased lipopolysaccharides (LPS), aspartate aminotransferase (AST), gamma-glutamyltransferase (GGT), haptoglobin (HPT), serum amyloid-A (SAA), interleukin-1β (IL1-β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) serum concentrations (p < 0.05). Compared with the CON diet, the HG diet decreased rumen pH (p < 0.05), and increased total volatile fatty acids concentration, and proportion of butyrate (p < 0.05). The relative abundance of Firmicutes and Saccharibacteria were higher (p < 0.05), while Bacteroidetes was lower (p < 0.05) in the HG group than those in the CON group. At the genus level, the relative abundance of Christensenelaceae_R-7_group, Ruminococcaceae_NK4A214_group, Lachnospiraceae_NK3A20_group, and Acetitomaculum were higher than in those in the HG diet (p < 0.05). Compared with the CON group, the HG diet increased the concentrations of biogenic amines (histamine, tyramine, and putrescine), common amino acids (phenylalanine, threonine, serine, etc.), and arachidonic acid (prostaglandin H2, prostaglandin E2, 12(S)-HPETE, etc.). Collectively, these findings demonstrate that the HG diet altered the microbiota and metabolites, as well as potentially damaged their rumen health and induced inflammation in yaks.

Dynamic changes in fecal microbiota in donkey foals during weaning: From pre-weaning to post-weaning

Introduction

A better understanding of the microbiota community in donkey foals during the weaning transition is a prerequisite to optimize gut function and improve feed efficiency. The objective of the present study was to investigate the dynamic changes in fecal microbiota in donkey foals from pre-to post-weaning period.

Methods

A total of 27 fecal samples of donkey foals were collected in the rectum before morning feeding at pre-weaning (30 days of age, PreW group, n = 9), dur-weaning (100 days of age, DurW group, n = 9) and post-weaning (170 days of age, PostW group, n = 9) period. The 16S rRNA amplicon sequencing were employed to indicate the microbial changes during the weaning period.

Results

In the present study, the cessation of breastfeeding gradually and weaning onto plant-based feeds increased the microbial diversity and richness, with a higher Shannon, Ace, Chao and Sobs index in DurW and PostW than in PreW (p < 0.05). The predominant bacterial phyla in donkey foal feces were Firmicutes (>50.5%) and Bacteroidota (>29.5%), and the predominant anaerobic fungi and archaea were Neocallimastigomycota and Euryarchaeota. The cellulolytic related bacteria including phylum Firmicutes, Spirochaetota and Fibrobacterota and genus norank_f_F082, Treponema, NK4A214_group, Lachnospiraceae_AC2044_group and Streptococcus were increased from pre-to post-weaning donkey foals (p < 0.05). Meanwhile, the functions related to the fatty acid biosynthesis, carbohydrate metabolism and amino acid biosynthesis were significantly enriched in the fecal microbiome in the DurW and PostW donkeys. Furthermore, the present study provided the first direct evidence that the initial colonization and establishment of anaerobic fungi and archaea in donkey foals began prior to weaning. The relative abundance of Orpinomyces were the highest in DurW donkey foals among the three groups (p < 0.01). In terms of archaea, the abundance of Methanobrevibacter were higher in PreW than in DurW and PostW (p < 0.01), but the abundance of Methanocorpusculum were significantly increased in DurW and PostW compared to PreW donkey foals (p < 0.01).

Discussion

Altogether, the current study contributes to a comprehensive understanding of the development of the microbiota community in donkey foals from pre-to post-weaning period, which may eventually result in an improvement of the digestion and feed efficiency in donkeys.

Effects of dietary crude protein levels in the concentrate supplement after grazing on rumen microbiota and metabolites by using metagenomics and metabolomics in Jersey-yak

Introduction

The crude protein level in the diet will affect the fermentation parameters, microflora, and metabolites in the rumen of ruminants. It is of great significance to study the effect of crude protein levels in supplementary diet on microbial community and metabolites for improving animal growth performance. At present, the effects of crude protein level in supplementary diet on rumen fermentation parameters, microbial community, and metabolites of Jersey-Yak (JY) are still unclear.

Methods

The purpose of this experiment was to study the appropriate crude protein level in the diet of JY. The rumen fermentation indexes (volatile fatty acids and pH) were determined by supplementary diets with crude protein levels of 15.16 and 17.90%, respectively, and the microbial community and metabolites of JYs were analyzed by non-target metabonomics and metagenome sequencing technology, and the changes of rumen fermentation parameters, microbial flora, and metabolites in the three groups and their interactions were studied.

Results and Discussion

The crude protein level in the supplementary diet had significant effects on pH, valeric acid, and the ratio of acetic acid to propionic acid (p < 0.05). The protein level had no significant effect on the dominant microflora at the phylum level (p > 0.05), and all three groups were Bacteroides and Firmicutes. The results of metabolite analysis showed that the crude protein level of supplementary diet significantly affected the metabolic pathways such as Bile secretion and styrene degradation (p < 0.05), and there were different metabolites between the LP group and HP group, and these different metabolites were related to the dominant microbial to some extent. To sum up, in this experiment, the effects of crude protein level in supplementary diet on rumen microorganisms and metabolites of JY and their relationship were studied, which provided the theoretical basis for formulating a more scientific and reasonable supplementary diet in the future.