Long-term high-grain diet altered the ruminal pH, fermentation, and composition and functions of the rumen bacterial community, leading to enhanced lactic acid production in Japanese Black beef cattle during fattening

Associations of rumen and rectum bacteria with the sustained productive performance of dairy cows

The gut bacterial community is essential for maintaining lifelong health and productivity in ruminants, but the relationship between the gut microbiota and the sustained productivity of ruminants remains inadequately understood. In this study, we selected long-lived dairy cows in mid-lactation (≥5 parities) with different levels of milk production (n = 10). Significant differences were observed in the rumen bacterial structures between the two groups of dairy cows, whereas no significant differences were detected in the rectum bacterial communities. Additionally, there were no significant differences in serum oxidative stress biomarkers, inflammatory markers, or immunological markers between the long-lived high-yield (LH) and long-lived low-yield (LL) dairy cows. Furthermore, the concentrations of propionate (Pr) in the rumen and butyrate (Bu) in the rectum were elevated in the high-yield group. Spearman correlation and microbial co-occurrence network analyses revealed that several rumen-enriched bacteria, such as Syntrophococcus, Lachnospira, Shuttleworthia, Erysipelotrichaceae_UCG-2, and Roseburiaare associated with rumen propionate (Pr) production. In the rectum, the reduced abundance of Christensenellaceae_R-7_group and Moryella favors butyrate production. Furthermore, Random Forest machine learning analysis demonstrated that six bacterial taxa in the rumen combined with one serum biomarker, as well as three bacterial taxa in the rectum combined with three serum biomarkers, can serve as potential biomarkers for distinguishing between LH and long- LL dairy cows, achieving prediction accuracies of 92 and 99%, respectively. The findings of this study indicate that rumen and rectum bacteria are associated with the milk production phenotypes of dairy cows with sustained productivity. The rumen microbes are closely linked to the long-term productive capacity of dairy cows and represent a key target for the development of gut microbiota-based interventions. The unique bacterial communities of the rumen and rectum of long-lived high-yielding dairy cows contribute to maintaining their productive capacity.

Impact of Dietary-Forage-to-Concentrate Ratio on Podolian Young Bulls' Performance and Nutritional Properties of Meat

Animal feeding has a great impact on the management of beef farms, also affecting the nutritional properties of the meat. Therefore, in this study, the following two forage-to-concentrate ratios were tested on twenty farmed Podolian young bulls: high forage-to-concentrate (HF:C) ratio of 65:35 vs. low forage-to-concentrate (LF:C) ratio of 45:55. The fatty acid profile, bioactive compounds, α-tocopherol content, and oxidative stability were evaluated on Longissimus thoracis muscle vacuum-packaged and aged at 2 °C for 11 and 18 days, respectively. Feeding the highest forage-to-concentrate ratio improved the fatty acid profile by decreasing the saturated fatty acids (p < 0.01) and increasing the monounsaturated (p < 0.05) and n-3 polyunsaturated fatty acids (p < 0.001). In particular, the percentages of linolenic acid (C18:3n-3), eicosapentaenoic acid (EPA-C20:5n-3), DPA (C22:5n-3), and docosahexaenoic acid (DHA-C22:6n3) were significantly higher (p < 0.01) in the HF:C group than the LF:C group. The highest forage-to-concentrate ratio also increased the contents of bioactive compounds, such as creatine (p < 0.001), carnosine (p < 0.01), and anserine (p < 0.05). This study suggests that a diet composed of 65% forage may be a feasible strategy to enrich meat with healthy bioactive compounds.

Effect of changing the proportion of C16:0 and cis-9 C18:1 in fat supplements on rumen fermentation, glucose and lipid metabolism, antioxidation capacity, and visceral fatty acid profile in finishing Angus bulls

This study evaluated the effects of different proportions of palmitic (C16:0) and oleic (cis-9 C18:1) acids in fat supplements on rumen fermentation, glucose (GLU) and lipid metabolism, antioxidant function, and visceral fat fatty acid (FA) composition in Angus bulls. The design of the experiment was a randomized block design with 3 treatments of 10 animals each. A total of 30 finishing Angus bulls (21 ± 0.5 months) with an initial body weight of 626 ± 69 kg were blocked by weight into 10 blocks, with 3 bulls per block. The bulls in each block were randomly assigned to one of three experimental diets: (1) control diet without additional fat (CON), (2) CON + 2.5% palmitic calcium salt (PA; 90% C16:0), (3) CON + 2.5% mixed FA calcium salts (MA; 60% C16:0 + 30% cis-9 C18:1). Both fat supplements increased C18:0 and cis-9 C18:1 in visceral fat (P < 0.05) and up-regulated the expression of liver FA transport protein 5 (FATP5; P < 0.001). PA increased the insulin concentration (P < 0.001) and aspartate aminotransferase activity (AST; P = 0.030) in bull's blood while reducing the GLU concentration (P = 0.009). PA increased the content of triglycerides (TG; P = 0.014) in the liver, the content of the C16:0 in visceral fat (P = 0.004), and weight gain (P = 0.032), and up-regulated the expression of liver diacylglycerol acyltransferase 2 (DGAT2; P < 0.001) and stearoyl-CoA desaturase 1 (SCD1; P < 0.05). MA increased plasma superoxide dismutase activity (SOD; P = 0.011), reduced the concentration of acetate and total volatile FA (VFA) in rumen fluid (P < 0.05), and tended to increase plasma non-esterified FA (NEFA; P = 0.069) concentrations. Generally, high C16:0 fat supplementation increased weight gain in Angus bulls and triggered the risk of fatty liver, insulin resistance, and reduced antioxidant function. These adverse effects were alleviated by partially replacing C16:0 with cis-9 C18:1.

Effect of Adding Yeast Cultures to High-Grain Conditions on Production Performance, Rumen Fermentation Profile, Microbial Abundance, and Immunity in Goats

It is a common practice among farmers to utilize high-grain diets with the intention of promoting ruminant growth. However, this approach bears the risk of inducing rumen disorders and nutrient metabolism diseases. Yeast culture (YC) showed advantages in ruminant applications. The objective of this study was to evaluate the effects of adding two different types of YC to high-grain conditions on production performance, rumen fermentation profile, microbial abundance, and immunity in goats. A total of 30 male goats with similar body condition were randomly distributed into 3 dietary treatments with 10 replicates per treatment as follows: basic diet group (CON); basic diet + 0.5% yeast culture 1 (YC1) group; basic diet + 0.5% yeast culture 2 (YC2) group. The trial lasted for 36 days. The results demonstrated that dietary YC supplementation led to an increase in the average daily gain and a reduction in feed intake and weight gain ratio in goats. It increased the apparent digestibility of crude protein, NDF, and ADF (p < 0.05). The serum concentrations of interleukin (IL)-1β, IL-6, and Tumor Necrosis Factor-α in the control group were significantly higher than those of the YC groups (p < 0.05). The serum concentrations of Immunoglobulin (Ig)A and IgG in the control group were significantly lower than those in the YC groups (p < 0.05). The rumen concentration of microbial protein (MCP) in the control group was significantly lower than that in the YC groups (p < 0.05). There was a negative correlation between the concentration of IL-10 and Bacteroidota, Spirochaetota, and Succinivibrio, while there was a positive correlation between concentrations of IL-10 and Firmicutes. Nevertheless, discrepancies were observed in the impact of the two different types of YC on the physiological and biochemical indicators of the animals. The concentration of triglyceride in the YC1 group was significantly higher than that of the CON and YC2 groups, while the concentration of urea in the YC2 group was significantly higher than that of the CON and YC1 groups (p < 0.05). At the phylum level, the addition of YC2 to the diet significantly increased the relative abundance of Bacteroidota and Fibrobacterota and significantly decreased Firmicutes compared to the control. At the genus level, the addition of YC1 to the HGD significantly reduced the relative abundance of Rikenellaceae_RC9_gut_group, while the addition of YC2 to the HGD significantly increased the relative abundance of Prevotellace-ae_UCG-001, Fibrobacter, and Prevotellaceae_UCG-003 (p < 0.05). The addition of YC significantly improved growth performance, increased nutrient digestibility, beneficially manipulated ruminal fermentation and microbial diversity, and improved immune function. The choice of yeast cultures can be customized according to specific production conditions.

The Impact of Different Dietary Ratios of Soluble Carbohydrate-to-Neutral Detergent Fiber on Rumen Barrier Function and Inflammation in Dumont Lambs

Appropriate soluble carbohydrate (SCHO)-to-NDF ratios in the diet are essential for rumen health. The effects of different SCHO-to-NDF ratios (1.0, 1.5, and 2.0) on rumen barrier function and inflammation in Dumont lambs (n = 18, 6 replicates per treatment) was investigated. The SCHO:NDF ratio was altered by replacing the forage (Leynus chinensis) with corn grain. With an increase in the proportion of SCHO, the final body weight (FBW), average daily gain (ADG), soluble carbohydrate intake (SCHOI), and LPS level increased; and the neutral detergent fiber intake (NDFI), ruminal papillae height, papillae area, and pH decreased (p < 0.05, plin < 0.05). The medium CHO:NDF group had increased claudin-1 mRNA (p < 0.05, plin = 0.005, pquad = 0.003) and protein (p < 0.05, pquad < 0.001) levels; the high CHO:NDF group had increased occludin mRNA and protein (p < 0.05, plin = 0.001) levels. The level of the anti-inflammatory cytokine IL-10 was significantly greater in the medium CHO:NDF group than in the high CHO:NDF group (p < 0.05, pquad < 0.001). With an increase in the ratio of SCHO, the mRNA level and concentration of the proinflammatory cytokines IL-1β, IL-6, and TNF-α linearly increased (p < 0.05, plin < 0.05), and those in the high CHO:NDF group were significantly greater than those in the low CHO:NDF group. The levels of phosphorylated p65 (plin = 0.003), IκB-α (plin < 0.001), and JNK (plin = 0.001) increased linearly, and those in the high CHO:NDF group were significantly greater than those in the other two groups (p < 0.05). Therefore, when the SCHO-to-NDF ratio was increased to 1.5, the rumen epithelium was not affected, but when the ratio was increased to 2.0, NF-κB and MAPK were activated in the rumen epithelium, leading to impaired barrier function and inflammation. The suitable NFC:NDF ratio for the short-term fattening of Dumont lambs was found to be 1.50.

Assessing the impact of three feeding stages on rumen bacterial community and physiological characteristics of Japanese Black cattle

In Japan, Japanese Black cattle, known for their exceptional meat quality owing to their abundant intramuscular fat, undergo a unique three-stage feeding system with varying concentrate ratios. There is limited research on physiological and rumen microbial changes in Japanese Black cattle during these stages. Therefore, this study aimed to examine Japanese Black steers in these three stages: early (T1, 12-14 months), middle (T2, 15-22 months), and late (T3, 23-30 months). The rumen bacteria of 21 cattle per phase was analyzed using 16S rRNA gene sequencing. Rumen bacterial diversity was significantly higher in T1, with a distinct distribution, than in T2 and T3. Specific phyla and genera were exclusive to each stage, reflecting the shifts in feed composition. Certain genera dominated each stage: T1 had Flexilinea, Streptococcus, Butyrivibrio, Selenomonas, and Kandleria; T2 had Bifidobacterium, Shuttleworthia, and Sharpea; and T3 had Acetitomaculum, Mycoplasma, Atopobium, and Howardella. Correlation analysis revealed significant associations between certain microbial populations and physiological parameters. These findings indicate that changes in energy content and feed composition are associated with physiological and ruminal alterations. This study may guide strategies to improve rumen health and productivity in Japanese Black cattle by modifying diets to specific fattening stages.

A Comparative Study of Growth Performance, Blood Biochemistry, Rumen Fermentation, and Ruminal and Fecal Bacterial Structure between Yaks and Cattle Raised under High Concentrate Feeding Conditions

This study compared the growth performance, serum biochemical indicators, rumen fermentation parameters, rumen bacterial structure, and fecal bacterial structure of cattle and yaks fed for two months and given a feed containing concentrate of a roughage ratio of 7:3 on a dry matter basis. Compared with cattle, yak showed better growth performance. The serum biochemical results showed that the albumin/globulin ratio in yak serum was significantly higher than that in cattle. Aspartate aminotransferase, indirect bilirubin, creatine kinase, lactate dehydrogenase, and total cholesterol were significantly lower in yaks than in cattle. The rumen pH, acetate to propionate ratio, and acetate were lower in yaks than in cattle, whereas the lactate in yaks was higher than in cattle. There were significant differences in the structure of ruminal as well as fecal bacteria between cattle and yaks. The prediction of rumen bacterial function showed that there was a metabolic difference between cattle and yaks. In general, the metabolic pathway of cattle was mainly riched in a de novo synthesis of nucleotides, whereas that of yaks was mainly riched in the metabolic utilization of nutrients. This study provides a basis for understanding a rumen ecology under the condition of a high concentrate diet.

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.

Predicted functional analysis of rumen microbiota suggested the underlying mechanisms of the postpartum subacute ruminal acidosis in Holstein cows

BACKGROUND

The relationships between the postpartum subacute ruminal acidosis (SARA) occurrence and predicted bacterial functions during the periparturient period are still not clear in Holstein cows.

OBJECTIVES

The present study was performed to investigate the alterations of rumen fermentation, bacterial community structure, and predicted bacterial functional pathways in Holstein cows.

METHODS

Holstein cows were divided into the SARA (n = 6) or non-SARA (n = 4) groups, depending on whether they developed SARA during the first 2 weeks after parturition. Reticulo-ruminal pH was measured continuously during the study period. Reticulo-ruminal fluid samples were collected 3 weeks prepartum, and 2 and 6 weeks postpartum, and blood samples were collected 3 weeks before, 0, 2, 4 and 6 weeks postpartum.

RESULTS

The postpartum decline in 7-day mean reticulo-ruminal pH was more severe and longer-lasting in the SARA group compared with the non-SARA group. Changes in predicted functional pathways were identified in the SARA group. A significant upregulation of pathway "PWY-6383" associated with Mycobacteriaceae species was identified at 3 weeks after parturition in the SARA group. Significantly identified pathways involved in denitrification (DENITRIFICATION-PWY and PWY-7084), detoxification of reactive oxygen and nitrogen species (PWY1G-0), and starch degradation (PWY-622) in the SARA group were downregulated.

CONCLUSIONS

The postpartum SARA occurrence is likely related to the predicted functions of rumen bacterial community rather than the alterations of rumen fermentation or fluid bacterial community structure. Therefore, our result suggests the underlying mechanisms, namely functional adaptation of bacterial community, causing postpartum SARA in Holstein cows during the periparturient period.

Increasing buffering capacity enhances rumen fermentation characteristics and alters rumen microbiota composition of high-concentrate fed Hanwoo steers

The buffering capacity of buffer agents and their effects on in vitro and in vivo rumen fermentation characteristics, and bacterial composition of a high-concentrate fed Hanwoo steers were investigated in this study. Treatments were comprised of CON (no buffer added), BC0.3% (low buffering capacity, 0.3% buffer), BC0.5% (medium buffering capacity, 0.5% buffer), and BC0.9% (high buffering capacity, 0.9% buffer). Four Hanwoo steers in a 4 × 4 Latin square design were used for the in vivo trial to assess the effect of treatments. Results on in vitro experiment showed that buffering capacity, pH, and ammonia-nitrogen concentration (NH3-N) were significantly higher in BC0.9% and BC0.5% than the other treatments after 24 h incubation. Individual and total volatile fatty acids (VFA) concentration of CON were lowest compared to treatment groups. Meanwhile, in vivo experiment revealed that Bacteroidetes were dominant for all treatments followed by Firmicutes and Proteobacteria. The abundances of Barnesiella intestinihominis, Treponema porcinum, and Vibrio marisflavi were relatively highest under BC0.9%, Ruminoccocus bromii and Succiniclasticum ruminis under BC0.5%, and Bacteroides massiliensis under BC0.3%. The normalized data of relative abundance of observed OTUs' representative families have grouped the CON with BC0.3% in the same cluster, whereas BC0.5% and BC0.9% were clustered separately which indicates the effect of varying buffering capacity of buffer agents. Principal coordinate analysis (PCoA) on unweighted UniFrac distances revealed close similarity of bacterial community structures within and between treatments and control, in which BC0.9% and BC0.3% groups showed dispersed community distribution. Overall, increasing the buffering capacity by supplementation of BC0.5% and and BC0.9% buffer agents enhanced rumen fermentation characteristics and altered the rumen bacterial community, which could help prevent ruminal acidosis during a high-concentrate diet.

Effects of high concentrate rations on ruminal fermentation and microbiota of yaks

Ruminal microflora is closely correlated with the ruminant’s diet. However, information regarding the effect of high concentrate diets on rumen microflora in yaks is lacking. In the current study, 24 healthy male yaks were randomly assigned to two groups, each fed with different diets: less concentrate (LC; concentrate: coarse = 40: 60) and high concentrate (HC; concentrate: coarse = 80: 20) diets. Subsequently, a 21-day feeding trial was performed with the yaks, and rumen fluid samples were collected and compared using 16 s rRNA sequencing. The results showed that NH3-N, total VFA, acetate, butyrate, isobutyrate, and isovalerate were significantly higher in the HC group than that in the LC group (p &lt; 0.05), while microbial diversity and richness were significantly lower in the HC group (p &lt; 0.05). Principal coordinate analysis indicated that rumen microflora was significantly different in LC and HC groups (p &lt; 0.05). In the rumen, phyla Firmicutes and Bacteroidota were the most abundant bacteria, with Firmicutes being more abundant, and Bacteroidota being less abundant in the HC group than those found in the LC group. Christensenellaceae_R-7_group and Prevotella are the highest abundant ones at the genus level. The relative abundance of Acetitomaculum, Ruminococcus, and Candidatus_Saccharimonas were significantly higher in the HC group than that in the LC group (p &lt; 0.05), while the relative abundance of Olsenella was significantly lower in the HC group than in the LC group (p &lt; 0.05). Compared to the LC group, the relative abundance of Prevotella, Ruminococcus, and Candidatus_Saccharimonas was significantly higher in the HC group. The relative abundances of Prevotella, Prevotellaceae_UCG-003, Olsenella, Ruminococcus, Acetitomaculum, Candidatus_Saccharimonas, and NK4A214_group were correlated with ruminal fermentation parameters (p &lt; 0.05). Furthermore, PICRUSt 2 estimation indicated that microbial genes associated with valine, leucine, and isoleucine biosynthesis were overexpressed in the rumen microflora of yaks in the HC group (p &lt; 0.05). Conclusively, our results suggest that high concentrate diets affect the microflora composition and fermentation function in yak rumen. The present findings would provide new insights into the health of yaks under high concentrate feeding conditions and serve as a potent reference for the short-term fattening processes of yaks.

Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome

Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.

Parturition and postpartum dietary change altered ruminal pH and the predicted functions of rumen bacterial communities but did not alter the bacterial composition in Holstein cows

We investigated the temporal dynamics of ruminal pH and the composition and predicted functions of the rumen bacterial community in Holstein cows during the periparturient period. Eight multiparous Holstein cows (body weight; 707.4 ± 29.9 kg, parity; 3.6 ± 0.6) were used for continuous reticulo-ruminal pH measurement, among which five were also used for bacterial community analysis. Rumen fluid samples were collected at 3 weeks before and 2 and 6 weeks after parturition, and blood samples were collected 3 weeks before and 0, 2, 4, and 6 weeks after parturition. After the parturition, reduction in the 1-h mean reticulo-ruminal pH was associated with a significant (P < 0.05) increase in total volatile fatty acid concentration. However, with the exception of a significant change in an unclassified genus of Prevotellaceae (P < 0.05), we detected no significant changes in the compositions of major bacterial phyla or genera or diversity indices during the periparturient period. On the basis of predicted functional analysis, we identified a total of 53 MetaCyc pathways (45 upregulated), 200 enzyme commissions (184 upregulated), and 714 Kyoto Encyclopedia of Genes and Genomes orthologs (667 upregulated) at 6 weeks postpartum that were significantly (P < 0.05) different to those at 3 weeks prepartum. Among the 14 MetaCyc pathways (P < 0.05) in which pyruvate is an end product, PWY-3661 [log2-fold change (FC) = 5.49, false discovery rate (FDR) corrected P < 0.001] was the most highly upregulated pyruvate-producing pathway. In addition, P381-PWY [adenosylcobalamin biosynthesis II (aerobic); FC = 5.48, FDR corrected P < 0.001] was the second most upregulated adenosylcobalamin (Vitamin B12)-producing pathway. In contrast, PWY-2221 (FC = −4.54, FDR corrected P = 0.003), predominantly found in pectinolytic bacteria, was the most downregulated pathway. Our findings indicate that changes in rumen bacterial community structure are not strictly associated with transitions in parturition or diet; however, we did observe changes in reticulo-ruminal pH and the metabolic adaptation of predicted functional pathways. Consequently, predictive analysis of postpartum functional pathways may enable us to gain insights into the underlying functional adaptations of bacterial communities in Holstein cows during the periparturient period.

Maternal Fecal Microbes Contribute to Shaping the Early Life Assembly of the Intestinal Microbiota of Co-inhabiting Yak and Cattle Calves

The Qinghai-Tibetan Plateau offers one of the most extreme environments for yaks (Bos grunniens). Although the genetic adaptability of yak and rumen metagenomes is increasingly understood, the relative contribution of host genetics and maternal symbiotic microbes throughout early intestinal microbial successions in yaks remains elusive. In this study, we assessed the intestinal microbiota succession of co-inhabiting yak and cattle (Bos taurus) calves at different weeks after birth as well as the modes of transmission of maternal symbiotic microbes (i.e., rumen fluid, feces, oral cavity, and breast skin) to their calves' intestinal microbiota colonization. We found that the fecal microbiota of yak and cattle calves after birth was dominated by members of the families Ruminococcaceae, Bacteroidaceae, and Lachnospiraceae. The Source Tracker model revealed that maternal fecal microbes played an important role (the average contribution was about 80%) in the intestinal microbial colonization of yak and cattle calves at different weeks after birth. Unlike cattle calves, there was no significant difference in the fecal microbiota composition of yak calves between 5 and 9 weeks after birth (Wilcoxon test, P > 0.05), indicating that yak may adapt to its natural extreme environment to stabilize its intestinal microbiota composition. Additionally, our results also find that the intestinal microbial composition of yak and cattle calves, with age, gradually tend to become similar, and the differences between species gradually decrease. The findings of this study are vital for developing strategies to manipulate the intestinal microbiota in grazing yaks and cattle for better growth and performance on the Qinghai-Tibetan Plateau.

Effect of high-concentrate diets on mRNA expression of genes related to muscle fiber type and metabolism of psoas major muscle in goats

In the process of modern breeding, high-concentrate diets are widely used to meet the high energy nutritional requirements of animals but change the form of access to energy and nutrients and the way the organism metabolizes them. Goat psoas major (PM) muscle is a hybrid skeletal muscle whose characteristics are important for the motility and meat quality of goats. However, there are few studies on the effects of high-concentrate diets on the muscle type and metabolic characteristics of PM in goats. In this study, two treatment groups were set up: high concentrate group (HC) and control group (C). The expression of genes related to muscle type and metabolism of the PM was examined by quantitative PCR. The results showed that high concentrate promoted the conversion of PM fibers from intermediate to slow type at the mRNA level, improved the absorption, transport, and oxidation of fat by PM, and upregulated the expression of calpain system. These changes may be regulated by the involvement of differential expression of MSTN, Myf-5, and IGF-2. These results suggest that high concentrate may exert a positive effect on skeletal muscle function, metabolism, and meat quality in goats by affecting the expression of muscle type and metabolism-related genes.

Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan

The rumen contains a complex microbial ecosystem that degrades plant materials, such as cellulose and hemicellulose. We herein reconstructed 146 nonredundant, rumen-specific metagenome-assembled genomes (MAGs), with ≥50% completeness and <10% contamination, from cattle in Japan. The majority of MAGs were potentially novel strains, encoding various enzymes related to plant biomass degradation and volatile fatty acid production. The MAGs identified in the present study may be valuable resources to enhance the resolution of future taxonomical and functional studies based on metagenomes and metatranscriptomes.

Fecal Microbiota Dynamics Reveal the Feasibility of Early Weaning of Yak Calves under Conventional Grazing System

Simple Summary

Yak (Bos grunniens) is the most economically and culturally important domestic bovine species adapted to the extreme ecological environment of the Qinghai–Tibetan Plateau (QTP), which provides milk, meat, transportation, fuel (yak dung), and wool for local nomads as well as major sources of income. Calves are an important part of the sustainable development of the yak industry on the QTP, and the quality of calf rearing directly determines the production performance of adult animals. Under the traditional grazing management, late weaning (>180 days) of yak calves seriously affects the improvement of their production performance. A comparative study of fecal microbiota dynamics of yak and cattle (Bos taurus) calves in different months after weaning will help to understand the changes in intestinal microbiota structure, and will aid in in improving growth rate and survivability of early weaned calves. Our research will contribute to the development of appropriate strategies to regulate the gut microbiome and thus improve the growth and health of the grazing ruminants on the QTP.

Abstract

Background: The gut microbiota plays an important role in the health and production of animals. However, little information is available on the dynamic variations and comparison of intestinal microbiota in post-weaning yak calves living on the QTP. Methods: We explored the fecal bacterial microbiota succession of yak calves at different months after early weaning (60 d) compared with cattle calves by 16S rRNA gene amplicon sequencing and functional composition prediction. Results: We found no significant difference in blood biochemical parameters related to glucose and lipid metabolism between yaks and calves in different months after weaning. The core fecal bacterial microbiota from both species of calves was dominated by Ruminococcaceae, Rikenellaceae, and Bacteroidaceae. The fecal microbial community has a great alteration within the time after weaning in both cattle and yak calves, but cattle showed a larger change. After five months, the microbiota achieves a stable and concentrated state. This is also similar to the functional profile. Conclusions: Based on the exploration of dynamic changes in the fecal microbiota at an early stage of life, our results illustrated that there were no negative effects of intestinal microbiota succession on yak calves when early weaning was employed.

Taxonomic and functional characterization of the rumen microbiome of Japanese Black cattle revealed by 16S rRNA gene amplicon and metagenome shotgun sequencing

This study aimed to determine the taxonomic and functional characteristics of the Japanese Black (JB) steer rumen microbiome. The rumen microbiomes of six JB steers (age 14.7 ± 1.44 months) and six JB sires × Holstein dams crossbred (F1) steers (age 11.1 ± 0.39 months), fed the same diet, were evaluated. Based on 16S rRNA gene sequencing, the beta diversity revealed differences in microbial community structures between the JB and F1 rumen. Shotgun sequencing showed that Fibrobacter succinogenes and two Ruminococcus spp., which are related to cellulose degradation were relatively more abundant in the JB steer rumen than in the F1 rumen. Furthermore, the 16S rRNA gene copy number of F. succinogenes was significantly higher in the JB steer rumen than in the F1 rumen according to quantitative real-time polymerase chain reaction analysis. Genes encoding the enzymes that accelerate cellulose degradation and those associated with hemicellulose degradation were enriched in the JB steer rumen. Although Prevotella spp. were predominant both in the JB and F1 rumen, the genes encoding carbohydrate-active enzymes of Prevotella spp. may differ between JB and F1.

Effects of Saccharomyces cerevisiae Culture on Ruminal Fermentation, Blood Metabolism, and Performance of High-Yield Dairy Cows

Simple Summary

Nowadays, the lifetime milk production of dairy cows, as well as the fat and protein contents of milk, has reached an unprecedented high. These improvements pose threats and challenges to animal health and welfare due to metabolic stress. The cows, during the high-yielding period, are especially susceptible to metabolic diseases such as digestive alterations, rumen acidosis, and lameness. This study assessed the effects of Saccharomyces cerevisiae culture (SC), a food supplement, on ruminal pH, volatile fatty acid (VFA), inflammatory cytokines, and the performance of high-yield dairy cows. The results show that supplementing high-yield lactating cows with the SC of 100 g/d increases milk yield, milk fat content, and milk lactose content, but does not affect protein content. SC supplementation affects overall ruminal VFA concentration and induces a significantly greater ruminal pH. It has the potential to enhance the rumen microbial growth and decrease the inflammation response. Our research suggests that SC supplementation has a positive effect on the productivity and health of dairy cows.

Abstract

High-yield dairy cows with high-concentrate diets are more prone to experiencing health problems associated with rumen microbial imbalance. This study assessed the effects of Saccharomyces cerevisiae culture (SC), a food supplement, on ruminal pH, volatile fatty acid (VFA), inflammatory cytokines, and performance of high-yield dairy cows. Forty Holstein cows with similar characteristics (e.g., milk yield, days of milk, and parity) were randomly divided into two groups: an experimental group fed the basal ration supplemented with the SC of 100 g of SC per cow per day (hour, SC group), and a control group fed the same basal ration diet without SC (i.e., CON group). On average, the supplementation of SC started at 73 days of lactation. The experimental period lasted approximately 70 days (from 18 January to 27 March 2020), including 10 days for dietary adaptation. Milk yield was recorded daily. Rumen fluid and milk samples were collected after 2 h of feeding in the morning of day 0, 15, 30, and 60. The data showed that rumen pH increased (p < 0.05) when cows were provided with SC. On average, the cows in the SC group produced 1.36 kg (p < 0.05) more milk per day than those in the CON group. Milk fat content of cows in the SC group was also higher (4.11% vs. 3.96%) (p < 0.05). Compared with the CON group, the concentration of acetic acid in the rumen fluid of dairy cows in the SC group was significantly higher (p < 0.05). There were no differences (p > 0.05) found in milk protein content and propionic acid between groups. The SC group had a tendency increase in butyric acid (p = 0.062) and total VFA (p = 0.058). The result showed that SC supplementation also enhanced the ratio between acetic and propionic. Most of the mean inflammatory cytokine (IL-2, IL-6, γ-IFN, and TNF-α) concentrations (p < 0.05) of the SC group were lower than CON group. This study demonstrated that high-yield cows receiving supplemental SC could produce more milk with higher fat content, have higher rumen acetate, and potentially less inflammatory cytokines.

Identification of the core rumen bacterial taxa and their population dynamics during the fattening period in Japanese Black cattle

The rumen microbiota comprises a vast range of bacterial taxa, which may affect the production of high‐quality meat in Japanese Black cattle. The aim of this study was to identify core rumen microbiota in rumen fluid samples collected from 74 Japanese Black cattle raised under different dietary conditions using 16S rRNA gene amplicon sequencing. In the rumen of fattening Japanese Black cattle, 10 bacterial taxa, showing >1% average relative abundance and >95% prevalence, irrespective of the dietary conditions and the fattening periods, were identified as the core rumen bacterial taxa, which accounted for approximately 80% of the rumen microbiota in Japanese Black cattle. Additionally, population dynamics of the core rumen bacterial taxa revealed two distinct patterns: Prevotella spp. and unclassified Bacteroidales decreased in the mid‐fattening period, whereas unclassified Clostridiales, unclassified Ruminococcaceae, Ruminococcus spp., and unclassified Christensenellaceae increased during the same period. Therefore, the present study reports the wide distribution of the core rumen bacterial taxa in Japanese Black cattle, and the complementary nature of the population dynamics of these core taxa, which may ensure stable rumen fermentation during the fattening period.

Changes in the predicted function of the rumen bacterial community of Japanese Black beef cattle during the fattening stages according to Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses

We investigated changes in the predicted functions of the rumen bacterial community in Japanese Black beef cattle during fattening. Nine cattle were fed a high-concentrate diet during the early, middle, and late fattening stages consecutively (10–14, 15–22, and 23–30 months of age, respectively). The rumen fluid and solid samples collected at each stage were subjected to sequencing analyses. The sequencing results were clustered and classified into operational taxonomic units (OTUs). Representative sequences and a raw counting table for each OTU were submitted to the Piphillin website. The predicted functions were revealed by the Kyoto Encyclopedia of Genes and Genomes database as the ratio of the total sequence. In the early stage, “Biosynthesis of secondary metabolites” was significantly higher in the fluid fraction than in the solid fraction. “Two-component system” in the middle stage was significantly lower and “Purine metabolism” in the late stage was significantly higher in the fluid fraction than those in the solid fraction. The fluid fraction was significantly correlated with acetic acid, propionic acid, and bacterial metabolism, such as “Biosynthesis of secondary metabolites” and “Sugar metabolism.” Moreover, the solid fraction was correlated with “Purine metabolism” and “Biosynthesis of secondary metabolism”. These results suggest that the rumen bacterial community in Japanese Black beef cattle adapts to changes in rumen conditions by altering their functions in response to a long-term high-grain diet.

Effect of dietary concentrate content on feed intake, feed efficiency, and meat quality of Holstein steers fattened in a hot environment

The objective of this study was to investigate the effect of feeding high and low concentrate diets on feed intake and feed efficiency, the morphological characteristics of the rumen papillae, and meat quality of Holstein steers fattened under hot climate conditions in Oman. Ten male Holstein calves, of 5 months of age, were selected for the experiment. The animals were fed concentrate and Rhodes grass hay and were divided into two groups of high concentrate (HC, n = 5) and low concentrate diets (LC, n = 5), in which their feed intake, weight gain, and feed efficiency were evaluated across three growing periods. Feed intake and efficiency and average daily gain (ADG) of the HC group were significantly greater than for the LC group and were affected by the diet (p < .01) and the period (p < .001). Across the fattening periods, ADG declined in both groups, with ADG improved by 35% for steers on the HC diet compared to steers on the LC diet. Carcass meat quality was not affected significantly by the dietary concentrate level. In conclusion, our results can be used to make improvements in feed efficiency of Holstein steers under hot climate conditions.

Diet Transition from High-Forage to High-Concentrate Alters Rumen Bacterial Community Composition, Epithelial Transcriptomes and Ruminal Fermentation Parameters in Dairy Cows

Effects of changing diet on rumen fermentation parameters, bacterial community composition, and transcriptome profiles were determined in three rumen-cannulated Holstein Friesian cows using a 3 × 4 cross-over design. Treatments include HF-1 (first high-forage diet), HC-1 (first high-concentrate diet), HC-2 (succeeding high-concentrate diet), and HF-2 (second high-forage diet as a recovery period). Animal diets contained Klein grass and concentrate at ratios of 8:2, 2:8, 2:8, and 8:2 (two weeks each), respectively. Ammonia-nitrogen and individual and total volatile fatty acid concentrations were increased significantly during HC-1 and HC-2. Rumen species richness significantly increased for HF-1 and HF-2. Bacteroidetes were dominant for all treatments, while phylum Firmicutes significantly increased during the HC period. Prevotella, Erysipelothrix, and Galbibacter significantly differed between HF and HC diet periods. Ruminococcus abundance was lower during HF feeding and tended to increase during successive HC feeding periods. Prevotellaruminicola was the predominant species for all diets. The RNA sequence analysis revealed the keratin gene as differentially expressed during the HF diet, while carbonic-anhydrase I and S100 calcium-binding protein were expressed in the HC diet. Most of these genes were highly expressed for HC-1 and HC-2. These results suggested that ruminal bacterial community composition, transcriptome profile, and rumen fermentation characteristics were altered by the diet transitions in dairy cows.

Comparison of pH and bacterial communities in the rumen and reticulum during fattening of Japanese Black beef cattle

We used castrated and fistulated Japanese Black beef cattle (n = 9) to measure the pH and bacterial communities in the rumen liquid, rumen solid, and reticulum liquid during early, middle, and late fattening stages (10-14, 15-22, and 23-30 months of age, respectively). The pH was measured in the rumen and reticulum during the last 13 days of each fattening stage and was significantly lower in the rumen at the early and middle fattening stage and in the reticulum during the late stage. Sequencing analysis indicated similar bacterial compositions in the rumen and reticulum liquid fractions and stability of bacterial diversity in the rumen and reticulum liquid fractions and rumen solid fraction. By contrast, major operational taxonomic units (OTUs), such as Ruminococcus bromii strain ATCC 27255 (OTU1, OTU10, and OTU15), were differently correlated to the fermentation parameters among the rumen and reticulum liquid fractions. Therefore, the long-term feeding of Japanese Black beef cattle with a high-concentrate diet might reverse the trend of pH in the rumen and reticulum during the late fattening stage, and the bacterial communities adapted to changes in fermentation by preserving their diversity throughout fattening.

Forestomach developmental failure in an 11-month-old Japanese Black steer with severely retarded growth and chronic ruminal tympany

This study reports findings from the pathological examination of the forestomach of an 11-month-old Japanese Black steer with severely retarded growth (41% of expected weight) and chronic ruminal tympany. The ruminal papillae were weakly formed (0.3–0.5 cm long) and unevenly distributed. The cellulae and cristae reticuli were underdeveloped; the cristae were 0.4–0.7 cm in height and milky white. The keratinized layer in the stratified squamous epithelium was thickened. Ruminal pH was 5.25, and ruminal volatile fatty acid concentration was 11.7 mM. The steer’s severely retarded growth was considered to be caused by malnutrition due to developmental and functional failure of the forestomach.

Association between Rumen Microbiota and Marbling Score in Korean Native Beef Cattle

Simple Summary

The ruminal microbiome affects various metabolic processes associated with animal development; however, few studies have focused on its correlation with marbling. Results of the present study show differences in ruminal microbiomes among Hanwoo Korean beef cattle, which have low or high marbling scores. By elucidating the effect of the ruminal microbiome on the marbling of Hanwoo, differentially abundant microbial taxa, ruminal taxonomic drivers of lipid metabolism, and the correlation with meat quality indices, the present study provides insights into the potential effects of microbial factors on marbling in beef cattle.

Abstract

This study demonstrated the potential effects of the rumen microbiota on the deposition of intramuscular fat, known as marbling. Previous studies on fatty acid metabolism in beef cattle have mostly focused on biohydrogenating rumen bacteria, whereas those on the overall rumen microbiota—to understand their roles in marbling—have not been systematically performed. The rumen microbiota of 14 Korean beef cattle (Hanwoo), which showed similar carcass characteristics and blood metabolites but different marbling scores, were analyzed by 16S rRNA gene sequencing. The rumen samples were grouped into two extreme marbling score groups of host animals as follows: LMS, marbling score≤ 4 or HMS, marbling score ≥7. Species richness tended to be higher in the HMS group, whereas the overall microbiota differed between LMS and HMS groups. RFP12, Verrucomicrobia, Oscillospira, Porphyromonadaceae, and Paludibacter were differentially abundant in the HMS group, whereas Olsenella was abundant in the LMS group. Some marbling-associated bacterial taxa also contributed to the enrichment of two lipid metabolic pathways including “alpha-linolenic acid metabolism” and “fatty acid biosynthesis” in the HMS microbiome. Taxonomic drivers of fatty acid biosynthesis, particularly in the rumen microbiome of high-marbled meat, could thus be further studied to increase the intramuscular fat content.

Long-term high-grain diet alters ruminal pH, fermentation, and epithelial transcriptomes, leading to restored mitochondrial oxidative phosphorylation in Japanese Black cattle

To increase intramuscular fat accumulation, Japanese Black beef cattle are commonly fed a high-grain diet from 10 to 30 months of age. Castrated and fistulated cattle (n = 9) were fed a high-concentrate diets during the early, middle, and late stages consecutively (10-14, 15-22, 23-30 months of age, respectively). Ruminal pH was measured continuously, and rumen epithelium and fluid samples were collected on each stage. The 24-h mean ruminal pH during the late stage was significantly lower than that during the early stage. Total volatile fatty acid (VFA) and lactic acid levels during the late stage were significantly lower and higher, respectively, than those during the early and middle stages. In silico analysis of differentially expressed genes showed that "Oxidative Phosphorylation" was the pathway inhibited most between the middle and early stages in tandem with an inhibited upstream regulator (PPARGC1A, also called PGC-1α) but the most activated pathway between the late and middle stages. These results suggest that mitochondrial dysfunction and thereby impaired cell viability due to acidic irritation under the higher VFA concentration restored stable mitochondrial oxidative phosphorylation and cell viability by higher lactic acid levels used as cellular oxidative fuel under a different underlying mechanism in subacute ruminal acidosis.