Interpretation of the effects of rumen acidosis on the gut microbiota and serum metabolites in calves based on 16S rDNA sequencing and non-target metabolomics

Introduction

Rumen acidosis is one of the most common diseases in beef cattle. It severely affects the normal development of calves and poses a significant threat to the farming industry. However, the influence of rumen acidosis on the gut microbiota and serum metabolites of calves is currently unclear.

Objective

The aim of this study is to investigate the changes in the gut microbiota and serum metabolites in calves after rumen acidosis and analyse the correlation.

Methods

Eight calves were selected as the rumen acidosis group, and eight health calves were selected as the healthy group. The faecal gut microbiota and serum metabolites of calves were detected respectively using 16S rDNA high-throughput sequencing and non-target metabolomics. The correlation between gut microbiota and serum metabolites was analyzed by Spearman correlation analysis.

Results

Differential analysis of the diversity and composition of gut microbiota between eight male healthy (Health) and eight male rumen acidosis (Disease) calves revealed that rumen acidosis increased the abundance of the gut microbiota in calves. At the phylum level, compared to the Healthy group, the relative abundance of Proteobacteria in the Disease group significantly decreased (P<0.05), while the relative abundance of Desulfobacterota significantly increased in the Disease group (P<0.05). At the genus level, compared to the Disease group, the relative abundance of Alloprevotella, Muribaculaceae, Succinivibrio, Prevotella, Agathobacter and Parabacteroides significantly increased in the Healthy group (P<0.05), while the relative abundance of Christensenellaceae_R-7 and Monoglobus significantly decreased in the Healthy group (P<0.05). Differential analysis results showed the Healthy group had 23 genera with higher abundance, while the Disease group had 47 genera with higher abundance. Serum metabolomics results revealed the differential metabolites associated with rumen acidosis, including nicotinamide, niacin, L-glutamic acid and carnosine, were mainly enriched in the nicotinate and nicotinamide pathway and the histidine pathway.

Conclusion

The occurrence of rumen acidosis can induce changes in the gut microbiota of calves, with a significant increase of the Christensenellaceae_R-7 genus and a significant decrease of Prevotella and Succinivibrio genera. In addition, the occurrence of rumen acidosis can also induce changes in serum metabolites including niacin, niacinamide, L-glutamine, and carnosine, which may serve as the diagnostic biomarkers of rumen acidosis of calves.

Invited review: "Probiotic" approaches to improving dairy production: Reassessing "magic foo-foo dust"

The gastrointestinal microbial consortium in dairy cattle is critical to determining the energetic status of the dairy cow from birth through her final lactation. The ruminant's microbial community can degrade a wide variety of feedstuffs, which can affect growth, as well as production rate and efficiency on the farm, but can also affect food safety, animal health, and environmental impacts of dairy production. Gut microbial diversity and density are powerful tools that can be harnessed to benefit both producers and consumers. The incentives in the United States to develop Alternatives to Antibiotics for use in food-animal production have been largely driven by the Veterinary Feed Directive and have led to an increased use of probiotic approaches to alter the gastrointestinal microbial community composition, resulting in improved heifer growth, milk production and efficiency, and animal health. However, the efficacy of direct-fed microbials or probiotics in dairy cattle has been highly variable due to specific microbial ecological factors within the host gut and its native microflora. Interactions (both synergistic and antagonistic) between the microbial ecosystem and the host animal physiology (including epithelial cells, immune system, hormones, enzyme activities, and epigenetics) are critical to understanding why some probiotics work but others do not. Increasing availability of next-generation sequencing approaches provides novel insights into how probiotic approaches change the microbial community composition in the gut that can potentially affect animal health (e.g., diarrhea or scours, gut integrity, foodborne pathogens), as well as animal performance (e.g., growth, reproduction, productivity) and fermentation parameters (e.g., pH, short-chain fatty acids, methane production, and microbial profiles) of cattle. However, it remains clear that all direct-fed microbials are not created equal and their efficacy remains highly variable and dependent on stage of production and farm environment. Collectively, data have demonstrated that probiotic effects are not limited to the simple mechanisms that have been traditionally hypothesized, but instead are part of a complex cascade of microbial ecological and host animal physiological effects that ultimately impact dairy production and profitability.

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.

Integrating Omics Technologies for a Comprehensive Understanding of the Microbiome and Its Impact on Cattle Production

Ruminant production holds a pivotal position within the global animal production and agricultural sectors. As population growth escalates, posing environmental challenges, a heightened emphasis is directed toward refining ruminant production systems. Recent investigations underscore the connection between the composition and functionality of the rumen microbiome and economically advantageous traits in cattle. Consequently, the development of innovative strategies to enhance cattle feed efficiency, while curbing environmental and financial burdens, becomes imperative. The advent of omics technologies has yielded fresh insights into metabolic health fluctuations in dairy cattle, consequently enhancing nutritional management practices. The pivotal role of the rumen microbiome in augmenting feeding efficiency by transforming low-quality feedstuffs into energy substrates for the host is underscored. This microbial community assumes focal importance within gut microbiome studies, contributing indispensably to plant fiber digestion, as well as influencing production and health variability in ruminants. Instances of compromised animal welfare can substantially modulate the microbiological composition of the rumen, thereby influencing production rates. A comprehensive global approach that targets both cattle and their rumen microbiota is paramount for enhancing feed efficiency and optimizing rumen fermentation processes. This review article underscores the factors that contribute to the establishment or restoration of the rumen microbiome post perturbations and the intricacies of host-microbiome interactions. We accentuate the elements responsible for responsible host-microbiome interactions and practical applications in the domains of animal health and production. Moreover, meticulous scrutiny of the microbiome and its consequential effects on cattle production systems greatly contributes to forging more sustainable and resilient food production systems, thereby mitigating the adverse environmental impact.

Stall-Feeding of Sheep on Restricted Grazing: Effects on Performance and Serum Metabolites, Ruminal Fermentation, and Fecal Microbiota

This study investigated the effects of three feeding systems, indoor feeding (CONT), indoor feeding with time-restricted grazing artificial pasture (4 h/day, G4H), and indoor feeding with an eight-hour daily grazing artificial pasture (G8H), on the growth performance, serum metabolites, ruminal fermentation, and fecal microbiota composition of lambs. Average daily gain showed a tendency (p = 0.081) to be higher for the G4H group compared with the CONT group. Moreover, feeding systems did not have a significant effect on most of the serum biochemical indicators in lambs. Concentrations of serum glutathione peroxidase and immunoglobulins (IgA, gG, and IgM) were significantly lower (p < 0.01) in the CONT group. Additionally, a tendency towards higher levels of volatile fatty acids, acetate, and butyrate was found in animals of the G4H group compared to the CONT group. Furthermore, fecal microbiota composition was altered in G4H and G8H groups, resulting in the increased relative abundance of Firmicutes and Ruminococcaceae UCG-005, as well as the decreased relative abundance of Ruminobacter compared with the CONT group. Overall, these results suggest that indoor feeding with restricted grazing time does not significantly affect fattening performance or rumen fermentation but enhances antioxidation and immune function activity and also alters fecal microbiota composition.

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), BC_0.3% (low buffering capacity, 0.3% buffer), BC_0.5% (medium buffering capacity, 0.5% buffer), and BC_0.9% (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 BC_0.9% and BC_0.5% 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 BC_0.9%, Ruminoccocus bromii and Succiniclasticum ruminis under BC_0.5%, and Bacteroides massiliensis under BC_0.3%. The normalized data of relative abundance of observed OTUs' representative families have grouped the CON with BC_0.3% in the same cluster, whereas BC_0.5% and BC_0.9% 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 BC_0.9% and BC_0.3% groups showed dispersed community distribution. Overall, increasing the buffering capacity by supplementation of BC_0.5% and and BC_0.9% 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.

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.

Utilizing the Gastrointestinal Microbiota to Modulate Cattle Health through the Microbiome-Gut-Organ Axes

The microorganisms inhabiting the gastrointestinal tract (GIT) of ruminants have a mutualistic relationship with the host that influences the efficiency and health of the ruminants. The GIT microbiota interacts with the host immune system to influence not only the GIT, but other organs in the body as well. The objective of this review is to highlight the importance of the role the gastrointestinal microbiota plays in modulating the health of a host through communication with different organs in the body through the microbiome-gut-organ axes. Among other things, the GIT microbiota produces metabolites for the host and prevents the colonization of pathogens. In order to prevent dysbiosis of the GIT microbiota, gut microbial therapies can be utilized to re-introduce beneficial bacteria and regain homeostasis within the rumen environment and promote gastrointestinal health. Additionally, controlling GIT dysbiosis can aid the immune system in preventing disfunction in other organ systems in the body through the microbiome-gut-brain axis, the microbiome-gut-lung axis, the microbiome-gut-mammary axis, and the microbiome-gut-reproductive axis.

Influence of the Gut Microbiome on Feed Intake of Farm Animals

With the advancement of microbiome research, the requirement to consider the intestinal microbiome as the “last organ” of an animal emerged. Through the production of metabolites and/or the stimulation of the host’s hormone and neurotransmitter synthesis, the gut microbiota can potentially affect the host’s eating behavior both long and short-term. Based on current evidence, the major mediators appear to be short-chain fatty acids (SCFA), peptide hormones such as peptide YY (PYY) and glucagon-like peptide-1 (GLP-1), as well as the amino acid tryptophan with the associated neurotransmitter serotonin, dopamine and γ-Aminobutyrate (GABA). The influence appears to extend into central neuronal networks and the expression of taste receptors. An interconnection of metabolic processes with mechanisms of taste sensation suggests that the gut microbiota may even influence the sensations of their host. This review provides a summary of the current status of microbiome research in farm animals with respect to general appetite regulation and microbiota-related observations made on the influence on feed intake. This is briefly contrasted with the existing findings from research with rodent models in order to identify future research needs. Increasing our understanding of appetite regulation could improve the management of feed intake, feed frustration and anorexia related to unhealthy conditions in farm animals.

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.

Liver transcriptome response to periparturient hormonal and metabolic changes depends on the postpartum occurrence of subacute ruminal acidosis in Holstein cows

We investigated changes in rumen fermentation, peripheral blood metabolites and hormones, and hepatic transcriptomic dynamics in Holstein cows with and those without subacute ruminal acidosis (SARA) during the periparturient period. Sixteen multiparous Holstein cows were categorized in the SARA (n = 8) or non-SARA (n = 8) groups depending on whether they developed SARA during the 2 wk after parturition. Reticulo-ruminal pH was measured continuously throughout the study. Rumen fluid, blood, and liver tissue samples were collected at 3 wk prepartum and 2 and 6 wk postpartum, with an additional blood sample collected at 0 and 4 wk postpartum. The 1-h mean pH was depressed postpartum in both groups, whereas depression was more severe in the SARA group simultaneously with significantly longer duration of time (for pH <5.6 and 5.8). Significant expression of differentially expressed genes in liver tissue (DEGs; false discovery rate corrected P < 0.1) were identified only in the non-SARA group and were further analyzed by Ingenuity Pathway Analysis software. Among the top expressed DEGs, the hepatic genes encoding lipid and cholesterol secretion (APOA1, APOA4, and G0S2) and gluconeogenesis (PC, G6PC, and PCK1) were upregulated postpartum. In silico analysis revealed the significant postpartum activation of upstream regulators, such as INSR, PPARG, and PPARGC1A. These results suggested that hepatic transcriptomic responsiveness to postpartum metabolic load and hormones were likely discouraged in cows with SARA when compared with the significant activation of genes and signaling pathways for adequate metabolic adaption to postpartum high-grain diet feeding in Holstein cows without SARA.

Anti-lipopolysaccharide antibody administration mitigates ruminal lipopolysaccharide release and depression of ruminal pH during subacute ruminal acidosis challenge in Holstein bull cattle

The effects of anti-lipopolysaccharide (LPS) antibody on rumen fermentation and LPS activity were investigated during subacute ruminal acidosis (SARA) challenge. Eleven Holstein cattle (164 ± 14 kg) were used in a 3 × 3 Latin square design. Cattle were fed a roughage diet on days −11 to −1 (pre-challenge) and day 2 (post-challenge), and a high-grain diet on days 0 and 1 (SARA challenge). For 14 days, 0-, 2-, or 4-g of anti-LPS antibody was administered once daily through a rumen fistula. Ruminal pH was measured continuously, and rumen fluid and blood samples were collected on days −1, 0, 1, and 2. Significantly lower ruminal LPS activity on day 1 was observed in the 2- and 4-g groups than those in the 0-g group. In addition, significantly higher 1-hr mean ruminal pH on SARA challenge period (days 0 and 1) was identified in the 4-g group than in the 0-g group. However, rumen fermentation measurements (total volatile fatty acid [VFA], VFA components, NH₃-N and lactic acid) and peripheral blood metabolites (glucose, free fatty acid, beta-hydroxybutyrate, total cholesterol, blood urea nitrogen, aspartate aminotransferase and gamma-glutamyl transferase) were not different among the groups during the experimental periods. Therefore, anti-LPS antibody administration mitigates LPS release and pH depression without the depression of rumen fermentation and peripheral blood metabolites during SARA challenge in Holstein cattle.

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.

The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi

This work investigated the changes of the rumen microbiome of goats switched from a forage to a concentrate diet with special attention to anaerobic fungi (AF). Female goats were fed an alfalfa hay (AH) diet (0% grain; n = 4) for 20 days and were then abruptly shifted to a high-grain (HG) diet (40% corn grain, 60% AH; n = 4) and treated for another 10 days. Rumen content samples were collected from the cannulated animals at the end of each diet period (day 20 and 30). The microbiome structure was studied using high-throughput sequencing for bacteria, archaea (16S rRNA gene) and fungi (ITS2), accompanied by qPCR for each group. To further elucidate unclassified AF, clone library analyses were performed on the ITS1 spacer region. Rumen pH was significantly lower in HG diet fed goats, but did not induce subacute ruminal acidosis. HG diet altered prokaryotic communities, with a significant increase of Bacteroidetes and a decrease of Firmicutes. On the genus level Prevotella 1 was significantly boosted. Methanobrevibacter and Methanosphaera were the most abundant archaea regardless of the diet and HG induced a significant augmentation of unclassified Thermoplasmatales. For anaerobic fungi, HG triggered a considerable rise in Feramyces observed with both ITS markers, while a decline of Tahromyces was detected by ITS2 and decrease of Joblinomyces by ITS1 only. The uncultured BlackRhino group revealed by ITS1 and further elucidated in one sample by LSU analysis, formed a considerable part of the AF community of goats fed both diets. Results strongly indicate that the rumen ecosystem still acts as a source for novel microorganisms and unexplored microbial interactions and that initial rumen microbiota of the host animal considerably influences the reaction pattern upon diet change.

Spatial and temporal organization of jejunal microbiota in goats during animal development process

AIMS

This research aimed to investigate the temporal bacterial colonization relating to non-rumination, transition and rumination phases, together with the spatial organization of microbial community in the jejunal mucosa and digesta of goats.

METHODS AND RESULTS

This study explored the colonization programme of the jejunal microbiota by employing 16S rRNA amplicon sequencing. The colonization pattern of jejunal bacterial community exhibited an age- and gut region-dependent progression during animal development process. Approximately 268 bacterial signatures contributed to the discrimination between gut regions, with Lactobacillus, Ruminococcus, Eubacterium and Clostridium_sensu_stricto were enriched in the jejunal digesta, and Bacteroides and unclassified bacteria were enriched in the jejunal mucosa. Intriguingly, a shift from Lactobacillus to Butyrivibrio, Eubacterium and Ruminococcus after d 20 was observed for jejunal digesta. In mucosa, Bifidobacterium, Corynebacterium, Faecalibacterium and Roseburia increased with age (P < 0·05) while Arcobacter, Bacteroides and Porphyromonas peaked at d 10.

CONCLUSIONS

The jejunal bacterial community was settled after solid starter provision, which may mark the potential boundary of a timeframe for intervention in goats. The spatial heterogeneity highlighted the complicacy of ecological niches during manipulation of gut microbiota.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study extended the understanding of microbial programming and niche specific in the jejunum among different life stages and the basal cognition of persistent enhancement of nutrient utilization and decline of enteric diseases in ruminants.

Non-Invasive Indicators Associated with Subacute Ruminal Acidosis in Dairy Cows

The aim of the study was to characterize the interrelationship between decreased ruminal fluid pH during subacute ruminal acidosis (SARA) and concentrations of principal constituents of milk and biochemical indices associated with nitrogen utilizations such as rumen ammonia nitrogen (RAN), blood urea nitrogen (BUN) and milk urea nitrogen (MUN). Ruminal fluid samples were obtained by rumenocentesis from 305 cows representing 13 dairy herds. The cows were divided according to ruminal fluid pH into three groups: low, moderate, and high rumen pH cows. The herds were divided into three groups on the basis of the percentages of cows with an assigned value of ruminal fluid pH: SARA-positive, SARA-risk and SARA-negative. SARA-positive herds were characterized by higher concentrations of RAN (12.6 vs. 6.9 mg/dL), BUN (16.2 vs. 10.1 mg/dL) and MUN (12.4 vs. 9.1 mg/dL) compared to SARA-negative herds. Similarly, low-rumen pH cows had greater concentrations of RAN, BUN and MUN than high-rumen pH cows (11.9 vs. 5.8 mg/ dL, 19.9 vs. 14.1 mg/dL, and 12.3 vs. 9.5 mg/dL, respectively). Moreover, SARA-positive herds and low-rumen pH cows had the highest lactose and the lowest fat concentrations in milk. The study demonstrated that the concentration of milk urea nitrogen could be considered one of the indirect and non-invasive indicators of the occurrence of subacute ruminal acidosis in dairy herds.

Effects of short-term fasting on ruminal pH and volatile fatty acids in cattle fed high-roughage versus high-concentrate diets

We evaluated whether the dietary roughage-to-concentrate ratio affects ruminal pH and volatile fatty acids (VFAs) in response to a one-time morning fast. Four healthy rumen-cannulated Holstein steers 4–5 months old were used. Cattle were subjected to 2 weeks of adaptation (high-roughage or high-concentrate diet), and morning feed restriction was performed on the day after the adaptation period ended (Day 0). Thereafter, each diet was reintroduced on the evening of Day 0. Our results showed that the 1-hr mean ruminal pH from 0800 to 1900 on Day 0 was higher, and that from 1700 to 1900 on Day 1 was lower (P<0.05) than pH on 1 day before fasting (Day −1) in cattle fed both diets. On Day 0, total VFA levels decreased after morning fasting and were lower (P<0.05) than those on Day −1 irrespective of evening refeeding. Furthermore, blood non-esterified fatty acid and beta-hydroxybutyric acid levels on Day 0 increased and decreased, respectively, compared to Day −1 in cattle fed both diets. These results indicate that even a one-time feed restriction can disrupt ruminal fermentation, and the changes can persist to the next day after fasting.

The Role of the Gut Microbiome in Cattle Production and Health: Driver or Passenger?

Ruminant production systems face significant challenges currently, driven by heightened awareness of their negative environmental impact and the rapidly rising global population. Recent findings have underscored how the composition and function of the rumen microbiome are associated with economically valuable traits, including feed efficiency and methane emission. Although omics-based technological advances in the last decade have revolutionized our understanding of host-associated microbial communities, there remains incongruence over the correct approach for analysis of large omic data sets. A global approach that examines host/microbiome interactions in both the rumen and the lower digestive tract is required to harness the full potential of the gastrointestinal microbiome for sustainable ruminant production. This review highlights how the ruminant animal production community may identify and exploit the causal relationships between the gut microbiome and host traits of interest for a practical application of omic data to animal health and production.

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.

Notice of RETRACTION: Changes in rumen fermentation, bacterial community, and predicted functional pathway in Holstein cows with and without subacute ruminal acidosis during the periparturient period

The authors have elected to retract this paper in accordance with the following points. The article as written contains misleading information and omits important details. Cows in this study were assigned to groups based on the current definition of subacute ruminal acidosis; they were housed on two different farms and fed two different sets of rations in this study. However, multiple farms were not described in the materials and methods and this was not accounted for in the statistical analysis as published. The diets shown in Table 1 were not actually fed to animals; rather, the proportions of ingredients listed represent an average of the two farms housing the cows. The authors regret the errors.

Fermentation Pattern of Several Carbohydrate Sources Incubated in an In Vitro Semicontinuous System with Inocula from Ruminants Given Either Forage or Concentrate-Based Diets

Simple Summary

A sudden change from a milk/forage diet to a high concentrate diet in young ruminants increases the rate and extent of rumen microbial fermentation, leading to digestive problems, such as acidosis. The magnitude of this effect depends on the nature of the ingredients. Six carbohydrate sources were tested: three cereal grains (barley, maize and brown sorghum), as high starch sources of different availability, and three byproducts (sugarbeet pulp, citrus pulp and wheat bran), as sources of either insoluble or soluble fibre. An in vitro semicontinuous incubation system was used to compare the fermentation pattern of substrates incubated with inocula-simulating concentrate or forage diets, under the pH and liquid outflow rate conditions of intensive feeding systems. The magnitude of microbial fermentation was higher with the concentrate than the forage inoculum, and the drop in pH in the first part of incubation was more profound. Among the substrates, citrus pulp had a greater acidification potential and was fermented at a higher extent, followed by wheat bran and barley. In conclusion, the acidification capacity of substrates plays an important role in the environmental conditions, depending on the type of diet given to the ruminant. This in vitro system allows us to compare the substrates under conditions simulating high-concentrate feeding.

Abstract

The fermentation pattern of several carbohydrate sources and their interaction with the nature of microbial inoculum was studied. Barley (B), maize (M), sorghum, (S), sugarbeet pulp (BP), citrus pulp (CP) and wheat bran (WB) were tested in an in vitro semicontinuous system maintaining poorly buffered conditions from 0 to 6 h, and being gradually buffered to 6.5 from 8 to 24 h to simulate the rumen pH pattern. Rumen fluid inoculum was obtained from lambs fed with either concentrate and barley straw (CI) or alfalfa hay (FI). The extent of fermentation was higher with CI than FI throughout the incubation (p < 0.05). Among the substrates, S, BP and M maintained the highest pH (p < 0.05), whereas CP recorded the lowest pH with both inocula. Similarly, CP recorded the highest gas volume throughout the incubation, followed by WB and B, and S recorded the lowest volume (p < 0.05). On average, the total volatile fatty acid (VFA), as well as lactic acid concentration, was higher with CP than in the other substrates (p < 0.05). The microbial structure was more affected by the animal donor of inoculum than by the substrate. The in vitro semicontinuous system allows for the study of the rumen environment acidification and substrate microbial fermentation under intensive feeding conditions.

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

To increase intramuscular fat accumulation, Japanese Black cattle are commonly fed a high-grain diet from 10 to 30 months of age although it can result in the abnormal accumulation of organic acids in the rumen. We explored the effect of long-term high-concentrate diet feeding on ruminal pH and fermentation, and its effect on the rumen bacterial community in Japanese Black beef cattle during a 20-month fattening period. Nine castrated and fistulated Japanese Black beef cattle were housed with free access to food and water throughout the study period (10-30 months of age). The fattening stages included Early, Middle, and Late stages (10-14, 15-22, and 23-30 months of age, respectively). Cattle were fed high-concentrate diets for the experimental cattle during fattening. The body weight of the cattle was 439 ± 7.6, 561 ± 11.6, and 712 ± 18.5 kg (mean ± SE) during the Early, Middle, and Late stages, respectively. Ruminal pH was measured continuously during the final 7 days of each stage, and rumen fluid and blood samples were collected on day 4 (fourth day during the final 7 days of the pH measurements). The 24-h mean ruminal pH during the Late stage was significantly lower than that during the Early stage. Total volatile fatty acid (VFA) during the Late stage was significantly lower than during the Early and Middle stages, but no changes were noted in individual VFA components. The lactic acid concentration during the Late stage was significantly higher than that during the Early and Middle stages. The bacterial richness indices decreased significantly during the Late stage in accordance with the 24-h mean ruminal pH. Among the 35 bacterial operational taxonomic units (OTUs) shared by all samples, the relative abundances of OTU8 (Family Ruminococcaceae) and OTU26 (Genus Butyrivibrio) were positively correlated with the 24-h mean ruminal pH. Total VFA concentration was negatively correlated with OTU167 (Genus Intestinimonas), and lactic acid concentration was correlated positively with OTU167 and OTU238 (Family Lachnospiraceae). These results suggested that long-term high-grain diet feeding gradually lowers ruminal pH and total VFA production during the Late fattening stage. However, the ruminal bacterial community adapted to feeding management and the lower pH during the Late stage by preserving their diversity or altering their richness, composition, and function, to enhance lactic acid production in Japanese Black beef cattle.

Influence of the microbiota-gut-brain axis on behavior and welfare in farm animals: A review

There is increasing evidence of a pivotal role of the gut microbiota (GUT-M) in key physiological functions in vertebrates. Many studies discuss functional implications of the GUT-M not only on immunity, growth, metabolism, but also on brain development and behavior. However, while the influence of the microbiota-gut-brain axis (MGBA) on behavior is documented in rodents and humans, data on farm animals are scarce. This review will first report the well-known influence of the MGBA on behavior in rodent and human and then describe its influence on emotion, memory, social and feeding behaviors in farm animals. This corpus of experiments suggests that a better understanding of the effects of the MGBA on behavior could have large implications in various fields of animal production. Specifically, animal welfare and health could be improved by selection, nutrition and management processes that take into account the role of the GUT-M in behavior.

Effects of an increased concentrate diet on rumen pH and the bacterial community in Japanese Black beef cattle at different fattening stages

This study evaluated the effects of increasing the proportion of concentrate in the diet on the rumen pH and bacterial community in Japanese Black beef cattle at different fattening stages. Six rumen-cannulated beef cattle were studied in the middle (Mid group, n=3, age 21–22 months) and late (Late group, n=3, age 31 months) fattening stages. The cattle were fed rice straw with control (CON period) or high-concentrate (HC period) diets for 14 consecutive days in each period. Rumen pH was measured continuously and the rumen fluids were collected on the last day of each period. The 24-hr mean and minimum rumen pH in the Mid group were significantly (P<0.05) lower during the HC period compared with the CON period, whereas those in the Late group were continuously low during both periods. In the Late group, the ruminal volatile fatty acid and lactic acid concentrations were significantly (P<0.05) higher during the HC period. During the HC period, the proportions of Prevotella and Caloramator were significantly (P<0.05) higher and lower, respectively, in the Mid group. From these findings, significant changes in the rumen pH and bacterial community induced by dietary changes were mainly observed in the Mid group. Therefore, the ruminal fermentative function in response to a higher concentrate diet might adapt differently in Japanese Black beef cattle at the two different fattening stages.