Factors that alter rumen microbial ecology

Potential role of key rumen microbes in regulating host health and growth performance in Hu sheep

BACKGROUND

Average daily gain (ADG) is an important component affecting the profitability of sheep. However, research on the relationship between rumen microbes and sheep growth phenotype is still very lacking. Therefore, in this study, 16 Hu sheep were selected from a cohort of 318 sheep assigned to the same feeding and management conditions, and divided into high growth rate (HADG, n = 8) group and low growth rate (LADG, n = 8) group according to the extreme ADG value. Then, the differences in rumen microbes, rumen fermentation and animal immune parameters were further compared between groups to explore the potential role of rumen key microbes in regulating the health and growth performance of Hu sheep hosts.

RESULTS

The results showed that specific pathogenic bacteria associated with ADG, including Anaerotruncus, Sediminibacterium and Glaesserella, exhibited significant correlations with interleukin-6 (IL-6) and immunoglobulin G (IgG). These interactions disrupt immune homeostasis in the host, leading to a metabolic prioritization of energy resources toward immune responses, thereby impairing growth and development. Succinivibrio_dextrinosolvens was enriched in HADG sheep and exhibited a significant positive correlation with propionate levels. This promoted propionate production in the rumen, enhancing the metabolic activity of carbohydrate, amino acid and energy metabolism, ultimately contributing to higher ADG in sheep. Importantly, random forest analysis results showed that Succinivibrio_dextrinosolvens could classify sheep into HADG and LADG with a prediction accuracy of 81.2%. Additionally, we identified 34 bacteria belonged to connectors in the HADG co-occurrence network, including Alloprevotella, Phascolarctobacterium, Anaerovibrio, Butyricicoccus, Ruminococcaceae_noname, and Roseburia, etc., which play an important role in the degradation of carbohydrates and convert them into short-chain fatty acids (SCFAs), maintaining rumen health, and modulating inflammation.

CONCLUSIONS

In summary, key microbes in the rumen affect the overall healthy homeostasis and rumen fermentation of the host, leading to changes in energy utilization, which in turn affects the average daily gain of Hu sheep. Succinivibrio_dextrinosolvens is a promising biomarker for selecting high growth rate sheep in the future. This study provides a new method to manipulate rumen bacteria to improve growth performance in sheep.

Effects of cellulase or Lactobacillus plantarum on ensiling performance and bacterial community of sorghum straw

This study aimed to evaluate the effects of cellulase or Lactobacillus plantarum (L. plantarum) on the fermentation characteristics and microbial community structure of the sorghum straw silage. Sorghum straw was treated with the following four experimental conditions: distilled water (control, CK), cellulase (CEL), Lactobacillus plantarum (LP), and a combined treatment of Lactobacillus plantarum with cellulase (LPCEL). These results indicated that the LP treatment could markedly (p < 0.05) preserve the crude protein content compared to that in other treatments, whereas the CEL significantly (p < 0.05) reduced the acid detergent fiber content, while the LPCEL had the highest lactic acid content and lowest pH value. Proteobacteria and Pantoea were identified as the dominant phylum and genus in fresh materials, respectively. This phylum level dominance transitioned to Firmicutes post-treatment, while at the genus level, the community shifted from Pantoea to co-dominance of Lactobacillus and Prevotella, with Lactobacillus being the most abundant in both the CEL and LPCEL treatments. In conclusion, adding L. plantarum and cellulase to sorghum straw can significantly improve the fermentation quality of sorghum straw silage, and improve the nutritional value of silage by affecting the microbial community structure and metabolic pathways.

Invited Review: Unlocking Growth and Development Potential in Dairy Calves through Precision Protein Feeding

Optimizing protein nutrition is pivotal for enhancing growth, metabolic efficiency and long-term productivity of dairy calves. This review summarizes current research on precision protein feeding based on the NASEM (2021) model, which aligns metabolizable protein (MP) and metabolizable energy (ME) with calf developmental stages to optimize nutrient utilization. In the pre-weaning phase, the crude protein (CP) requirement of Holstein calves (<125 kg BW) increases with increasing average daily gain (ADG), with a 50 kg calf requires 102 g CP (18.2% DMI) for 0.2 kg/d ADG and 315 g CP (25.5% DMI) for 1.0 kg/d ADG, while ME intake increases from 2.56 to 5.66 Mcal/d. The review underscores the importance of adjusting the CP to ME ratio, adequate supply of limiting AA such as Lys, Met and Thr and a balanced ratio of rumen degradable protein (RDP) and rumen undegradable protein (RUP) to optimize growth and metabolism. Amino acids are essential for muscle development, immune response and enzyme function. Protein intake in the pre-weaning phase improves growth performance, weight gain and feed efficiency, although excess protein in the diet can reduce overall growth efficiency. The balance between RDP and RUP is critical for microbial protein synthesis and nitrogen retention, with RDP becoming the dominant protein source after weaning due to increased reliance on microbial protein. Furthermore, macronutrient-specific adjustments in milk replacers (MR), such as the addition of protein, fat or lactose, lead to different metabolic responses, with protein primarily supporting lean tissue building, while fat and lactose promote energy storage. These findings emphasize the need for precise nutritional strategies that consider protein quality and AA availability to ensure optimal growth and metabolic efficiency. Furthermore, protein levels in calf starter diets ideally between 20 and 23% CP (DM basis) lead to optimal growth, especially when combined with moderate to high milk feeding, although higher protein levels are not always growth promoting, highlighting the need for precise nutritional adjustments according to the developmental needs of the calf. For growing heifers, protein nutrition after weaning continues to be a critical factor in optimizing growth, efficiency and later lactation performance. Stage-specific adjustments to the balance between RDP and RUP are important to support microbial protein synthesis and nitrogen retention, with RDP becoming the dominant protein source as heifers mature and transition to a more energy-driven fat deposition phase. These findings are critical for refining protein and energy utilization strategies, optimizing calf development and supporting long-term lactation performance. In summary, this review provides insights into the optimal protein feeding strategies to improve calf growth and metabolic efficiency in the pre- and post-weaning phases.

Studies on the concerted interaction of microbes in the gastrointestinal tract of ruminants on lignocellulose and its degradation mechanism

The complex structure of lignocellulose, one of the most abundant renewable resources on earth, makes biodegradation challenging. Ruminant gastrointestinal microbiota achieves efficient lignocellulose degradation through a highly synergistic ecosystem, which provides an important research model for sustainable energy development and high value-added chemical production. This review systematically summarizes the key mechanisms of lignocellulose degradation by ruminant gastrointestinal microorganisms, focusing on the synergistic roles of rumen and hindgut (including cecum, colon, and rectum) microorganisms in cellulose, hemicellulose, and lignin degradation. The study focuses on the functional differentiation and cooperation patterns of bacteria, fungi and protozoa in lignocellulose decomposition, and summarizes the roles of carbohydrate-active enzymes (CAZymes) and their new discoveries under the histological techniques. In addition, this manuscript explores the potential application of gastrointestinal tract (GIT) microbial degradation mechanisms in improving the utilization of straw-based feeds. In the future, by revealing the mechanism of microbe-host synergy and integrating multi-omics technologies, the study of ruminant gastrointestinal microbial ecosystems will provide new solutions to promote the efficient utilization of lignocellulose and alleviate the global energy crisis.

Gender and age-related variations in rumen fermentation and microbiota of Qinchuan cattle

OBJECTIVE

Our study aimed to investigate the gender and age-related variations in rumen fermentation, serum metabolites, and microbiota in Qinchuan cattle.

METHODS

A total of 38 Qinchuan beef cattle were selected and maintained on a uniform diet for three months. Rumen fluid and blood samples were collected to determine rumen fermentation, serum metabolites, and microbial 16S rRNA sequencing.

RESULTS

The results revealed that the concentration of rumen butyrate in female Qinchuan cattle was significantly higher than in males (p<0.05). Isobutyrate, butyrate, and isovalerate exhibited significant age-related differences. Females exhibited lower serum glucose (GLU) and higher triglycerides (TG), nonesterifiedfatty acid (NEFA) levels compared to males (p<0.05). Serum albumin (ALB) and urea (UA) levels increased with age (p<0.05). Furthermore, the alpha diversity of rumen bacteria improved with age (p<0.05), with no gender differences observed. Males had higher relative abundances of Bacteroidota, Verrucomicrobiota, and Cyanobacteria, while females had higher Firmicutes and Desulfobacterota (p<0.05). The cellulose-degrading genus Ruminococcus and propionateproducing genus Succiniclasticum were more abundant in females, whereas the antiinflammatory genus Lachnospiraceae_NK4A136_group and the hemicellulose-degrading genus Prevotella were more abundant in males (p<0.05). Age-related differences in bacteria were found in Pseudobutyrivibrio and several members of the Lachnospiraceae. Functional prediction indicated that "Amino acid metabolism" and "Lipid metabolism" were mainly enriched in females, whereas "Carbohydrate metabolism" and "Glycan biosynthesis and metabolism" were enriched in males (p<0.05). RDA analysis highlighted butyrate as a key factor influencing the rumen bacterial community. NK4A214_group and Ruminococcus were positively correlated with butyrate, while Prevotella and Pseudobutyrivibrio were negatively correlated with butyrate (p<0.05).

CONCLUSION

We observed a significant improvement in the diversity and stability of rumen microbiota as age increased. Ruminococcus, NK4A214_group, and Prevotella were likely contributors to variations in energy utilization and fat deposition between male and female Qinchuan cattle.

Asparagopsis taxiformis mitigates ruminant methane emissions via microbial modulation and inhibition of methyl-coenzyme M reductase

Introduction

Asparagopsis taxiformis (A. taxiformis) has shown great potential to mitigate methane (CH4) emissions in recent years. This study aims to evaluate the impact of A. taxiformis on methane emissions and to fill the knowledge gap regarding its mechanisms of action in affecting CH4 metabolism and rumen fermentation.

Methods

The experimental design consisted of a control group (CON) and test groups supplemented with 2% (Low), 5% (Mid), and 10% (High) of dried and freeze-dried treatment A. taxiformis, respectively, for 48 h of in vitro rumen fermentation. The optimal combination strategy for mitigating CH4 emissions was confirmed by analyzing nutrient degradation, CH4 production and rumen fermentation parameters, and the mechanism of action was analyzed by metagenomic and metabolomic approaches.

Results and discussion

The results showed that freeze-dried treatment had better potential to mitigate CH4 emissions than dried treatment, and supplementation of freeze-dried treatments at Low, Mid, and High groups significantly reduced CH4 production by 32.44%, 98.53%, and 99.33%, respectively. However, the High group exhibited a huge negative impact on rumen fermentation. Therefore, subsequent analyses focused on the Low and Mid groups to explore the underlying mechanisms. Metagenomics analyses showed that supplementation of freeze-dried treatment with the Mid-level supplementation significantly increased the relative abundance of propionate-producing bacteria such as Prevotella, Ruminobacter, and Succinivibrio, while inhibited acetate-producing bacteria such as Ruminococcus, altered the pattern of volatile fatty acid (VFA) synthesis in the rumen, and reduced H2 availability for methanogenesis and promoted propionate production, indirectly alleviating CH4 production. Moreover, by suppressing the relative abundance of Methanobrevibacter, CH4 production in the rumen was directly suppressed. Furthermore, KEGG pathway analysis showed that A. taxiformis significantly inhibited the abundance of K00399, methyl-coenzyme M reductase alpha subunit, which directly inhibited CH4 synthesis. Metabolomics analysis of A. taxiformis supplementation significantly enriched ketoglutarate, malate, isocitrate, and melatonin, which may have reduced the release of rumen fermented H2, thereby mitigating CH4 emissions. In summary, freeze-dried treatment A. taxiformis at the 5% supplementation level achieved the optimal balance between CH4 mitigation and rumen fermentation efficiency.

Boosting volatile fatty acids (VFAs) production during anaerobic digestion of rich lignocellulose pulp mill excess sludge by inoculating rumen fluid and the study on the microbial community structures and functions

Hydrolysis is the rate-limiting step in the anaerobic digestion of lignocellulose. In the present study, pulp and paper mill sludge (PPMS), a lignocellulose-rich, high-volume waste, which is difficult to be treated by traditional anaerobic digestion, was inoculated with rumen microorganisms for VFAs production. The maximum extent of VFA accumulation was 3839 mg/L after 84 h in the rumen fluid-inoculated digester, versus 2338 mg/L after 96 h in the digester without rumen fluid addition. The amount was 1.64 times higher than that of digester leachate inoculum. During VFAs production, the hydrolysable of lignocellulose and extracellular polymers were promoted by inoculating rumen liquid. High-throughput sequencing results (16S rRNA genes) showed that there was a significant succession of dominant microbial community during in vitro fermentation of PPMS by rumen fluid. Fermentation by rumen fluid is a potentially effective technology to boost VFAs production from a lignocellulose-rich biomass.

Gastrointestinal Microorganisms and Blood Metabolites in Holstein Calves with Different Heat Stress Responses in the Same Hot Environment

This study investigated differences in gastrointestinal microbiota and blood metabolomes in calves with different heat stress (HS) responses in the same hot environment. Ten high (H) and ten low (L) HS response preweaning Holstein calves were selected based on their heat stress level (respiratory rate and rectal temperature), jugular vein blood samples and ruminal and fecal samples were collected. Notable variations were observed in the serum levels of heat shock protein 70 (HSP-70) and IL-2 between the two calf groups (p < 0.05). In group H, rumen and fecal microbiota synergism was disrupted. In the H group, the host metabolome exhibited enrichment in pyruvate metabolism and the tricarboxylic acid cycle (p < 0.05). Key factors bridging the relationship between gastrointestinal microbiota and serum metabolites included the rumen bacterial genus g__Ruminococcus, serum HSP-70, malic acid, and fumaric acid. These hubs served as potential indicators for distinguishing the response to heat stress in calves (p < 0.05). In conclusion, this study identified the relationship between gastrointestinal microbiota characteristics and different HS responses of the host, thus providing evidence and new directions for future studies aimed at understanding HS in individual calves (gut microbiota-host interactions).

The characteristics, influence factors, and regulatory strategies of growth retardation in ruminants: a review

Growth retardation represents a main barrier to affect the productivity and efficiency of ruminants production, which is characterized by low growth rate, a disparity between skeletal and physiological maturation, gastrointestinal dysfunction and reduced reproductive performance. This review provides a concise overview of growth retardation in ruminants, and summarizes the key factors that influence their growth and development, including genetics, nutrition, microbiota and environment. Also, this review emphasizes the central role of nutritional management and gastrointestinal development, as well as the regulatory mechanisms involved in growth processes. In addition, recent advances in these aspects are discussed to form an integrative framework aimed at improving physiological function in ruminants. This review provides a comprehensive perspective for understanding the complex mechanism of growth retardation in ruminants, puts forward a theoretical basis for optimizing the production efficiency of ruminants industry and emphasizes the importance of multidisciplinary collaboration to provide a reference for advancing systematic research on growth and development of ruminants.

Effects of Dietary Protein and Fat Levels on Growth Performance, Nutrient Digestibility, Serum Indexes, and Rectal Fecal Microbiota of Sika Deer (Cervus nippon) Fawns in Early Wintering Period

This study examined the effects of dietary crude protein (CP: 18%, 15%) and crude fat (EE: 8%, 4%) levels, and their interactions, on growth performance, nutrient digestibility, serum indices, and rectal fecal microbiota in sika deer fawns during early wintering. A two-month 2 × 2 factorial experiment was conducted using 32 healthy five-month-old male fawns randomly assigned to four groups: P18E8 (18% CP, 8% EE), P18E4 (18% CP, 4% EE), P15E8 (15% CP, 8% EE), and P15E4 (15% CP, 4% EE). The P18E4 group showed the highest total weight gain and average daily gain (p < 0.05), along with greater apparent digestibility of dry matter, crude protein, calcium, and fiber fractions (p < 0.05). Serum urea content was significantly lower in this group, indicating improved nitrogen utilization (p < 0.05). Dominant fecal microbiota at the phylum level across all groups included Firmicutes_A and Bacteroidota, with the P18E4 group showing a unique genus composition within Bacteroidota, known for enhancing fiber digestion. In summary, a diet with 18% CP and 4% EE optimized growth performance, nutrient digestibility, and gut microbiota composition, providing a strategy for improving the health and productivity of sika deer fawns during overwintering.

Effects of increasing n3:n6 ratio by replacing extruded soybeans with extruded flaxseed on dry matter intake, rumen fluid bacteria, and liver lipid metabolism in transition cows

BACKGROUND

The drop of dry matter intake (DMI) and rise of milk production in transitional dairy cows would mobilize reserved fat and disrupt lipid metabolism, eventually attributed to negative energy balance (NEB) and immune injury. The positive effect of n-3 polyunsaturated fatty acids (PUFA) on regulating energy metabolism and inflammation has been elucidated, however, the lack of regulatory mechanism of dairy cows deserves further investigation. In this study, 30 Holstein transition cows were divided into the control (CON) and HN3 groups based on the n-3: n-6 PUFA ratio in the diet.

RESULTS

The results showed that compared to the CON group, high n-3: n-6 PUFA ratio-supplemented cows in the prepartum phase reduced the relative abundance of gram-negative bacteria in the rumen, the concentration of lipopolysaccharide in the plasma and liver also significantly decreased (P < 0.05). Transcriptomic analysis of the liver showed that the NF-κB signaling pathway significantly down-regulated and the taste transduction pathway up-regulated (P < 0.05) in the HN3 group. In the postpartum phase, a high n-3/n-6 PUFA ratio in the diet increased the relative abundance of Prevotella, Succinimonas and Treponema in the rumen, at the same time, orexins in plasma were also changed (P < 0.05). Further, the insulin resistance pathway significantly down-regulated and the taste transduction pathway up-regulated (P < 0.05) in the liver.

CONCLUSIONS

Overall, these results showed that a high n-3: n-6 PUFA ratio in the diet attenuates inflammatory responses in the prepartum phase and increases milk protein in the postpartum phase of transitional dairy cows. Appropriate increase in the proportion of n-3: n-6 PUFA ratio in the diet may be an effective measure to alleviate postpartum metabolic disease in dairy cows.

Gut Microbiota of Ruminants and Monogastric Livestock: An Overview

The diversity and composition of the gut microbiota are widely recognized as fundamental factors influencing the well-being and productivity of domestic animals. Advancements in sequencing technologies have revolutionized studies in this research field, allowing for deeper insights into the composition and functionality of microbiota in livestock. Ruminants and monogastric animals exhibit distinct digestive systems and microbiota characteristics: ruminants rely on fermentation, while monogastrics use enzymatic digestion, and monogastric animals have simpler stomach structures, except for horses and rabbits, where both processes coexist. Understanding the gut microbiota's impact and composition in both animal types is essential for optimizing production efficiency and promoting animal health. Following this perspective, the present manuscript review aims to provide a comprehensive overview of the gut microbiota in ruminants (such as cattle, sheep, and goats) and monogastric animals (including horses, pigs, rabbits, and chickens).

Comparative Analysis of Health, Inflammatory Markers, and Rumen Microbiota Between Mildly Lame and Healthy Cows

Bovine lameness leads to significant economic losses in the dairy industry. This study investigated the relationship between rumen microbiota and lameness in Holstein cows. Rumen fluid and blood samples were collected from 11 cows with mild lameness and 10 healthy cows before morning feeding. Using high-throughput sequencing and ELISA kits, we found that cows with lameness exhibited decreased rumen pH and increased lameness scores compared to healthy cows. Additionally, cows with lameness had higher blood concentrations of LPS, IL-1, IL-8, and TNF-α. Although there were no significant differences in microbial alpha diversity, principal coordinate analysis (PCoA) revealed significant differences in the rumen microbial structure between the two groups. Further analysis showed that the relative abundances of ruminal Clostridium_IV, Streptococcus, Bacillus, Acinetobacter, Desulfobulbus, Methanobrevibacter, and Mogibacterium were significantly higher in the lameness group, whereas Succinivibrio, Lachnobacterium, Elusimicrobium, Succiniclasticum, and Prevotella were significantly more abundant in the rumen of healthy cows. Importantly, the microbial interaction network in the rumen of cows with lameness was more complex, with key bacteria such as Mogibacterium dominating the microbial interaction network. This study highlights the relationship between rumen microbiota and lameness, providing insights into the prevention and treatment of bovine lameness.

Impact of Feed Composition on Rumen Microbial Dynamics and Phenotypic Traits in Beef Cattle

The rumen microbiome is central to feed digestion and host performance, making it an important target for improving ruminant productivity and sustainability. This study investigated how feed composition influences rumen microbial abundance and phenotypic traits in beef cattle. Fifty-nine Angus bulls were assigned to forage- and grain-based diets in a randomized block design, evaluating microbial dynamics, methane emissions, and feed efficiency. Quantitative PCR (qPCR) quantified bacterial, archaeal, fungal, and protozoal populations. Grain-based diets reduced bacterial and fungal counts compared to forage diets (1.1 × 1011 vs. 2.8 × 1011 copies of 16S rRNA genes and 1.5 × 103 vs. 3.5 × 104 copies of 18S rRNA genes/mL, respectively), while protozoan and methanogen populations remained stable. Microbial abundance correlated with feed intake metrics, including dry matter and neutral detergent fiber intakes. Methane emissions were lower in grain-fed bulls (14.8 vs. 18.0 L CH4/kg DMI), though feed efficiency metrics showed no direct association with microbial abundance. Comparative analysis revealed adaptive microbial shifts in response to dietary changes, with functional redundancy maintaining rumen stability and supporting host performance. These findings provide insights into how feed composition shapes rumen microbial dynamics and host phenotypes, highlighting the functional adaptability of the rumen microbiome during dietary transitions.

Effects of Dietary Coated Folic Acid and Folic Acid Addition on Lactation Performance, Rumen Fermentation, and Hepatic Lipid Content in Early Lactation Dairy Cows

This study evaluated the influences of coated folic acid (CFA) and folic acid (FA) on lactation performance, apparent digestibility, rumen volatile fatty acid (VFA) production, blood metabolism, and hepatic lipid content in cows. A total of 140 Holstein cows were allocated to seven groups in a randomized block design. Cows in the control received no addition, those in the in low CFA (LCFA), medium CFA (MCFA), and high CFA (HCFA) groups received CFA at 135, 270, and 405 mg FA/d, and those in the low FA (LFA), medium FA (MFA), and high FA (HFA) groups received FA at 135, 270, and 405 mg/d. The experiment began 5 weeks before calving to 6 weeks after calving. When increasing the level of CFA, the fat-corrected milk (FCM), fat and protein yields, de novo fatty acid content, and feed efficiency increased linearly. A linear increase was observed for nutrient digestibility and ruminal total VFAs. The blood total protein, albumin, superoxide dismutase, glutathione peroxidase, and folate increased linearly, but blood non-esterified fatty acids and β-hydroxybutyric acid and hepatic lipids decreased linearly. When increasing the level of FA, the FCM and milk fat yields increased linearly, but the rumen total VFA increased quadratically. Compared with MFA, cows receiving MCFA had a greater milk yield and lower hepatic lipids. Overall, the addition of CFA increased the milk yield and decreased the hepatic lipid content in cows.

Effects of phyto-phenolic compounds on ammonia production by select amino acid fermenting bacteria

Bacteria that ferment amino acids to ammonia can be categorized as generalists or specialist hyper-ammonia-producing bacteria. In the rumens of ruminant animals, most of the ammonia produced is eventually excreted as urea in urine. This process can be controlled with off-label use of antibiotics, but the practice can lead to antibiotic resistance; therefore, discovery of antibiotic alternatives is pertinent. Plant-derived phenolic compounds have demonstrated antimicrobial efficacy for such purposes. This study investigated the antimicrobial and metabolic suppressive potential of six phenolic compounds on five amino acid fermenting bacteria: Clostridium sporogenes MD1, C. aminophilum F, Acetoanaerobium sticklandii SR, Peptostreptococcus sp. BG1, and Prevotella bryantii B14. Inhibitory action of the compounds was determined using a 10% v/v serial dilution method in basal media. Carvacrol (1 mM), thymol (1 mM), and eugenol (10 mM) demonstrated the greatest antimicrobial potential, where carvacrol and eugenol inhibited growth of all five species and thymol four species except BG1. The cinnamic acids (trans and hydro) demonstrated variable activity against all organisms. Suppression of metabolic activity was determined via colorimetric assay quantifying ammonia in washed stationary phase culture supernatant after 24 h of metabolism on fresh substrate. Carvacrol and eugenol yielded the greatest reduction of ammonia by all organisms except B14, which produced no ammonia under the growth conditions. Thymol greatly reduced ammonia production of four organisms except F. These data demonstrate that eugenol, carvacrol, and thymol may be worthy antimicrobial candidates for the control of ammonia-producing organisms.

Capsaicin Modulates Ruminal Fermentation and Bacterial Communities in Beef Cattle with High-Grain Diet-Induced Subacute Ruminal Acidosis

This study was developed with the goal of exploring the impact of capsaicin on ruminal fermentation and ruminal bacteria in beef cattle affected by high-grain diet-induced subacute ruminal acidosis (SARA). In total, 18 healthy Simmental crossbred cattle were randomized into three separate groups (n = 6/group): (1) control diet (CON; forage-to-concentrate ratio = 80:20); (2) high-grain diet (SARA; forage-to-concentrate ratio = 20:80); and (3) high-grain diet supplemented with capsaicin (CAP; 250 mg/cattle/day). The study was conducted over a 60-day period. The results showed that the SARA model was successfully induced in the SARA group with a high-grain diet. Relative to the SARA group, the addition of capsaicin elevated the ruminal pH from 5.40 to 6.36 (p < 0.01), and decreased the total volatile fatty acids (VFAs) from 133.95 to 82.86 mmol/L (p < 0.01), aligning closely with the levels observed in the CON group. The addition of capsaicin increased the alpha diversity of ruminal bacteria relative to the SARA group, as evidenced by a lower Simpson index (p < 0.05), together with increases in the Ace, Chao, and Shannon indices (p < 0.05). Bacteroidota and Firmicutes were the most common phyla across all treatment groups, while Prevotella was the predominant genera. The unique bacterial genera (LDA scores > 4) identified within the SARA group comprised Succinivibrionaceae_UCG-001, Succinivibrio, NK4A214_group, Lachnospiraceae_NK3A20_group, and Ruminococcus, which may serve as potential biomarkers for the diagnosis of SARA. The unique genera associated with the CON group included Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-003, and U29-B03, while those for the CAP group included Succiniclasticum and Prevotellaceae_UCG-004. In summary, these results suggest that dietary capsaicin supplementation can limit the adverse effects of SARA through the modulation of bacterial communities within the rumen, thus altering ruminal fermentation in beef cattle.

Whole stillage inclusion level influences in vitro fiber digestibility and ruminal fermentation of tall fescue hay

With the growing bourbon industry in the southeastern U.S. leading to increased production of liquid distillery byproducts, there is a pressing need to explore sustainable uses for whole stillage [containing residual grain (corn, rye, malted barley) and liquid after ethanol separation] in livestock nutrition. The objectives of this study were to evaluate the effects of increasing whole stillage inclusion on the in vitro fiber digestibility and ruminal fermentation of tall fescue hay. Ruminal contents were obtained from 2 ruminally cannulated Angus × Holstein steers (390 ± 4.49 kg BW) fed a basal diet consisting of 90% tall fescue hay and 10% cracked corn. Whole stillage was obtained from a local distillery, homogenized, and replaced water in the Goering and Van Soest buffer preparation at 0.00%, 9.06%, 18.1%, or 36.3% on a v/v basis to simulate ruminal fill of whole stillage under practical conditions. Tall fescue hay was used as the substrate and vessels were incubated for 48 h. Results were analyzed with the GLM procedure of SAS using polynomial contrast statements for statistical comparison. Increasing whole stillage inclusion linearly decreased (P = 0.002) apparent dry matter (DM) digestibility, with the lowest (quadratic: P = 0.03) coefficients for true DM and neutral detergent fiber (NDF) digestibility occurring at 36.3% whole stillage inclusion. The rate and extent of gas production, methane production, and total volatile fatty acid (VFA) concentration increased (P < 0.05) with increasing whole stillage inclusion. The final pH of the fermentation media linearly decreased (P < 0.001) with increasing whole stillage inclusion. The molar acetate, valerate, isovalerate, and isobutyrate proportions decreased (P < 0.05) with increasing whole stillage inclusion. The molar propionate proportion responded quadratically (P < 0.01), with the peak proportion occurring at 36.3% whole stillage inclusion. Increasing whole stillage inclusion linearly decreased (P < 0.001) the viable number of cellulolytic and 2-deoxyglucose-resistant cellulolytic bacteria in the fermentation media. Peptide- and amino acid-utilizing bacteria increased linearly (P < 0.001) and hyper-ammonia-producing bacterial concentration peaked (quadratic: P = 0.05) at 36.3% whole stillage inclusion. Increasing whole stillage inclusion in the in vitro ruminal media demonstrated negative effects on the fermentation of tall fescue hay, as indicated by decreased NDF digestibility, cellulolytic bacteria, pH, and branched-chain VFA proportions.

The Holobiont concept in ruminant physiology - more of the same, or something new and meaningful to food quality, food security, and animal health?

The holobiont concept has emerged as an attempt to recognize and describe the myriad interactions and physiological signatures inherent to a host organism, as impacted by the microbial communities that colonize and/or co-inhabit the environment within which the host resides. The field acknowledges and draws upon principles from evolution, ecology, genetics, and biology, and in many respects has been "pushed" by the advent of high throughput DNA sequencing and, to a lesser extent, other "omics"-based technologies. Despite the explosion in data generation and analyses, much of our current understanding of the human and ruminant "holobiont" is based on compositional forms of data and thereby, restricted to describing host phenotypes via associative or correlative studies. So, where to from here? We will discuss some past findings arising from ruminant and human gut microbiota research and seek to evaluate the rationale, progress, and opportunities that might arise from the "holobiont" approach to the ruminant and human host. In particular, we will consider what is a "good" or "bad" host gastrointestinalmicrobiome in different scenarios, as well as potential avenues to sustain or alter the holobiont. While the holobiont approach might improve food quality, food security and animal health, these benefits will be most likely achieved via a judicious and pragmatic compromise in data generation, both in terms of its scale, as well as its generation in context with the "forgotten" knowledge of ruminant and human physiology.

Circadian Rhythm Enhances mTORC1/AMPK Pathway-Mediated Milk Fat Synthesis in Dairy Cows via the Microbial Metabolite Acetic Acid

Livestock may respond differently to circadian rhythms, leading to differences in the composition of the animal products. Nevertheless, the circadian effects on rumen microorganisms and animal products are poorly understood. In the study, it was found that dairy cows exhibited increased milk fat levels, decreased acetic acid concentrations in the rumen fluid, and elevated acetic acid levels in the blood during the night compared to those of the day. Correlational analyses suggested a high association between Succiniclasticum, Lactobacillus, Prevotellacene NK3B31_group, Muribaculaceae_unclassified, etc., which were significantly enriched in rumen fluid at night, and milk fat levels. The differential metabolite Vitamin B6, significantly elevated at night, promoted the translocation of acetic acid into the circulation by increasing the level of rumen epithelial MCT1 protein expression. In addition, we found that both acetic acid treatment time and dose modulated the expression of lipid metabolism transcription factors (PPARγ, PPARα, and SREBP1c) and downstream genes (FASN, SCD1, ACCα, and CPT1A). Additionally, the mTORC1 and AMPK pathways were responsible for the effects of acetic acid on transcription factors and genes involved in lipid metabolism. Differences in rumen microbial taxa were observed between the day and night. Microbial metabolite (acetic acid) was found to be absorbed into the bloodstream and entered the mammary gland at night at a significantly elevated level. This regulation impacted the expression of lipid metabolism-related transcription factors (PPARγ, PPARα, and SREBP1c), as well as downstream genes through the mTORC1 and AMPK signaling pathways, ultimately affecting milk fat synthesis. These findings provide a new perspective for the microbial regulation of milk synthesis.

Temporal Changes in Faecal Microbiota Composition and Diversity in Dairy Cows Supplemented with a Lactobacillus-Based Direct-Fed Microbial

The rumen microbiota of dairy cows plays a crucial role in fermenting fibrous material, essential for nutrient extraction and overall productivity, detoxification of anti-nutritional toxic compounds, synthesis of vital nutrients, and is essential for optimal animal health. This study investigated the impact of Lentilactobacillus-, Lactocaseibacillus-, and Lacticaseibacillus-based direct-fed microbial (DFM) supplementation on dairy cows' faecal microbial composition and diversity. The study was carried out on a commercial dairy farm using 50 Holstein-Friesian cows randomly assigned into control (CON) and treatment (TRT) groups. Faecal samples were collected directly from the rectum every two months from September 2021 to January 2023. The bacterial 16S rRNA gene and fungal ITS-1 regions were amplified, sequenced, and analysed. Microbial diversity was assessed through alpha- and beta-diversity metrics. Linear discriminant analysis effect size (LEfSe) was performed to identify which taxa were driving the changes seen in the microbiota over time and treatment. Bacteroidaceae were the most prevalent bacterial family, followed by Lachnospiraceae and Muribaculaceae in both CON and TRT cows. Ascomycota, Basidiomycota, and Mucoromycota were the dominant three fungal phyla in the faeces of both CON and TRT cows. Bacterial genera Fructilactobacillus was abundant in the CON and Absicoccus in the TRT groups. Fungal taxa Chaetothryriales_incertae_sedis and Pseudomentella were absent in the faeces of TRT cows. Significant temporal and specific taxonomic differences were observed between the CON and TRT groups. The study's findings underscore the dynamic nature of microbial communities and the importance of targeted dietary interventions. Further research is necessary to elucidate these microbial shifts, long-term impacts, and functional implications, aiming to optimise ruminant nutrition and enhance dairy cow performance.

Feed efficiency and enteric methane emissions indices are inconsistent with the outcomes of the rumen microbiome composition

The correlation between enteric methane emissions (eME) and feed efficiency (FE) in cattle is linked to the anaerobic fermentation of feedstuffs that occurs in the rumen. Several mathematical indices have been developed to predict feed efficiency and identify low methane emitters in herds. To investigate this, the current study aimed to evaluate the rumen microbial composition in the same group of animals ranked according to six different indices (three indices for FE and three for eME). Thirty-three heifers were ranked into three groups, each consisting of 11 animals, based on FE (feed conversion efficiency - FCE, residual weight gain - RG, and residual feed intake - RFI) and eME indices (production, yield, and intensity). Rumen fluids were collected using a stomach tube and analyzed using 16S rRNA and 18S rRNA, targeting rumen bacteria, archaea, and protozoa. The sequencing analysis revealed that the presence of unique microbial species in the rumen varies across animals ranked by the FE and eME indices. The High RG group harbored 17 unique prokaryotic taxa, while the High FCE group contained only seven. Significant differences existed in the microbial profiles of the animals based on the FE and eME indices. For instance, Raoultibacter was more abundant in the Intermediate RFI group but less so in the Intermediate RG and Intermediate FCE groups. The abundance of Entodinium was higher while Diplodinium was lower in the High FCE group, in contrast to the High RG and High RFI groups. Methanobrevibacter exhibited similar abundances across eME indices. However, the heifers did not demonstrate the same production, yield, and intensity of eME. The present findings underscore the importance of standardizing the FE and eME indices. This standardization is crucial for ensuring consistent and reliable assessments of the composition and function of the rumen microbiome across different herds.

Microbiological Characteristics of the Gastrointestinal Tracts of Jersey and Holstein Cows

The gastrointestinal bacterial microbiota is essential for maintaining the health of dairy cows and ensuring their production potential, and it may also help explain the breed-related phenotypic differences. Therefore, investigating the differences in gastrointestinal bacterial microbiota between breeds is critical for deciphering the mechanisms behind these differences and exploring the potential for improving milk production by regulating the gastrointestinal bacterial microbiota. This study holistically examined the differences between rumen and hindgut bacterial microbiota in a large cohort of two breeds of dairy cows, comprising 184 Jersey cows and 165 Holstein cows. Significant distinctions were identified between the rumen and hindgut bacterial microbiota of dairy cows, with these differences being consistent across breeds. A total of 20 breed-differentiated microorganisms, comprising 14 rumen microorganisms and 6 hindgut microorganisms, were screened, which may be the primary drivers of the observed differences in lactation performance between Jersey and Holstein cows. The present study revealed the spatial heterogeneity of the gastrointestinal bacterial microbiota of Jersey and Holstein cows and identified microbial biomarkers of different breeds. These findings enhance our understanding of the differences in the gastrointestinal bacterial microbiota between Jersey and Holstein cows and may provide useful information for optimizing the composition of the intestinal bacterial microbiota of the two breeds of dairy cows.

Effects of Different Dietary Combinations on Blood Biochemical Indicators and Rumen Microbial Ecology in Wenshan Cattle

With the continuous optimization of feed ingredients in livestock production, barley has garnered significant attention as a potential substitute for corn in feed. This study aims to investigate the effects of replacing part of the corn and soybean meal with barley, wheat bran, and rapeseed meal on Wenshan cattle, focusing on the rumen microbial community, blood physiological and biochemical indicators, and growth traits. Through an intensive feeding experiment with two different dietary ratios, we found that adding barley to the diet significantly reduced the host's blood lipid concentration and significantly increased the height, body length, heart girth, and average daily weight gain of Wenshan cattle. Analysis of the rumen microbial community structure showed that the addition of barley significantly affected the relative abundance of Firmicutes, Proteobacteria, and Bacteroidetes, with the relative abundance of Spirochaetes being significantly lower than that of the control group (p < 0.05). The dominant bacterial groups mainly included Acinetobacter, Solibacillus, and Lysinibacillus. In summary, this study reveals the potential of different feed ingredient ratios involving barley, wheat bran, and rapeseed meal in the production performance of Wenshan cattle. By regulating blood physiology and improving the rumen micro-ecological structure, it provides new scientific evidence for optimizing livestock and poultry feeding management strategies. Future research will further explore the optimal application ratio of barley under different feeding conditions and its long-term impact on animal health and production performance.

Effects of fermented and unfermented aging corn on ruminal fermentation, bacterial communities, lactation performance and plasma metabolites in Holstein cows

Aging reduces the nutritional value of corn grain, which may be improved by fermentation prior to use. This study investigated the effects of replacing conventional corn (CC) with aging corn (AC) and fermented aging corn (FAC) in the diets of lactating Holstein cows. Six healthy third-parity Holstein cows were used in a replicated 3 × 3 Latin square experiment with 21-day periods. Cows were fed twice and milked twice daily. The cows were randomly divided into three treatment groups: (1) CC diet: a diet with 23.6% starch in diet DM containing 24.0% conventional corn; (2) AC diet: a diet with 23.5% starch in diet DM containing 24.0% aging corn replacing conventional corn; and (3) FAC diet: a diet with 23.2% starch in diet DM containing 24.6% fermented aging corn replacing conventional corn. The diets were formulated to be isonitrogenous and contained identical roughage. The FAC treatment increased the starch digestibility compared with AC. Feeding FAC increased the concentrations of total volatile fatty acid compared with CC and AC and decreased the molar proportion of acetate compared with AC. At the family level, the relative abundance of Prevotellaceae was higher on FAC than CC. The relative abundance of Succinivibrionaceae was lower on FAC than on CC and AC. Besides, at the genera level, the relative abundance of Succinivibrionaceae_UCG_002 in the rumen was higher on AC than CC and FAC. The relative abundance of Prevotella and Ruminococcus was higher on FAC than CC and AC. The relative abundance of Succinivibrionaceae_UCG_001 was lower on FAC than CC. The Simpson index was lower on FAC than CC and AC. The FAC treatment increased the milk yield (34.0, 33.7, and 35.2 kg/d for CC, AC, and FAC group, respectively) and protein yield, and thus, energy-corrected milk production was increased, and at the same time, decreased the somatic cell score compared with CC and AC. The AC treatment increased the malondialdehyde concentration in plasma compared with CC and FAC. The concentrations in plasma of triglyceride and malondialdehyde were lower on FAC than AC. The immunoglobulin G concentration in plasma was higher on FAC than CC and AC. Overall, feeding AC resulted in decreased plasma antioxidant capacity compared with CC, whereas feeding FAC altered the relative abundance of bacteria in the rumen and improved starch digestibility, ruminal bacterial diversity, lactation performance, plasma antioxidant capacity and immune competence compared with AC in dairy cows.

Profiling the dynamic adaptations of CAZyme-Producing microorganisms in the gastrointestinal tract of South African goats

The gastrointestinal tract of goats serves as a habitat for anaerobic microbial populations that work together to break down complex plant material, including lignocellulose. This study explored the microbial diversity and metabolic profiles across different gastrointestinal tract compartments. Significant diversity differences among the compartments were observed (ANOSIM p < 0.006), with the abomasum showing a distinct species composition and a decreased alpha diversity (Mann-Whitney/Kruskal-Wallis test p = 0.00096), possibly due to its acidic environment. Dominant microbial phyla included Proteobacteria, Bacteroidetes, and Firmicutes, with Proteobacteria being the most prevalent in the abomasum (50.06 %). Genera like Proteus and Bacteroides were particularly prominent in the rumen and reticulum, highlighting their significant role in feed degradation and fermentation processes. Over 65 % of genes at Kyoto Encyclopedia of Genes and Genomes level 1 were involved in metabolism with significant xenobiotic biodegradation in the abomasum. The dbCAN2 search identified Glycoside Hydrolases as the most prevalent CAZyme class (79 %), followed by Glycosyltransferases, Polysaccharide Lyases, and Carbohydrate Esterases, with Carbohydrate-Binding Modules and Auxiliary Activities accounting for 1 % of the hits. Higher CAZyme abundance was observed in the reticulum and omasum compartments, possibly due to MAGs diversity. In conclusion, the gastrointestinal tract of South African goats harbors diverse CAZyme classes, with Glycoside Hydrolases predominating. Interestingly, higher CAZyme abundance in specific compartments suggested compartmentalized microbial activity, reflecting adaptation to dietary substrates.

Tea Polyphenols Inhibit Methanogenesis and Improve Rumen Epithelial Transport in Dairy Cows

This study systematically investigated the effects of tea polyphenols on methane (CH4) production and the rumen epithelial cell transport capability in cattle using both in vitro and animal experiments, employing multi-omics techniques. The in vitro results demonstrated that, compared to the control group, tea polyphenols significantly reduced CH4 production and the acetate/propionate ratio (p < 0.05). Tea polyphenols reduced CH4 production by inhibiting the relative abundance of unclassified_d_Archaea methanogens and the protozoa Pseudoentodinium and g__Balantioides. The animal experiments showed that tea polyphenols significantly increased the concentrations of T-AOC and GSH-PX in bovine blood (p < 0.05). In addition, microbial groups such as Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, and Butyrivibrio_2 were significantly enriched in the ruminal fluid of the tea polyphenol group (p < 0.05). The proteomic results indicated significant upregulation of proteins such as COIII, S100A8, FABP1, SLC2A8, and SLC29A1 (p < 0.05) and downregulation of proteins including HBB, RAB4A, RBP4, LOC107131172, HBA, and ZFYVE19 (p < 0.05), with FABP1 showing a positive correlation with propionate concentration, and RAB4A had a negative correlation (p < 0.05). Overall, tea polyphenols modulate the microbial composition within the rumen, inhibiting CH4 production and enhancing the host's rumen epithelial cell transport capacity for volatile fatty acids.

Feeding limestone buffer to limit-fed dairy steers fed a high inclusion rate of distiller grains

The study objective was to evaluate dietary limestone buffer inclusion rates for impacting nutrient digestibility and excretion when growing dairy cattle are fed high distiller grains with solubles (DDGS) limit-fed ration. The hypothesis was that feeding more limestone buffer would offset a low rumen pH when feeding a high DDGS inclusion rate. Five ruminally cannulated Holstein and Brown Swiss steers were used in a crossover design having 2-wk periods to evaluate high and low buffer inclusion rates when limit-fed. Treatments were similar in ingredient composition being: 1) 40% DDGS at 0.80% high CaCO3 buffer inclusion (HIGH) and 2) 40% DDGS with 0.25% low CaCO3 buffer inclusion (LOW) with the remaining ration consisting of grass hay with minerals and vitamins. Rations were limit-fed at 2.50% of body weight (BW) using Calan feeding doors with steers being weighed every 2 wk with ration amounts adjusted accordingly. Rumen fluid was collected via the ruminal cannula at the start and end of each period for pH, ammonia-n, and volatile fatty acid (VFA)s. Fecal grab samples were collected at the end of each period for measurement of total-tract nutrient digestibility. There were no treatment-by-period interactions (P > 0.10) for any of the growth parameters measured. Gains in frame growth parameters were similar (P > 0.10) for steers fed both rations. BWs and gains were similar (P > 0.10) for steers fed both rations. Steers fed the LOW ration demonstrated a numeric improvement in average daily gain combined with a tendency (P < 0.06) for lower dry matter intake resulting in an improved (P < 0.01) feed efficiency (gain:feed) compared with steers fed the HIGH ration. Steers fed HIGH demonstrated greater (P < 0.01) ruminal ammonia-N and isovalerate concentrations compared with steers fed the LOW buffer ration. Steers fed both buffer inclusion rates were similar (P > 0.10) for ruminal pH and remaining VFAs concentrations. Steers fed both buffer inclusion rates were similar (P > 0.10) in DM and organic matter digestibilities. Limit-feeding a high DDGS inclusion rate ratio combined with a low buffer inclusion rate improved feed efficiency while maintaining growth performance. The study hypothesis was rejected in that feed efficiency can be enhanced when feeding a high DDGS ration by feeding a low calcium carbonate buffer.

Postbiotics from Saccharomyces cerevisiae fermentation stabilize rumen solids microbiota and promote microbial network interactions and diversity of hub taxa during grain-based subacute ruminal acidosis (SARA) challenges in lactating dairy cows

Background

High-yielding dairy cows are commonly fed high-grain rations. However, this can cause subacute ruminal acidosis (SARA), a metabolic disorder in dairy cows that is usually accompanied by dysbiosis of the rumen microbiome. Postbiotics that contain functional metabolites provide a competitive niche for influential members of the rumen microbiome, may stabilize and promote their populations, and, therefore, may attenuate the adverse effects of SARA.

Methods

This study used a total of 32 rumen-cannulated lactating dairy cows, which were randomly assigned into four treatments: no SCFP (control), 14 g/d Original XPC (SCFPa), 19 g/d NutriTek (SCFPb-1X), and 38 g/d NutriTek (SCFPb-2X) (Diamond V, Cedar Rapids, IA) from 4 weeks before until 12 weeks after parturition. Grain-based SARA challenges were conducted during week 5 (SARA1) and week 8 (SARA2) after parturition by replacing 20% dry matter of the base total mixed ration (TMR) with pellets containing 50% ground barley and 50% ground wheat. The DNA of rumen solids digesta was extracted and subjected to V3-V4 16S rRNA gene sequencing. The characteristics of rumen solids microbiota were compared between non-SARA (Pre-SARA1, week 4; Post-SARA1, week 7; and Post-SARA2, weeks 10 and 12) and SARA stages (SARA1/1, SARA1/2, SARA2/1, SARA2/2), as well as among treatments.

Results

Both SARA challenges reduced the richness and diversity of the microbiota and the relative abundances of the phylum Fibrobacteres. Supplementation with SCFP promoted the growth of several fibrolytic bacteria, including Lachnospiraceae UCG-009, Treponema, unclassified Lachnospiraceae, and unclassified Ruminococcaceae during the SARA challenges. These challenges also reduced the positive interactions and the numbers of hub taxa in the microbiota. The SCFPb treatment increased positive interactions among microbial members of the solids digesta and the number of hub taxa during the SARA and non-SARA stages. The SCFPb-2X treatment prevented changes in the network characteristics, including the number of components, clustering coefficient, modularity, positive edge percentage, and edge density of the microbiota during SARA challenges. These challenges reduced predicted carbohydrate and nitrogen metabolism in microbiota, whereas SCFP supplementation attenuated those reductions.

Conclusions

Supplementation with SCFP, especially the SCFPb-2X attenuated the adverse effects of grain-based SARA on the diversity and predicted functionality of rumen solids microbiota.

Integrating host and microbiome biology using holo-omics

Holo-omics is the use of omics data to study a host and its inherent microbiomes - a biological system known as a "holobiont". A microbiome that exists in such a space often encounters habitat stability and in return provides metabolic capacities that can benefit their host. Here we present an overview of beneficial host-microbiome systems and propose and discuss several methodological frameworks that can be used to investigate the intricacies of the many as yet undefined host-microbiome interactions that influence holobiont homeostasis. While this is an emerging field, we anticipate that ongoing methodological advancements will enhance the biological resolution that is necessary to improve our understanding of host-microbiome interplay to make meaningful interpretations and biotechnological applications.

Examining homoacetogens in feces from adult and juvenile kangaroos with the aim of finding competitive strains to hydrogenotrophic methanogens

We examined the microbial populations present in fecal samples of macropods capable of utilizing a mixture of hydrogen and carbon dioxide (70:30) percent. The feces samples were cultured under anaerobic conditions, and production of methane or acetic acids characteristic for methanogenesis and homoacetogenesis was measured. While the feces of adult macropods mainly produced methane from the substrate, the sample from a 2-month-old juvenile kangaroo only produced acetic acid and no methane. The stable highly enriched culture of the joey kangaroo was sequenced to examine the V3 and V4 regions of the 16S rRNA gene. The results showed that over 70% of gene copies belonged to the Clostridia class, with Paraclostridium and Blautia as the most predominant genera. The culture further showed the presence of Actinomyces spp., a genus which has only been identified in the GI tract of macropods in a few studies, and where none, to our knowledge, have been classified as homoacetogenic. The joey kangaroo mixed culture showed a doubling time of 3.54 h and a specific growth rate of 0.199/h, faster than what has been observed for homoacetogenic bacteria in general.

IMPORTANCE

Enteric methane emissions from cattle are a significant contributor to greenhouse gas emissions worldwide. Methane emissions not only contribute to climate change but also represent a loss of energy from the animal's diet. However, methanogens play an important role as hydrogen sink to rumen systems; without it, the performance of hydrolytic organisms diminishes. Therefore, effective strategies of methanogen inhibition would be enhanced in conjunction with the addition of alternative hydrogen sinks to the rumen. The significance of our research is to identify homoacetogens present in the GI tract of kangaroos and to present their performance in vitro, demonstrating their capability to serve as alternatives to rumen methanogens.

Metagenomics-Metabolomics Exploration of Three-Way-Crossbreeding Effects on Rumen to Provide Basis for Crossbreeding Improvement of Sheep Microbiome and Metabolome of Sheep

The objective of this experiment was to explore the effects of three-way hybridization on rumen microbes and metabolites in sheep using rumen metagenomics and metabolomics. Healthy Hu and CAH (Charolais × Australian White × Hu) male lambs of similar birth weight and age were selected for short-term fattening after intensive weaning to collect rumen fluid for sequencing. Rumen metagenomics diversity showed that Hu and CAH sheep were significantly segregated at the species, KEGG-enzyme, and CAZy-family levels. Moreover, the CAH significantly increased the ACE and Chao1 indices. Further, correlation analysis of the abundance of the top 80 revealed that the microorganisms were interrelated at the species, KEGG-enzyme, and CAZy-family levels. Overall, the microbiome significantly affected metabolites of the top five pathways, with the strongest correlation found with succinic acid. Meanwhile, species-level microbial markers significantly affected rumen differential metabolites. In addition, rumen microbial markers in Hu sheep were overall positively correlated with down-regulated metabolites and negatively correlated with up-regulated metabolites. In contrast, rumen microbial markers in CAH lambs were overall negatively correlated with down-regulated metabolites and positively correlated with up-regulated metabolites. These results suggest that three-way crossbreeding significantly affects rumen microbial community and metabolite composition, and that significant interactions exist between rumen microbes and metabolites.

Structural, Biochemical, and Phylogenetic Analysis of Bacterial and Fungal Carbohydrate Esterase Family 15 Glucuronoyl Esterases in the Rumen

Glucuronoyl esterases (GEs) are carbohydrate active enzymes in carbohydrate esterase family 15 which are involved in the hydrolysis of lignin-carbohydrate complexes. They are encoded by a wide range of aerobic and anaerobic fungi and bacteria inhabiting diverse environments. The rumen microbiome is a complex microbial community with a wide array of enzymes that specialize in deconstructing plant cell wall carbohydrates. Enzymes from the rumen tend to show low similarity to homologues found in other environments, making the rumen microbiome a promising source for the discovery of novel enzymes. Using a combination of phylogenetic and structural analysis, we investigated the structure-function relationship of GEs from the rumen bacteria Fibrobacter succinogenes and Ruminococcus flavefaciens, and from the rumen fungus, Piromyces rhizinflata. All adopt a canonical α/β hydrolase fold and possess a structurally conserved Ser-His-Glu/Asp catalytic triad. Structural variations in the enzymes are localized to loops surrounding the active site. Analysis of the active site structures in these enzymes emphasized the importance of structural plasticity in GEs with non-canonical active site conformations. We hypothesize that interkingdom HGT events may have contributed to the diversity of GEs in the rumen, and this is demonstrated by the phylogenetic and structural similarity observed between rumen bacterial and fungal GEs. This study advances our understanding of the structure-function relationship in glucuronoyl esterases and illuminates the evolutionary dynamics that contribute to enzyme diversity in the rumen microbiome.

Postbiotics from Saccharomyces cerevisiae fermentation stabilize microbiota in rumen liquid digesta during grain-based subacute ruminal acidosis (SARA) in lactating dairy cows

BACKGROUND

Subacute ruminal acidosis (SARA) is a common metabolic disorder of high yielding dairy cows, and it is associated with dysbiosis of the rumen and gut microbiome and host inflammation. This study evaluated the impact of two postbiotics from Saccharomyces cerevisiae fermentation products (SCFP) on rumen liquid associated microbiota of lactating dairy cows subjected to repeated grain-based SARA challenges. A total of 32 rumen cannulated cows were randomly assigned to 4 treatments from 4 weeks before until 12 weeks after parturition. Treatment groups included a Control diet or diets supplemented with postbiotics (SCFPa, 14 g/d Original XPC; SCFPb-1X, 19 g/d NutriTek; SCFPb-2X, 38 g/d NutriTek, Diamond V, Cedar Rapids, IA, USA). Grain-based SARA challenges were conducted during week 5 (SARA1) and week 8 (SARA2) after parturition by replacing 20% DM of the base total mixed ration (TMR) with pellets containing 50% ground barley and 50% ground wheat. Total DNA from rumen liquid samples was subjected to V3-V4 16S rRNA gene amplicon sequencing. Characteristics of rumen microbiota were compared among treatments and SARA stages.

RESULTS

Both SARA challenges reduced the diversity and richness of rumen liquid microbiota, altered the overall composition (β-diversity), and its predicted functionality including carbohydrates and amino acids metabolic pathways. The SARA challenges also reduced the number of significant associations among different taxa, number of hub taxa and their composition in the microbial co-occurrence networks. Supplementation with SCFP postbiotics, in particular SCFPb-2X, enhanced the robustness of the rumen microbiota. The SCFP supplemented cows had less fluctuation in relative abundances of community members when exposed to SARA challenges. The SCFP supplementation promoted the populations of lactate utilizing and fibrolytic bacteria, including members of Ruminococcaceae and Lachnospiraceae, and also increased the numbers of hub taxa during non-SARA and SARA stages. Supplementation with SCFPb-2X prevented the fluctuations in the abundances of hub taxa that were positively correlated with the acetate concentration, and α- and β-diversity metrics in rumen liquid digesta.

CONCLUSIONS

Induction of SARA challenges reduced microbiota richness and diversity and caused fluctuations in major bacterial phyla in rumen liquid microbiota in lactating dairy cows. Supplementation of SCFP postbiotics could attenuate adverse effects of SARA on rumen liquid microbiota.

Faecal microbial diversity in a cattle herd infected by Mycobacterium avium subsp. paratuberculosis: a possible effect of production status

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, or paratuberculosis (PTB) in ruminants, besides having zoonotic potential. It possibly changes the gut microbiome, but no conclusive data are available yet. This study aimed at investigating the influence of MAP on the faecal microbiome of cattle naturally infected with PTB. In a follow up period of 10 months, PTB status was investigated in a herd of dairy cattle with history of clinical cases. Each animal was tested for MAP infection using serum and milk ELISA for MAP anti-bodies and IS900 real-time PCR and recombinase polymerase amplification assays for MAP DNA in the faeces and milk monthly for 4 successive months, then a last one after 6 months. The faecal samples were subjected to 16S rDNA metagenomic analysis using Oxford Nanopore Sequencing Technology. The microbial content was compared between animal groups based on MAP positivity rate and production status. All animals were MAP positive by one or more tests, but two animals were consistently negative for MAP DNA in the faeces. In all animals, the phyla firmicutes and bacteroidetes were highly enriched with a small contribution of proteobacteria, and increased abundance of the families Oscillospiraceae, Planococcaceae, and Streptococcacaceae was noted. Animals with high MAP positivity rate showed comparable faecal microbial content, although MAP faecal positivity had no significant effect (p > 0.05) on the microbiome. Generally, richness and evenness indices decreased with increasing positivity rate. A significantly different microbial content was found between dry cows and heifers (p < 0.05). Particularly, Oscillospiraceae and Rikenellaceae were enriched in heifers, while Planococcaceae and Streptococcaceae were overrepresented in dry cows. Furthermore, abundance of 72 genera was significantly different between these two groups (p < 0.05). Changes in faecal microbiome composition were notably associated with increasing MAP shedding in the faeces. The present findings suggest a combined influence of the production status and MAP on the cattle faecal microbiome. This possibly correlates with the fate of the infection, the concern in disease control, again remains for further investigations.

Interaction of a source rich in phytonutrients (fruits peel pellets) and polyunsaturated oil (Tung oil) on in vitro ruminal fermentation, methane production, and nutrient digestibility

Tropical fruit peels from mangosteen, rambutan, and banana are rich in phytonutrients. Several studies reported that the phytonutrients improved rumen fermentation. Nevertheless, the combination of phytonutrients and essential fatty acids on rumen fermentation have not yet been investigated. Hence, the aim of this research was to investigate the influence of fruit peel pellets (mangosteen, rambutan, and banana peel; MARABAC) containing phytonutrients and tung oil supplementation on rumen fermentation and the degradability of nutrients. Four levels of MARABAC (0, 2, 4, and 6 %) and four levels of tung oil (0, 2, 4, and 6 %) were supplemented with concentrate according to a 4 × 4 factorial arrangement in a completely randomized design (CRD). Rumen fermentation parameters, including gas production, ammonia nitrogen (NH3-N), volatile fatty acids (VFA), nutrient degradability (IVDMD and IVOMD), and in vitro methane (CH4) production were determined. The results showed that there were no interactions between MARABAC and Tung oil treatments for all terms of kinetic gas and cumulative gas, IVDMD and IVOMD, and in vitro ammonia-nitrogen (NH3-N). However, when combining MARABAC and tung oil beyond the 4 % level, VFA and in vitro CH4 production was severely affected. The supplementation of MARABAC and tung oil decreased gas production and rumen nutrient degradability (p < 0.05). Acetate (C2) and propionate (C3) production were significantly affected by the level of MARABAC supplementation. NH3-N was dropped when levels of MARABAC and tung oil supplementation were increased. There were interactions between MARABAC and tung oil on total VFA and in vitro CH4 production at 8 h (h). In addition, in vitro CH4 production decreased (p < 0.05) with higher levels of MARABAC supplementation. It could be concluded that MARABAC and tung oil supplementation significantly contributed to improving the production of gas and could be applied to decrease rumen CH4 production, thereby reducing the emission of greenhouse gases.

Changes in the rumen development, rumen fermentation, and rumen microbiota community in weaned calves during steviol glycosides treatment

Early weaning leads to weaning stress in calves, which hinders healthy growth and development. As an excellent sweetener applied in food, steviol glycosides (STE) has also been shown to exhibit positive biological activity in monogastric animals. Therefore, this study aimed to evaluate the impact of incorporating STE as a dietary supplement on rumen development, fermentation, and microbiota of rumen in weaned calves. This study selected 24 healthy Holstein bull calves and randomly allocated them into two groups (CON and STE). The results indicated that supplementation STE group improved rumen development in weaned calves, as demonstrated by a marked increase in the weight of the rumen, as well as the length and surface area of the rumen papilla. Compared with the CON group, the concentrations of total volatile fatty acids (TVFA), propionate, butyrate, and valerate were higher in the STE group. Moreover, STE treatment increased the relative abundance of Firmicutes and Actinobacteria at the phylum level. At the genus level, the STE group showed a significantly increased relative abundance of Succiniclasticum, Lachnospiraceae_NK3A20_group, and Olsenella, and a decreased relative abundance of Acinetobacter compared to the CON group. Pusillimonas, Lachnospiraceae_NK3A20_group, Olsenella, and Succiniclasticum were significantly enriched in rumen chyme after supplementation with STE, as demonstrated by LEfSe analysis. Overall, our findings revealed that rumen bacterial communities altered in response to the dietary supplementation with STE, and some bacterial taxa in these communities may have positive effects on rumen development during this period.

Effects of grain intervention on hypothalamic function and the metabolome of blood and milk in dairy cows

BACKGROUND

The hypothalamus plays a crucial role in the health and productivity of dairy cows, yet studies on its functionality and its impact on peripheral circulation in these animals are relatively scarce, particularly regarding dietary interventions. Therefore, our study undertook a comprehensive analysis, incorporating both metabolomics and transcriptomics, to explore the effects of a grain-based diet on the functionality of the hypothalamus, as well as on blood and milk in dairy cows.

RESULTS

The hypothalamic metabolome analysis revealed a significant reduction in prostaglandin E2 (PGE2) level as a prominent response to the grain-based diet introduction. Furthermore, the hypothalamic transcriptome profiling showed a notable upregulation in amino acid metabolism due to the grain-based diet. Conversely, the grain-based diet led to the downregulation of genes involved in the metabolic pathway from lecithin to PGE2, including phospholipase A2 (PLA2G4E, PLA2G2A, and PLA2G12B), cyclooxygenase-2 (COX2), and prostaglandin E synthase (PTGES). Additionally, the plasma metabolome analysis indicated a substantial decrease in the level of PGE2, along with a decline in adrenal steroid hormones (tetrahydrocortisol and pregnenolone) following the grain-based diet introduction. Analysis of the milk metabolome showed that the grain-based diet significantly increased uric acid level while notably decreasing PGE2 level. Importantly, PGE2 was identified as a critical metabolic marker in the hypothalamus, blood, and milk in response to grain intervention. Correlation analysis demonstrated a significant correlation among metabolic alterations in the hypothalamus, blood, and milk following the grain-based diet.

CONCLUSIONS

Our findings suggest a potential link between hypothalamic changes and alterations in peripheral circulation resulting from the introduction of a grain-based diet.

Lyophilized rumen fluid as a ruminal fermentation modifier in high grain-fed acidotic goats

Rumen cud transfaunation re-establishes rumen micro environment and improves fermentation in recipient animals affected with digestive disorders. Preserving rumen cud or fluid will increase its availability for the treatment of rumen fermentation disorders, without having to maintain donor animals. Rumen fluid collected from healthy goats, fed standard ration having roughage 70% and concentrate 30%, was lyophilized (prefreezing -80 °C, 48 h; lyophilization -45 °C, 32 h) using 5% glycerol as cryoprotectant. The 16 S metagenome analysis of the lyophilized rumen fluid (LRF) revealed an abundance of Prevotella (33.2%). Selenomonas ruminantium (1.87%) and Megasphaera elsdenii (0.23%) were also present. Twenty-four goats having history of high grain feeding and exhibiting clinical symptoms of rumen fermentation disorders were randomly distributed into either one of the two treatment groups viz., T1 = oral administration of LRF 31 g/animal/day and T2 = oral administration of sodium bicarbonate (SB) 15 g/animal/day. Post intervention LRF and SB, improved animal body condition, feed intake, fecal consistency, elevated the ruminal pH at 48 h, reduced propionate and lactate at 48 h, reduced total volatile fatty acids (TVFA) and ammonia nitrogen at 24 h. Significant reduction in serum blood urea nitrogen (BUN) and urea levels were observed even from 24 h post intervention irrespective of the treatments. LRF significantly improved acetate and decreased propionate production compared to SB. LRF at 7.5% (v/v) can thus be used to counteract ruminal fermentation disorders in goats sequel to high grain ration.

Disturbances of Ruminal Microbiota and Liver Inflammation, Mediated by LPS and Histamine, in Dairy Cows Fed a High-Concentrate Diet

The ecosystem of ruminal microbiota profoundly affects the health and milk production of dairy cows. High-concentrate diets are widely used in dairy farms and evoke a series of metabolic disorders. Several studies have reported the effects of high-concentrate diets on the ruminal microbiome, while the effect of changes in ruminal microbial flora, induced by high-concentrate diet feeding, on the liver of dairy cows has not been studied before. In this study, 12 mid-lactating Holstein Friesian cows (weight of 455 ± 28 kg; parities of 2.5 ± 0.5; starting milk yield of 31.59 ± 3.2 kg/d; DMI of 21.7 ± 1.1 kg/d; and a DIM at the start of the experiment of 135 ± 28 d) were fitted with ruminal fistulas, as well as with portal and hepatic vein catheters. All cows were randomly divided into 2 groups; then, they fed with low-concentrate diets (LC, concentrate: forage = 40:60) and high-concentrate diets (HC, concentrate: forage = 60:40) for 18 weeks. The forage sources were corn silage and alfalfa hay. After the cows of two groups were euthanized over two consecutive days, ruminal microbiota; the concentration of LPS in the rumen content; cecum content; the levels of blood and histamine in rumen fluid, blood, and the liver; the histopathological status of the rumen and cecum; and the inflammatory response of the liver were assessed in dairy cows under conditions of subacute ruminal acidosis (SARA). These conditions were caused by high-concentrate diet feeding. All data were analyzed using the independent t-test in SPSS. The results showed that high-concentrate diet feeding increased the concentration of LPS and histamine in the rumen and plasma of veins (p < 0.05). The abundance of Bacteroidetes at the phylum level, and of both Bacteroidetes and Saccharibacteria at the genus level, was decreased, while the abundance of Firmicutes at the phylum level and Oscillibacter at the genus level was increased by high-concentrate diet feeding. The decreased pH values of ruminal contents (LC = 6.02, HC = 5.90, p < 0.05) and the increased level of LPS in the rumen (LC = 4.921 × 105, HC = 7.855 × 105 EU/mL, p < 0.05) and cecum (LC = 11.960 × 105, HC = 13.115 × 105 EU/mL, p < 0.01) induced the histopathological destruction of the rumen and cecum, combined with the increased mRNA expression of IL-1β (p < 0.05). The histamine receptor H1R and the NF-κB signaling pathway were activated in the liver samples taken from the HC group. In conclusion, the elevated concentrations of LPS and histamine in the gut may be related to changes in the ruminal microbiota. LPS and histamine induced the inflammatory response in the ruminal epithelium, cecum epithelium, and liver. However, the cause-effect mechanism needs to be proved in future research. Our study offers a novel therapeutic strategy by manipulating ruminal microbiota and metabolism to decrease LPS and histamine release and to improve the health of dairy cows.

Metagenomic and metabolomic analyses reveal differences in rumen microbiota between grass- and grain-fed Sanhe heifers

Introduction

The aim of this study was to investigate the effects of diets on the composition and function of rumen microbiome and metabolites in Sanhe heifers.

Methods

Metagenomic and metabolomic analyses were performed using rumen fluid samples collected from Sanhe heifers (n = 20) with similar body weights and ages from grass-fed and grain-fed systems.

Results

The grain-fed group exhibited more intensive rumen fermentation than the grass-fed group. However, the grass-fed group exhibited carbohydrate metabolism and methane production higher than that of the grain-fed group; these increases were observed as a higher abundance of various bacterial phyla (Firmicutes, Bacteroidetes, Actinobacteria, Lentisphaerae, and Verrucomicrobia), families (Lachnospiraceae, Eubacteriaceae, and Eggerthellaceae), and the archaeal family Methanobacteriaceae. A comparison of genes encoding carbohydrate-active enzymes, using Kyoto Encyclopedia of Genes and Genome profiles, revealed noteworthy differences in the functions of rumen microbiota; these differences were largely dependent on the feeding system.

Conclusion

These results could help manipulate and regulate feed efficiency in Sanhe cattle.

Isobutyramide and Slow-Release Urea as Substitutes for Soybean Meal in the Finishing Diet of Beef Cattle

Two experiments were conducted to investigate the effects of isobutyramide (IBA) and slow-release urea (SRU) as substitutes for soybean meal (SBM) in the finishing diet of beef cattle. The completely randomized design in vitro experiment with five treatments, i.e., control, 0.9% SRU group, 0.6% SRU + 0.3% IBA group (SRU-I), 0.3% SRU + 0.6% IBA group (IBA-S), 0.9% IBA group was conducted. The results showed that the IBA-S and IBA increased (p ≤ 0.05) substrate disappearance of dry matter (DM), neutral detergent fiber (NDF), acid detergent fiber (ADF), total gas, and total volatile fatty acids (TVFA). The SRU group had the highest (p < 0.01) crude protein disappearance and ammonia nitrogen concentration, but the IBA contrarily decreased (p < 0.01) them compared with the control. Inclusion of IBA increased isobutyrate concentrations (p = 0.01) with the highest value for the IBA group. Then, an 84-day replicate 4 × 4 Latin square design with 8 Angus steers and four treatments, i.e., control, SRU, SRU-I, IBA-S was performed. The results showed that the treatments did not affect DM intake (p > 0.05) but tended (p = 0.09) to increase average daily gain. The inclusion of IBA increased (p < 0.05) the apparent digestibility of DM, organic matter, NDF, ADF, TVFA, and microbial crude protein with the highest values for the IBA-S group. The IBA-contained groups also increased (p ≤ 0.01) isobutyrate concentration, activities of carboxymethyl cellulase and xylanase, and the relative abundance of Butyrivibrio fibrisolvens with the highest values for the IBA-S group. The SRU had no effect on animal growth and nutrient apparent digestibility. In conclusion, IBA was developed as a new substitute for SBM in the finishing diet of beef cattle, and the optimal strategy was the isonitrogenous substitution of SBM with 0.3% SRU and 0.6% IBA of the diet.

Effects of complete substitution of dietary grain and protein sources with by-products on the production performance of mid-lactation dairy cows fed diets based on barley silage under heat-stress conditions

This study evaluated the effects of replacing cereal grains and soybean meal with by-products (BY) on production performance, nutrient digestibility, ruminal fermentation, nutrient recovery, and eating and chewing behavior of moderate-producing dairy cows under heat-stress conditions. Twelve multiparous Holstein cows (116.7 ± 12.01 d in milk; 42.7 ± 5.06 kg/d milk yield; 665 ± 77 kg body weight; mean ± SD) were used in a replicated 3 × 3 Latin square with 28-d periods (21 d for diet adaptation and 7 d for sampling and data collection). Cows were fed a total mixed ration containing a 39.2:60.8 ratio of forage to concentrate throughout the experiment. All diets were formulated to be isoenergetic and isonitrogenous, with different concentrates. Diets were (1) control diet based on cereal grains (CON: ground corn and ground barley, plus soybean meal); (2) sugar-rich BY diet (S-BY-CM: beet pulp, citrus pulp, and liquid molasses, plus canola meal); and (3) cereal grain BY diet (CG-BY: rice bran, corn germ meal, wheat bran, barley sprout, and broken corn). Our results showed that replacing grains with BY increased neutral detergent fiber intake and digestibility but decreased starch intake, human-edible energy, and human-edible protein. Milk yield and dry matter intake (DMI) decreased more in cows fed the CG-BY diet compared with the other 2 treatments. In contrast, no significant differences were observed between the CON and S-BY-CM diets in terms of milk yield and DMI. The S-BY-CM diet increased energy-corrected milk production compared with the CG-BY diet (36.2 vs. 34.3 kg/d), but CG-BY enhanced feed conversion efficiency compared with the other 2 treatments. Although the S-BY-CM diet prolonged the eating and sorting of small particles, neither of the dietary treatments affected chewing activity or ruminal pH 4 h after feeding. Furthermore, both diets containing BY contributed to an increase in milk fat content in comparison to the CON group. Additionally, the CG-BY and S-BY-CM diets demonstrated better performance than the CON diet in terms of human-edible feed conversion efficiency for protein and energy. The results indicated that S-BY-CM can completely replace barley and corn grain in the diet of mid-lactating dairy cows exposed to heat-stress conditions without any negative effect on production and ruminal pH. However, the inclusion of CG-BY did impair DMI, milk yield, and digestibility of nutrients and is not recommended during heat-stress conditions.

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.

Ruminal inocula with distinct fermentation profiles differentially affect the in vitro fermentation pattern of a commercial algal blend

The in vitro rumen batch technique is widely used for screening novel feed sources; however, it remains unclear to what extent the in vitro fermentability of non-conventional feed sources is affected by non-adapted ruminal inocula. Thus, in this study, we evaluated the effects of distinct ruminal inocula on the in vitro fermentation parameters of a sustainable non-conventional feed, a commercially available algal blend composed of microalgae (Chlorella vulgaris and Nannochloropsis oceanica) and seaweeds (Ulva sp. and Gracilaria gracilis). First, four late-lactation Holstein cows were fed four forage-based diets varying only in the proportions of basal forage (100% corn silage, 70% corn silage and 30% haylage, 30% corn silage and 70% haylage, and 100% haylage) in a 4 × 4 Latin square design with the last square omitted. After 3 weeks of adaptation, haylage-based diets resulted in ruminal fermentation parameters distinct from those promoted by corn silage-based diets, as reflected in increased pH, ammonia-N contents, and acetate proportions. Individual ruminal fluids derived from each of the four diets were further used as inocula in in vitro incubations. Here, a 1:1 mixture of corn silage and haylage was supplemented with 0, 5, 10, or 15% algal blend and incubated with each inoculum for 24 h in a 4 × 4 factorial design. Total gas and methane production decreased with inocula from cows fed haylage-based diets and with increasing algal blend supplementation levels. The fermentation pH increased and the ammonia-N contents decreased with inocula from cows fed haylage-based diets; however, these parameters were not affected by algal blend inclusion levels. The interaction between the ruminal inoculum source and the algal blend supplementation level affected the total volatile fatty acids (VFA) and the proportions of most individual VFA. Total VFA production decreased with increasing algal supplementation levels, particularly with inocula from cows fed 30% corn silage and 70% haylage; the acetate, propionate, and valerate proportions were only affected by algal blend levels under incubation with 100% corn silage inocula. Overall, our findings highlight the importance of the ruminal inoculum source when assessing the fermentability of non-conventional feed as well as the potential of the algal blend as a natural modulator of ruminal fermentation.

Early-life ruminal microbiome-derived indole-3-carboxaldehyde and prostaglandin D2 are effective promoters of rumen development

BACKGROUND

The function of diverse ruminal microbes is tightly linked to rumen development and host physiology. The system of ruminal microbes is an excellent model to clarify the fundamental ecological relationships among complex nutrient-microbiome-host interactions. Here, neonatal lambs are introduced to different dietary regimes to investigate the influences of early-life crosstalk between nutrients and microbiome on rumen development.

RESULTS

We find starchy corn-soybean starter-fed lambs exhibit the thickest ruminal epithelia and fiber-rich alfalfa hay-fed lambs have the thickest rumen muscle. Metabolome and metagenome data reveal that indole-3-carboxaldehyde (3-IAld) and prostaglandin D2 (PGD2) are the top characteristic ruminal metabolites associated with ruminal epithelial and muscular development, which depend on the enhanced ruminal microbial synthesis potential of 3-IAld and PGD2. Moreover, microbial culture experiment first demonstrates that Bifidobacterium pseudolongum is able to convert tryptophan into 3-IAld and Candida albicans is a key producer for PGD2. Transcriptome sequencing of the ruminal epithelia and smooth muscle shows that ruminal epithelial and muscular development is accompanied by Wnt and Ca2+ signaling pathway activation. Primary cell cultures further confirm that 3-IAld promotes ruminal epithelial cell proliferation depending on AhR-wnt/β-catenin signaling pathway and PGD2 accelerates ruminal smooth muscle cell proliferation via Ca2+ signaling pathway. Furthermore, we find that 3-IAld and PGD2 infusion promote ruminal epithelial and musculature development in lambs.

CONCLUSIONS

This study demonstrates that early-life ruminal microbiome-derived 3-IAld and PGD2 are effective promoters of rumen development, which enhances our understanding of nutrient-microbiome-host interactions in early life.

Excess fermentation and lactic acidosis as detrimental functions of the gut microbes in treatment-naive TB patients

Introduction

The link between gut microbiota and host immunity motivated numerous studies of the gut microbiome in tuberculosis (TB) patients. However, these studies did not explore the metabolic capacity of the gut community, which is a key axis of impact on the host's immunity.

Methods

We used deep sequencing of fecal samples from 23 treatment-naive TB patients and 48 healthy donors to reconstruct the gut microbiome's metabolic capacity and strain/species-level content.

Results

We show that the systematic depletion of the commensal flora of the large intestine, Bacteroidetes, and an increase in Actinobacteria, Firmicutes, and Proteobacteria such as Streptococcaceae, Erysipelotrichaceae, Lachnospiraceae, and Enterobacteriaceae explains the strong taxonomic divergence of the gut community in TB patients. The cumulative expansion of diverse disease-associated pathobionts in patients reached 1/4 of the total gut microbiota, suggesting a heavy toll on host immunity along with MTB infection. Reconstruction of metabolic pathways showed that the microbial community in patients shifted toward rapid growth using glycolysis and excess fermentation to produce acetate and lactate. Higher glucose availability in the intestine likely drives fermentation to lactate and growth, causing acidosis and endotoxemia.

Discussion

Excessive fermentation and lactic acidosis likely characterize TB patients' disturbed gut microbiomes. Since lactic acidosis strongly suppresses the normal gut flora, directly interferes with macrophage function, and is linked to mortality in TB patients, our findings highlight gut lactate acidosis as a novel research focus. If confirmed, gut acidosis may be a novel potential host-directed treatment target to augment traditional TB treatment.

An artificial intelligence approach of feature engineering and ensemble methods depicts the rumen microbiome contribution to feed efficiency in dairy cows

Genetic selection has remarkably helped U.S. dairy farms to decrease their carbon footprint by more than doubling milk production per cow over time. Despite the environmental and economic benefits of improved feed and milk production efficiency, there is a critical need to explore phenotypical variance for feed utilization to advance the long-term sustainability of dairy farms. Feed is a major expense in dairy operations, and their enteric fermentation is a major source of greenhouse gases in agriculture. The challenges to expanding the phenotypic database, especially for feed efficiency predictions, and the lack of understanding of its drivers limit its utilization. Herein, we leveraged an artificial intelligence approach with feature engineering and ensemble methods to explore the predictive power of the rumen microbiome for feed and milk production efficiency traits, as rumen microbes play a central role in physiological responses in dairy cows. The novel ensemble method allowed to further identify key microbes linked to the efficiency measures. We used a population of 454 genotyped Holstein cows in the U.S. and Canada with individually measured feed and milk production efficiency phenotypes. The study underscored that the rumen microbiome is a major driver of residual feed intake (RFI), the most robust feed efficiency measure evaluated in the study, accounting for 36% of its variation. Further analyses showed that several alpha-diversity metrics were lower in more feed-efficient cows. For RFI, [Ruminococcus] gauvreauii group was the only genus positively associated with an improved feed efficiency status while seven other taxa were associated with inefficiency. The study also highlights that the rumen microbiome is pivotal for the unexplained variance in milk fat and protein production efficiency. Estimation of the carbon footprint of these cows shows that selection for better RFI could reduce up to 5 kg of diet consumed per cow daily, potentially reducing up to 37.5% of CH4. These findings shed light that the integration of artificial intelligence approaches, microbiology, and ruminant nutrition can be a path to further advance our understanding of the rumen microbiome on nutrient requirements and lactation performance of dairy cows to support the long-term sustainability of the dairy community.

From transients to permanent residents: the existence of obligate aerobic microorganisms in the goat rumen

The rumen serves as a complex ecosystem, harboring diverse microbial communities that play crucial ecological roles. Because previous studies have predominantly focused on anaerobic microorganisms, limited attention has been given to aerobic microorganisms in the goat rumen. This study aims to explore the diversity of aerobic microorganisms in the rumen and understand their niche and ecological roles. Rumen fluid samples were collected from 6 goats at different time points post-morning feeding. pH, NH3-N, and volatile fatty acid (TVFA) concentrations were measured, while In vitro cultivation of aerobic microorganisms was performed using PDA medium. Internal Transcribed Spacer (ITS) and 16S sequencing unveiled microbial diversity within the rumen fluid samples. Evidence of obligate aerobic microorganisms in the goat rumen suggests their potential contribution to ecological functionalities. Significantly, certain aerobic microorganisms exhibited correlations with TVFA levels, implying their involvement in TVFA metabolism. This study provides evidence of the existence and potential ecological roles of obligate aerobic microorganisms in the goat rumen. The findings underscore the significance of comprehensively deciphering goat rumen microbial communities and their interactions, with aerobes regarded as permanent residents rather than transients. These insights form a solid foundation for advancing our understanding of the intricate interplay between goat and their aerobic microorganisms in the rumen.

Characterization of the ruminal microbiota in sheep and goats fed different levels of tannin-rich Sericea lespedeza hay

Understanding ruminal microbiota and diet-host breed interactions under forage feeding conditions is essential for optimizing rumen fermentation and improving feed efficiency in small ruminants. This study aimed to investigate the effects of different ratios of condensed tannin-rich Sericea lespedeza (SL; Lespedeza cuneata) in the diets on changes and interactions of ruminal microbiota and host species (i.e., sheep and goats). Katahdin sheep (n = 12) and Alpine goats (n = 12) at approximately 10 to 12 mo of age were blocked by body weight (BW = 30.3 and 25.5 kg, respectively) and randomly assigned to one of the 3 treatments. Diets contained 75% coarsely ground forage and 25% concentrate. The forages were 1) 100% alfalfa hay (AL), 2) 100% SL, and 3) 50% AL + 50% SL (ASL). In the present study, the diversity and composition of ruminal microbiota differed between sheep and goats fed similar diets. Based on the taxonomic analysis, there was a distinct clustering pattern (P < 0.05) for sheep by diets, but such a pattern was not observed for goats (P > 0.1). The most predominant phyla were Firmicutes, Bacteroidetes, Ascomycota, and methanogen species of Methanobrevibactor sp. in the rumen of sheep and goats, regardless of diets. The Bacteroidetes and Ascomycota were enriched in sheep fed AL and ASL. In contrast, these microbial phyla were enhanced in goats fed tannin-rich SL diets, with the diet-by-host species interaction (P < 0.02) for the Bacteroidetes phylum. Sheep rumen fluid samples showed a higher degree of variability in microbial community composition compared to goat rumen fluid samples. The relative proportion of the Aspergillus fungi population was reduced to 90.7% in the SL group compared with the AL group, regardless of host species. The antimicrobial activity of tannins and greater sensitivities of selected microbiota species to these tannin compounds during SL feeding in sheep and goats perhaps caused this difference. The results from this study suggest that differences in the microbiota were associated with differences in diets and host species. Therefore, this study provides a better understanding of ruminal microbiota and diet-host species interactions under various tannin-rich diets, which could advance consolidative information on rumen microbiome community diversity changes and may improve sheep and goat production.