Specific inhibition of Streptococcus bovis by endolysin LyJH307 supplementation shifts the rumen microbiota and metabolic pathways related to carbohydrate metabolism

Rumen protozoa and viruses: New insights into their diversity and potential roles through omics lenses-A review

The rumen microbiome is essential for breaking down indigestible plant material, supplying ruminants with most of their metabolizable energy and protein. While research has primarily focused on bacteria and archaea, protozoa and viruses (phages) have only gained attention in recent years. Protozoa contribute to feed digestion and fermentation, but as predators, they regulate microbial populations by lysing large quantities of microbial cells (the primary protein source for ruminants) and influence the amount of microbial protein reaching the small intestines, along with other mechanisms of interactions. While rumen viruses (or phages) are abundant and diverse, they remain the least understood component of the rumen ecosystem. They can profoundly affect the rumen microbiome by directly lysing their hosts and reprogramming host metabolism through multiple mechanisms, including gene transfer and alteration of central carbon metabolism. Recent advances in omics technologies have deepened our understanding of these viruses, revealing their complex roles in rumen function. This review integrates current knowledge and recent discoveries from omics studies, highlighting the transformative impact of omics-based approaches. It also identifies critical knowledge gaps and outlines future research directions, including selective inhibition of rumen protozoa, development of phages as potential intervention tools to manage specific undesirable rumen microbes, and the causal impacts of rumen viruses on microbial dynamics and animal productivity.

Direct On-Chip Diagnostics of Streptococcus bovis/Streptococcus equinus Complex in Bovine Mastitis Using Bioinformatics-Driven Portable qPCR

This study introduces an innovative on-site diagnostic method for rapidly detecting the Streptococcus bovis/Streptococcus equinus complex (SBSEC), crucial for livestock health and food safety. Through a comprehensive genomic analysis of 206 genomes, this study identified genetic markers that improved classification and addressed misclassifications, particularly in genomes labeled S. equinus and S. lutetiensis. These markers were integrated into a portable quantitative polymerase chain reaction (qPCR) that can detect SBSEC species with high sensitivity (down to 101 or 100 colony-forming units/mL). The portable system featuring a flat chip and compact equipment allows immediate diagnosis within 30 min. The diagnostic method was validated in field conditions directly from cattle udders, farm environments, and dairy products. Among the 100 samples, 51 tested positive for bacteria associated with mastitis. The performance of this portable qPCR was comparable to laboratory methods, offering a reliable alternative to whole-genome sequencing for early detection in clinical, agricultural, and environmental settings.

Effects of Active Dry Yeast Supplementation in In Vitro and In Vivo Nutrient Digestibility, Rumen Fermentation, and Bacterial Community

This study assessed the impact of active dry yeast (ADY) on nutrient digestibility and rumen fermentation, using both in vitro and in vivo experiments with lambs. In vitro, ADYs were incubated with rumen fluid and a substrate mixture to assess gas production, pH, volatile fatty acid (VFA) profiles, and lactate concentration. In vivo, Hu lambs were randomly assigned to five dietary treatments: a control group and four groups receiving one of two dosages of either Vistacell or Procreatin7. Growth performance, nutrient digestibility, rumen fermentation parameters, and bacterial community composition were measured. Pro enhanced the propionate molar proportion while it decreased the n-butyrate molar proportion. Vis reduced the lactate concentration in vitro. In the in vivo experiment, Vis increased the propionate molar proportion and the Succinivibrionaceae_UCG-001 abundance while it decreased the n-butyrate molar proportion and the Lachnospiraceae_ND3007 abundance. Additionally, Vis showed a greater impact on improving the NDF digestibility and total VFA concentration in vivo compared to Pro. Overall, the effects of ADYs on rumen fermentation were found to vary depending on the specific ADY used, with Vis being the most suitable for lamb growth. It was observed that Vis promoted propionate fermentation and Succinivibrionaceae_UCG-001 abundance at the expense of reduced n-butyrate fermentation and Lachnospiraceae_ND3007 abundance. Importantly, differences were noted between the outcomes of the in vitro and in vivo experiments concerning the effects of ADYs on rumen fermentation, highlighting the need for caution when generalizing batch culture results to the in vivo effects of ADYs.

Clinical predictive significance of biomarker molecules elevation during the transition period in cattle suffering from different pathological states: A review

The transition period (TP), which extends from 3 weeks before 3 weeks post parturition, is a critical period regarding the health, productivity, and profitability of dairy animals, during which most health disorders arise, including lameness, mastitis, rumen acidosis, ketosis, hypocalcemia (HC) (milk fever), left-displaced abomasum, fatty liver, hypophosphatemia and post-parturient hemoglobinuria, subacute ruminal acidosis, RP, and metritis. Biomarkers are biological molecules distributed in blood, body fluids, or tissues that represent physiological or pathophysiological indicators of events, processes, or conditions happening within the animal's body. In the field of veterinary medicine, biomarkers are thought to have enormous valuable potential in the field of clinical diagnosis, therapeutical research, surgery, and obstetrical outcome. This review article aims to explore the significance of biomarkers used to predict pathological conditions and health status of cattle during the TP to facilitate the early clinical diagnosis and prompt treatment of TP-related diseases/or conditions and thus improve animal welfare and health and increase productivity.

Rumen protozoa and viruses: The predators within and their functions-A mini-review

The rumen microbiome digests plant feedstuff that would be otherwise indigestible and provides most of the metabolizable energy and protein the host animals need. Until recently, research efforts have primarily been directed to bacteria and archaea, leaving the protozoa, fungi, and viruses much less understood. Protozoa contribute to feed digestion and fermentation, but as predators, they affect the microbiome and its function by regulating the abundance and activities of other rumen microbes both in a top-down (by directly killing the prey) and bottom-up (by affecting the metabolism of other microbes) manner. Rumen viruses (or phages, used interchangeably below) are diverse and abundant but the least understood. They are also predators (intracellular "predators") because of their lytic lifecycle, although they can co-exist peacefully with their hosts and reprogram host metabolism, buttressing host ecological fitness. In doing so, rumen viruses also affect the rumen microbiome in both a top-down and a bottom-up manner. Here we review the recent advancement in understanding both types of predators, focusing on their potential impact on the rumen microbiome and functions.

Integrated multi-omics profiling highlights the benefits of resveratrol hydroxypropyl-β-cyclodextrin inclusion complex for A53T transgenic mice through the microbiota-gut-brain axis

Parkinson's disease (PD) is a neurological disorder characterized by motor and gastrointestinal dysfunctions. Resveratrol is a potent antioxidant and anti-inflammatory phytoalexin known for its health-promoting benefits. However, little is known about its potential in treating PD by modulating the microbial gut-brain axis, and its clinical application has been limited due to poor water solubility, rapid metabolism, and limited systemic bioavailability. Our study aimed to evaluate the therapeutic potential of RHSD, a resveratrol-cyclodextrin inclusion complex, in treating PD through the gut-brain axis in human SNCA-transgenic (A53T) mice PD models. Building on our previous study, we prepared RHSD and compared its efficacy with uncoated resveratrol for PD treatment. The study results demonstrated that RHSD exhibited several advantages in improving motor function, alleviating cognitive impairment, restoring intestinal barrier function, and inhibiting neuropathy. Subsequently, a series of analyses, including fecal microbiota metagenomic sequencing, non-target metabolic assays, host transcriptome sequencing, and integrative analysis were performed to reveal the potential therapeutic pathways of RHSD in A53T mice. The metagenomic sequencing results indicated a significant increase in the levels of Lactobacillus murinus, Lactobacillus reuteri, Enterorhabduscaecimuris, Lactobacillus taiwanensis, and Lactobacillus animals following RHSD administration. Furthermore, metabolomics profiling showed that the levels of gut microbiome metabolites were reversed after RHSD treatment, and differential metabolites were significantly correlated with motor function and intestinal function in PD mice. The integrated analysis of microbial metabolites and host transcriptomics suggested that abnormal amino acid metabolism, mitochondrial dysfunction, oxidative stress, and neuroinflammation in the PD model were associated with the diffusion of abnormal metabolites. This study illustrates the profound impact of RHSD administration on rectifying gut microbiota dysbiosis and improving the A53T mouse model. Notably, we observed significant alterations in the proliferation and metabolism of multiple probiotic strains of Lactobacillus. Furthermore, our research supports the hypothesis that microbiota-related metabolites may regulate the transcription of host genes, including dopamine receptors and calcium stabilization. Consequently, our findings underscore the potential of RHSD as a promising therapeutic candidate for the treatment of PD through the modulation of several signaling pathways within the microbiota-gut-brain axis.

Differences in serum metabolome profile explain individual variation in growth performance of young goats

High growth rates and body weight are important traits of young dairy goats that can shorten generation intervals, improve animal performance, and increase economic benefits. In the present study, ninety-nine, 6-month-old, female goats were fed with the same diet and kept under the same management condition. The ten goats with highest average daily gain (ADG, HADG, 135.27 ± 4.59 g/d) and ten goats with lowest ADG (LADG, 87.74 ± 3.13 g/d) were selected to identify the key serum metabolites associated with ADG, and to investigate the relationships of serum metabolome profiles with digestive tract microbiota. The results showed that a total of 125 serum metabolites were significantly different between HADG and LADG. Of these, 43 serum metabolites were significantly higher levels in HADG, including D-ornithine, l-glutamine, L-histidine, carnosine, LysoPC (16:1(9Z)/0:0), DCTP and hydroxylysine, while, 82 serum metabolites were significantly higher levels in LADG, including P-salicylic acid and deoxycholic acid 3-glucuronide. Pathway analysis indicated that these different metabolites were mainly involved in amino acid and lipid metabolism. Furthermore, Spearman's rank correlation analysis revealed that these differential serum metabolites were correlated with ADG and ADG-related bacteria. Notably, serum hydroxylysine and L-histidine could be used as biomarkers for distinguishing HADG and LADG goats, with an accuracy of >92.0%. SIGNIFICANCE: Our study confirms that individual microbiota and metabolic differences contribute to the variations of growth rate in young goats. Some serum metabolites may be useful in improving the growth performance of young goats, which provides directions for developing further nutritional regulation in the goat industry to achieve healthy feeding and efficiency enhancement.

Ruminal fermentation pattern of acidosis-induced cows fed either monensin or polyclonal antibodies preparation against several ruminal bacteria

This study was designed to evaluate a spray-dried multivalent polyclonal antibody preparation (PAP) against lactate-producing bacteria as an alternative to monensin (MON) to control ruminal acidification. Holstein cows (677 ± 98 kg) fitted with ruminal cannulas were allocated in an incomplete Latin square design with two 20 days period. Cows were randomly assigned to control (CTL), PAP, or MON treatments. For each period, cows were fed a forage diet in the first 5 days (d−5 to d−1), composed of sugarcane, urea and a mineral supplement, followed by a 74% concentrate diet for 15 days (d 0 to d 14). There were no treatment main effects (P > 0.05) on dry matter intake (DMI) and microbial protein synthesis. However, there was a large peak (P < 0.01) of intake on d 0 (18.29 kg), followed by a large decline on d 1 (3.67 kg). From d2, DMI showed an increasing pattern (8.34 kg) and stabilized around d 8 (12.96 kg). Higher mean pH was measured (P < 0.01) in cattle-fed MON (6.06 vs. PAP = 5.89 and CTL = 5.91). The ruminal NH3-N concentration of CTL-fed cows was lower (P < 0.01) compared to those fed MON or PAP. The molar concentration of acetate and lactate was not affected (P > 0.23) by treatments, but feeding MON increased (P = 0.01) propionate during the first 4 days after the challenge. Feeding MON and PAP reduced (P = 0.01) the molar proportion of butyrate. MON was effective in controlling pH and improved ruminal fermentation of acidosis-induced cows. However, PAP was not effective in controlling acidosis. The acidosis induced by the challenge was caused by the accumulation of SCFAs. Therefore, the real conditions for evaluation of this feed additive were not reached in this experiment, since this PAP was proposed to work against lactate-producing bacteria.

The impact of protein source and grain inclusion on digestibility, fecal metabolites, and fecal microbiome in adult canines

This study was conducted to determine the effect of animal protein inclusion rate and grain-free or grain-inclusive diets on macronutrient digestibility, fecal characteristics, metabolites, and microbiota in mixed-breed hounds and Beagles. Four experimental extruded kibble diets were made with varying amounts of animal protein and carbohydrates: 1) high animal protein, grain-inclusive (HA-GI), 2) low animal protein, grain-free (LA-GF), 3) low animal protein, grain-inclusive (LA-GI), and 4) high animal protein, grain-free (HA-GF). Thirty-two Beagles and 33 mixed-breed hounds were assigned to 1 of the 4 treatment groups in a completely randomized design that lasted 180 d. All diets were similar in chemical composition and well-digested by the animals. In general, for fecal metabolites, mixed-breed hounds had a greater concentration of total short-chain fatty acid (SCFA) and ammonia and lower indole concentration than Beagles (P < 0.05). In mixed-breed hounds, LA-GF had a greater (P < 0.05) total SCFA concentration than HA-GI and LA-GI; however, this was not observed in Beagles. There were greater concentrations of ammonia, phenol, and indole in HA-GI than in LA-GF (P < 0.05). Breed-affected fecal primary bile acid (BA) concentration, as mixed-breed hounds had a greater concentration of cholic acid (CA) than Beagles (P < 0.05). Mixed-breed hounds fed LA-GF resulted in greater CA concentrations than HA-GI and LA-GI (P < 0.05). Dogs who consumed LA-GF had lower fecal secondary BA content than the other groups (P < 0.05). The distribution of the fecal microbiota community differed in LA-GF compared with the other groups, with lower α-diversity. However, dogs fed LA-GF had the largest difference in composition with greater Selenomonadaceae, Veillonellaceae, Lactobacillaceae, Streptococcus, Ligilactobacillus, Megamonas, Collinsella aerofaciens, and Bifidobacterium sp. than the other groups. A significant breed effect was noted on nutrient digestibility, fecal metabolites, and microbiota. A treatment effect was observed in LA-GF as it resulted in greater fecal SCFA, lower protein fermentative end products, greater fecal primary BAs, lower fecal secondary BA concentrations, and shifts in fecal microbiota.

Effects of Replacing Alfalfa Hay with Oat Hay in Fermented Total Mixed Ration on Growth Performance and Rumen Microbiota in Lambs

The use of the fermented total mixed ration (FTMR) is a promising approach for the preservation of feedstuff, but the effect of FTMR on the between growth performance and ruminal microflora of lambs are still limited. This study aimed to assess the effects of different roughage types in the FTMR on growth performance and rumen microbiota of lambs. Forty-five six-month-old Small tail Han sheep × Ujumqin male lambs were randomly allocated into three groups (three pens per treatment and five lambs per pen) with the initial body weight (BW) of 28.50 ± 1.50 kg. The three treatments were as follows: the low oat percentages group (LO) contained 200 g/kg oat hay + 400 g/kg alfalfa hay, the medium oat percentages group (MO) contained 300 g/kg oat hay + 300 g/kg alfalfa hay, and the high oat percentages group (HO) contained 400 g/kg oat hay + 200 g/kg alfalfa hay. The result revealed that the dry matter intake and average daily gain were markedly (p < 0.05) higher in the MO treatment than in the LO and HO treatments, whereas no significant difference (p > 0.05) was found in the final body weight. There were no significant (p > 0.05) differences on the Shannon and Simpson index among the three treatments. The PCoA score plot illustrated the individual separation in the LO, MO, and HO treatments. At the phylum level, the presence of Bacteroidetes and Firmicutes belonging to the dominant phyla is widely described in rumen communities among the three treatments. The relative abundances of Prevotella, Fibrobacter, and Succinivibrio in the level of the genes were remarkably higher (p < 0.05) in MO treatment than that in LO and HO treatments, while the relative abundance of Sediminispirochaeta was remarkably higher (p < 0.05) in LO treatment than that in MO and HO treatments. These results indicated that the MO treatments could more effectively improve growth performance than the LO and HO treatments, and also revealed that the different forage types in diets reshaped the compositions and function of the rumen microbiota. Consequently, the findings presented in this study provide a reference for the application of FTMR in animal production and the understanding of the interaction between diet, animal performance, and ruminal microbiota.

In Situ Rumen Degradation Characteristics and Bacterial Colonization of Corn Silages Differing in Ferulic and p-Coumaric Acid Contents

In plant cell wall, ferulic acid (FA) and p-coumaric acid (pCA) are commonly linked with arabinoxylans and lignin through ester and ether bonds. These linkages were deemed to hinder the access of rumen microbes to cell wall polysaccharides. The attachment of rumen microbes to plant cell wall was believed to have profound effects on the rate and the extent of forage digestion in rumen. The objective of this study was to evaluate the effect of bound phenolic acid content and their composition in corn silages on the nutrient degradability, and the composition of the attached bacteria. Following an in situ rumen degradation method, eight representative corn silages with different FA and pCA contents were placed into nylon bags and incubated in the rumens of three matured lactating Holstein cows for 0, 6, 12, 24, 36, 48, and 72 h, respectively. Corn silage digestibility was assessed by in situ degradation methods. As a result, the effective degradability of dry matter, neutral detergent fibre, and acid detergent fibre were negatively related to the ether-linked FA and pCA, and their ratio in corn silages, suggesting that not only the content and but also the composition of phenolic acids significantly affected the degradation characteristics of corn silages. After 24 h rumen fermentation, Firmicutes, Actinobacteria, and Bacteroidota were observed as the dominant phyla in the bacterial communities attached to the corn silages. After 72 h rumen fermentation, the rumen degradation of ester-linked FA was much greater than that of ester-linked pCA. The correlation analysis noted that Erysipelotrichaceae_UCG-002, Olsenella, Ruminococcus_gauvreauii_group, Acetitomaculum, and Bifidobacterium were negatively related to the initial ether-linked FA content while Prevotella was positively related to the ether-linked FA content and the ratio of pCA to FA. In summary, the present results suggested that the content of ether-linked phenolic acids in plant cell walls exhibited a more profound effect on the pattern of microbial colonization than the fibre content.

Gut microbiota-directed intervention with high-amylose maize ameliorates metabolic dysfunction in diet-induced obese mice

Obesity is a chronic disease that may lead to the development of metabolic diseases, cardiovascular diseases, and cancers and has been predicted to affect one billion adults by 2030. Owing to the pivotal role of the gut microbiota in health, including metabolism and energy homeostasis, dietary fiber, the primary energy resource for the gut microbiota, not only helps reduce appetite and short-term food intake but also modulates the structure of the gut microbiota. In this study, we investigated whether high-amylose maize (HAM), with a particular amount of dietary fiber, improves dysmetabolism and gut microbiota dysbiosis in diet-induced obese mice. Promisingly, the HAM dietary intervention not only reduced body weight gain, adipocyte hypertrophy, and dyslipidemia but also mitigated non-alcoholic fatty liver disease, insulin resistance, impaired glucose tolerance, and inflammation in the liver and epididymal white adipose tissues in high-fat diet (HFD)-fed obese mice. In addition, the HAM dietary intervention ameliorated gut microbiota dysbiosis in HFD-fed mice. Changes in families, genera, and species of gut biota that have a relative abundance of 0.01% in at least one group were scrutinized. At the species level, HAM dietary intervention increased Bifidobacterium pseudolongum, Bifidobacterium animalis, Bifidobacterium bifidum, and Lactobacillus paraplantarum and decreased Streptococcus agalactiae, Mucispirillum schaedleri, and Alistipes indistinctus. This change in the gut microbiota driven by the HAM diet was strongly associated with obesity-related indices, highlighting the nutraceutical potential of HAM for improving overall metabolic health. Taken together, this study demonstrates the potential of the HAM diet for mediating metabolic syndrome and gut microbiota dysbiosis.

Endolysin, a Promising Solution against Antimicrobial Resistance

Antimicrobial resistance (AMR) is a global crisis for human public health which threatens the effective prevention and control of ever-increasing infectious diseases. The advent of pandrug-resistant bacteria makes most, if not all, available antibiotics invalid. Meanwhile, the pipeline of novel antibiotics development stagnates, which prompts scientists and pharmacists to develop unconventional antimicrobials. Bacteriophage-derived endolysins are cell wall hydrolases which could hydrolyze the peptidoglycan layer from within and outside of bacterial pathogens. With high specificity, rapid action, high efficiency, and low risk of resistance development, endolysins are believed to be among the best alternative therapeutic agents to treat multidrug resistant (MDR) bacteria. As of now, endolysins have been applied to diverse aspects. In this review, we comprehensively introduce the structures and activities of endolysins and summarize the latest application progress of recombinant endolysins in the fields of medical treatment, pathogen diagnosis, food safety, and agriculture.