Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model

Konjac glucomannan and κ-carrageenan improve hepatic fatty acid metabolism and colonic microbiota in suckling piglet

Konjac glucomannan (KGM) and κ-carrageenan are polysaccharides that have garnered attention for their potential health benefits. This study aimed to evaluate the maternal supplementation of KGM and κ-carrageenan (SF) during later gestation and lactation on the effect of hepatic lipid metabolism and colonic microflora in offspring. Regarding antioxidant and inflammatory factors in the suckling piglet liver, our results showed that nuclear factor erythroid 2-related factor 2 (Nrf2) and interleukin (IL)-10 levels were significantly increased in the SF group (P < 0.05). In liver mitochondrial function, the mRNA levels of voltage-dependent anion channel 1 (VDAC1), fission 1 (Fis1), and peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α) were significantly up-regulated in the SF group compared to the control (Con) group (P < 0.05). The mRNA level of peroxisome proliferator-activated receptor alpha (PPARα) was remarkably down-regulated in the SF group (P < 0.05). In the colonic microflora of suckling piglets, we found that the SF group increased the abundance of Megasphaera and reduced the abundance of Erysipelotrichaceae_unclassified. The occludin level was significantly increased in the SF group than in the Con group (P < 0.05). In summary, maternal supplementation with SF improves hepatic lipid metabolism and colonic microflora in suckling piglets.

Metagenomics reveals the characteristics and potential spread of microbiomes and virulence factor genes in the dairy cattle production system

Virulence factor genes (VFGs) pose a potential threat to ecological security and animal health, and have attracted increasing attention in the livestock industry. As one of the primary livestock types, dairy cattle may be an important source of VFG transmission. However, the distribution, transmission, and evolution of VFGs in the gastrointestinal tract and surrounding environment of dairy cattle remain unclear. In the present study, a total of 263 samples were collected from cows, calves, colostrum, farm wastewater, and soil. Metagenomics was conducted to analyze changes in the microbiome and VFGs characteristics in these ecological niches. The VFGs of the cows showed distinct differences between the rumen and feces, and were influenced by the region. The dominant VFG hosts was regulated by their microbial structure. Colostrum administration of cows increased VFG abundance in their newborn calf feces sharply and Enterobacteriaceae became the primary host. While diet was the primary driving force for the temporal variation in calf VFGs. For samples of the surrounding environment, water and soil had higher VFG concentrations and were more structurally stable. Moreover, extensive interactions between the mobile genetic elements and VFGs and gene mobile analysis map based on metagenomic binning both displayed the potential horizontal transfer ability of VFGs in the cows and environment. Our study revealed the prevalence, diffusion, and regulatory factors of VFGs in dairy cattle production systems, providing novel insights into reducing livestock VFGs and limiting their spread.

Early concentrate starter introduction induces rumen epithelial parakeratosis by blocking keratinocyte differentiation with excessive ruminal butyrate accumulation

INTRODUCTION

Rumen epithelial parakeratosis, a common disease in ruminants caused by abnormalities in the ruminal stratified squamous epithelial keratinization process, negatively impacts ruminant health and performance. However, we still lack a comprehensive perception of the underlying mechanisms and the predisposing factors for this disorder.

OBJECTIVES

Here, we investigated rumen epithelial cell heterogeneity, differentiation trajectories, and cornification to clarify the rumen epithelial keratinization process and discern the key ruminal metabolites contributing to rumen epithelial parakeratosis.

METHODS

Twenty-four 14-day-old lambs were divided into three groups, including only milk feeding, milk plus alfalfa hay feeding, and milk plus corn-soybean concentrate starter feeding. At 42 days of age, the lambs were slaughtered, and rumen tissues were collected for single-cell RNA-sequencing (scRNA-seq), immunofluorescence, and quantitative real-time PCR (qRT-PCR) analyses. Ruminal fluid samples were collected for metabolomic analyses. Rumen epithelial organoid was used to verify the key ruminal metabolites contributing to parakeratosis.

RESULTS

As expected, we observed that concentrate starter introduction resulted in rumen epithelial parakeratosis. Moreover, scRNA-seq analysis revealed a developmental impediment in the transition from differentiated keratinocytes to terminally differentiated keratinocytes (TDK) in lambs with concentrate starter introduction. Immunofluorescence and qRT-PCR analyses further verified the location and expression of marker genes of TDK. Metabolomic analysis showed a robust positive correlation between ruminal butyrate levels and rumen epithelial keratinization. More importantly, we successfully established a rumen organoid model capable of facilitating the study of the keratinization process in the rumen epithelia and further confirmed that high dose butyrate indeed contributed to rumen epithelial parakeratosis.

CONCLUSION

Collectively, concentrate starter introduction induces ruminal epithelial parakeratosis by blocking keratinocyte differentiation with excessive ruminal butyrate accumulation in a neonatal lamb model. These findings enhance our understanding of rumen epithelial keratinization and provide valuable insights for addressing rumen epithelial parakeratosis using early nutritional intervention strategies.

Butyrate metabolism in rumen epithelium affected by host and diet regime through regulating microbiota in a goat model

The rumen is an important organ that enables ruminants to digest nutrients. However, the biological mechanism by which the microbiota and its derived fatty acids regulate rumen development is still unclear. In this study, 18 female Haimen goats were selected and slaughtered at d 30, 60, and 90 of age. Multi-omics analyses (rumen microbial sequencing, host transcriptome sequencing, and rumen epithelial metabolomics) were performed to investigate host-microbe interactions from preweaning to postweaning in a goat model. With increasing age, and after the introduction of solid feed, the increased abundances of Prevotella and Roseburia showed positive correlations with volatile fatty acid (VFA) levels and morphological parameters (P < 0.05). Epithelial transcriptomic analysis showed that the expression levels of hub genes, including 3-hydroxy-3-methylglutaryl-CoA synthase isoform 2 (HMGCS2), enoyl-CoA hydratase, short chain 1 (ECHS1), and peroxisome proliferator activated receptor gamma (PPARG), were positively associated with animal phenotype (P < 0.05). These hub genes were mainly correlated to VFA metabolism, oxidative phosphorylation, and the mammalian target of rapamycin (mTOR) and peroxisome proliferator activated receptor (PPAR) signaling pathways (P < 0.05). Moreover, the primary metabolites in the epithelium changed from glucose preweaning to (R)-3-hydroxybutyric acid (BHBA) and acetoacetic acid (ACAC) postweaning (P < 0.05). Diet and butyrate were the major factors shaping epithelial metabolomics in young ruminants (P < 0.05). Multi-omics analysis showed that the rumen microbiota and VFA were mainly associated with the epithelial transcriptome, and that alterations in gene expression influenced host metabolism. The "butanoate metabolism" pathway, which transcriptomic and metabolomic analyses identified as being upregulated with age, produces ketones that regulate the "oxidative phosphorylation" pathway, which could provide energy for the development of rumen papillae. Our findings reveal the changes that occur in the rumen microbiota, host transcriptome, and metabolome with age, and validate the role of microbiota-derived VFA in manipulating host gene expression and subsequent metabolism. This study provides insight into the molecular mechanisms of host-microbe interactions in goats and supplies a theoretical basis and guidance for precise nutritional regulation during the critical time window for rumen development of young ruminants.

Comparison of the Physicochemical Properties, Microbial Communities, and Hydrocarbon Composition of Honeys Produced by Different Apis Species

The chemical composition and quality of honey are influenced by its botanical, geographic, and entomological origins, as well as climatic conditions. In this study, the physicochemical characteristics, microbial communities, and hydrocarbon compounds of honey produced by Apis mellifera, Apis cerana, Apis laboriosa, Apis dorsata, and Apis florea were elucidated. The physicochemical profile of the honey exhibited significant differences across species, including moisture content (18.27-23.66%), fructose (33.79-38.70%), maltose (1.10-1.93%), electrical conductivity (0.37-0.74 mS/cm), pH (3.36-3.72), diastase activity (4.50-29.97 diastase number), and color (37.90-102.47 mm). Microbial analysis revealed a significant abundance of lactic acid bacteria, particularly the Apilactobacillus genus in A. laboriosa honey and the Lactobacillus in A. florea honey, indicating significant probiotic potential. Chemometric methods, principal component analysis, hierarchical cluster analysis, and orthogonal partial least squares discriminant analysis (OPLS-DA) were used to classify the honey samples based on the 12 beeswax-derived hydrocarbons. The OPLS-DA model demonstrated 100% accuracy in predicting the entomological origin of honey, indicating that specific hydrocarbons are reliable markers for honey classification.

Effects of Glutamine or Glucose Deprivation on Inflammation and Tight Junction Disruption in Yak Rumen Epithelial Cells

Yak is a special free-ranging cattle breed in the plateau areas of Qinghai and Tibet. Pasture withering in cold-season pastures results in energy deficiency in yaks, which undermines the rumen epithelial barrier. However, the leading factor causing rumen epithelial injury remains unknown. Glutamine (Gln), a conditionally essential amino acid, is insufficient under pathological conditions. Glucose (GLU) is an important energy source. Thus, we explored the effects of Gln or GLU deprivation on the barrier function of yak rumen epithelial cells and investigated the underlying mechanisms, as well as the differences in rumen epithelial barrier function between Gln deprivation (Gln-D) and GLU deprivation (GLU-D). In previous work, we constructed the yak rumen epithelial cells (YRECs) line by transferring the human telomerase reverse transcriptase gene (hTERT) and simian virus 40 large T antigen (SV40T) into primary YRECs. The YRECs were exposed to normal, Gln-D, GLU-D, and serum replacement (SR) media for 6, 12, and 24 h. Our data displayed that cell viability and tight junction protein expression in the SR group were not significantly changed compared to the normal group. Whereas, compared with the SR group, Gln-D treated for more than 12 h reduced cell viability and proliferation, and GLU-D treated for more than 12 h damaged the cell morphology and reduced cell viability and proliferation. The cell proliferation and cell viability were decreased more in GLU-D than in Gln-D. In addition, Gln-D treated for more than 12 h disrupted YREC cellular partially tight junctions by inducing oxidative stress and inflammation, and GLU-D treated for more than 12 h disrupted YREC cellular tight junctions by inducing apoptosis, oxidative stress, and inflammation. Compared with Gln-D, GLU-D more significantly induced cell injury and reduced tight junction protein levels. Our results provided evidence that GLU-D induced damage through the p38 mitogen-activated protein kinase (p38 MAPK)/c-junN-terminal kinase (JNK) signaling pathway, which was more serious than Gln-D treated for more than 12 h.

Comparative Analysis of Microbiota in Jiani Yaks with Different Rib Structures

The Jiani yak is a nationally renowned species that is known for its meat which is rich in various minerals, amino acids, and proteins. The rumen microbiota plays a critical role in gastrointestinal health and feed degradation, contributing proteins, lipids, and volatile fatty acids (VFAs) essential for milk and meat production. However, there is limited knowledge about the microbiota of free-ranging Jiani yaks, especially those with 15 ribs. Rumen fluid samples were collected from yaks with 14 (PL) ribs and 15 (DL) ribs from a slaughterhouse in Jiani County, China. The total DNA of rumen fluid microorganisms was extracted for microbiota sequencing. Our results revealed 643,713 and 656,346 raw sequences in DL and PL animals, respectively, with 611,934 and 622,814 filtered sequences in these two yak groups. We identified 13,498 Amplicon Sequence Variants (ASVs), with 2623 shared between DL and PL animals. The ratio of Bacteroidota to Firmicutes differed between PL (3.04) and DL (2.35) animals. Additionally, 6 phyla and 21 genera showed significant differences between yaks with 14 and 15 ribs, leading to altered microbiota functions, with 51 and 35 notably different MetaCyc and KEGG pathways, respectively. Hence, the microbiota of yaks with 15 ribs differs from those with 14 ribs. Therefore, these microbiota-related comparative investigations will provide insights into yak husbandry practices and genetic selection strategies for their improved productivity in harsh environments.

A metagenomic catalogue of the ruminant gut archaeome

While the ruminant gut archaeome regulates the gut microbiota and hydrogen balance, it is also a major producer of the greenhouse gas methane. However, ruminant gut archaeome diversity within the gastrointestinal tract (GIT) of ruminant animals worldwide remains largely underexplored. Here, we construct a catalogue of 998 unique archaeal genomes recovered from the GITs of ruminants, utilizing 2270 metagenomic samples across 10 different ruminant species. Most of the archaeal genomes (669/998 = 67.03%) belong to Methanobacteriaceae and Methanomethylophilaceae (198/998 = 19.84%). We recover 47/279 previously undescribed archaeal genomes at the strain level with completeness of >80% and contamination of <5%. We also investigate the archaeal gut biogeography across various ruminants and demonstrate that archaeal compositional similarities vary significantly by breed and gut location. The catalogue contains 42,691 protein clusters, and the clustering and methanogenic pathway analysis reveal strain- and host-specific dependencies among ruminant animals. We also find that archaea potentially carry antibiotic and metal resistance genes, mobile genetic elements, virulence factors, quorum sensors, and complex archaeal viromes. Overall, this catalogue is a substantial repository for ruminant archaeal recourses, providing potential for advancing our understanding of archaeal ecology and discovering strategies to regulate methane production in ruminants.

Effects of moringa polysaccharides on growth performance, immune function, rumen morphology, and microbial community structure in early-weaned goat kids

The aim of this research was to investigate the effects of adding moringa polysaccharides (MOP) on the growth performance, immune function, rumen tissue morphology, and rumen microbial community in early-weaned goat kids. Twenty-one 7-day-old Leizhou male goat kids weighing (3.05 ± 0.63) kg, were randomly divided into a control group (CON group), a low-dose group (LOW group), and a high-dose group (HIG group). MOP was added to the goat kids' milk replacer (MR) at 0, 0.15, and 0.3% (on dry matter basis),fed until 60 days of age, and four goat kids in each group with body weights close to the mean of each group were selected for slaughter. The results showed that, compared to the CON group, the MOP groups significantly improved final body weight, body measurements, daily weight gain, and feed intake of the early weaned goat kids; significantly reduced the content of propionic acid, butyric acid, valeric acid, and ammoniacal nitrogen; and in addition, the addition of MOP could significantly increase the height of rumen nipple, the content of immunoglobulin G (IgG) in the serum. The HIG group significantly increased rumen pH, rumen muscularis layer thickness, rumen wall thickness, and serum immunoglobulin A (IgA), and immunoglobulin M (IgM). In conclusion, the addition of MOP positively impacted the growth performance, serum immune function, and rumen tissue morphology in early-weaned goat kids.

Negative energy balance affects perinatal ewe performance, rumen morphology, rumen flora structure, and placental function

This study investigated the effects of negative energy balance (NEB) on perinatal ewes, with a focus on changes in growth performance, serum biochemical parameters, rumen fermentation, ruminal bacteria composition, placental phenotype-related indicators, and expression levels of genes related to placental function. Twenty ewes at 130 days of gestation were randomly allocated to either the positive energy balance (PEB) or NEB groups. In the experiment, ewes in the PEB group were fed the same amount as their intake during the pre-feeding baseline period, while ewes in the NEB group were restricted to 70% of their individual baseline feed intake. The experiment was conducted until 42 days postpartum, and five double-lamb ewes per group were selected for slaughter. The results demonstrated that NEB led to a significant decrease in body weight, carcass weight, and the birth and weaning weights of lambs (P < 0.05). Additionally, NEB caused alterations in serum biochemical parameters, such as increased non-esterified fatty acids and β-hydroxybutyrate levels and decreased cholesterol and albumin levels (P < 0.05). Rumen fermentation and epithelial parameters were also affected, with a reduction in the concentrations of acetic acid, butyric acid, total acid and a decrease in the length of the rumen papilla (P < 0.05). Moreover, NEB induced changes in the structure and composition of ruminal bacteria, with significant differences in α-diversity indices and rumen microbial community composition (P < 0.05). Gene expression in rumen papilla and ewe placenta was also affected, impacting genes associated with glucose and amino acid transport, proliferation, apoptosis, and angiogenesis (P < 0.05). These findings screened the key microbiota in the rumen of ewes following NEB and highlighted the critical genes associated with rumen function. Furthermore, this study revealed the impact of NEB on placental function in ewes, providing a foundation for investigating how nutrition in ewes influences reproductive performance. This research demonstrates how nutrition regulates reproductive performance by considering the combined perspectives of rumen microbiota and placental function.

Differential immunological responses in lamb rumen and colon to alfalfa hay and wheat straw in a concentrate-rich diet: insights into microbe-host interactions

The impact of a concentrate-rich (CR) diet on the gut microbiome and epithelium homeostasis is well documented. However, it has not been systematically studied whether and how host-microbial interaction contributes to the immune homeostasis in the rumen and colon of lambs fed alfalfa hay and wheat straw, alone or combined, in a CR diet. In all, 63 lambs (initial body weight, 16.69 ± 1.50 kg) were randomly allotted to three dietary groups, each consisting of three pens with seven lambs per pen. Over 14 weeks, the lambs were fed diets as follows: 60% concentrate supplemented with either 40% wheat straw (WG), 20% alfalfa hay combined with 20% wheat straw (MG), or 40% alfalfa hay (AG). The present findings showed that lambs in the AG group had greater (P < 0.05) IgG and lower (P = 0.067) tumor necrosis factor-alpha concentrations relative to those in the MG and WG groups. The 16S rRNA analysis highlighted that various bacterial phyla and genera in the rumen and colon preferentially degrade fiber and starch derived from alfalfa hay and wheat straw. The weighted gene co-expression network analysis revealed that the bacterial genera from the Firmicutes are broadly associated with genes involved in various signaling pathways, underscoring the potential role of Firmicutes as key drivers of host-microbial interactions under the present feeding conditions. These findings shed light on the fact that the rumen and colon immune homeostasis is distinctively influenced by diets of alfalfa hay, wheat straw, or their combination in a CR diet. Further studies should examine the prolonged effects of replacing wheat straw with alfalfa hay in a concentrate-rich diet formulated to provide equivalent neutral detergent fiber levels. This could reveal how various forage fibers influence host-microbial interactions and gut health.IMPORTANCEIn contemporary feedlots, a growing trend is to feed animals a concentrate-rich (CR) diet that could disrupt the synchronized interplay between microbes and host metabolism, leading to altered metabolic functions. Wheat straw and alfalfa hay have different levels of protein and neutral detergent fiber, each with varying rates of digestion. It is unclear how including alfalfa hay and wheat straw, alone or combined in a CR diet, influences the host-microbial consortia and immune homeostasis. Herein, we showed that rumen and colon showed differential immune responses to the alfalfa hay, wheat straw, or both. Bacterial genera preferentially degrade fiber and starch derived from alfalfa hay, wheat straw, or both. Bacterial genera from Firmicutes phylum play a pivotal role in driving the host-microbial interactions, as indicated by their extensive association with genes across various signaling pathways.

Dietary Conversion from All-Concentrate to All-Roughage Alters Rumen Bacterial Community Composition and Function in Yak, Cattle-Yak, Tibetan Yellow Cattle and Yellow Cattle

The experiment was to compare the effects of switching all-concentrate to all-roughage diets on rumen microflora and functional metabolism of yak, cattle-yak, Tibetan yellow cattle and yellow cattle living in different altitudes. A total of 24 yaks, cattle-yaks, Tibetan yellow cattle and yellow cattle with a similar weight and good body condition aged 3.5 years were selected and divided into four groups according to species. They were fed a concentrate diet with 40% soybean meal and 60% corn meal for the first month (C group) and a roughage diet with dry corn stalks (100%) for the second month (R group); the formal experimental period was 60 d. These results showed that the conversion had a significant effect on the rumen microflora structure of the four herds, and the biggest difference between concentrate and roughage diets was yak and cattle-yak, followed by Tibetan yellow cattle and yellow cattle. At the phylum level, Bacteroidetes and Firmicutes still predominate in all groups. Compared with the C groups, the relative abundance of Lentisphaerae and Kiritimatiellaeota increased in all R groups, and Lentisphaerae was significantly increased in yak and cattle-yak (p < 0.05). At the genus and species levels, Prevotella had the highest abundance, and the relative abundances of Prevotella, Ruminococcus, Sarcina and Ruminobacter in R groups were lower, while the abundances of other differential genera, including Methanobrevibacter, Fibrobacter, Treponema, Eubacterium, Butyrivibrio, Succinivibrio and Succinimonas, were all higher. Roughage diets increased the number of unique genes and functional genes encoding different CAZymes in rumen microorganisms in all four herds. In the functional contribution analysis, with the exception of ABC transporters and methane metabolism, Prevotella was the main contributor to almost all of these functions. In methane metabolism, Methanobrevibacter had the highest relative abundance, followed by Prevotella, Clostridia and Bacteroidales in all groups. Compared with Tibetan yellow cattle and yellow cattle, yaks and cattle-yaks have better adaptability to roughage, and its utilization rate can be fully improved to reduce methane emission. The study indicates that when four herds are converted to high roughage at the later stage of feeding, the growth and reproduction of rumen microorganisms are affected, and the abundance and diversity of rumen microorganisms are increased to varying degrees. The transformation of concentrate to roughage diet can change the metabolic pathways of rumen microorganisms in yaks and finally affect the fermentation mode of rumen. The above results provide a theoretical basis for the research and development of fattening feeds for yaks, cattle-yaks, Tibetan yellow cattle and yellow cattle and the intensive feeding of livestock on the plateau.

Unique rumen micromorphology and microbiota-metabolite interactions: features and strategies for Tibetan sheep adaptation to the plateau

The rumen microbiota-a symbiont to its host and consists of critical functional substances-plays a vital role in the animal body and represents a new perspective in the study of adaptive evolution in animals. This study used Slide Viewer slicing analysis system, gas chromatography, RT-qPCR and other technologies, as well as 16S and metabolomics determination methods, to measure and analyze the microstructure of rumen epithelium, rumen fermentation parameters, rumen transport genes, rumen microbiota and metabolites in Tibetan sheep and Hu sheep. The results indicate that the rumen nipple height and cuticle thickness of Tibetan sheep are significantly greater than those of Hu sheep (p < 0.01) and that the digestion and absorption of forage are greater. The levels of carbohydrate metabolism, lipid metabolism, and protein turnover were increased in Tibetan sheep, which enabled them to ferment efficiently, utilize forage, and absorb metabolic volatile fatty acids (VFAs). Tibetan sheep rumen metabolites are related to immune function and energy metabolism, which regulate rumen growth and development and gastrointestinal homeostasis. Thus, compared with Hu sheep, Tibetan sheep have more rumen papilla and cuticle corneum, and the synergistic effect of the microbiota and its metabolites is a characteristic and strategy for adapting to high-altitude environments.

Branched Short-Chain Fatty Acid-Rich Fermented Protein Food Improves the Growth and Intestinal Health by Regulating Gut Microbiota and Metabolites in Young Pigs

The diet in early life is essential for the growth and intestinal health later in life. However, beneficial effects of a diet enriched in branched short-chain fatty acids (BSCFAs) for infants are ambiguous. This study aimed to develop a novel fermented protein food, enriched with BSCFAs and assess the effects of dry and wet ferment products on young pig development, nutrient absorption, intestinal barrier function, and gut microbiota and metabolites. A total of 18 young pigs were randomly assigned to three groups. The dry corn gluten-wheat bran mixture (DFCGW) and wet corn gluten-wheat bran mixture (WFCGW) were utilized as replacements for 10% soybean meal in the basal diet. Our results exhibited that the WFCGW diet significantly increased the growth performance of young pigs, enhanced the expression of tight junction proteins, and regulated associated cytokines expression in the colonic mucosa. Simultaneously, the WFCGW diet led to elevated levels of colonic isobutyric and isovaleric acid, as well as the activation of GPR41 and GPR109A. Furthermore, more potential probiotics including Lactobacillus, Megasphaera, and Lachnospiraceae_ND3007_group were enriched in the WFCGW group and positively associated with the beneficial metabolites such as 5-hydroxyindole-3-acetic acid. Differential metabolite KEGG pathway analysis suggested that WFCGW might exert gut health benefits by modulating tryptophan metabolism. In addition, the WFCGW diet significantly increased ghrelin concentrations in serum and hypothalamus and promoted the appetite of young pigs by activating hypothalamic NPY/AGRP neurons. This study extends the knowledge of BSCFAs and provides a reference for the fermented food application in the infant diet.

Performance, ruminal and fecal microbiome of lambs fed diets supplemented with probiotics

The present study aimed to investigate the impact of adding two doses of a commercial probiotic on productive performance, ruminal and fecal microbiome in growing lambs. Forty-two Texel or Ile de France crossbred lambs aged 86.9 ± 8.0 days (body weight: 27.4 ± 3.7 kg) were distributed into three groups: basal diet without probiotic supplementation (CG); basal diet + 1 g/animal/day of probiotic (GP1) and basal diet + 5 g/animal/day of probiotic (GP5). The experimental period was 84 days. The weight was evaluated weekly and dry matter intake (DMI) and leftovers were measured daily. At the end of the experiment, lambs were slaughtered. Feces and rumen fluid were collected for microbiome analysis and rumen fragments for histological evaluation. The use of probiotics did not affect weight gain, but GP1 showed a higher silage and DMI intake than CG (p < 0.001). The CG had a greater thickness of keratinized epithelium and stratum corneum (< 0.001) than GP1 and GP5, and greater total papilla width (p = 0.039) than GP1. There was no difference in the general abundance in the rumen and fecal microbiomes. GP5 had a higher proportion of Azoarcus and Dialister taxa in the rumen fluid (p = 0.012 and p = 0.017, respectively) and higher proportion of Treponema and Fibrobacter taxa in the fecal microbiome (p = 0.015 and p = 0.026, respectively), whereas CG had a higher proportion of Anaeroplasma than the other groups (p = 0.032). These results demonstrated the benefits of probiotics for ruminal epithelium protection and microbial diversity. However, there was no effect on performance parameters.

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.

Short- and long-term effects of different forage types supplemented in preweaning dairy calves on performance and milk production into first lactation

We investigated the short- and long-term effects of different forage types supplemented in preweaning dairy calves on growth performance, blood metabolites, rumen fermentation, bacterial community, and milk production during first lactation. A total of 60 healthy 30-d-old female Holstein calves were blocked by birth date and body weight and randomly assigned to 1 of 3 groups (n = 20): normal milk and pelleted starter feeding (CON), supplemented with chopped oat hay (OAH; 75.0 g/d per calf [DM basis]), or alfalfa hay (ALF; 75.0 g/d per calf [DM basis]). The forage supplementation started when calves were 30 d old (d 1 of the experimental period) and ended when they were 73 d old (d 44 of the experimental period, when calves were weaned). Milk and feed intakes and fecal consistency scores were recorded daily. Growth performance, rumen fluid, and blood samples were collected biweekly. After weaning, all the calves were integrated with the same barn and diets. After calving, the milk production was recorded daily. During the experimental period, the OAH group had greater solid feed and total DM intakes and greater rumen pH than the CON group (P ≤ 0.04), but had lower forage intake and CP digestibility than the ALF group (P ≤ 0.04). The ALF group had higher rumen pH and blood BHB concentration (P ≤ 0.04), lower fecal score (P = 0.02), and greater ether extract digestibility (P = 0.02) than the CON group. The ALF and OAH groups had lower concentrations of ruminal total VFA (P = 0.01). Still, the ALF group had a greater proportion of acetate and a relative abundance of cellulose degradation-related bacteria (Lachnoclostridium_1 and Oribacterium) and a lower relative abundance of inflammation-related bacteria (Erysipelotrichaceae_UCG-009) in the rumen compared with CON. Interestingly, the average milk production from 6 to 200 DIM was greater in the ALF group (P < 0.01), even though no significant effects were found on the rumen fermentation parameters and blood metabolites at 200 DIM. Generally, alfalfa hay supplementation in preweaning dairy calves had positive effects in the short- and long-term for rumen development, health status, and future milk production.

Effects of Dietary Energy Levels on Growth Performance, Nutrient Digestibility, Rumen Barrier and Microflora in Sheep

Dietary energy is crucial for ruminants' performance and health. To determine optimal dietary energy levels for growing sheep, we evaluated their growth performance, nutrient digestibility, rumen fermentation, barrier function, and microbiota under varying metabolic energy (ME) diets. Forty-five growing Yunnan semi-fine wool sheep, aged 10 months and weighing 30.8 ± 1.9 kg, were randomly allocated to five treatments, each receiving diets with ME levels of 8.0, 8.6, 9.2, 9.8 or 10.4 MJ/kg. The results showed that with increasing dietary energy, the average daily gain (ADG) as well as the digestibility of dry matter (DM) and organic matter (OM) increased (p < 0.05), while the feed conversion ratio (FCR) decreased linearly (p = 0.01). The concentration of total VFA (p = 0.03) and propionate (p = 0.01) in the rumen increased linearly, while rumen pH (p < 0.01) and the acetate-propionate ratio (p = 0.01) decreased linearly. Meanwhile, the protein contents of Claudin-4, Claudin-7, Occludin and ZO-1 as well as the relative mRNA expression of Claudin-4 and Occludin also increased (p < 0.05). In addition, rumen bacterial diversity decreased with the increase of dietary energy, and the relative abundance of some bacteria (like Saccharofermentans, Prevotella and Succiniclasticum) changed. In conclusion, increasing dietary energy levels enhanced growth performance, nutrient digestibility, rumen fermentation, and barrier function, and altered the rumen bacterial community distribution. The optimal dietary ME for these parameters in sheep at this growth stage was between 9.8 and 10.4 MJ/kg.

Fermented total mixed ration enhances nutrient digestibility and modulates the milk components and fecal microbial community in lactating Holstein dairy cows

Fermented total mixed ration (FTMR) is an effective method of preserving high-moisture byproducts with higher aerobic stability after fermentation. FTMR has the potential to fulfill the daily nutritional requirements of cattle and enhance their production performance. The objective of this research was to examine the influence of FTMR on lactation performance, total tract apparent digestibility, fecal microbiota communities, and fermentation profiles in lactating dairy cows. A total of 12 cows were randomly assigned into two groups: the TMR group and the FTMR group. The TMR group was fed a total mixed ration (TMR) diet, and the FTMR group was fed an FTMR diet. The FTMR did not impact milk yield in dairy cows despite a decrease in dry matter intake, which increased the efficiency of the feed. In contrast to that in the TMR group, the milk fat content in the FTMR group was greater. The FTMR group showed greater digestibility of neutral detergent fiber (NDF), organic matter (OM), dry matter (DM), crude protein (CP), and acid detergent fiber (ADF) in the total digestive tract than did the TMR group. The FTMR increased the concentration of butyrate in the fecal matter and reduced the pH of the feces. The Chao1, ACE, and Shannon indices of the archaeal community in dairy cow feces were significantly higher in cow fed the FTMR compared to those fed the TMR. LefSe analysis revealed higher levels of Oscillospira, Lactobacillus, Prevotella, and Dehalobacterium in the feces of dairy cows fed the FTMR than in those fed the TMR. However, the abundances of Roseburia, rc4-4, Bulleidia and Sharpea exhibited the opposite trend. The abundances of Halobacteria, Halobacteriales, and Halobacteriaceae, which are biomarkers for distinguishing fecal archaea in the TMR from the FTMR, were substantially greater in the feces of dairy cows that consumed the TMR than in those that consumed the FTMR. Therefore, FTMR can improve the milk fat content, total tract apparent feed digestibility efficiency, and diversity of archaea in the feces. Additionally, this work provides a theoretical basis for the feasibility of FTMR feeding for dairy cows.

Fructo-oligosaccharide supplementation enhances the growth of nursing dairy calves while stimulating the persistence of Bifidobacterium and hindgut microbiome's maturation

The colonization and development of the gut microbiome in dairy calves play a crucial role in their overall health and future productivity. Despite the widely proposed benefits of inulin-related products on the host, there is insufficient information about how supplementing fructo-oligosaccharides (FOS) affects the colonization and development of the gut microbiome in calves. In a randomized intervention trial involving newborn male Holstein dairy calves, we investigated the effect of FOS on the calf hindgut microbiome, short-chain fatty acids (SCFA), growth performance, and the incidence of diarrhea. The daily administration of FOS exhibited a time-dependent increase in the ADG and the concentration of SCFA. Concurrently, FOS delayed the natural decline of Bifidobacterium, promoting the maturation and stabilization of the hindgut microbiome. These findings not only contribute to a theoretical understanding of the judicious application of prebiotics but also hold significant practical implications for the design of early life dietary interventions in the rearing of dairy calves.

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.

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.

Microbial Metagenomes and Host Transcriptomes Reveal the Dynamic Changes of Rumen Gene Expression, Microbial Colonization and Co-Regulation of Mineral Element Metabolism in Yaks from Birth to Adulthood

Yaks are the main pillar of plateau animal husbandry and the material basis of local herdsmen's survival. The level of mineral elements in the body is closely related to the production performance of yaks. In this study, we performed a comprehensive analysis of rumen epithelial morphology, transcriptomics and metagenomics to explore the dynamics of rumen functions, microbial colonization and functional interactions in yaks from birth to adulthood. Bacteria, eukaryotes, archaea and viruses colonized the rumen of yaks from birth to adulthood, with bacteria being the majority. Bacteroidetes and Firmicutes were the dominant phyla in five developmental stages, and the abundance of genus Lactobacillus and Fusobacterium significantly decreased with age. Glycoside hydrolase (GH) genes were the most highly represented in five different developmental stages, followed by glycosyltransferases (GTs) and carbohydrate-binding modules (CBMs), where the proportion of genes coding for CBMs increased with age. Integrating host transcriptome and microbial metagenome revealed 30 gene modules related to age, muscle layer thickness, nipple length and width of yaks. Among these, the MEmagenta and MEturquoise were positively correlated with these phenotypic traits. Twenty-two host genes involved in transcriptional regulation related to metal ion binding (including potassium, sodium, calcium, zinc, iron) were positively correlated with a rumen bacterial cluster 1 composed of Alloprevotella, Paludibacter, Arcobacter, Lactobacillus, Bilophila, etc. Therefore, these studies help us to understand the interaction between rumen host and microorganisms in yaks at different ages, and further provide a reliable theoretical basis for the development of feed and mineral element supplementation for yaks at different ages.

Postnatal Growth and Development of the Rumen: Integrating Physiological and Molecular Insights

The rumen plays an essential role in the physiology and production of agriculturally important ruminants such as cattle. Functions of the rumen include fermentation, absorption, metabolism, and protection. Cattle are, however, not born with a functional rumen, and the rumen undergoes considerable changes in size, histology, physiology, and transcriptome from birth to adulthood. In this review, we discuss these changes in detail, the factors that affect these changes, and the potential molecular and cellular mechanisms that mediate these changes. The introduction of solid feed to the rumen is essential for rumen growth and functional development in post-weaning calves. Increasing evidence suggests that solid feed stimulates rumen growth and functional development through butyric acid and other volatile fatty acids (VFAs) produced by microbial fermentation of feed in the rumen and that VFAs stimulate rumen growth and functional development through hormones such as insulin and insulin-like growth factor I (IGF-I) or through direct actions on energy production, chromatin modification, and gene expression. Given the role of the rumen in ruminant physiology and performance, it is important to further study the cellular, molecular, genomic, and epigenomic mechanisms that control rumen growth and development in postnatal ruminants. A better understanding of these mechanisms could lead to the development of novel strategies to enhance the growth and development of the rumen and thereby the productivity and health of cattle and other agriculturally important ruminants.

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments

BACKGROUND

Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species.

RESULTS

We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea.

CONCLUSIONS

The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.

Effects of dietary energy levels on microorganisms and short-chain fatty acids of rumen and tight junction proteins in Honghe Yellow cattle

This study was conducted to investigate the effects of dietary energy levels on microorganisms and short-chain fatty acids (SCFAs) of rumen and the expression of tight junction proteins in Honghe Yellow cattle. A total of fifteen male Honghe Yellow cattle were randomly divided into three treatments (five replicates per treatment), consisting of formulated energy concentrations of 5.90 MJ/kg (high-energy diet, group H), 5.60 MJ/kg (medium-energy diet, group M) and 5.30 MJ/kg (low-energy diet, group L). The results showed that compared with group H, the expression of Claudin-1 in rumen epithelium of groups M and L was increased, but the expression of ZO-1 was decreased (p < 0.05). Moreover, compared with group H, group M down-regulated the expression of Occludin and Claudin-1 in the brain (p < 0.05). For rumen bacteria, the dominant phyla included Bacteroidetes and Firmicutes, the abundance of Actinobacteriota in groups M and L was significantly increased compared with group H (p < 0.05). At the genus level, the relative abundance of Corynebacterium, Eubacterium_nodatum_group and Neisseraceae in groups M and L was significantly decreased compared with group H (p < 0.05). For rumen fungi, the dominant phyla included Basidiomycota, Ascomycota and Neocariastigomycota, the relative abundance of Ascomycetes was significantly higher than that of groups M and L compared with group H (p < 0.05). At the genus level, the relative abundance of Neocelimastigaceae and Myceliophthora in groups M and L was significantly reduced compared with group H (p < 0.05). Furthermore, the expression of Claudin-1 in rumen epithelium was significantly positively correlated with Actinobacteriota, Corynebacterium and Neisseriaceae. The expression of ZO-1 in the spinal cord was significantly positively correlated with Myceliophthora. The expression of Occludin in brain was positively correlated with valerate content (p < 0.05). In summary, dietary energy levels affected the rumen microbiota of Honghe Yellow cattle. The expression of Claudin-1 in rumen epithelium and the total SCFAs concentration were increased with decreasing dietary energy levels, but the expression of Claudin-1 in brain and ZO-1 in the spinal cord were reduced with decreasing dietary energy levels. Meanwhile, the rumen microbiota and SCFAs were significantly correlated with the expression of TJP.

Effects of Grape Pomace on Growth Performance, Nitrogen Metabolism, Antioxidants, and Microbial Diversity in Angus Bulls

Polyphenol-rich grape pomace (GP) represents a valuable processing by-product with considerable potential as sustainable livestock feed. This study aimed to investigate the effects of different levels of GP on the growth performance and nitrogen utilization efficiency, antioxidant activity, and rumen and rectum microbiota of Angus bulls. Thirty Angus bulls were allocated three dietary treatments according to a completely randomized design: 0% (G0), 10% (G10), and 20% (G20) corn silage dry matter replaced with dried GP dry matter. The results showed that the average daily gain (ADG) of the G0 group and G10 group was higher than that of the G20 group (p < 0.05); urinary nitrogen levels decreased linearly with the addition of GP (linear, p < 0.05). In terms of antioxidants, the levels of catalase (CAT) in the G10 group were higher than in the G0 and G20 groups (p < 0.05), and the total antioxidative capacity (T-AOC) was significantly higher than that in the G20 group (p < 0.05). In addition, in the analysis of a microbial network diagram, the G10 group had better microbial community complexity and stability. Overall, these findings offer valuable insights into the potential benefits of incorporating GP into the diet of ruminants.

Coping with extremes: the rumen transcriptome and microbiome co-regulate plateau adaptability of Xizang goat

The interactions between the rumen microbiota and the host are crucial for the digestive and absorptive processes of ruminants, and they are heavily influenced by the climatic conditions of their habitat. Owing to the harsh conditions of the high-altitude habitat, little is known about how ruminants regulate the host transcriptome and the composition of their rumen microbiota. Using the model species of goats, we examined the variations in the rumen microbiota, transcriptome regulation, and climate of the environment between high altitude (Lhasa, Xizang; 3650 m) and low altitude (Chengdu, Sichuan, China; 500 m) goats. The results of 16 S rRNA sequencing revealed variations in the abundance, diversity, and composition of rumen microbiota. Papillibacter, Quinella, and Saccharofermentans were chosen as potential microbes for the adaptation of Xizang goats to the harsh climate of the plateau by the Spearman correlation study of climate and microbiota. Based on rumen transcriptome sequencing analysis, 244 genes were found to be differentially expressed between Xizang goats and low-altitude goats, with 127 genes showing up-regulation and 117 genes showing down-regulation. SLC26A9, GPX3, ARRDC4, and COX1 were identified as potential candidates for plateau adaptation in Xizang goats. Moreover, the metabolism of fatty acids, arachidonic acids, pathway involving cytokines and their receptors could be essential for adaptation to plateau hypoxia and cold endurance. The expression of GPX3, a gene linked to plateau acclimatization in Xizang goats, was linked to the abundance of Anaerovibrio, and the expression of SLC26A9 was linked to the quantity of Selenomonas, according to ruminal microbiota and host Spearman correlation analysis. Our findings imply that in order to adapt harsh plateau conditions, Xizang goats have evolved to maximize digestion and absorption as well as to have a rumen microbiota suitable for the composition of their diet.

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.

Supplementation with Astragalus Root Powder Promotes Rumen Microbiota Density and Metabolome Interactions in Lambs

The gut microbiota is highly symbiotic with the host, and the microbiota and its metabolites are essential for regulating host health and physiological functions. Astragalus, as a feed additive, can improve animal immunity. However, the effects of Astragalus root powder on the rumen microbiota and their metabolites in lambs are not apparent. In this study, thirty healthy Hu sheep lambs with similar body weights (17.42 ± 2.02 kg) were randomly selected for the feeding experiment. Lambs were fed diets supplemented with 0.3% Astragalus root powder, and the rumen microbiota density and metabolome were measured to determine the effects of Astragalus on the health of lambs in the rumen. The results showed that the relative abundance of Butyrivibrio fibrisolvens (Bf), Ruminococcus flavefaciens (Rf), Succiniclasticum (Su), and Prevotella (Pr) in the rumen was increased in the Astragalus group (p < 0.01), and metabolic profiling showed that the metabolites, such as L-lyrosine and L-leucine, were upregulated in the Astragalus group (p < 0.01). KEGG functional annotation revealed that upregulated metabolites were mainly enriched in the pathways of amino acid metabolism, lipid metabolism, fatty acid biosynthesis, and bile secretion in the Astragalus group, and downregulated metabolites were enriched in the pathways of methane metabolism and other pathways. Correlation analysis revealed that butyric acid was positively correlated with Roseburia and Blautia (p < 0.05) and negatively correlated with Desulfovibrio (p < 0.05). Thus, by analyzing the interactions of Astragalus root powder with the density of rumen microorganisms and their metabolites in lambs, it was shown that Astragalus root powder could improve the structure of rumen microbiota and their metabolites and then participate in the regulation of amino acid metabolism, lipid metabolism, immune metabolism, and other pathways to improve the efficiency of energy absorption of the lambs.

Crosstalk between innate immunity and rumen-fecal microbiota under the cold stress in goats

The balance of the microbiome, which is sensitive to temperature changes, plays a crucial role in maintaining overall health and reducing the risk of diseases. However, the specific mechanisms by which immunity and microbiota interact to adapt to cold stress have yet to be addressed. In this study, Nanjiang Yellow goats were chosen as a model and sampled during the cold (winter, cold stress) and warm (spring) seasons, respectively. Analyses of serum immune factors, as well as the composition of rumen and fecal microbial communities, were conducted to explore the crosstalk between microbiota and innate immunity under cold stress. Significantly increased levels of IgA (P < 0.01) were observed in the cold season compared to the warm season. Conversely, the levels of IL-2 (P = 0.02) and IL-6 (P < 0.01) diminished under cold stress. However, no significant differences were observed in IgG (P = 0.89), IgM (P = 0.42), and IL-4 (P = 0.56). While there were no significant changes in the diversity of bacterial communities between the warm and cold seasons, positive correlations between serum IgA, IL-2, IL-6 concentrations and several genera were observed. Furthermore, the weighted gene co-expression network analysis indicated that the microbiota enriched in the MEbrown module positively correlated with IgA, while the microbiota enriched in the MEblue module positively correlated with IL-2 and IL-6. The strong correlation between certain probiotics, including Alistipes, Bacteroides, Blautia, and Prevotellaceae_UCG.004, and the concentration of IL-2, and IL-6 suggests their potential role in immunomodulatory properties. This study provides valuable insights into the crosstalk between microbial communities and immune responses under the challenge of cold stress. Further studies on the immunomodulatory properties of these probiotics would contribute to the development of strategies to enhance the stress resistance of animals for improved overall health and survival.

Diet and monensin influence the temporal dynamics of the rumen microbiome in stocker and finishing cattle

BACKGROUND

Stocker cattle diet and management influence beef cattle performance during the finishing stage, but knowledge of the dynamics of the rumen microbiome associated with the host are lacking. A longitudinal study was conducted to determine how the feeding strategy from the stocker to the finishing stages of production affects the temporal dynamics of rumen microbiota. During the stocker phase, either dry hay or wheat pasture were provided, and three levels of monensin were administrated. All calves were then transported to a feedlot and received similar finishing diets with or without monensin. Rumen microbial samples were collected on d 0, 28, 85 during the stocker stage (S0, S28 and S85) and d 0, 14, 28, 56, 30 d before slaughter and the end of the trial during the finishing stage (F0, F14, F28, F56, Pre-Ba, and Final). The V4 region of the bacterial 16S rRNA gene of 263 rumen samples was sequenced.

RESULTS

Higher alpha diversity, including the number of observed bacterial features and the Shannon index, was observed in the stocker phase compared to the finishing phase. The bacterial amplicon sequence variants (ASVs) differentiating different sampling time points were identified. Dietary treatments during the stocker stage temporally impact the dynamics of rumen microbiota. For example, shared bacteria, including Bacteroidales (ASV19) and Streptococcus infantarius (ASV94), were significantly higher in hay rumen on S28, S85, and F0, while Bacteroidaceae (ASV11) and Limivicinus (ASV15) were more abundant in wheat. Monensin affected rumen microbial composition at a specific time. Transportation to feedlot significantly influenced microbiome structure and diversity in hay-fed calves. Bacterial taxa associated with body weight were classified, and core microbiotas interacted with each other during the trial.

CONCLUSIONS

In summary, the temporal dynamics of the rumen microbiome in cattle at the stocker and finishing stage are influenced by multiple factors of the feeding strategy. Diet at the stocker phase may temporarily affect the microbial composition during this stage. Modulating the rumen microbiome in the steers at the stocker stage affects the microbial interactions and performance in the finishing stage.

Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer

IMPORTANCE

Yaks, as ruminants inhabiting high-altitude environments, possess a distinct rumen microbiome and are resistant to extreme living conditions. This study investigated the microbiota, resistome, and functional gene profiles in the rumen of yaks fed milk or milk replacer (MR), providing insights into the regulation of the rumen microbiome and the intervention of antimicrobial resistance in yaks through dietary methods. The abundance of Prevotella members increased significantly in response to MR. Tetracycline resistance was the most predominant. The rumen of yaks contained multiple antimicrobial resistance genes (ARGs) originating from different bacteria, which could be driven by MR, and these ARGs displayed intricate and complex interactions. MR also induced changes in functional genes. The enzymes associated with fiber degradation and butyrate metabolism were activated and showed close correlations with Prevotella members and butyrate concentration. This study allows us to deeply understand the ruminal microbiome and ARGs of yaks and their relationship with rumen bacteria in response to different milk sources.

Multi-omics revealed the effects of dietary energy levels on the rumen microbiota and metabolites in yaks under house-feeding conditions

Yak (Bos grunniens) is a unique large ruminant species in the Qinghai-Tibetan Plateau (QTP). Changing the energy levels of their rations can significantly improve their growth performance. Therefore, studying the effects of dietary energy levels on the rumen microflora and metabolites of yak is crucial for enhancing the development of the yak industry. Currently, there is a lack of understanding regarding the impact of feeding energy diets on rumen fermentation parameters, microbial functions, and metabolites. This study was designed to determine the appropriate energy level for feeding yak. Three test diets with metabolizable energy levels of 7.57 MJ/kg, 9.44 MJ/kg, and 11.9 MJ/kg were used and the concentration of volatile fatty acids (VFA) in rumen fluid was measured. The microbial communities, functions, and metabolites in yaks were studied by 16S rRNA sequencing, metagenome, and LC-MS non-targeted metabolomics to investigate the relationships among rumen fermentation parameters, microbial diversity, and metabolites. Ration energy levels significantly affect total VFA, acetate, propionate, butyrate, iso-valerate, valerate, and acetate/propionate (p < 0.05). At the phylum level, the dominant phyla in all three treatment groups were Bacteroidota, Firmicutes, and Actinobacteriota. At the genus level, the abundance of the unclassified_o__Bacteroidales, norank_f_Muribaculaceae, Lachnospiraceae_NK4A136_group, and Family _XIII_AD3011_group showed significant differences (p < 0.05) and were significantly correlated with differential metabolites screened for phosphatidylcholine [PC(16:0/0:0), PC(18:3/0:0)], uridine 3'-monophosphate, and adenosine monophosphate, etc. CAZymes family analysis showed that GHs and CEs differed significantly among the three groups. In addition, differential metabolites were mainly enriched in the pathways of lipid metabolism, nucleotide metabolism, and biosynthesis of other secondary metabolites, and the concentrations of differential metabolites were correlated with microbial abundance. In summary, this study analyzed the effects of ration energy levels on rumen microorganisms and metabolites of yaks and their relationships. The results provided a scientific basis for the selection of dietary energy for yaks in the house feeding period in the future.

Dietary β-hydroxybutyric acid improves the growth performance of young ruminants based on rumen microbiota and volatile fatty acid biosynthesis

Introduction

The ketone body β-hydroxybutyric acid (BHB) plays critical roles in cellular proliferation and metabolic fuel utilization; however, its effects on the rumen microbiota remain unknown.

Methods

Here, three doses of BHB (low, medium, and high) were supplemented to early-weaned goat kids.

Results

Compared with controls, the beneficial effects of BHB on growth and rumen development were observed in goats at 90 days of age (d). The low dose of dietary BHB increased the concentration of rumen acetate, propionate, and butyrate on d90. The sequencing results of the rumen microbiota revealed marked shifts in rumen microbial community structure after early-weaned goat kids consumed BHB for 2 months. The signature bacterial ASVs for each treatment were identified and were the main drivers contributing to microbial interactions in the rumen. The bacteria associated with rumen weight were also correlated with body weight. Some classified bacterial signatures, including Prevotella, Olsenella umbonate, and Roseburia faecis, were related to rumen volatile fatty acids and host development.

Conclusion

Overall, dietary BHB altered rumen microbiota and environments in young goats, which contributed to rumen development and growth.

Transcriptomic and metabolomic insights into the roles of exogenous β-hydroxybutyrate acid for the development of rumen epithelium in young goats

Beta-hydroxybutyric acid (BHBA), as one of the main metabolic ketones in the rumen epithelium, plays critical roles in cellular growth and metabolism. The ketogenic capacity is associated with the maturation of rumen in young ruminants, and the exogenous BHBA in diet may promote the rumen development. However, the effects of exogenous BHBA on rumen remain unknown. This is the first study to investigate the mechanisms of BHBA on gene expression and metabolism of rumen epithelium using young goats as a model through multi-omics techniques. Thirty-two young goats were divided into control, low dose, middle dose, and high dose groups by supplementation of BHBA in starter (0, 3, 6, and 9 g/day, respectively). Results demonstrated the dietary of BHBA promoted the growth performance of young goats and increased width and length of the rumen papilla (P < 0.05). Hub genes in host transcriptome that were positively related to rumen characteristics and BHBA concentration were identified. Several upregulated hub genes including NDUFC1, NDUFB4, NDUFB10, NDUFA11 and NDUFA1 were enriched in the gene ontology (GO) pathway of nicotinamide adenine dinucleotide (NADH) dehydrogenase (ubiquinone) activity, while ATP5ME, ATP5PO and ATP5PF were associated with ATP synthesis. RT-PCR revealed the expression of genes (HMGCS2, BDH1, SLC16A3, etc.) associated with lipolysis increased significantly by BHBA supplementation (P < 0.05). Metabolomics indicated that some metabolites such as glucose, palmitic acid, cortisol and capric acid were also increased (P < 0.05). This study revealed that BHBA promoted rumen development through altering NADH balance and accelerating lipid metabolism, which provides a theoretical guidance for the strategies of gastrointestinal health and development of young ruminants.

Benefits of tributyrin on growth performance, gastrointestinal tract development, ruminal bacteria and volatile fatty acid formation of weaned Small-Tailed Han lambs

This study aimed to determine the effects of tributyrin on growth performance, gastrointestinal tract development, ruminal bacteria and volatile fatty acid (VFA) formation. Thirty healthy weaned Small-Tailed Han female lambs at 3 months old with BW 27.5 ± 4.1 kg (mean ± SD) were randomly assigned to five groups of six lambs each, and each group received tributyrin at 0, 0.5, 1.0, 2.0 and 4.0 g/kg in feed. Weights were measured before the start and end of the study. After 15 d adaptation, DMI, feed, faeces and urine were recorded every week. Lambs were sacrificed at d 75. Compared to lambs fed no tributyrin, lambs fed 4.0 g/kg tributyrin had higher average daily BW gain (P = 0.04) and DMI (P < 0.01). Tributyrin reduced nitrogen (P < 0.01), Ca (P < 0.01) and P (P < 0.01) losses derived from faeces and urine. The mostly important, tributyrin increased dorsal sac thickness (P < 0.01), papillae length (P = 0.04) and width (P < 0.01), ventral sac papillae length (P < 0.01) and width (P < 0.01), caudodorsal blind sac thickness (P = 0.02), papillae length (P < 0.01) and width (P < 0.01). Furthermore, tributyrin increased thicknesses of both the duodenum (P < 0.01) and ileum (P = 0.01), and villus heights of the duodenum (P = 0.01), ileum (P < 0.01), jejunum (P < 0.01) and caecum (P = 0.02), but tributyrin decreased duodenal (P < 0.01) and caecal crypt depths (P < 0.01). Tributyrin reduced rumen pH (P < 0.01) while promoting total VFA concentration (P < 0.01). Tributyrin improved the structure of rumen bacteria by enhancing Clostridium (P = 0.04), Butyrivibrio (P < 0.01), Streptococcus (P = 0.04), Prevotella (P = 0.04), Ruminobacter (P = 0.02) and Fibrobacter (P = 0.03). In conclusion, tributyrin could stimulate gastrointestinal tract development by enhancing colonization of rumen VFA-producing bacteria, and dietary supplementation of tributyrin at 4.0 g/kg of DM was recommended for the weaned lambs.

The effect of early colonized gut microbiota on the growth performance of suckling lambs

The early colonized gut microbiota during the newborn period has been reported to play important roles in the health and immunity of animals; however, whether they can affect the growth performance of suckling lambs is still unclear. In this study, a total of 84 newborn lambs were assigned into LF-1 (top 15%), LF-2 (medium 70%), and LF-3 (bottom 15%) groups according to their average body weight gain at 30 days of age. Fecal samples of lambs (LF) as well as feces (MF), vagina (VAG), colostrum (COL), teat skin (TEAT) samples of ewes, and the air sediment (AIR) in the delivery room were collected 72 h after birth, and then the 16S rRNA gene was sequenced on the Illumina MiSeq platform. The results showed that the early colonized gut microbiota had a significant effect on the growth performance of suckling lambs with alpha and beta diversity (p < 0.05), and we observed that the contribution of early colonized bacteria on the growth performance of lambs increased with age (from BW30 at 25.35% to BW45 at 31.10%; from ADG30 at 33.02% to ADG45 at 39.79% by measuring the relative effects of factors that influence growth performance). The early colonized gut microbiota of suckling lambs with high growth performance was similar to that in VAG, MF, and AIR (p < 0.05). With the RandomForest machine learning algorithm, we detected 11, 11, 6, and 4 bacterial taxa at the genus level that were associated with BW30, BW45, ADG30, and ADG45 of suckling lambs, respectively, and the correlation analysis showed that Butyricicoccus, Ruminococcus_gnavus_group, Ruminococcaceae_Other, and Fusobacterium could significantly affect the growth performance (BW30, BW45, ADG30, and ADG45) of suckling lambs (p < 0.05). In conclusion, the early colonized gut microbiota could significantly affect the growth performance of suckling lambs, and targeting the early colonized gut microbiota might be an alternative strategy to improve the growth performance of suckling lambs.

Bacillus subtilis and Macleaya cordata extract regulate the rumen microbiota associated with enteric methane emission in dairy cows

BACKGROUND

Ruminant livestock production is a considerable source of enteric methane (CH4) emissions. In a previous study, we found that dietary inclusions of Bacillus subtilis (BS) and Macleaya cordata extract (MCE) increased dry matter intake and milk production, while reduced enteric CH4 emission in dairy cows. The objective of this study was to further elucidate the impact of feeding BS and MCE on rumen methanogenesis in dairy cows using rumen metagenomics techniques.

RESULTS

Sixty dairy cows were blocked in 20 groups of 3 cows accordingly to their live weight, milk yield, and days in milk, and within each group, the 3 cows were randomly allocated to 1 of 3 treatments: control diet (CON), control diet plus BS (BS), and control diet plus MCE (MCE). After 75 days of feeding experimental diets, 12 cows were selected from each treatment for collection of rumen samples for the metagenomic sequencing. Results showed that BS decreased ruminal acetate and butyrate, while increased propionate concentrations, resulting in decreased acetate:propionate ratio. The metagenomics analysis revealed that MCE reduced relative abundances of Methanobrevibacter wolinii, Methanobrevibacter sp. AbM4, Candidatus Methanomassiliicoccus intestinalis, Methanobrevibacter cuticularis, Methanomicrobium mobile, Methanobacterium formicicum, and Methanobacterium congolense. Both BS and MCE reduced relative abundances of Methanosphaera sp. WGK6 and Methanosphaera stadtmanae. The co-occurrence network analysis of rumen bacteria and archaea revealed that dietary treatments influenced microbial interaction patterns, with BS and MCE cows having more and stronger associations than CON cows. The random forest and heatmaps analysis demonstrated that the Halopenitus persicus was positively correlated with fat- and protein-corrected milk yield; Clostridium sp. CAG 269, Clostridium sp. 27 14, Haloarcula rubripromontorii, and Methanobrevibacter curvatus were negatively correlated with rumen acetate and butyrate concentrations, and acetate:propionate ratio, whereas Selenomonas rumiantium was positively correlated with those variables.

CONCLUSIONS

The present results provided new information for mitigation of enteric methane emissions of dairy cows by feeding BS and MCE to influence rumen microbial activities. This fundamental knowledge is essential for developing enteric CH4 reduction strategies to mitigate climate change and reduce dietary energy waste. Video Abstract.

Synergistic Responses of Tibetan Sheep Rumen Microbiota, Metabolites, and the Host to the Plateau Environment

Plateau adaptation in animals involves genetic mechanisms as well as coevolutionary mechanisms of the microbiota and metabolome of the animal. Therefore, the characteristics of the rumen microbiome and metabolome, transcriptome, and serum metabolome of Tibetan sheep at different altitudes (4500 m, 3500 m, and 2500 m) were analyzed. The results showed that the rumen differential metabolites at 3500 m and 4500 m were mainly enriched in amino acid metabolism, lipid metabolism, and carbohydrate metabolism, and there was a significant correlation with microbiota. The differentially expressed genes and metabolites at middle and high altitudes were coenriched in asthma, arachidonic acid metabolism, and butanoate and propanoate metabolism. In addition, the serum differential metabolites at 3500 m and 4500 m were mainly enriched in amino acid metabolism, lipid metabolism, and metabolism of xenobiotics by cytochrome P450, and they were also related to microbiota. Further analysis revealed that rumen metabolites accounted for 7.65% of serum metabolites. These common metabolites were mainly enriched in metabolic pathways and were significantly correlated with host genes (p < 0.05). This study found that microbiota, metabolites, and epithelial genes were coenriched in pathways related to lipid metabolism, energy metabolism, and immune metabolism, which may be involved in the regulation of Tibetan sheep adaptation to plateau environmental changes.

A Preliminary Study of the Potential Molecular Mechanisms of Individual Growth and Rumen Development in Calves with Different Feeding Patterns

At present, it is common to feed calves with "Concentrate", "Concentrate + hay" and TMR "Total Mixed Rations" feeding patterns in China, which achieved well feeding efficiency, but the three feeding patterns molecular regulation mechanism in actual production is still unclear. The study aimed to explore the most suitable feeding pattern for Chinese Holstein calves to improve the rumen fermentation function and growth performance of calves. In this regard, the interactions between rumen microorganisms and host metabolism were investigated. The rumen volume and weight of calves in the GF group were significantly higher than those in the GFF and TMR groups (p < 0.05), and the rumen pH of calves in the GF group was 6.47~6.79. Metagenomics analysis revealed that the rumen microbiome of GF and GFF calves had higher relative abundances of Methanobrevibacter, Methanosphaera, and Methanolacinia (p < 0.05). Prevotella multisaccharivorax was significantly more abundant in the rumen of GF calves (p < 0.05), indicating that GF group calves had a stronger ability to ferment sugars. Notably, in the pyruvate metabolic pathway, phosphoenolpyruvate carboxylase was significantly up-regulated in GF calves compared with the TMR group, and pyruvate-phosphate dikinase was significantly down-regulated. Metabolomic results showed that Ursodeoxycholic acid was significantly up-regulated in GF calves, and most of the differential metabolites were enriched in Bile secretion pathways. The association analysis study found that the microorganisms of Prevotella and Ruminococcaceae might cooperate with the host, which was helpful for the digestion and absorption of lipids and made the calves have better growth. The three feeding modes had similar effects, but the 'GF' feeding pattern was more beneficial to the individual growth and ruminal development regarding ruminal morphology, contents physiology and microorganisms. Furthermore, the synergistic effect of rumen microorganisms and the host could more effectively hydrolyze lipid substances and promote the absorption of lipids, which was of great significance to the growth of calves.

Physical, Metabolic, and Microbial Rumen Development in Goat Kids: A Review on the Challenges and Strategies of Early Weaning

The digestive system of newborn ruminant functions is similar to monogastric animals, and therefore milk flows into the abomasum instead of rumen for digestion. The rumen undergoes tremendous changes over time in terms of structure, function, and microbiome. These changes contribute to the smooth transition from the dependence on liquid diets to solid diets. Goat kids are usually separated at early ages from their dams in commercial intensive systems. The separation from dams minimizes the transfer of microbiota from dams to newborns. In this review, understanding how weaning times and methodologies could affect the normal development and growth of newborn goats may facilitate the development of new feeding strategies to control stress in further studies.

Exploring the elevation dynamics of rumen bacterial communities in Barn feeding cattle from 900 to 3,600 meters by full-length 16S sequencing

The diversity and abundance of rumen microorganisms serve as indicators not only of the host's digestive and metabolic capacity but also of its health status. The complex microbial communities in the rumen are influenced to varying degrees by environmental adaptability. In this study, we collected 24 rumen fluid samples from 24 healthy male cattle in three regions of Yunnan, China. Using 16S rRNA amplicon sequencing data analysis, we examined the variations in rumen microorganisms among cattle fed at altitudes of 900 m, 1800 m, and 3,600 m. Altitude-related environmental factors did not surpass phylogeny as the main driving force behind the convergent evolution of yellow cattle rumen microbiome composition. However, they did have an impact on the alpha diversity of the rumen microbiome and the coevolution of the core microbiome. The change in altitude noticeably influenced the diversity and richness of the rumen microbiota, highlighting the environmental effect of altitude. As altitude increased, there was an observed increase in the abundance of Firmicutes and Bacteroidetes, while the abundance of ruminal Proteobacteria and Kiritimatiellaeota decreased. Importantly, at the genus level, the core genus exhibited distinct dynamic changes as altitude increased. Ruminants exhibit the ability to adapt their gut type in accordance with altitude, thereby optimizing energy utilization, especially in high-altitude settings. These discoveries offer valuable insights into the coevolution of host-microbe interactions during ruminant adaptation to various altitudinal environments.

Effects of Chromium Propionate and Calcium Propionate on Lactation Performance and Rumen Microbiota in Postpartum Heat-Stressed Holstein Dairy Cows

Chromium propionate (Cr-Pro) and calcium propionate (Ca-Pro) are widely applied in dairy production, especially in the alleviation of heat stress (HS). HS can reduce the abundance of rumen microbiota and the lactation performance of dairy cows. The present work mainly focused on evaluating the effects of Cr-Pro and Ca-Pro on the performance, ruminal bacterial community, and stress of postpartum HS dairy cows as well as identifying the differences in their mechanisms. Fifteen multiparous postpartum Holstein cows with equivalent weights (694 ± 28 kg) and milk yields (41.2 ± 1.21 kg/day) were randomly divided into three groups: control (CON), Cr-Pro (CRPR), and Ca-Pro (CAPR). The control cows received the basal total mixed ration (TMR) diet, while the CRPR group received TMR with 3.13 g/day of Cr-Pro, and the CAPR group received TMR with 200 g/day of Ca-Pro. The rumen microbial 16S rRNA was sequenced using the Illumina NovaSeq platform along with the measurement of ruminal volatile fatty acids (VFAs) and milking performance. Cr-Pro and Ca-Pro improved lactation performance, increased the rumen VFA concentration, and altered the rumen microbiota of the HS dairy cows. Cr-Pro significantly improved the milk yield (p < 0.01). The richness and diversity of the microbial species significantly increased after feeding on Ca-Pro (p < 0.05). Gene function prediction revealed increased metabolic pathways and biological-synthesis-related function in the groups supplemented with Cr-Pro and Ca-Pro. Our results indicate that the application of Cr-Pro or Ca-Pro can provide relief for heat stress in dairy cows through different mechanisms, and a combination of both is recommended for optimal results in production.

Transmission of fungi and protozoa under grazing conditions from lactating yaks to sucking yak calves in early life

Microbiota from mothers is an essential source of microbes in early-life rumen microbiota, but the contribution of microbiota from different maternal sites to the rumen microbiota establishment in neonates needs more data. To fill this gap, we collected samples from the mouth, teat skin, and rumen of lactating yaks and from the rumen of sucking calves concomitantly on seven occasions between days 7 and 180 after birth under grazing conditions. We observed that the eukaryotic communities clustered based on sample sites, except for the protozoal community in the teat skin, with negative correlations between fungal and protozoal diversities in the rumen of calves. Furthermore, fungi in the dam's mouth, which is the greatest source of the calf's rumen fungi, accounted for only 0.1%, and the contribution of the dam's rumen to the calf's rumen fungi decreased with age and even disappeared after day 60. In contrast, the average contribution of the dam's rumen protozoa to the calf's rumen protozoa was 3.7%, and the contributions from the dam's teat skin (from 0.7 to 2.7%) and mouth (from 0.4 to 3.3%) increased with age. Thus, the divergence in dam-to-calf transmissibility between fungi and protozoa indicates that the foundation of these eukaryotic communities is shaped by different rules. This study provides the first measurements of the maternal contribution to the fungal and protozoal establishment in the rumen of sucking and grazing yak calves in early life, which could be beneficial for future microbiota manipulation in neonatal ruminants. KEY POINTS: • Dam to calf transfer of rumen eukaryotes occurs from multiple body sites. • A minor proportion of rumen fungi in calves originated from maternal sites. • The inter-generation transmission between rumen fungi and protozoa differs.

Growth performance, blood metabolites, ruminal fermentation, and bacterial community in preweaning dairy calves fed corn silage-included starter and total mixed ration

The objective of this study was to evaluate the effects of the inclusion of whole-plant corn silage (WPCS) in a starter or total mixed ration (TMR) on growth, blood metabolites, ruminal fermentation, and microbial community in preweaning dairy calves. A total of 45 healthy dairy calves were blocked by date of birth and randomly assigned to 1 of 3 treatments: 100% calf starter (CONS), a mix of 85% calf starter and 15% WPCS [dry matter (DM) basis; CSCS], or 100% WPCS-based lactation TMR (CTMR). Pasteurized normal milk was fed to all the animals under the same regimen. The experiment ran from when the calves were 2 d old to weaning at 63 d. Milk and feed intakes were recorded daily. Growth performance data and blood samples were collected on wk 3, 5, 7, and 9 of the experiment. Rumen fluid was sampled at 40 and 60 d. The 3 treatments had different particle size fractions. The CSCS group had greater medium fraction (<19 mm, >8 mm) and particles retained on 8-mm sieves than the other 2 groups, whereas the CTMR group had the greatest long (>19 mm) and fine (<4 mm) fractions and physically effective neutral detergent fiber (NDF) on 8- and 4-mm sieves, but had the smallest short fraction (<8 mm, >4 mm) and particles retained on 4-mm sieves. The 24-h in vitro digestibility of DM, crude protein (CP), NDF, and acid detergent fiber (ADF) were decreased in order by the CONS, CSCS, and CTMR groups. Compared with the CONS group, the digestibility of ether extract (EE) was lower in the CSCS and CTMR groups, whereas the digestibility of starch was similar among treatments. During the experimental period, the DM, CP, and metabolizable energy intakes from milk, solid feed, and total feed were not affected by treatments. The NDF, ADF, and EE intakes and potentially digestible intakes were greater in the CTMR group than in the other 2 groups. With the exception that body barrel was greater for calves fed CSCS, growth parameters and blood metabolites were similar among treatments. Compared with the CSCS group, the CTMR group had greater rumen pH and total volatile fatty acids, propionate, and isovalerate concentrations, but a lower acetate:propionate ratio. The CTMR group had greater relative abundances of some cellulolytic bacteria (Rikenellaceae RC9 gut group, Christensenellaceae R7, Ruminococcaceae NK4A214, Ruminococcaceae UCG, Ruminococcus, and Erysipelotrichaceae UCG) in the rumen, which may be beneficial for the early acquisition of specific adult-associated microorganisms. In summary, a WPCS-based lactation TMR, but not the WPCS-included starter, had the potential to be an alternative starter in preweaning calves without having significant adverse effects. These findings provide theoretical and practical implications for the rational application of TMR in the early life of dairy calves.

Early Solid Diet Supplementation Influences the Proteomics of Rumen Epithelium in Goat Kids

It is well known that solid diet supplementation in early life can significantly promote rumen development and metabolic function in young ruminants. However, the changes in the expressed proteome and related metabolism in rumen epithelium in response to a supplemented solid diet remain unclear. In this study, rumen epithelial tissue from goats in three diet regimes including milk replacer only (MRO), milk replacer supplemented concentrate (MRC), and milk replacer supplemented concentrate plus alfalfa pellets (MCA) were collected for measurement of the expression of epithelial proteins using proteomic technology (six per group). The results showed that solid diet significantly improved the growth performance of goats, enhanced the ability of rumen fermentation, and promoted the development of epithelial papilla (p < 0.05). Proteome analysis revealed the distinct difference in the expressed protein in the MRC and MCA group compared with the MRO group (42 upregulated proteins and 79 downregulated proteins in MRC; 38 upregulated proteins and 73 downregulated proteins in MCA). Functional analysis showed that solid diet supplementation activated a variety of molecular functions in the epithelium, including protein binding, ATP binding, structural constituent of muscle, etc., in the MRC and MCA groups. Meanwhile, the expression of proteins related to fatty acid metabolism, the PPAR signaling pathway, valine, leucine, and isoleucine degradation, and butanoate metabolism were upregulated, being stimulated by solid feed. In contrast, the proteins associated with carbohydrate digestion and absorption and glycosaminoglycan degradation were downregulated. In addition, the protein expression of enzymes involved in ketone body synthesis in the rumen was generally activated, which was caused by solid feed. In summary, solid feed promoted the development of rumen epithelium by changing the expression of proteins related to fatty acid metabolism, energy synthesis, and signal transduction. The ketone body synthesis pathway might be the most important activated pathway, and provides energy for rumen development.

Effects of artificial diet breeding on intestinal microbial populations at the young stage of silkworm (Bombyx mori)

The silkworm (Bombyx mori) is an economically important insect and serves as a model organism for Lepidoptera. To investigate the effects of the intestinal microbial population on the growth and development of larvae fed an artificial diet (AD) during the young stages, we analyzed the characteristics of the intestinal microbial population using 16S rRNA gene sequencing technology. Our results revealed that the intestinal flora of the AD group tended to be simple by the 3rd-instar, which Lactobacillus accounting for 14.85% and leading to a decreased pH in the intestinal fluid. In contrast, the intestinal flora of silkworms in the mulberry leaf (ML) group showed continuous growth of diversity, with Proteobacteria accounting for 37.10%, Firmicutes accounting for 21.44%, and Actinobacteria accounting for 17.36%. Additionally, we detected the activity of intestinal digestive enzymes at different instars and found that the activity of digestive enzymes in the AD group increased by larval instar. Protease activity in the AD group was lower during the 1st- to 3rd-instars compared to the ML group, while α-amylase and lipase activities were significantly higher in the AD group during the 2nd- and 3rd-instar compared to the ML group. Furthermore, our experimental results indicated that changes in the intestinal population decreased the pH and affected the activity of proteases, which might contribute to the slower growth and development of larvae in the AD group. In summary, this study provides a reference for investigating the relationship between artificial diet and intestinal flora balance.

Metagenomic Sequencing Reveals the Taxonomic and Functional Characteristics of Rumen Micro-organisms in Gayals

As a semi-wild breed, Gayals have a strong fiber degradation capacity, which is unique to the microbial structure and function of their rumen. In this study, the unique rumen microbial composition and function of Gayals were investigated by metagenomic sequencing, with the Yunnan yellow cattle as the control. We compared the differences in rumen micro-organisms between Gayals and the Yunnan Yellow cattle, and the results showed that there were differences in bacteria, archaea and fungi between Gayals and the Yunnan Yellow cattle, while no significant abundance changes were observed in the protozoa. In addition, the ratio of Firmicutes to Bacteroidetes (1.06) in Gayals was higher than that of the Yunnan Yellow cattle (0.66). Three enzymes (PTA, ACH and FTHFS) related to the acetate production pathway and five enzymes (BHBD, THL, PTB, BK and BCACT) involved in butyric acid production were annotated in this study. The CAZymes search results showed that the abundance of GH5, GH26, GH94, CBM11 and CBM63 in Gayals was higher than in the Yunnan Yellow cattle (p < 0.05). Furthermore, this research constructed a model of rumen micro-organisms degrading fibers according to the characteristics and differences in the rumen microbiota structures and functions of the two breeds. This study expands our knowledge of the rumen microbiota and the mechanisms of fiber degradation in Gayals.