Transcriptomic analysis reveals the molecular mechanisms of rumen wall morphological and functional development induced by different solid diet introduction in a lamb model

Sex-specific microbiota associations with backfat thickness, eye muscle area, and rumen fermentation in Qinchuan cattle

BACKGROUND

Ruminant livestock are essential for global food production, and understanding sex-specific rumen fermentation and microbial differences is key to improving production efficiency and meat quality. This study explored sex-specific variations in backfat thickness, eye muscle area, rumen fermentation, and microbiota in Qinchuan cattle.

RESULTS

The results revealed that heifers exhibited higher backfat thickness, butyrate concentrations, and acetate/propionate ratio, whereas bulls had larger eye muscle areas and higher propionate concentrations. Volatile fatty acids (VFAs) transport-related genes (CA4, DRA, and NHE1) were more highly expressed in bulls. Heifers showed greater microbial diversity with distinct sex-specific community structures. Bulls had a higher abundance of Prevotella, while butyrate-producing bacteria like Butyrivibrio and Pseudobutyrivibrio were more abundant in heifers. Functional predictions revealed that bulls were enriched in glycan biosynthesis and amino acid metabolism pathways, whereas heifers showed enhanced lipid metabolism pathways. Correlation analyses showed that backfat thickness was positively correlated with acetate and butyrate production, and acetate/propionate ratio, but negatively correlated with Veillonellaceae_UCG-001. Eye muscle area was negatively correlated with isobutyrate production and the abundance of Elusimicrobium and Anaeroplasma, but positively correlated with Lachnospiraceae_NK3A20_group. Redundancy analysis (RDA) identified propionate and butyrate as key drivers of microbial community differences. The Random Forest model identified key predictors for backfat thickness, including rumen fermentation parameters, microbial taxa, and metabolic pathways, explaining 28% of the variation. However, eye muscle area was not well predicted by the current parameters.

CONCLUSION

These findings enhance our understanding of sex-specific microbial and metabolic profiles, offering potential strategies for optimizing livestock management and breeding programs.

Wheat straw and alfalfa hay alone or combined in a high-concentrate diet alters microbial-host interaction in the rumen of lambs

The inclusion of various forages in a normal forage-to-concentrate ratio has widely been reported to reveal the changes that occur in the foregut tissues. However, the mechanism by which the wheat straw, alfalfa hay, or both alter the orchestrated crosstalk of microbiome and host-transcriptome in the rumen of lambs fed a high-concentrate diet is elusive. Sixty-three Hulunbuir lambs were randomly allotted to 3 dietary groups, and each dietary group had 3 pens with 7 lambs. The lambs were fed high-concentrate diets (70%) supplemented with either 30% wheat straw (30S), a mixture of 15% alfalfa hay and 15% wheat straw (30M), or 30% alfalfa hay (30A) over a 2-week adaptation period and a 12-week formal trial. Compared with the 30S and 30A groups, the 30M group had greater (P < 0.05) levels of plasma glucagon-like peptide (GLP-2), interleukin-2 (IL-2). Humoral immunity showed a tendency to increase in the 30M group, as evidenced by the greater levels of plasma immunoglobulins (Ig) A and IgG (P > 0.05). The 16S rRNA result showed that the abundance of Lachnospiraceae (NK3A20 group and unclassified), Olsenella, Shuttleworthia, and Succiniclasticum were enriched in the 30M group. Meanwhile, the abundances of Ruminococcaceae NK4A214 and prevetolla_7 were enriched in 30S and 30A, respectively. The RNA-seq identified 35 shared differentially expressed genes (DEGs) between the "30S vs. 30M" and "30S vs. 30A," enriched in lipid metabolism pathways, including glycerophospholipid and arachidonic acid metabolism. The weighted gene co-expression network analysis results revealed that the expression of genes in the darkred (194 genes) and darkgreen (134 genes) modules showed a strong positive correlation with phenotypic traits and bacterial genera, respectively. The genes in the darkgreen module were involved in carbohydrate, lipid, and amino acid metabolism and showed a wide range of associations with Prevotella_7, Shuttleworthia, and Succiniclasticum, indicating that ruminal microbes might act as a vital driver in the microbiome-host interaction, likely through fermentation of end-products or metabolites. In conclusion, the results indicate that microbiome enrichment in response to feeding wheat straw and alfalfa hay might drive microbiome-host crosstalk to regulate rumen function in lambs fed a high-concentrate diet.

Dietary secoisolariciresinol diglucoside crude extract improves growth through modulating rumen bacterial community and epithelial development in lambs

BACKGROUND

Flaxseed lignans, types of polyphenolic compounds, primarily consist of secoisolariciresinol diglucoside (SDG). Natural plant extracts are becoming increasingly important as feed for ruminant animals. An underutilized plant bioactive component, SDG shows promising benefits for young ruminant production. The objective of this study was to assess the impact of SDG on rumen fermentation using an in vitro rumen simulation technology. Additionally, we tested the effects of SDG (0.20 g kg-1 body weight) on rumen development and production performance of lambs in a production setting.

RESULTS

The in vitro addition of 100 mg L-1 SDG demonstrated significant regulatory effects, with a notable decrease in the acetate/propionate ratio (P < 0.05). Feeding trials revealed that SDG significantly increased average daily feed intake and average daily weight gain (P < 0.05), and reduced the acetate/propionate ratio (P < 0.05). This led to a significant increase in the relative abundance of Eubacterium ruminantium (P = 0.038) and Butyrivibrio (P = 0.002). Furthermore, it promoted rumen development and upregulated the relative expression of mRNA of Cyclin E1 and CDK2 in rumen epithelial cells (P < 0.05).

CONCLUSION

The SDG extract optimizes the composition of rumen microbiota and the development of rumen epithelial cells, promoting the growth of pre-weaning lambs. The SDG additive exhibits potential as a novel growth promoter for ruminant animals, offering a promising solution for sustainable livestock production. © 2024 Society of Chemical Industry.

Transcriptomic characterization of the functional and morphological development of the rumen wall in weaned lambs fed a diet containing yeast co-cultures of Saccharomyces cerevisiae and Kluyveromyces marxianus

Introduction

In lambs, the function of the rumen is incompletely developed at weaning, and the inclusion of yeast cultures in the diet can profoundly influence the morphological and functional development of the rumen.

Methods

In this study, the effects of Saccharomyces cerevisiae and Kluyveromyces marxianus (NM) yeast co-cultures on ruminal histomorphology were assessed, and corresponding transcriptomic changes within the rumen epithelium were identified. In total, 24 lambs were grouped into four groups of six lambs including a control (C) group fed a basal diet, and N, M, and NM groups in which lambs were fed the basal diet, respectively, supplemented with Saccharomyces cerevisiae yeast cultures (30 g/d per head), Kluyveromyces marxianus yeast cultures (30 g/d per head), and co-cultures of both yeasts (30 g/d per head), the experiment lasted for 42 d.

Results

In morphological analyses, lambs from the NM group presented with significant increases in papilla length, papilla width, and epithelial thickness in the rumen relative to lambs in the C group (p < 0.05). Transcriptomic analyses revealed 202 genes that were differentially expressed between samples from the C and NM groups, with the largest proportion of these genes being associated with the oxidative phosphorylation pathway. In a weighted gene coexpression network analysis, a positive correlation was observed between the MEgreen and MEpurple modules and rumen morphology. Of these modules, the MEgreen module was found to be more closely linked to fatty acid metabolism and oxidative phosphorylation, whereas the MEpurple module was linked to oxidative phosphorylation and fatty acid degradation. Ultimately, these results suggest that dietary supplementation with NM has driven the degradation of fatty acids, the induction of oxidative phosphorylation, the acceleration of lipid metabolism, the production of ATP to sustain ruminal growth, and the maintenance of intracellular NADH/NAD+ homeostasis on weaned lambs and is superior to single yeast fermentation.

Discussion

These results thus offer a theoretical foundation for further studies examining the mechanisms through which NM cultures can influence ruminal development in lambs.

Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction

With extreme nutritional substrate deficiency, the adaptive responses of the gastrointestinal microbiota and host metabolism are largely unknown. Here, we successfully established a microbial substrate deficiency model in the rumen without solid diet introduction in neonatal lambs. In the absence of solid diet, we observed a reduction in the Simpson Index of rumen bacteria, along with a marked decline in the abundance of keystone microorganisms such as Prevotella, Selenomonas, Megasphaera, and Succiniclasticum, indicating a simplified microbial interaction network. Additionally, more urea and NH3-N production facilitated microbial efficient nitrogen utilization to prioritize ammonia as a nitrogen source for survival, reallocating energy to overcome nutritional limitations and sustain their viability. In addition, enriched archaea (Methanosarcina, Methanomicrobium, Methanobrevibacter, and Methanobacterium) promoted hydrogen removal and the growth of nitrogen-producing microorganisms (Pecoramyces, Piromyces, Caecomyces, and Orpinomyces). It also reinforced the glutamate-glutamine pathway, as evidenced by the higher expression of glnA, GLUL, gdhA, and ureAB, suggesting enhanced internal cycling of nitrogen for microbial survival. This selfish microbial survival strategy deprived the host of adequate volatile fatty acids for energy metabolism, resulting in the downregulation of rumen epithelial cell cycle proteins (CCNB1, CCNE), abnormal mitochondrial morphology, and reduced mitochondrial deoxyribonucleic acid copy number and adenosine triphosphate production. Overall, these findings revealed the adaptive survival strategies of rumen microbiota with solid diet deficiency in early life, which caused alterations in epithelial cell mitochondrial function.

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.

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.

Multi-omics insights into the energy compensation of rumen microbiota of grazing yaks in cold season

Background

The ability of yaks to adapt to the extreme environment of low temperatures and hypoxia at cold seasons on the Qinghai-Tibet Plateau (QTP) is related to the host genome; however, the convergent evolution of rumen microbiomes in host adaption is unknown.

Methods

Here, we conducted a multi-omics study on the rumen fluid of grazing yaks from warm (July) and cold (December) seasons on the QTP to evaluate the convergent evolution of rumen microbiomes in the adaptation of grazing yaks to cold-seasons environments.

Results

The results showed that grazing yaks at cold seasons had higher fibrolytic enzyme activities and volatile fatty acids (VFAs) concentrations, and the relative abundance of Firmicutes and the ratio Firmicutes to Bacteroidetes was significantly higher than that of yaks at warm seasons. Macrogenomic analyses showed that genes involved in forming VFAs and arginine were significantly enriched in cold-season yaks. Transcriptome analyses of the rumen epithelium showed that 72 genes associated with VFAs absorption and transport were significantly upregulated in cold-season yaks. Metabolomic analyses showed that the levels of ornithine, related to efficient nitrogen utilization, were significantly upregulated in cold-season yaks.

Conclusion

The synergistic role of rumen microbiomes in the adaptation of grazing yaks to extreme environments at cold seasons was revealed by multi-omics study.

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.

Investigating the impact of feed-induced, subacute ruminal acidosis on rumen epimural transcriptome and metatranscriptome in young calves at 8- and 17-week of age

Introduction

With the goal to maximize intake of high-fermentable diet needed to meet energy needs during weaning period, calves are at risk for ruminal acidosis. Using the calves from previously established model of feed-induced, ruminal acidosis in young calves, we aimed to investigate the changes in rumen epimural transcriptome and its microbial metatranscriptome at weaning (8-week) and post-weaning (17-week) in canulated (first occurred at 3 weeks of age) Holstein bull calves with feed-induced subacute ruminal acidosis.

Methods

Eight bull calves were randomly assigned to acidosis-inducing diet (Treated, n = 4; pelleted, 42.7% starch, 15.1% neutral detergent fiber [NDF], and 57.8% nonfiber carbohydrates), while texturized starter was fed as a control (Control, n = 4; 35.3% starch, 25.3% NDF, and 48.1% nonfiber carbohydrates) starting at 1 week through 17 weeks. Calves fed acidosis-inducing diet showed significantly less (p < 0.01) body weight over the course of the experiment, in addition to lower ruminal pH (p < 0.01) compared to the control group. Rumen epithelial (RE) tissues were collected at both 8 weeks (via biopsy) and 17 weeks (via euthanasia) and followed for whole transcriptome RNA sequencing analysis. Differentially expressed genes (DEGs) analysis was done using cufflinks2 (fold-change ≥2 and p < 0.05) between treated and control groups at 8-week of age, and between 8- and 17-week for the treated group.

Results

At 8-week of age, DEGs between treatment groups showed an enrichment of genes related to the response to lipopolysaccharide (LPS) (p < 0.005). The impact of prolonged, feed-induced acidosis was reflected by the decreased expression (p < 0.005) in genes involved in cell proliferation related pathways in the RE at 17-week of age in the treated group. Unique sets of discriminant microbial taxa were identified between 8-and 17-week calves in the treated group and the treatment groups at 8-week, indicating that active microbial community changes in the RE are an integral part of the ruminal acidosis development and progression.

Ruminal microbiota-host crosstalks promote ruminal epithelial development in neonatal lambs with alfalfa hay introduction

Ruminal microbiota is gradually established after birth, while microbiota maturation could be highly diverse because of varied solid dietary accessibility. However, how the ruminal microbiota accreted from postnatal hay diets alters rumen epithelial development, and how this affects animal health remains largely unknown. Here, neonatal lambs were introduced to starchy corn-soybean starter or corn-soybean starter + alfalfa hay (AH) to investigate the influences of early life ruminal microbiome on rumen epithelial development using integrated 16s rRNA sequencing-metagenome-transcriptome approaches. The results showed that AH introduction elevated average daily weight gain, rumen weight and volume, rumen epithelial papillae length, and rumen muscle layer thickness. Meanwhile, the relative abundance of fibrolytic bacteria (Christensenellaceae R-7 group, Prevotellaceae UCG-001, and Succinivibrio), acetate producer (Acetitomaculum and Mitsuokella), and propionate producer Succiniclasticum was increased in the rumen content by AH supplementation (P < 0.05). Moreover, AH introduction decreased the relative abundance of total CAZymes, CBM, and GH and increased the abundance of KO genes related to volatile fatty acid (VFA) generation in the rumen content. AH lambs had a higher relative abundance of Succiniclasticum, Megasphaera, Succinivibrio, and Suttonella (P < 0.05), while a lower relative abundance of Cloacibacillus, Desulfovibrio, Dialister, Intestinimonas, Parabacteroides, and Pseudoscardovia (P < 0.05) in the rumen epithelial samples. Furthermore, these alterations in ruminal microbial structure and function resulted in ruminal epithelial cell proliferation and development pathways activation. In summary, AH introduction benefited ruminal fiber degradation and VFA generation bacteria colonization and promoted ruminal epithelial development. These findings provide new insights into ruminal microbial-host interactions in the early life.IMPORTANCEWhile it is established that a fiber-rich diet promotes rumen development in lambs, further research is needed to investigate the precise response of rumen microbiota and epithelium to high-quality alfalfa hay. Here, we observed that the inclusion of alfalfa hay led to a discernible alteration in the developmental trajectory of the rumen. Notably, there was a favorable shift in the rumen's volume, morphology, and the development of rumen papillae. Furthermore, ruminal microbial structure and function resulted in ruminal epithelial cell proliferation and development pathways activation, collectively provide compelling evidence supporting the capacity of alfalfa hay to enhance rumen development and health through ruminal micrbiota-host crosstalks. Our findings elucidate the functional response of the rumen to alfalfa hay introduction, providing new insights into strategies for promoting healthy development of the rumen in young ruminants.

Transcriptomic analysis reveals that non-forage or forage fiber source promotes rumen development through different metabolic processes in lambs

Dietary fiber supplementation can stimulate rumen development in lambs during the pre-weaning period. However, it is unclear whether different sources of fiber have varying effects on rumen development. This study aimed to investigate the molecular mechanism of rumen morphological and functional development based on non-forage or forage as a starter dietary fiber source. Twenty-four male Hu lambs with similar body weights (BW, 3.67 ± 0.08 kg) were selected and divided into two groups that received diets supplemented with either alfalfa hay (AH) or soybean hull (SH). At the age of 70 days, six lambs were slaughtered from each treatment group for rumen fermentation and morphological analyses. Three samples of the rumen tissue from the ventral sac were collected for transcriptomic analysis. The results identified 633 differentially expressed genes (DEGs), of which 210 were upregulated and 423 were downregulated in the SH group compared with those in the AH group. The upregulated DEGs were most enriched in the immune function and proteolysis pathways, whereas the downregulated DEGs were mainly involved in cell proliferation, apoptosis, and differentiation pathways. These findings indicated that non-forage as a starter dietary fiber source improved immune function and enhanced nitrogen utilization, whereas forage facilitated rumen morphological development.

The type of lipid supplement has crucial implications for forage particle size in calf starter diets

BACKGROUND

Forage inclusion in starters of young dairy calves has become an acceptable strategy in the last decade. To compensate for the lower energy provided by forage, concurrent lipid supplementation can be proposed. However, ruminal microbial activity and forage digestibility may be decreased by lipid supplementation. We hypothesized that the composite effect of forage and lipid supplements may be dependent on forage particle size and the type of lipid supplement. Therefore, we evaluated the effect of long (LP; geometric mean, 4.97 mm) vs. short alfalfa hay particle sizes (SP; geometric mean, 1.26 mm) with either soybean oil (SBO) or palm fatty acids (PLF) as lipid source in a 2 × 2 factorial design with treatments SP-SBO, SP-PLF, LP-SBO, and LP-PLF. Treatments (n = 13 with 6 males and 7 females each) were offered to Holstein calves (3 days old) with equal amounts of lipid (25 g/kg DM) throughout the experimental period. The milk offering scheme (d 1 to 53) was equal for all groups. Data collection continued until 20 d post-weaning.

RESULTS

Interaction between forage particle size and lipid supplement was significant for the following readouts: the highest and lowest starter intakes during the pre-weaning period occurred in LP-PLF and LP-SBO, respectively. This was associated with similarly contrasting changes in average daily gain (ADG) during the post-weaning period, body weight at the end of experiment, withers height, digestibility of organic matter and neutral detergent fiber, and blood serum concentrations of glucose, beta-hydroxybutyrate, and insulin during the pre-weaning period. During both pre- and post-weaning periods, the highest and lowest urinary excretion of allantoin and total purine derivatives, representing microbial protein synthesis, were observed in LP-PLF and LP-SBO, respectively, indicating that those diets were most and least favorable for rumen development. Irrespective of forage particle size, supplemental SBO vs. PLF increased serum malondialdehyde as an oxidative stress indicator across periods, increased blood urea nitrogen and feed efficiency in the pre-weaning period, and reduced hip height during the post-weaning period.

CONCLUSIONS

It can be concluded that feeding a rumen-inert, mostly saturated fatty acid source with alfalfa hay as long particle size is recommended with view on performance, whereas a combination soybean oil rich in unsaturated fatty acids should not be provided to milk-fed Holstein calves together with long particle forage. Feeding soybean oil and alfalfa hay as long particles is not advisable mainly due to lower starter consumption and impaired development of ruminal function. If dietary supplementation of soybean oil is applied, incorporation of forage as small particles should be preferred to support rumen development.

Effects of rearing mode on gastro-intestinal microbiota and development, immunocompetence, sanitary status and growth performance of lambs from birth to two months of age

BACKGROUND

Artificial rearing system, commonly used in prolific sheep breeds, is associated to increased mortality and morbidity rates before weaning, which might be linked to perturbations in digestive tract maturation, including microbiota colonization. This study evaluated the effect of rearing mode (mothered or artificially reared) on the establishment of the rumen and intestinal microbiome of lambs from birth to weaning. We also measured immunological and zootechnical parameters to assess lambs' growth and health. GIT anatomy as well as rumen and intestinal epithelium gene expression were also analysed on weaned animals to assess possible long-term effects of the rearing practice.

RESULTS

Total VFA concentrations were higher in mothered lambs at 2 months of age, while artificially-reared lambs had lower average daily gain, a more degraded sanitary status and lower serum IgG concentration in the early growth phase. Metataxonomic analysis revealed higher richness of bacterial and eukaryote populations in mothered vs. artificially-reared lambs in both Rumen and Feces. Beta diversity analysis indicated an evolution of rumen and fecal bacterial communities in mothered lambs with age, not observed in artificially-reared lambs. Important functional microorganisms such as the cellulolytic bacterium Fibrobacter succinogenes and rumen protozoa did not establish correctly before weaning in artificially-reared lambs. Enterobacteriaceae and Escherichia coli were dominant in the fecal microbiota of mothered lambs, but main E. coli virulence genes were not found differential between the two groups, suggesting they are commensal bacteria which could exert a protective effect against pathogens. The fecal microbiota of artificially-reared lambs had a high proportion of lactic acid bacteria taxa. No difference was observed in mucosa gene expression in the two lamb groups after weaning.

CONCLUSIONS

The rearing mode influences gastrointestinal microbiota and health-associated parameters in offspring in early life: rumen maturation was impaired in artificially-reared lambs which also presented altered sanitary status and higher risk of gut dysbiosis. The first month of age is thus a critical period where the gastrointestinal tract environment and microbiota are particularly unstable and special care should be taken in the management of artificially fed newborn ruminants.

Dietary spirulina supplementation modifies rumen development, fermentation and bacteria composition in Hu sheep when consuming high-fat dietary

Introduction

This study aims to investigate the long-term effects of spirulina supplementation in a high-fat diet (HFD) on rumen morphology, rumen fermentation, and the composition of rumen microbiota in lambs. Spirulina is a blue-green microalgae that has been shown to have high nutritional value for livestock.

Methods

Fifty-four lambs were randomly divided into three groups: a normal chow diet (NCD) group, a high-fat diet (HFD) group, and a high-fat diet supplemented with 3% spirulina (HFD+S) group. Rumen morphology, rumen fermentation, and rumen microbiota were analyzed at the end of the study.

Results

Spirulina supplementation improved the concentration of volatile fatty acids and rumen papilla length. Additionally, there was a tendency for an increase in rumen weight and an upregulation of the genes Claudin-1, Claudin-4, and Occludin in the HFD+S group. Pyrosequencing of the 16S ribosomal RNA gene also showed that spirulina supplementation significantly changed the rumen microbiota composition in the HFD group, with a decrease in richness and diversity. Specifically, the relative abundance of Prevotella 9 and Megasphaera was significantly increased in the HFD group compared to the NCD group, while spirulina supplementation reversed these changes.

Discussion

This study suggests that 3% spirulina supplementation can improve rumen development and fermentation, and effectively relieve rumen microbe disorders in lambs caused by a high-fat diet. However, further research is needed to confirm the findings and to examine the long-term effects of spirulina supplementation in different types of livestock and under different dietary conditions.

Transcriptomics Based Network Analyses and Molecular Docking Highlighted Potentially Therapeutic Biomarkers for Colon Cancer

In this study, machine learning-based multiple bioinformatics analysis was carried out for the purpose of the deep and efficient mining of high-throughput transcriptomics data from the TCGA database. Compared with normal colon tissue, 2469 genes were significantly differentially expressed in colon cancer tissue. Gene functional annotation and pathway analysis suggested that most DEGs were functionally related to the cell cycle and metabolism. Weighted gene co-expression network analysis revealed a significant module and the enriched genes that were closely related to fatty acid degradation and metabolism. Based on colon cancer progression, the trend analysis highlighted that several gene sets were significantly correlated with disease development. At the same time, the most specific genes were functionally related to cancer cell features such as the high performance of DNA replication and cell division. Moreover, survival analysis and target drug prediction were performed to prioritize reliable biomarkers and potential drugs. In consideration of a combination of different evidence, four genes (ACOX1, CPT2, CDC25C and PKMYT1) were suggested as novel biomarkers in colon cancer. The potential biomarkers and target drugs identified in our study may provide new ideas for colonic-related prevention, diagnosis, and treatment; therefore, our results have high clinical value for colon cancer.

Integrated multi-omics of the gastrointestinal microbiome and ruminant host reveals metabolic adaptation underlying early life development

BACKGROUND

The gastrointestinal tract (GIT) microbiome of ruminants and its metabolic repercussions vastly influence host metabolism and growth. However, a complete understanding of the bidirectional interactions that occur across the host-microbiome axis remains elusive, particularly during the critical development stages at early life. Here, we present an integrative multi-omics approach that simultaneously resolved the taxonomic and functional attributes of microbiota from five GIT regions as well as the metabolic features of the liver, muscle, urine, and serum in sika deer (Cervus nippon) across three key early life stages.

RESULTS

Within the host, analysis of metabolites over time in serum, urine, and muscle (longissimus lumborum) showed that changes in the fatty acid profile were concurrent with gains in body weight. Additional host transcriptomic and metabolomic analysis revealed that fatty acid β-oxidation and metabolism of tryptophan and branched chain amino acids play important roles in regulating hepatic metabolism. Across the varying regions of the GIT, we demonstrated that a complex and variable community of bacteria, viruses, and archaea colonized the GIT soon after birth, whereas microbial succession was driven by the cooperative networks of hub populations. Furthermore, GIT volatile fatty acid concentrations were marked by increased microbial metabolic pathway abundances linked to mannose (rumen) and amino acids (colon) metabolism. Significant functional shifts were also revealed across varying GIT tissues, which were dominated by host fatty acid metabolism associated with reactive oxygen species in the rumen epithelium, and the intensive immune response in both small and large intestine. Finally, we reveal a possible contributing role of necroptosis and apoptosis in enhancing ileum and colon epithelium development, respectively.

CONCLUSIONS

Our findings provide a comprehensive view for the involved mechanisms in the context of GIT microbiome and ruminant metabolic growth at early life. Video Abstract.

Effects of Oil Supplements on Growth Performance, Eating Behavior, Ruminal Fermentation, and Ruminal Morphology in Lambs during Transition from a Low- to a High-Grain Diet

The objectives of this study were to investigate the effect of a maximum recommended oil supplementation on growth performance, eating behavior, ruminal fermentation, and ruminal morphological characteristics in growing lambs during transition from a low- to a high-grain diet. A total of 21 Afshari male lambs with an initial body weight (BW) of 41.4 ± 9.1 kg (mean ± SD) and at 5−6 months of age were randomly assigned to one of three dietary treatments (n = 7 per group), including (1) a grain-based diet with no fat supplement (CON), (2) CON plus 80 g/d of prilled palm oil (PALM), and (3) CON plus 80 g/d soybean oil (SOY); oils were equivalent to 50 g/kg of dry matter based on initial dry matter intake (DMI). All lambs were adapted to the high-grain diet for 21 d. In the adaptation period, lambs were gradually transferred to a dietary forage-to-concentrate ratio of 20:80 by replacing 100 g/kg of the preceding diet every 3 d. Thereafter, lambs were fed experimental diets for another 22 days. Fat-supplemented lambs had greater DMI, body weight (BW), and average daily gain (ADG), with a lower feed to gain ratio (p < 0.05), compared to CON lambs. The highest differences of DMI between fat-supplemented and CON-lambs were observed in week 3 of the adaptation period (p = 0.010). PALM- or SOY-supplementation lowered DM and NDF digestibility compared with CON (p < 0.05), and SOY caused the lowest organic matter (OM) digestibility compared with CON and PALM lambs (62.0 vs. 67.6 and 66.9; p < 0.05). Ruminal pH was higher for PALM and SOY compared with CON (p = 0.018). Lambs in SOY tended to have the highest ammonia-N concentrations (p = 0.075), together with a trend for higher concentrations of propionic acid, at the expense of acetic acid in ruminal fluid, on the last day of the adaptation period (diet × time, p = 0.079). Fat-supplemented lambs had lower isovaleric and valeric acid concentrations compared with CON on d 40 (diet × time, p < 0.05). PALM and SOY-fed lambs had a longer eating time (min/d and min/kg of DMI), chewing activity (min/d), meal frequency (n), and duration of eating the first and second meals after morning feeding (p < 0.05), and the largest meal size (p < 0.001). Fat supplemented lambs had greater ruminal papillary length (p < 0.05) and width (p < 0.01), and thicker submucosal, epithelial, and muscle layers, compared with the CON (p < 0.01). Blood metabolites were not influenced by dietary treatments (p > 0.05). The results from this study suggest that fat supplementation to high-grain diets may improve the development of ruminal epithelia and modify ruminal fermentation via optimized eating behavior or the direct effect of oils on the ruminal environment, resulting in better growth performance in growing lambs.

Early feeding strategies in lambs affect rumen development and growth performance, with advantages persisting for two weeks after the transition to fattening diets

This study aimed to explore the effects of early feeding strategies on the growth and rumen development of lambs from pre-weaning to the transition to fattening diets. Ninety-six newborn, male lambs with similar body weights were randomly assigned to three treatments: fed starter at 42 days old + weaned at 56 days old (Ctrl, n = 36), fed starter at 7 days old + weaned at 56 days old (ES, n = 36), and fed starter at 7 days old + weaned at 28 days old (ES + EW, n = 24). The fattening diets of all lambs were gradually replaced from 60 to 70 days of age. Six randomly selected lambs from each treatment were slaughtered at 14, 28, 42, 56, 70, and 84 days of age. The results showed that the richness and diversity of rumen microbiota of lambs in the Ctrl group were distinct from those of lambs in the other groups at 42 days of age. Moreover, transcriptome analysis revealed 407, 219, and 1,211 unique differentially expressed genes (DEGs) in the rumen tissue of ES vs. Ctrl, ES vs. ES + EW, and ES + EW vs. Ctrl groups, respectively, at 42 days of age. Different early feeding strategies resulted in differences in ruminal anatomy, morphology, and fermentation in lambs from 42 to 84 days of age (P < 0.05). Lambs in the ES + EW group had a higher average starter diet intake than those in the other groups (P < 0.05) from 28 to 56 days of age, which affected their growth performance. After 42 days of age, the body and carcass weights of lambs in the ES and ES + EW groups were higher than those in the Ctrl group (P < 0.05). These findings demonstrate that feeding lambs with a starter diet at 7 days of age and weaning them at 28 days of age can promote rumen development and improve growth performance, and this advantage persists for up to 2 weeks after transition to the fattening diet.

Fermented Wheat Bran Polysaccharides Intervention Alters Rumen Bacterial Community and Promotes Rumen Development and Growth Performance in Lambs

There is growing interest in the utilization of plant polysaccharides for the modulation of the rumen bacterial community and enhancement of growth performance in ruminants. Fermented wheat bran polysaccharides (FWBPs), plant polysaccharides, have been shown to improve the growth performance of lambs, but little is known about their effect on rumen bacteria. The aim of this study was to investigate the effects of FWBPs supplementation to milk replacer (MR) on the growth performance, blood metabolites, weight and morphology of rumen, rumen fermentation, and rumen bacterial community which were investigated in lambs. Twelve 1.5-month-old crossbred lambs (Dorper × Small-tailed Han Sheep) with an initial body weight (BW) of 11.38 ± 0.19 kg were randomly divided into two groups, namely, the control group and FWBPs group. Compared with the control group, the FWBPs group had a higher average daily weight gain and serum total protein concentrations, and a lower feed: gain ratio. A tendency of increase in final BW and carcass BW was also observed. Administration of FWBPs increased the ruminal papillae width and ruminal butyrate proportion and decreased the concentration of ammonia nitrogen and the proportion of isobutyrate and isovalerate. In addition, the epithelial cell thickness had an increased trend in the FWBPs group. High-throughput sequencing data showed that the relative abundance of Lachnospiraceae_NK3A20_group and Solobacterium was enhanced by FWBP treatment; meanwhile, the relative abundance of NK4A214_group, Megasphaera, and Treponema showed a tendency to be higher than that of the control group. Furthermore, Spearman's correlation analysis revealed that the relative abundances of NK4A214_group, Treponema, and Lachnospiraceae_NK3A20_group were positively correlated with butyrate proportion. Collectively, FWBPs supplementation to MR on lambs altered the rumen bacterial community, promoted rumen development, and improved growth performance.

Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages

Rumen development is a crucial physiological challenge for ruminants. However, the molecular mechanism regulating rumen development has not been clearly elucidated. In this study, we investigated genes involved in rumen development in 13 rumen tissues from three developmental stages (birth, youth, and adult) using RNA sequencing. We identified that 6,048 genes were differentially expressed among three developmental stages. Using weighted correlation network analysis, we found that 12 modules were significantly associated with developmental stages. Functional annotation and protein–protein interaction (PPI) network analysis revealed that CCNB1, CCNB2, IGF1, IGF2, HMGCL, BDH1, ACAT1, HMGCS2, and CREBBP involved in rumen development. Integrated transcriptome with GWAS information of carcass weight (CW), stomach weight (SW), marbling score (MS), backfat thickness (BFT), ribeye area (REA), and lean meat weight (LMW), we found that upregulated DEGs (fold change 0∼1) in birth–youth comparison were significantly enriched with GWAS signals of MS, downregulated DEGs (fold change >3) were significantly enriched with GWAS signals of SW, and fold change 0∼1 up/downregulated DEGs in birth–adult comparison were significantly enriched with GWAS signals of CW, LMW, REA, and BFT. Furthermore, we found that GWAS signals for CW, LMW, and REA were enriched in turquoise module, and GWAS signals for CW was enriched in lightgreen module. Our study provides novel insights into the molecular mechanism underlying rumen development in cattle and highlights an integrative analysis for illustrating the genetic architecture of beef complex traits.

Longitudinal investigations of anatomical and morphological development of the gastrointestinal tract in goats from colostrum to postweaning

The digestive tract development in goat kids around weaning is vital to the establishment of digestion and absorption function, growth, and health of adults. The objective was to explore the effects of age and solid feed on the anatomical and morphological development of the gastrointestinal tract of Laiwu Black goat kids. Forty-eight female Laiwu Black goats at 8 ages (1, 7, 14, 28, 42, 56, 70, and 84 d; 6 goats per group) were selected and killed for anatomical and morphological analysis. The goats experienced the following 4 diet phases: maternal colostrum (MC; d 1, d 7), maternal milk (MM; d 14, d 28), maternal milk plus solid diet (MMSD; d 42, d 56) and only solid diet (OSD; d 70, d 84). The body and carcass weights were not significantly changed during MC and MM phases but changed during the MMSD phase. The absolute growth of body and carcass weights were higher in the MMSD phase than in MM phase. In addition, the dressing percentage was the highest in the MMSD phase. The body size indices evolved progressively and increased over time. The percentage of internal and external organs to body weight decreased over time, whereas the percentage to complex stomach percentage increased. The rumen and omasum weight experienced synchronous absolute growth over time, especially in the OSD phase. In contrast, the absolute growth of the reticulum and abomasum was the highest in MMSD and MC phases, respectively. After weaning, the goats showed the highest papillae height, lamina propria, muscle layer thickness, and epithelial thickness. The OSD phase showed the highest colonic mucosa thickness, ileal villus height, and ileal muscle layer thickness. The crypt depth was higher in the MMSD phase than in the MM phase. Moreover, the crypt depth and muscle layer thickness of jejunum increased over time. Furthermore, duodenal crypt depth, muscle layer thickness, and epithelial thickness increased in the OSD phase compared with other stages. In conclusion, the histological investigation supports the improvement of the morphological development of the digestive tract and the growth performance in the solid feed phase. It is recommended to add solid food as early as 4 wk old.

Transcriptome profiling reveals differential gene expression in the rumen of Hu lambs at different developmental stages

The development of the rumen is a critical physiological challenge in newborn ruminants. However, the molecular mechanism underlying different stages of rumen development in sheep remains poorly understood. Here, RNA sequencing and bioinformatics analysis were performed to compare the transcription profiles of rumen development at 7, 28 and 56 days of birth (D7, D28 and D56). We identified 1246, 2257 and 627 differentially expressed genes (DEGs) between D7 and D28, between D7 and D56, between D28 and D56, respectively. Also, 70 DGEs were co-expressed at these three time points. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated most DEGs mainly related to transporter activity, channel activity and metabolism pathways. Noteworthy, the expression levels of most genes (CA4, CA9, CA12 and CA14) in nitrogen metabolic pathways were negatively correlated with the papilla length and width, but the papilla length and width were positively correlated with the expression of genes (PLA2G3, SLC26A9, SLC34A3) in ion transport pathway, suggesting that these genes may be involved in nitrogen metabolic and ion transport pathway and thus affect rumen development. These results provide new insight into the changes in RNA expression at different time points of rumen development in Hu sheep.