Solid diet manipulates rumen epithelial microbiota and its interactions with host transcriptomic in young ruminants

Dataset of the rumen microbiota and epithelial transcriptomics and proteomics in goat affected by solid diets

Although early solid diet supplementation is a common practice to improve the growth and development in goat kids, its biological mechanism how solid diet induces rumen microbiota and epithelial development is still unknow. In this study, rumen fermentation parameters, 16S rRNA sequencing for rumen content and epithelial microbiota, transcriptomics and proteomics of epithelium were determined to classify the effects of solid diet supplementation. Here, we classified the changes of goat phenotypes (i.e., growth performance, rumen fermentation and development) and linked them to the changes of rumen microbiota, transcriptome and expressed proteins. The mechanism of solid diet improving rumen development was elucidated preliminarily. Moreover, different roles between the rumen content and epithelial microbiota were identified. Thess datasets expands our understanding of the association between the early diet intervention and rumen development, providing the useful information how nutrient strategy affects rumen function and subsequently improves the host growth. The generated data provides insights in the importance of rumen niche microbiota and microbe-host interactions, which benefits future studies.

Prickly ash seeds can promote healthy production of sheep by regulating the rumen microbial community

This study aimed to investigate the effect of prickly ash seeds (PAS) on the microbial community found in rumen microbes of Hu sheep by adding different percentages of prickly ash seeds and to carry out research on the relation between rumen flora and production performance. Twenty-seven male lambs of Hu sheep were classified into three groups based on the content of prickly ash seeds (PAS) fed for 90 days, i.e., 0%, 3%, and 6%. At the end of the feeding trial, rumen fluid samples were collected from six sheep in each group for 16S amplicon sequencing. The results showed that the addition of prickly ash seeds significantly increased both Chao1 and ACE indices (P < 0.05), and the differences between groups were greater than those within groups. The relative content of Bacteriodota decreased, and the relative content of Fusobacteriota, Proteobacteria, Acidobacteriota, and Euryarchaeota increased. The relative content of Papillibacter and Saccharofermentans was increased at the genus level, and the relative content of Bacteroides and Ruminococcus was decreased. The test group given 3% of prickly ash seeds was superior to the test group given 6% of prickly ash seeds. In addition, the addition of 3% of prickly ash seeds improved the metabolism or immunity of sheep. Fusobacteriota and Acidobacteriota were positively correlated with total weight, dressing percentage, and average daily gain (ADG) and negatively correlated with average daily feed intake (ADFI), feed-to-gain ratio (F/G), and lightness (L*). Methanobrevibacter and Saccharofermentans were positively correlated with ADG and negatively correlated with ADFI and L*. In conclusion, under the present experimental conditions, the addition of prickly ash seeds increased the abundance and diversity of rumen microorganisms in Hu sheep and changed the relative abundance of some genera. However, the addition of 6% prickly ash seeds may negatively affect the digestive and immune functions in sheep rumen.

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. Sixty healthy 1-mo-old female Holstein calves were blocked by birth date and body weight and randomly assigned to one of 3 groups (n = 20): normal milk and pelleted starter feeding (CON), supplemented with chopped oat hay [75.0 g/d/calf (dry matter (DM) basis); OAH], or alfalfa hay [75.0 g/d/calf (DM basis); ALF]. The forage supplementation started when calves were 30 d old (D1 of the experimental period) and ended when they were 73 d old (D44 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 bi-weekly. 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 crude protein digestibility than the ALF group (P ≤ 0.04). The ALF group had higher rumen pH and blood β-hydroxybutyrate 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 volatile fatty acids (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 d in milk (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 in terms of rumen development, health status, and future milk production.

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.

Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids

BACKGROUND

The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early stage of life under a conventional feeding system.

RESULTS

In our results, the rumen resistome of goat kids contained ARGs to 41 classes, and the richness of ARGs decreased with age. Four antibiotic compound types of ARGs, including drugs, biocides, metals, and multi-compounds, were found during milk feeding, while only drug types of ARGs were observed after supplementation with starter feed. The specific ARGs for each age and their temporal dynamics were characterized, and the network inference model revealed that the interactions among ARGs were related to age. A strong correlation between the profiles of rumen resistome and microbiome was found using Procrustes analysis. Ruminal Escherichia coli within Proteobacteria phylum was the main carrier of ARGs in goats consuming colostrum, while Prevotella ruminicola and Fibrobacter succinogenes associated with cellulose degradation were the carriers of ARGs after starter supplementation. Milk consumption was likely a source of rumen ARGs, and the changes in the rumen resistome with age were correlated with the microbiome modulation by starter supplementation.

CONCLUSIONS

Our data revealed that the temporal dynamics of the rumen resistome are associated with the microbiome, and the reservoir of ARGs in the rumen during early life is likely related to age and diet. It may be a feasible strategy to reduce the rumen and its downstream dissemination of ARGs in ruminants through early-life dietary intervention. Video Abstract.

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.

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.

The Effect of Feeding a Total Mixed Ration with an ad libitum or Restricted Pelleted Starter on Growth Performance, Rumination Behavior, Blood Metabolites, and Rumen Fermentation in Weaning Holstein Dairy Calves

The aim of the current study was to evaluate the effect of the starter restriction and of the ad libitum TMR (total mixed ration) inclusion on intake, growth performance, rumination time (RT), and health condition of Holstein dairy calves during weaning. We randomly assigned thirty female Holstein calves (with an average weight of 38.5 ± 1.96 kg at birth) to one of three treatments. From 21 days of age, the calves were fed one of three treatments as follows: a control diet (CTR) with an ad libitum calf starter but without TMR; Treatment 1 diet (TRT1) with both an ad libitum calf starter and ad libitum TMR; Treatment 2 diet (TRT2) with ad libitum TMR and a restricted amount of a calf starter (50% of the intake recorder in the control group day by day). Calves in the TRT2 group, between 56 and 63 days of age, had a lower body weight (80.1; 79.5; 75.6 kg for the CTR, TRT1, and TRT2 groups, respectively) compared with CTR and TRT1 calves. This outcome is ascribed to the average daily gain (0.759; 0.913; 0.508 kg/day for the CTR, TRT1, and TRT2 groups, respectively), resulting also in TRT2 being lower than CTR or TRT1 calves. The inclusion of ad libitum TMR increased the rumination time, especially after weaning (15.28 min/h, 18.38 min/h, and 18.95 min/h for the CTR, TRT1, and TRT2 groups, respectively). Concerning the rumen metabolism and inflammometabolic response, overall, no differences were observed between the three dietary treatments. In conclusion, the results indicated that a TMR could partially replace a calf starter in weaning dairy calves, since neither growth performance nor health status were impaired. In addition, providing TMR (with or without concentrate restriction) led to a better rumen development and likely a better rumen fermentation efficiency in post-weaning.

Integrated rumen microbiome and serum metabolome analysis responses to feed type that contribution to meat quality in lambs

BACKGROUND

Lifestyle factors, such as diet, are known to be a driver on the meat quality, rumen microbiome and serum metabolites. Rumen microbiome metabolites may be important for host health, the correlation between rumen microbiome and production of rumen metabolites are reported, while the impact of rumen microbiome on the serum metabolome and fatty acid of meat are still unclear. This study was designed to explore the rumen microbiome, serum metabolome and fatty acid of meat in response to the grass diet and concentrate diet to lambs, and the relationship of which also investigated.

METHODS

In the present study, 12 lambs were randomly divided into two groups: a grass diet (G) and a concentrate diet (C). Here, multiple physicochemical analyses combined with 16S rRNA gene sequences and metabolome analysis was performed to reveal the changes that in response to feed types.

RESULTS

The concentrate diet could improve the growth performance of lambs compared to that fed with the grass diet. The microbiome composition was highly individual, compared to the concentrate group, the abundance of Rikenellaceae_RC9_gut_group, F082_unclassified, Muribaculaceae_unclassified, Ruminococcaceae_NK4A214_group, Bacteroidetes_unclassified, and Bacteroidales_UCG-001_unclassified were significantly (P < 0.05) lower in the grass group, while, the abundance of Succinivibrio, Succinivibrionaceae_UCG-002, Fibrobacter and Christensenellaceae_R-7_group were significantly (P < 0.05) higher in the grass group. Serum metabolomics analysis combined with enrichment analysis revealed that serum metabolites were influenced by feed type as well as the metabolic pathway, and significantly affected serum metabolites involved in amino acids, peptides, and analogues, bile acids, alcohols and derivatives, linoleic acids derivatives, fatty acids and conjugates. Most of the amino acids, peptides, and analogues metabolites were positively associated with the fatty acid contents. Among the bile acids, alcohols and derivatives metabolites, glycocholic was positively associated with all fatty acid contents, except C18:0, while 25-Hydroxycholesterol and lithocholic acid metabolites were negatively associated with most of the fatty acid contents.

CONCLUSION

Correlation analysis of the association of microbiome with metabolite features, metabolite features with fatty acid provides us with comprehensive understanding of the composition and function of microbial communities. Associations between utilization or production were widely identified among affected microbiome, metabolites and fatty acid, and these findings will contribute to the direction of future research in lamb.

Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants

The rumen undergoes developmental changes during maturation. To characterize this understudied dynamic process, we profiled single-cell transcriptomes of about 308,000 cells from the rumen tissues of sheep and goats at 17 time points. We built comprehensive transcriptome and metagenome atlases from early embryonic to rumination stages, and recapitulated histomorphometric and transcriptional features of the rumen, revealing key transitional signatures associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. In addition, we identified and validated potential cross-talk between host cells and microbiomes and revealed their roles in modulating the spatiotemporal expression of key genes in ruminal cells. Cross-species analyses revealed convergent developmental patterns of cellular heterogeneity, gene expression, and cell-cell and microbiome-cell interactions. Finally, we uncovered how the interactions can act upon the symbiotic rumen system to modify the processes of fermentation, fiber digestion, and immune defense. These results significantly enhance understanding of the genetic basis of the unique roles of rumen.

Sodium butyrate promotes gastrointestinal development of preweaning bull calves via inhibiting inflammation, balancing nutrient metabolism, and optimizing microbial community functions

Butyrate promotes the growth and gastrointestinal development of calves. But, the mechanisms behind its effects on signaling pathways of the gastrointestinal tract and rumen microbiome is unclear. This study aimed to reveal transcriptomic pathways of gastrointestinal epithelium and microbial community in response to butyrate supplementation in calves fed a high fiber starter. Fourteen Holstein bull calves (39.9 ± 3.7 kg, 14 d of age) were assigned to 2 groups (sodium butyrate group, SB; control group, Ctrl). The SB group received 0.5% SB supplementation. At d 51, the calves were slaughtered to obtain samples for analysis of the transcriptome of the rumen and jejunum epithelium as well as ruminal microbial metagenome. Sodium butyrate supplementation resulted in a higher performance in average daily gain and development of jejunum and rumen papillae. In both the rumen and jejunum epithelium, SB down-regulated pathways related to inflammation including NF-κB (PPKCB, CXCL8, CXCL12), interleukin-17 (IL17A, IL17B, MMP9), and chemokine (CXCL12, CCL4, CCL8) and up-regulated immune pathways including the intestinal immune network for immunoglobulin A (IgA) production (CD28). Meanwhile, in the jejunum epithelium, SB regulated pathways related to nutritional metabolism including nitrogen metabolism (CA1, CA2, CA3), synthesis and degradation of ketone bodies (HMGCS2, BDH1, LOC100295719), fat digestion and absorption (PLA2G2F, APOA1, APOA4), and the PPAR signaling pathway (FABP4, FABP6, CYP4A11). The metagenome showed that SB greatly increased the relative abundance of Bacillus subtilis and Eubacterium limosum, activated ruminal microbial carbohydrate metabolism pathways and increased the abundance of carbohydrate hydrolysis enzymes. In conclusion, butyrate exhibited promoting effects on growth and gastrointestinal development by inhibiting inflammation, enhancing immunity and energy harvesting, and activating microbial carbohydrate metabolism. These findings provide new insights into the potential mechanisms behind the beneficial effects of butyrate in calf nutrition.

Multi-Omics Reveals the Impact of Exogenous Short-Chain Fatty Acid Infusion on Rumen Homeostasis: Insights into Crosstalk between the Microbiome and the Epithelium in a Goat Model

Emerging data have underscored the significance of exogenous supplementation of butyrate in the regulation of rumen development and homeostasis. However, the effects of other short-chain fatty acids (SCFAs), such as acetate or propionate, has received comparatively less attention, and the consequences of extensive exogenous SCFA infusion remain largely unknown. In our study, we conducted a comprehensive investigation by infusion of three SCFAs to examine their respective roles in regulating the rumen microbiome, metabolism, and epithelium homeostasis. Data demonstrated that the infusion of sodium acetate (SA) increased rumen index while also promoting SCFA production and absorption through the upregulation of SCFA synthetic enzymes and the mRNA expression of SLC9A1 gene. Moreover, both SA and sodium propionate infusion resulted in an enhanced total antioxidant capacity, an increased concentration of occludin, and higher abundances of specific rumen bacteria, such as "Candidatus Saccharimonas," Christensenellaceae R-7, Butyrivibrio, Rikenellaceae RC9 gut, and Alloprevotella. In addition, sodium butyrate (SB) infusion exhibited positive effects by increasing the width of rumen papilla and the thickness of the stratum basale. SB infusion further enhanced antioxidant capacity and barrier function facilitated by cross talk with Monoglobus and Incertae Sedis. Furthermore, metabolome and transcriptome data revealed distinct metabolic patterns in rumen contents and epithelium, with a particular impact on amino acid and fatty acid metabolism processes. In conclusion, our data provided novel insights into the regulator effects of extensive infusion of the three major SCFAs on rumen fermentation patterns, antioxidant capacity, rumen barrier function, and rumen papilla development, all achieved without inducing rumen epithelial inflammation. IMPORTANCE The consequences of massive exogenous supplementation of SCFAs on rumen microbial fermentation and rumen epithelium health remain an area that requires further exploration. In our study, we sought to investigate the specific impact of administering high doses of exogenous acetate, propionate, and butyrate on rumen homeostasis, with a particular focus on understanding the interaction between the rumen microbiome and epithelium. Importantly, our findings indicated that the massive infusion of these SCFAs did not induce rumen inflammation. Instead, we observed enhancements in antioxidant capacity, strengthening of rumen barrier function, and promotion of rumen papilla development, which were facilitated through interactions with specific rumen bacteria. By addressing existing knowledge gaps and offering critical insights into the regulation of rumen health through SCFA supplementation, our study holds significant implications for enhancing the well-being and productivity of ruminant animals.

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.

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.

In Vitro Modulation of Rumen Fermentation by Microbiota from the Recombination of Rumen Fluid and Solid Phases

Rumen microbiota transplantation (RMT) can improve rumen fermentation and ruminant performance. However, due to the microbial distinction in the fluid and solid phases, the current understanding of their specific roles in RMT is insufficient. Thus, this study was conducted to determine the effects of the microbiota from the recombination of the rumen fluid and solid phases on in vitro fermentation. The rumen fresh fluid (FF) and fresh solid (FS) phases were collected, and FS was washed for the fresh solid washing solution (FW). The fractions of FF, FS, and FW were autoclaved to obtain autoclaved fluid (AF), solid (AS), and washing solution (AW). Then, these phases were recombined to form eight treatments: FFFS, FFAS, FFFW, FFAW, AFFS, AFAS, AFFW, and AFAW. After 24 h of fermentation, the gas production in AFFS, FFFS, and FFAS was significantly higher than that of other groups. AFAS and AFAW had significantly lower alpha diversity than did other groups. The solid phase was enriched with fiber-degrading bacteria, including Treponema, Succinivibrio, and Ruminococcus. The fluid phase was dominated by Prevotella, Christensenellaceae R-7 group, and Rikenellaceae RC9 gut group. The washing solution had more Ruminobacter, Lachnospiraceae, and Fibrobacter. Moreover, the double-autoclaved phases displayed increased abundances of harmful bacteria, as AFAS and AFAW had higher Streptococcus and Prevotellaceae YAB2003 group abundances. A network analysis showed that the signature microbiota in AFAS and AFAW were negatively associated with the keystone microbiota in the other groups. In summary, the recombination of the solid phase and the autoclaved fluid phase had the best in vitro fermentation result, which provided certain references for RMT. IMPORTANCE This is the first study to systematically evaluate the in vitro fermentation efficiency of diets by bacteria harvested and recombined from the fluid and solid phases of rumen contents, and it took into account the effect of washing the rumen solid phase. Using "reconstituted rumen content", this study confirmed that bacteria from different fractions of the rumen digesta resulted in different fermentation production of diets and found the characteristic bacteria in each phase of rumen contents. Our data reveal that the bacteria in the solid phase have more positive effects on the in vitro fermentation parameters, that the combination of the autoclaved fluid phase and the fresh solid phase have the most ideal fermentation effect, and that the autoclave process significantly influenced the microbial composition and increased the abundance of harmful bacteria. This study provides a landmark reference for the future use of rumen microbiota transplantation to improve animal feed utilization and growth performance.

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

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

Effects of Replacing Alfalfa Hay With Native Grass Hay in Pelleted Total Mixed Ration on Physicochemical Parameters, Fatty Acid Profile, and Rumen Microbiota in Lamb

This study aimed to investigate the effects of replacing alfalfa with native grass on growth performance, meat quality, and rumen microbiota of lambs. Forty-five 6-month-old Ujimqin lambs with live body weight (BW) of 29.50 ± 0.26 kg were used for the experiment, and the lambs were assigned to three diet treatments (three pens per treatment and five lambs per pen) with 30 square meters per pen in semi-open housing based on similar BW. The lambs have received 30% alfalfa (HA, high alfalfa percentage group), 20% alfalfa (MA, moderate alfalfa percentage group), and 10% alfalfa (LA, low alfalfa percentage group) diets, respectively (dry matter basis). The diet treatments had a significant (P < 0.05) influence on the dry matter intake of lambs and the dry matter intake increased with the increasing percentages of native grass hay, while the significantly (P < 0.05) lower final BW and average daily gain were observed in the MA and LA groups compared with that in the HA group. The diet had a significant (P < 0.05) difference in meat pH value, water loss rate, cooked meat rate, moisture, and intramuscular fat, while no significant (P > 0.05) difference was found in protein. As native grass hay percentages increased in the diet, the contents of palmitic (C16:0) and palmitoleic (C16:1 cis-9) in the HA and MA groups were significantly (P < 0.05) lower than that in the LA groups, and compared with the HA group, the contents of elaidic (C18:1 trans-9), oleic (C18:1 cis-9), and linoleic (C18:2 cis-9–cis-12) were significantly (P < 0.05) increased in the MA and LA groups. The content of α-linolenic (C18:3n3) was significantly (P < 0.05) higher in the LA group than that in the HA and MA groups. The principal coordinate analysis profile displayed that the composition of the bacterial community of these groups was distinctly separated from each other. No significant (P > 0.05) difference was observed in the dominant rumen bacteria at the phyla and genus levels. In conclusion, the meat quality and fatty acid profile analysis revealed that replacing alfalfa hay with native grass hay is more beneficial for Mongolian lambs, and the meat from LA diet treatment is better than the others. In addition, correlation analysis of the association of rumen microbiome with growth performance, meat quality, and fatty acid profile provides us with a comprehensive understanding of the composition and function of rumen microbiota. These findings could provide knowledge of how the diet affects the animal performance, meat quality of lambs, and microbiota of the rumen, laying a theoretical basis for replacing alfalfa with native grass.

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.

The Temporal Dynamics of Rumen Microbiota in Early Weaned Lambs

Weaning affects the development of ruminal bacteria in lambs during early life. However, the temporal dynamics of rumen microbiota in early weaned lambs is unknown compared to conventionally weaned lambs. In this study, one group was reared with their dams (control, CON) and conventionally weaned at 49 days (d), while the other lambs were weaned at 21 d (early weaning, EW) using starter. Rumen microbial samples collected at 26, 35, and 63 d were used for next-generation sequencing. Here, we found that the abundance and diversity of rumen microbiota in EW were significantly lower at 26 and 35 d than the CON. Linear discriminant analysis Effect Size (LEfSe) analysis was performed to identify the signature microbiota for EW at these three ages. At 26 d, Prevotella 7, Syntrophococcus, Sharpea, Dialister, Pseudoscardovia, and Megasphaera in the rumen of the EW group had greater relative abundances. At 35 d, the Lachnospiraceae_NK3A20_group was enriched in CON. On 63 d, Erysipelotrichaceae_UCG-002 was abundant in EW. Syntrophococcus and Megaspheaera in EW lambs were abundant at 26 and 35 d, but kept similar to CON at 63 d. The relative abundance of Erysipelotrichaceae_UCG-002 at all-time points was consistently higher in the EW group. In conclusion, early weaning led to a significant decrease in rumen microbiota richness and diversity in the short term. The changes in rumen microbiota are associated with the persistence of weaning stress. The temporal dynamics of relative abundances of Syntrophococcus, Megasphaera, and Ruminococcaceae_UCG-014 reflect the weaning stress over a short period and rumen recovery after early weaning.