Rumen Microbiome Research Articles

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

BackgroundThe 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.ResultsIn 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.ConclusionsOur 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.ALjrPAe7hUkeePWTGYd3KaVideo

Rumen microbiome-driven insight into bile acid metabolism and host metabolic regulation.

Gut microbes play a crucial role in transforming primary bile acids (BAs) into secondary forms, which influence systemic metabolic processes. The rumen, a distinctive and critical microbial habitat in ruminants, boasts a diverse array of microbial species with multifaceted metabolic capabilities. There remains a gap in our understanding of BA metabolism within this ecosystem. Herein, through the analysis of 9371 metagenome-assembled genomes and 329 cultured organisms from the rumen, we identified two enzymes integral to BA metabolism: 3-dehydro-bile acid delta4,6-reductase (baiN) and the bile acid:Na + symporter family (BASS). Both in vitro and in vivo experiments were employed by introducing exogenous BAs. We revealed a transformation of BAs in rumen and found an enzyme cluster, including L-ribulose-5-phosphate 3-epimerase and dihydroorotate dehydrogenase. This cluster, distinct from the previously known BA-inducible operon responsible for 7α-dehydroxylation, suggests a previously unrecognized pathway potentially converting primary BAs into secondary BAs. Moreover, our in vivo experiments indicated that microbial BA administration in the rumen can modulate amino acid and lipid metabolism, with systemic impacts underscored by core secondary BAs and their metabolites. Our study provides insights into the rumen microbiome's role in BA metabolism, revealing a complex microbial pathway for BA biotransformation and its subsequent effect on host metabolic pathways, including those for glucose, amino acids, and lipids. This research not only advances our understanding of microbial BA metabolism but also underscores its wider implications for metabolic regulation, offering opportunities for improving animal and potentially human health.

Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield.

Ruminants are essential for global food security, but these are major sources of the greenhouse gas methane. Methane yield is controlled by the cycling of molecular hydrogen (H2), which is produced during carbohydrate fermentation and is consumed by methanogenic, acetogenic, and respiratory microorganisms. However, we lack a holistic understanding of the mediators and pathways of H2 metabolism and how this varies between ruminants with different methane-emitting phenotypes. Here, we used metagenomic, metatranscriptomic, metabolomics, and biochemical approaches to compare H2 cycling and reductant disposal pathways between low-methane-emitting Holstein and high-methane-emitting Jersey dairy cattle. The Holstein rumen microbiota had a greater capacity for reductant disposal via electron transfer for amino acid synthesis and propionate production, catalyzed by enzymes such as glutamate synthase and lactate dehydrogenase, and expressed uptake [NiFe]-hydrogenases to use H2 to support sulfate and nitrate respiration, leading to enhanced coupling of H2 cycling with less expelled methane. The Jersey rumen microbiome had a greater proportion of reductant disposal via H2 production catalyzed by fermentative hydrogenases encoded by Clostridia, with H2 mainly taken up through methanogenesis via methanogenic [NiFe]-hydrogenases and acetogenesis via [FeFe]-hydrogenases, resulting in enhanced methane and acetate production. Such enhancement of electron incorporation for metabolite synthesis with reduced methanogenesis was further supported by two in vitro measurements of microbiome activities, metabolites, and public global microbiome data of low- and high-methane-emitting beef cattle and sheep. Overall, this study highlights the importance of promoting alternative H2 consumption and reductant disposal pathways for synthesizing host-beneficial metabolites and reducing methane production in ruminants.

Alterations of rumen and fecal microbiome in growing beef and dairy steers fed rumen-protected Capsicum oleoresin.

The microbiome has been linked to animal health and productivity, and thus, modulating animal microbiomes is becoming of increasing interest. Antimicrobial growth promoters (AGP) were once a common technology used to modulate the microbiome, but regulation and consumer pressure have decreased AGP use in food animals. One alternative to antimicrobial growth promoters are phytotherapeutics, compounds derived from plants. Capsaicin is a compound from the Capsicum genus, which includes chili peppers. Capsaicin has antimicrobial properties and could be used to manipulate the gastrointestinal microbiome of cattle. Both the rumen and fecal microbiomes are essential to cattle health and production, and modulation of either microbiome can affect both cattle health and productivity. We hypothesized that the addition of rumen-protected capsaicin to the diet of cattle would alter the composition of the fecal microbiome, but not the rumen microbiome. To determine the impact of rumen-protected capsaicin in cattle, four Holstein and four Angus steers were fed rumen-protected Capsicum oleoresin at 0 (Control), 5, 10, or 15mg kg-1 diet dry matter. Cattle were fed in treatment groups in a 4 × 4 Latin Square design with a 21-d adaptation phase and a 7-d sample collection phase. Rumen samples were collected on day 22 at 0-, 2-, 6-, 12-, and 18-h post-feeding, and fecal swabs were collected on the last day of sample collection, day 28, within 1h of feeding. Sequencing data of the 16s rRNA gene was analyzed using the dada2 pipeline and taxa were assigned using the SILVA database. No differences were observed in alpha diversity among fecal or rumen samples for either breed (P > 0.08) and no difference between groups was detected for either breed in rumen samples or for Angus steers in fecal samples (P > 0.42). There was a difference in beta diversity between treatments in fecal samples of Holstein steers (P < 0.01), however, a pairwise comparison of the treatment groups suggests no difference between treatments after adjusting for multiple comparisons. Therefore, we were unable to observe substantial overall variation in the rumen or fecal microbiomes of steers due to increasing concentrations of rumen-protected capsaicin. We do, however, see a trend toward increased concentrations of capsaicin influencing the fecal microbiome structure of Holstein steers despite this lack of significance.

Roughage quality determines the production performance of post-weaned Hu sheep via altering ruminal fermentation, morphology, microbiota, and the global methylome landscape of the rumen wall

Roughage quality is a crucial factor influencing the growth performance and feeding cost of ruminants; however, a systematic investigation of the mechanisms underlying this is still lacking. In this study, we examined the growth performance, meat quality, ruminal fermentation parameters, rumen microbiome, and tissue methylomes of post-weaned Hu sheep fed low- or high-quality forage-based diets. Our results showed that sheep in the alfalfa hay (AG) and peanut vine (PG) groups exhibited better growth performance, slaughter performance, and meat quality than sheep in the wheat straw group (WG). The sheep in the AG possessed relatively higher contents of serum immunoglobins (IgA, IgG, and IgM) and lower contents of serum inflammation factors (TNF-α, IL-1β, IL-6, and IL-8) than those in the WG and the PG did. In addition, the levels of blood T lymphocytes (CD4+ and CD8+) and the CD4-to-CD8 ratio were significantly higher in the AG sheep than in the WG sheep and PG sheep. The concentration of ruminal NH3-N was highest in WG sheep, whereas the concentrations of individual and total short-chain fatty acids (SCFAs) were highest in the PG sheep. The length, width, and surface area of ruminal papillae were markedly different among the three groups, with the sheep in the PG being the most morphologically developed. The main ruminal microbes at the genus level include Prevotella 1, Rikenellaceae RC9 gut group, norank f F082, Ruminococcus 1, and Ruminococcus 2. The relative abundances of certain species are positively or negatively associated with fermentation parameters and growth index. For example, the fibrolytic bacteria Ruminococcaceae UGG-001 showed positive relationships with the concentration of SCFAs, except propionate. In addition, the relative abundances of fibrolytic bacteria (e.g., Ruminoccus 1) showed a negative relationship with starch-degrading bacteria (e.g., Prevotellaceae). The genome-wide DNA methylation analysis revealed that rumen tissues in the PG sheep and WG sheep occupied different global DNA methylomes. The genes with differentially methylated promoters were involved in known pathways (e.g., the FoxO signaling pathway) and the Gene Ontology (GO) terms (e.g., anatomical structure morphogenesis) pertaining to rumen development. Two candidate genes (ACADL and ENSOARG00020014533) with hyper- and hypo-methylated promoters were screened as potential regulators of rumen development. In conclusion, roughage quality determines sheep growth performance via directly influencing rumen fermentation and microbiome composition, and indirectly affecting rumen development at the epigenetic level.

Elucidating the factors and consequences of the severity of rumen acidosis in first-lactation Holstein cows during transition and early lactation.

First-lactation cows are particularly prone to subacute ruminal acidosis (SARA) during transition. Besides common risk factors of SARA, such as feeding of starch-rich diets, an individual severity of SARA in cows has been recently evidenced. Yet, the factors that play a role in SARA severity have not been elucidated. The main goal of this research was to evaluate the factors of SARA severity in first-lactation cows during transition and early lactation, which go beyond high-grain feeding, and to explore their impact on behavior, health, and fermentation in the rumen and hindgut. Twenty-four first-lactation Holstein cows with the same feeding regime were used starting from 3wk before the expected calving day until 10wk postpartum. Cows received a close-up diet (32% concentrate) until calving and were then transitioned to a lactation diet (60% concentrate) within 1 week. The SARA severity was assessed by cluster analysis of several rumen pH metrics, which revealed exceptionally longer and more severe SARA in cows denominated as high (n = 9), as compared to moderate (n = 9) and low (n = 6) SARA severity cows (P < 0.01). The logistic analysis showed that the length of close-up feeding, age at parturition, and the level of dry matter intake (DMI) were the main factors that influenced the cows' odds for high SARA severity (each P ≤ 0.01). Moreover, the ANOVA hinted differences in the metabolic activity of the ruminal microbiome to promote SARA severity, as indicated by highest ruminal propionate proportions (P = 0.05) in high SARA severity cows, also with similar DMI. The distinct SARA severity was marginally reflected in behavior and there were no effects of SARA severity or high-grain feeding on blood inflammation markers, which peaked at parturition regardless of SARA severity (P < 0.01). Still, ongoing high-grain feeding increased liver enzyme concentrations from 6wk postpartum on, compared to weeks before (P < 0.01), yet irrespectively of SARA severity. In conclusion, first-lactation cows differed in SARA severity under the same feeding regime, which was ascribed to management factors and differences in ruminal fermentation. Further research is warranted to validate these findings and to understand the mechanisms behind differences in the metabolic function of rumen microbiome, in particular in terms of evaluating markers for various SARA severity, as well as to evaluate potential long-term effects on health, performance, fertility, and longevity of dairy cows.

Rumen microbiome nutriomics: Harnessing omics technologies for enhanced understanding of rumen microbiome functions and ruminant nutrition

Abstract The rumen microbiome has attracted tremendous interest among microbiologists and ruminant nutritionists because of its crucial role in mediating feed digestion and fermentation and supplying most of the energy, nutrients, and precursors for producing ruminant products. The application of various omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metabolomics, have enabled unprecedented investigations into this ecosystem, shedding new light on its interactions with diet and animals and its relationships with key production traits. Despite the valuable insights these omics technologies provide, each has its unique utility and inherent limitations. Achieving a holistic characterization of the rumen microbiome and deciphering its causal relationship with diet and key animal production traits remain an ongoing endeavor. In this perspective review paper, we highlight the limitations of individual technologies and advocate for an integrated multi-omics approach and data analyses in studying the intricate relationships between diet, rumen microbes, and ruminant nutrition. This approach, termed “rumen microbiome nutriomics,” aims to comprehensively understand the rumen microbiome in the context of diets and animal productivity. Our emphasis lies in recognizing the necessity of integrated analysis across multiple data layers, encompassing data of diet, rumen microbiome features, animal genotypes, and production traits and identifying the causal relationship among them. We also call for collaborative efforts to develop a comprehensive rumen microbiome genome database, including prokaryotes, protozoa, fungi, and viruses. Furthermore, standardization of processes and analyses is crucial to address the variability observed in the literature, facilitating comparison of results among future studies and enabling robust data reanalysis through advanced data analytics.

Using a multi-omics approach to explore potential associations with rumen content and serum of cows with different milk production levels based on genomic predicted transmitting ability for milk and phenotypic milk production.

This study aims to compare rumen microbiome and metabolites between second lactation dairy cows in the 75th percentile (n = 12; 57.2 ± 5.08 kg/d) of production according to genomic predicted transmitting ability for milk (GPTAM) and their counterparts in the 25th percentile (n = 12; 47.2 ± 8.61 kg/d). It was hypothesized that the metagenome and metabolome would differ between production levels. Cows were matched by days in milk (DIM), sire, occurrence of disease, and days open in previous lactation. For an additional comparison, the cows were also divided by phenotype into high (n = 6; 61.3 ± 2.8 kg/d), medium (n = 10; 55 ± 1.2 kg/d), and low (n = 8; 41.9 ± 5.6 kg/d) based on their milk production. Samples were collected 65 ± 14 DIM. Rumen content was collected using an oro-gastric tube and serum samples were collected from the coccygeal vessels. High-resolution liquid chromatography-mass spectrometry (LC-MS) was used for rumen and serum metabolite profiling. Shotgun metagenomics was used for rumen microbiome profiling. Microbiome sample richness and diversity were used to determine alpha and Bray-Curtis dissimilarity index was used to estimate beta diversity. Differences in metabolites were determined using t-tests or ANOVA. Pearson correlations were used to consider associations between serum metabolites and milk production. There was no evidence of a difference in rumen metabolites or microbial communities by GPTAM or phenotype. Cows in the phenotypic low group had greater serum acetate to propionate ratio and acetate proportion compared to the cows in the phenotypic medium group. Likewise, serum propionate proportion was greater in the medium compared to the low phenotypic group. Serum acetate, butyrate, and propionate concentrations had a weak positive correlation with milk production. When investigating associations between rumen environment and milk production, future studies must consider the impact of the ruminal epithelium absorption and post-absorption processes in relation to milk production.

Effects of two types of Coccomyxa sp. KJ on in vitro ruminal fermentation, methane production, and the rumen microbiota.

Coccomyxa sp. KJ is a unicellular green microalga that accumulates abundant lipids when cultured under nitrogen-deficient conditions (KJ1) and high nitrogen levels when cultured under nitrogen-sufficient conditions (KJ2). Considering the different characteristics between KJ1 and KJ2, they are expected to have different effects on rumen fermentation. This study aimed to determine the effects of KJ1 and KJ2 on in vitro ruminal fermentation, digestibility, CH4 production, and the ruminal microbiome as corn silage substrate condition. Five treatments were evaluated: substrate only (CON) and CON + 0.5% dry matter (DM) KJ1 (KJ1_L), 1.0% DM KJ1 (KJ1_H), 0.5% DM KJ2 (KJ2_L), and 1.0% DM KJ2 (KJ2_H). DM degradability-adjusted CH4 production was inhibited by 48.4 and 40.8% in KJ2_L and KJ2_H, respectively, compared with CON. The proportion of propionate was higher in the KJ1 treatments than the CON treatment and showed further increases in the KJ2 treatments. The abundances of Megasphaera, Succiniclasticum, Selenomonas, and Ruminobacter, which are related to propionate production, were higher in KJ2_H than in CON. The results suggested that the rumen microbiome was modified by the addition of 0.5-1.0% DM KJ1 and KJ2, resulting in increased propionate and reduced CH4 production. In particular, the KJ2 treatments inhibited ruminal CH4 production more than the KJ1 treatments. These findings provide important information for inhibiting ruminal CH4 emissions, which is essential for increasing animal productivity and sustaining livestock production under future population growth.

Dietary resveratrol improves immunity and antioxidant defense in ewes by regulating the rumen microbiome and metabolome across different reproductive stages.

Resveratrol (Res), a natural plant antitoxin polyphenol, is widely used in animal husbandry due to its antioxidant and anti-inflammatory properties, and current research has focused on humans, sows, and female mice. This study aimed to analyze the effects of dietary Res supplementation in ewes on antioxidant activity, immune responses, hormone levels, rumen microbiota and metabolites across various reproductive stages (estrus, pregnancy, and lactation). Twenty-four healthy ewe lambs (Hu sheep, 2 months old) with a similar body weight (BW) (mean: 21.79 ± 2.09 kg) were selected and randomly divided into two groups: the control group (Con) and the Res group (Res). The Res group received 10 mg/kg Res (based on BW) in addition to their basal diet. Res increased the levels of follicle-stimulating hormone (FSH), luteinizing hormone (LH), and estradiol (E2) in ewes at sexual maturity (p < 0.05). Additionally, Res supplementation induced significant increases in serum glutathione peroxidase (GSH-Px), IgG, FSH, and LH levels during estrus (p < 0.05); serum IgA, IgG and IgM during pregnancy and lactation (p < 0.05); and serum LH, glucose, GSH-Px, and catalase (CAT) levels during lactation (p < 0.05). Meanwhile, serum interleukin 1β (IL-1β) (p =0.005) and cholesterol levels (p = 0.041) during the lactation stage decreased following Res supplementation. Notably, colostrum IgA, IgG, and fat concentrations were significantly higher in the Res group than in the Con group (p < 0.05). Moreover, Res altered the rumen microbiota in ewes. Specifically, the relative abundance of Prevotella (p < 0.05) during pregnancy and Rikenellaceae_RC9_gut_group (p < 0.001) during lactation were significantly increased in ewes under Res treatment. The abundance of Rikenellaceae_RC9_gut_group was positively correlated with the levels of Ig A, Ig M, E2, FSH, LH, GSH-PX, and CAT. Additionally, Res altered the activity of metabolic pathways such as progesterone-mediated oocyte maturation, the estrogen signaling pathway, ovarian steroidogenesis, and the AMPK signaling pathway, and the levels of AICAR and 2-hydroxyestradiol metabolites, both during pregnancy and lactation. There findings show that Res can improve health, antioxidant status, and immune activity throughout the reproductive cycle in ewes by regulating rumen microorganisms and metabolites.

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

High-yielding dairy cows are commonly fed high-grain rations. However, this can cause subacute ruminal acidosis (SARA), a metabolic disorder in dairy cows that is usually accompanied by dysbiosis of the rumen microbiome. Postbiotics that contain functional metabolites provide a competitive niche for influential members of the rumen microbiome, may stabilize and promote their populations, and, therefore, may attenuate the adverse effects of SARA. This study used a total of 32 rumen-cannulated lactating dairy cows, which were randomly assigned into four treatments: no SCFP (control), 14 g/d Original XPC (SCFPa), 19 g/d NutriTek (SCFPb-1X), and 38 g/d NutriTek (SCFPb-2X) (Diamond V, Cedar Rapids, IA) from 4 weeks before until 12 weeks after parturition. Grain-based SARA challenges were conducted during week 5 (SARA1) and week 8 (SARA2) after parturition by replacing 20% dry matter of the base total mixed ration (TMR) with pellets containing 50% ground barley and 50% ground wheat. The DNA of rumen solids digesta was extracted and subjected to V3-V4 16S rRNA gene sequencing. The characteristics of rumen solids microbiota were compared between non-SARA (Pre-SARA1, week 4; Post-SARA1, week 7; and Post-SARA2, weeks 10 and 12) and SARA stages (SARA1/1, SARA1/2, SARA2/1, SARA2/2), as well as among treatments. Both SARA challenges reduced the richness and diversity of the microbiota and the relative abundances of the phylum Fibrobacteres. Supplementation with SCFP promoted the growth of several fibrolytic bacteria, including Lachnospiraceae UCG-009, Treponema, unclassified Lachnospiraceae, and unclassified Ruminococcaceae during the SARA challenges. These challenges also reduced the positive interactions and the numbers of hub taxa in the microbiota. The SCFPb treatment increased positive interactions among microbial members of the solids digesta and the number of hub taxa during the SARA and non-SARA stages. The SCFPb-2X treatment prevented changes in the network characteristics, including the number of components, clustering coefficient, modularity, positive edge percentage, and edge density of the microbiota during SARA challenges. These challenges reduced predicted carbohydrate and nitrogen metabolism in microbiota, whereas SCFP supplementation attenuated those reductions. Supplementation with SCFP, especially the SCFPb-2X attenuated the adverse effects of grain-based SARA on the diversity and predicted functionality of rumen solids microbiota.

Methane emissions and rumen microbiome response during compensatory growth on either a forage or grain-based finishing diet in beef cattle.

The aim of this experiment was to evaluate the effect of the level of prior nutritional restriction during backgrounding in Angus steers on methane (CH4) emissions, diet digestibility, rumen fermentation, and ruminal microbiome under either a forage or grain-based finishing diet. Eighty steers (body weight [BW]: 444 ± 39kg, age: 18 ± 1 mo) were blocked and randomly assigned within the block to either an optimal (0.6 to 0.7kg/d) or suboptimal (0.3 to 0.4kg/d) growth rate to exploit compensatory growth (CG), during 97 d of backgrounding. Following, for 84 d, half of the steers in each group were finished on a forage diet while the other half were finished on a grain-based diet. During the backgrounding period, CH4 emissions tended (P ≤ 0.07) to be higher; however, CH4 intensity expressed by BW gain was 50% lower (P < 0.01) for optimal compared to suboptimal growth steers. BW gain, dry matter intake, diet digestibility, and ammonia nitrogen in the rumen were greater (P < 0.01) for optimal compared to suboptimal steers. During the finishing period, CH4 emissions in either forage or grain finishing diets were similar (P > 0.05) for both backgrounding treatments. However, due to greater BW gain in suboptimal steers (1.20 vs. 0.97kg/d), their CH4 intensity-related coefficient decreased (P < 0.05) during the finishing period. Diet digestibility or any fermentation parameter was unaffected (P > 0.05) by previous backgrounding during the finishing period. In fact, rumen microbial abundance measured during finishing was not modified (P > 0.05) by previous backgrounding. Steers finished under grain conditions, had lower (P < 0.01) daily CH4 emissions and CH4 intensity. Additionally, grain-fed steers increased (P < 0.05) BW gain, diet digestibility, propionic, lactic, and valeric acids, Succinivibrionaceae family and Succiniclasticum, Erysipelotrichaceae UCG-002, Sharpea, and Megasphaera bacteria genera, compared to forage-fed steers. In conclusion, ruminal microbiome and fermentation, diet digestibility, and CH4 emissions were unaffected during finishing between prior levels of backgrounding growth. However, given the higher BW gain in suboptimal steers in both finishing diets, CH4 intensity was reduced in comparison to the optimal backgrounded steers. Nevertheless, lifetime emissions of the steers need to be assessed with the different dietary regimens, since suboptimal steers reduced CH4 emissions during the backgrounding period but, additional days of finishing were required to achieve the same BW as their contemporaries.

Age-related compositional and functional changes in the adult and breastfed buffalo rumen microbiome.

The buffalo is an important domestic animal globally, providing milk, meat, and labor to more than 2 billion people in 67 countries. The rumen microorganisms of buffaloes play an indispensable role in enabling the healthy functionality and digestive function of buffalo organisms. Currently, there is a lack of clarity regarding the differences in the composition and function of rumen microorganisms among buffaloes at different growth stages. In this study, metagenomics sequencing technology was applied to examine the compositional and functional differences of rumen microorganisms in adult and breastfed buffaloes. The results revealed that the rumen of adult buffaloes had significantly higher levels of the following dominant genera: Prevotella, UBA1711, RF16, Saccharofermentans, F23-D06, UBA1777, RUG472, and Methanobrevibacter_A. Interestingly, the dominant genera specific to the rumen of adult buffaloes showed a significant positive correlation (correlation>0.5, p-value<0.05) with both lignocellulose degradation-related carbohydrate-active enzymes (CAZymes) and immune signaling pathways activated by antigenic stimulation. The rumen of breastfed buffaloes had significantly higher levels of the following dominant genera: UBA629, CAG- 791, Selenomonas_C, Treponema_D, Succinivibrio, and RC9. Simultaneously, the rumen-dominant genera specific to breastfed buffaloes were significantly positively correlated (correlation>0.5, p-value<0.05) with CAZymes associated with lactose degradation, amino acid synthesis pathways, and antibiotic-producing pathways. This indicates that rumen microorganisms in adult buffaloes are more engaged in lignocellulose degradation, whereas rumen microorganisms in breastfed buffaloes are more involved in lactose and amino acid degradation, as well as antibiotic production. In conclusion, these findings suggest a close relationship between differences in rumen microbes and the survival needs of buffaloes at different growth stages.

- Invited Review - Ruminal ciliates as modulators of the rumen microbiome.

Ruminal ciliates are a fundamental constituent within the rumen microbiome of ruminant animals. The complex interactions between ruminal ciliates and other microbial guilds within the rumen ecosystems are of paramount importance for facilitating the digestion and fermentation processes of ingested feed components. This review underscores the significance of ruminal ciliates by exploring their impact on key factors, such as methane production, nitrogen utilization efficiency, feed efficiency, and other animal performance measurements. Various methods are employed in the study of ruminal ciliates including culture techniques and molecular approaches. This review highlights the pressing need for further investigations to discern the distinct roles of various ciliate species, particularly relating to methane mitigation and the enhancement of nitrogen utilization efficiency. The promotion of establishing robust reference databases tailored specifically to ruminal ciliates is encouraged, alongside the utilization of genomics and transcriptomics that can highlight their functional contributions to the rumen microbiome. Collectively, the progressive advancement in knowledge concerning ruminal ciliates and their inherent biological significance will be helpful in the pursuit of optimizing rumen functionality and refining animal production outcomes.

- Invited Review - Chemical signalling within the rumen microbiome.

Ruminants possess a specialized four-compartment forestomach, consisting of the reticulum, rumen, omasum, and abomasum. The rumen, the primary fermentative chamber, harbours a dynamic ecosystem comprising bacteria, protozoa, fungi, archaea, and bacteriophages. These microorganisms engage in diverse ecological interactions within the rumen microbiome, primarily benefiting the host animal by deriving energy from plant material breakdown. These interactions encompass symbiosis, such as mutualism and commensalism, as well as parasitism, predation, and competition. These ecological interactions are dependent on many factors, including the production of diverse molecules, such as those involved in quorum sensing (QS). QS is a density-dependent signalling mechanism involving the release of autoinducer (AIs) compounds, when cell density increases AIs bind to receptors causing the altered expression of certain genes. These AIs are classified as mainly being N-acyl-homoserine lactones (AHL; commonly used by Gram-negative bacteria) or autoinducer-2 based systems (AI-2; used by Gram-positive and Gram-negative bacteria); although other less common AI systems exist. Most of our understanding of QS at a gene-level comes from pure culture in vitro studies using bacterial pathogens, with much being unknown on a commensal bacterial and ecosystem level, especially in the context of the rumen microbiome. A small number of studies have explored QS in the rumen using 'omic' technologies, revealing a prevalence of AI-2 QS systems among rumen bacteria. Nevertheless, the implications of these signalling systems on gene regulation, rumen ecology, and ruminant characteristics are largely uncharted territory. Metatranscriptome data tracking the colonization of perennial ryegrass by rumen microbes suggest that these chemicals may influence transitions in bacterial diversity during colonization. The likelihood of undiscovered chemicals within the rumen microbial arsenal is high, with the identified chemicals representing only the tip of the iceberg. A comprehensive grasp of rumen microbial chemical signalling is crucial for addressing the challenges of food security and climate targets.

Host and rumen microbiome contributions to feed efficiency traits in Holstein cows

It is now widely accepted that dairy cow performance is influenced by both the host genome and rumen microbiome composition. The contributions of the genome and the microbiome to the phenotypes of interest are quantified by heritability (h2) and microbiability (m2), respectively. However, if the genome and microbiome are included in the model, then the h2 reflects only the contribution of the direct genetic effects quantified as direct heritability (hd2), and the holobiont effect reflects the joint action of the genome and the microbiome, quantified as the holobiability (ho2). The objectives of this study were to estimate h2, hd2,m2, and ho2 for dry matter intake, milk energy, and residual feed intake; and to evaluate the predictive ability of different models, including genome, microbiome, and their interaction. Data consisted of feed efficiency records, SNP genotype data, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows from 2 research farms. Three kernel models were fit to each trait: one with only the genomic effect (model G), one with the genomic and microbiome effects (model GM), and one with the genomic, microbiome, and interaction effects (model GMO). The model GMO, or holobiont model, showed the best goodness-of-fit. The hd2 estimates were always 10% to 15% lower than h2 estimates for all traits, suggesting a mediated genetic effect through the rumen microbiome, and m2 estimates were moderate for all traits, and up to 26% for milk energy. The ho2 was greater than the sum of hd2 and m2, suggesting that the genome-by-microbiome interaction had a sizable effect on feed efficiency. Kernel models fitting the rumen microbiome (i.e., models GM and GMO) showed larger predictive correlations and smaller prediction bias than the model G. These findings reveal a moderate contribution of the rumen microbiome to feed efficiency traits in lactating Holstein cows and strongly suggest that the rumen microbiome mediates part of the host genetic effect.

Comparative analysis of functional diversity of rumen microbiome in bison and beef heifers.

Ruminants play a key role in the conversion of cellulolytic plant material into high-quality meat and milk protein for humans. The rumen microbiome is the driver of this conversion, yet there is little information on how gene expression within the microbiome impacts the efficiency of this conversion process. The current study investigates gene expression in the rumen microbiome of beef heifers and bison and how transplantation of ruminal contents from bison to heifers alters gene expression. Understanding interactions between the host and the rumen microbiome is the key to developing informed approaches to rumen programming that will enhance production efficiency in ruminants.

Effects of dietary supplementation of a blend of Saccharomyces cerevisiae, multiple live probiotic bacteria, and their fermentation products on performance, health, and rumen bacterial community of newly weaned beef steers during a 56-d receiving period.

We examined the effects of a blend of Saccharomyces cerevisiae, multiple live probiotic bacteria, and their fermentation products on performance, health, and the ruminal bacterial community of newly weaned beef steers during a 56-d receiving period. Forty newly weaned Angus crossbred steers (221 ± 25.6kg BW; 180 ± 17 d of age) were stratified by body weight (BW) into four pens (10 steers per pen) such that each pen had a similar average BW at the beginning of the experiment. The pens were randomly assigned to receive a corn silage basal diet (CON; n = 20) or the basal diet supplemented with 9g/steer/d of PRO feed additive (PRO; n = 20). The PRO additive is a blend of S. cerevisiae and the fermentation products of Enterococcus faecium, Bacillus licheniformis, B. subtilis, Lactobacillus animalis, and Propionibacterium freudenreichii. The DMI and water consumed were monitored using the GrowSafe intake nodes and custom flow meters, respectively. BWs were recorded weekly to calculate average daily gain (ADG). Before morning feeding, 10mL of blood was taken from each steer on days 0-7, and thereafter weekly for analyses of immune cells, plasma glucose, and NEFAs. On day 56, rumen fluid samples (200mL each) were collected from all the steers for microbiome analysis. Over the 56-d receiving period, the supplemental PRO had no effects on DMI, water intake, or ADG. However, compared to CON, beef steers fed supplemental PRO tended to have greater ADG (P = 0.08) and BW (P = 0.07) during the first 14 d of the study. There was a treatment × day interaction (P ≤ 0.05) for WBC, neutrophils and monocytes over the 56 d such that beef steers fed supplemental PRO had lower blood concentrations on certain days during the first 7 d after weaning, indicating reduced inflammation or stress response. The results of the rumen microbiome analysis revealed that the relative abundance of complex fiber degrading or obligate proton-reducing bacterial genera such as Bacteroides, Ruminococcus gauvreauii group, Desulfovibrio, Syntrophococcus, and Acetitomaculum were greater (P ≤ 0.05) in beef steers fed supplemental PRO compared to CON. This study demonstrated that dietary supplementation of PRO improved the growth performance, reduced stress or inflammatory response during the initial days after weaning, and altered the ruminal bacterial community toward increased relative abundance of bacterial genera associated with improved rumen function.

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

BackgroundLifestyle 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.MethodsIn 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.ResultsThe 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.ConclusionCorrelation 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.

Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle.

Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission. The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate. Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.