The ruminal microbiome associated with methane emissions from ruminant livestock

Solid-state fermentation through synthetic microbiome: An effective strategy for converting Chinese distillers' grains into functional protein feed

Chinese distillers' grains (CDGs), a byproduct of liquor production, have low protein, high fiber, and elevated alcohol/lactic acid levels, limiting their use as animal feed. This study utilised a synthetic microbiome composed of Candida utilis (protein enhancement), Trichoderma viride (fiber reduction), Bacillus subtilis (detoxification), and Lactobacillus casei (functional enhancement) for solid-state fermentation. The results showed that crude protein content increased to 23.61 %, and true protein content to 20.45 %. Crude fiber, ethanol, lactic acid, and acetic acid contents decreased by 22.31 %, 77.25 %, 85.08 %, and 73.89 %, respectively. Amino acid content increased by 23.80 %, and flavour compounds rose by 140.76 %. Mycotoxins like aflatoxin B1 (AFB1) and ochratoxin A (OTA) were undetectable, while vomitoxin (DON) remained below EU limits. In vitro digestibility of dry matter increased by 98.36 %. Pilot-scale trials showed a 1.42-fold increase in crude protein and a 1.34-fold increase in true protein, contributing to more efficient CDG utilisation and reduced agricultural costs.

Composition of the rumen archaeal community of growing camels fed different concentrate levels

Understanding the rumen fermentation and methanogenic community in camels fed intensively is critical for optimizing rumen fermentation, improving feed efficiency, and lowering methane emissions. Using Illumina MiSeq sequencing, quantitative real-time PCR, and high-performance liquid chromatography, this study evaluates the influence of different concentrate supplement levels in the diet on rumen fermentation as well as the diversity and structure of the rumen methanogenic community for growing dromedary camels. Twelve growing camels were divided into three groups and given three levels of concentrate supplement, 0.7% (C1), 1% (C2), and 1.3% (C3) based on their body weight. All animals were fed alfalfa hay ad libitum. The levels of total volatile fatty acid, rumen ammonia, and methanogen copy number were unaffected by the supplementation level. Increasing the concentrate supplement level increased the proportion of propionic acid while decreasing the proportion of acetic acid. Increasing the level of concentrate in the diet had no effect on alpha diversity metrics or beta diversity of rumen methanogens. Methanobrevibacter and Methanosphaera predominated the methanogenic community and were declined as concentrate supplement level increased. This study sheds new light on the effect of concentrate supplement level in growing camels' diet on rumen fermentation and methanogenic community, which could help in the development of a strategy that aimed to reduce methane emissions and enhance feed efficiency.

Effects of quercetin on in vitro rumen fermentation parameters, gas production and microflora of beef cattle

Methane is an important component of greenhouse gases, and ruminant production is a significant source of methane emissions. At present, flavonoid feed additives have certain applications in methane inhibition in ruminants. However, the effects of different doses of quercetin on rumen fermentation parameters, rumen bacteria and archaea are still unclear. Therefore, this study investigated the effects of quercetin on in vitro rumen fermentation parameters, methane production, and microflora in beef cattle. A completely randomized design was adopted. Quercetin was added to the fermentation substrates at 0% (group C), 0.5% (group Q1), 1% (group Q2) and 1.5% (group Q3). Anaerobic fermentation was carried out at 39°C for 48 h, gas production (GP) was recorded at different times, gas composition was determined, and methane (CH4) production was calculated. Fermentation parameters and dry matter digestibility (DMD) were determined after 48 h. Moreover, rumen fluid was collected for rumen bacterial and archaeal flora determination. The results were as follows: (1) After 32 h of fermentation, the GP decreased in response to the addition of quercetin. With increasing quercetin concentration, the theoretical maximum gas production decreased quadratically before 20 h (P quadratic = 0.032). There was a quadratic increase in gas production (P quadratic = 0.024). With increasing quercetin supplementation, the NH3-N content increased quadratically (P quadratic = 0.027). MCP increased linearly and quadratically with quercetin (P linear = 0.002, P quadratic = 0.005), whereas DMD decreased linearly and quadratically with quercetin (P linear = 0.013, P quadratic = 0.032). Both 0.5 and 1% quercetin significantly reduced the butyrate content (P quadratic = 0.002). With the addition of quercetin, the levels of butyrate, isobutyrate, isovalerate, and total volatile fatty acid (TVFA) first decreased but then increased (P quadratic < 0.05). (2) With increasing quercetin concentration, methane production (P quadratic = 0.009) and the methane proportion (P quadratic < 0.001) decreased quadratically. (3) The ACE index and Chao1 index increased quadratically with quercetin supplementation (P quadratic < 0.05). The relative abundance of Succiniclasticum in groups Q1 and Q3 increased, whereas the relative abundances of norank_f__norank_o__Rickettsiales and Curtobacterium decreased in all quercetin groups at the genus level (P < 0.05). (4) Quercetin supplementation did not affect the diversity of the archaeal community, but the relative abundance of Methanobrevibacter in group Q2 decreased. Overall, quercetin influenced in vitro rumen fermentation and the bacterial flora to decrease methane production and promote rumen nitrogen utilization and MCP synthesis.

Interplay of rumen microbiome and the cattle host in modulating feed efficiency and methane emissions

Given that the majority of energy and protein supplied to cattle arises as a result of ruminal fermentation, the rumen microbiome plays a key role in determining host feed efficiency and methane (CH4) emissions. Some reports suggests that a less diverse rumen microbiome is associated with improved feed efficiency, while other studies suggest that microbial diversity does not differ between low- and high-efficiency cattle of the same breed, fed identical diets. While reducing enteric CH4 emissions offers a dual benefit in terms of improved feed efficiency and a reduced environmental footprint; recent findings indicate that these outcomes are not always consistent in ruminants. The composition of the rumen microbiome is mainly determined by diet but is also influenced by host genetics and physiological parameters such as rumen volume, rate of passage and rumination. Reduced microbial diversity may impair the ability of cattle to adapt to frequent changes in diet and the environment. Hydrogen exchange and capture are the energetic foundation of the rumen microbiome, and considerable resources have been invested in developing additives that redirect hydrogen flow toward alternative sinks and away from the reduction of CO2 to CH4. These additives reduce enteric CH4 emissions by 30-80%, yet the anticipated gains in feed efficiency remain inconsistent. Strategies to improve the feed efficiency of cattle production must consider the multifaceted interactions among the host, rumen microbiome, and diet to ensure the sustainable intensification of cattle production while maintaining the social license for milk and meat production.

Network analyses unraveled the complex interactions in the rumen microbiota associated with methane emission in dairy cattle

BACKGROUND

Methane emissions from livestock, particularly from dairy cattle, represent a significant source of greenhouse gas, contributing to the global climate crisis. Understanding the complex interactions within the rumen microbiota that influence methane emissions is crucial for developing effective mitigation strategies.

RESULTS

This study employed Weighted Gene Co-expression Network Analysis to investigate the complex interactions within the rumen microbiota that influence methane emissions. By integrating extensive rumen microbiota sequencing data with precise methane emission measurements in 750 Holstein dairy cattle, our research identified distinct microbial communities and their associations with methane production. Key findings revealed that the blue module from network analysis was significantly correlated (0.45) with methane emissions. In this module, taxa included the genera Prevotella and Methanobrevibactor, along with species such as Prevotella brevis, Prevotella ruminicola, Prevotella baroniae, Prevotella bryantii, Lachnobacterium bovis, and Methanomassiliicoccus luminyensis are the key components to drive the complex networks. However, the absence of metagenomics sequencing is difficult to reveal the deeper taxa level and functional profiles.

CONCLUSIONS

The application of Weighted Gene Co-expression Network Analysis provided a comprehensive understanding of the microbiota-methane emission relationship, serving as an innovative approach for microbiota-phenotype association studies in cattle. Our findings underscore the importance of microbiota-trait and microbiota-microbiota associations related to methane emission in dairy cattle, contributing to a systematic understanding of methane production in cattle. This research offers key information on microbial management for mitigating environmental impact on the cattle population.

In vitro efficacy of cetyltrimethylammonium bromide (CETAB)-modified nano-montmorillonite against aflatoxin B1 associated toxicity and methanogenesis

BACKGROUND

Modified nano-montmorillonite is gaining attention as a feed additive for its benefits on ruminal fermentation. Chemical and mechanical methods were used to modify montmorillonite. Cetyltrimethylammonium bromide (CETAB) was utilized for chemical modification, while grounding was carried out to achieve the desired nanoscale particle size, resulting in the formation of the nanoscale powder known as MNMCETAB. Impacts of MNMCETAB supplementation on a basal diet, either contaminated with aflatoxin B1 (AFB1) or not at a level of 20 ppb were tested. Treatments included control (no supplements), a diet with 5 g per kilogram of dry matter (DM) of natural montmorillonite (NM), and diets with MNMCETAB at two doses, 0.5 (low) and 1 (high) grams per kilogram DM.

RESULTS

The MNMCETAB showed better physicochemical traits than NM clay, including narrower particle size range, higher cation exchange capacity (CEC), greater specific surface area (SSA), and more functional groups. A significant linear decreasing effect (P < 0.05) of MNMCETAB addition on methane (CH) production was observed by the increasing level of the MNMCETAB clay. The control diet contaminated with AFB1 resulted in lower fiber degradability than the other treatments (P < 0.05). No variations were observed in ruminal protozoal counts by both clay supplementations, although there was a noticeable trend (P = 0.08) towards reduced protozoal populations due to AFB1 contamination. AFB1-contaminated diets showed indications of reduced (P < 0.05) levels of total volatile fatty acids (VFA), and concentrations of butyrate and propionate (P < 0.05), alongside shifts towards elevated (P = 0.006) acetate levels, while the low dose of MNMCETAB exhibited higher (P < 0.01) propionate concentrations than the other treatments.

CONCLUSION

These findings underscored the anti-methanogenic properties and the favorable impacts of MNMCETAB in mitigating the adverse impacts of AFB1on ruminal fermentation and nutrient degradability.

Response of rumen methane production and microbial community to different abatement strategies in yaks

BACKGROUND

Developing region-specific dietary strategies is crucial for mitigating methane (CH4) emissions from yaks. However, there is a lack of tailored emission reduction strategies for yak production in the Qinghai-Tibet Plateau region. This study utilizes an in vitro rumen fermentation technique (Based on the ANKOMRF gas production measurement system) to investigate the effects of different dietary interventions on CH4 production from regional yaks. The selected strategies-Sodium Nitrate solution, regional Medicago sativa L., and regional Helianthus tuberosus L.-were chosen for their potential to reduce CH4 production through various mechanisms: Sodium Nitrate as a methanogenesis inhibitor, Medicago sativa L. for its high nutritional value and its ability to modulate microbial fermentation, and Helianthus tuberosus L. due to its inulin content, which promotes beneficial microbial activity. These dietary interventions aim not only to reduce CH4 production but also to support rumen health and productivity. In addition, gas chromatography and microbial sequencing techniques were employed to identify the optimal emission reduction strategy for regional yaks and to elucidate the key factors influencing the efficacy of these strategies.

RESULTS

The results indicate that supplementing the confined feeding ration (FR group) with Sodium Nitrate (12 mmol/L, FRN group), Medicago sativa L. (25%, FRM group), and Helianthus tuberosus L. (3%, FRH group) all have the effect of reducing CH4 production from yak rumen. Among these interventions, the FRM group exhibits the most significant reduction, with a decrease in rumen CH4 production by 42.76% compared to the FR group. The dry matter digestibility, total volatile fatty acids (TVFA), propionate, and butyrate levels in all groups were higher than those in the FR group. However, only the FRM group reached a significant level (P < 0.01). The pH values were significantly lower than those in the FR group (P < 0.01) across all groups. Each group exhibited distinct clustering patterns in bacterial and archaeal communities compared to the FR group (P < 0.05). The α diversity of bacterial communities was significantly lower than that of the FR group (P < 0.01), while the α diversity of archaeal communities was significantly higher than that of the FR group (P < 0.01). Taxa such as Lachnospiraceae, Clostridium, Treponema, Methanomicrobiaceae, Methanosphaera, and Methanoplanus were enriched in the FR group.

CONCLUSIONS

CH4 production from yak rumen were significantly negatively correlated with substrate crude protein (CP) levels, fermentation fluid TVFA levels, α diversity of archaeal communities, and the relative abundance of Selenomonas and Megasphaera in bacterial communities (P < 0.01). Conversely, CH4 production were significantly positively correlated with the relative abundance of Methanoplanus in archaeal communities (P < 0.01). From the perspective of CH4 gas production, the ranking of emission reduction effectiveness for different mitigation strategies is as follows: FRM group > FRH group > FRN group.

Hotspot Analysis of Rumen Microbiota and Methane Mitigation in Ruminants: A Bibliometric Analysis from 1998 to 2023

Methane (CH4) is the second-most abundant greenhouse gas, following carbon dioxide (CO2), and has a warming potential 28 times greater than CO2 [...].

Antiviral defense systems in the rumen microbiome

The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, the diversity and prevalence of antiviral defense systems in complex communities are still unknown. We therefore investigated the diversity and abundance of viral defense systems in 3,038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defense systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defense systems in the genomes. However, the number of defense systems, defense system families, and system density varied widely from genome to genome. Additionally, the number of defense system per genome correlated positively with the number of defense system families and the genome size. Restriction modification, Abi, and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defense systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage-host interaction.IMPORTANCEPhages may act antagonistically at the cell level but have a mutualistic interaction at the microbiome level. This interaction shapes the structure of microbial communities and is mainly driven by the defense mechanism. However, the diversity of such mechanism is larger than previously thought. Because of that, we described the abundance and diversity of the antiviral defense system of a collection of genomes, metagenome-assembled genomes (MAGs) and isolates, from the rumen. While defense mechanisms seem to be prevalent among bacteria and archaea, only a few were common. This suggests that most of these defense mechanisms are not present in many rumen microbes but could be shared among different members of the microbial community. This is consistent with the "pan-immune system" model, which appears to be common across different environments.

Designing host-associated microbiomes using the consumer/resource model

A key step toward rational microbiome engineering is in silico sampling of realistic microbial communities that correspond to desired host phenotypes, and vice versa. This remains challenging due to a lack of generative models that simultaneously capture compositions of host-associated microbiomes and host phenotypes. To that end, we present a generative model based on the mechanistic consumer/resource (C/R) framework. In the model, variation in microbial ecosystem composition arises due to differences in the availability of effective resources (inferred latent variables), while species' resource preferences remain conserved. Simultaneously, the latent variables are used to model phenotypic states of hosts. In silico microbiomes generated by our model accurately reproduce universal and dataset-specific statistics of bacterial communities. The model allows us to address three salient questions in host-associated microbial ecologies: (i) which host phenotypes maximally constrain the composition of the host-associated microbiomes? (ii) how context-specific are phenotype/microbiome associations, and (iii) what are plausible microbiome compositions that correspond to desired host phenotypes? Our approach aids the analysis and design of microbial communities associated with host phenotypes of interest.

IMPORTANCE

Generative models are extremely popular in modern biology. They have been used to model the variation of protein sequences, entire genomes, and RNA sequencing profiles. Importantly, generative models have been used to extrapolate and interpolate to unobserved regimes of data to design biological systems with desired properties. For example, there has been a boom in machine-learning models aiding in the design of proteins with user-specified structures or functions. Host-associated microbiomes play important roles in animal health and disease, as well as the productivity and environmental footprint of livestock species. However, there are no generative models of host-associated microbiomes. One chief reason is that off-the-shelf machine-learning models are data hungry, and microbiome studies usually deal with large variability and small sample sizes. Moreover, microbiome compositions are heavily context dependent, with characteristics of the host and the abiotic environment leading to distinct patterns in host-microbiome associations. Consequently, off-the-shelf generative modeling has not been successfully applied to microbiomes.To address these challenges, we develop a generative model for host-associated microbiomes derived from the consumer/resource (C/R) framework. This derivation allows us to fit the model to readily available cross-sectional microbiome profile data. Using data from three animal hosts, we show that this mechanistic generative model has several salient features: the model identifies a latent space that represents variables that determine the growth and, therefore, relative abundances of microbial species. Probabilistic modeling of variation in this latent space allows us to generate realistic in silico microbial communities. The model can assign probabilities to microbiomes, thereby allowing us to discriminate between dissimilar ecosystems. Importantly, the model predictively captures host-associated microbiomes and the corresponding hosts' phenotypes, enabling the design of microbial communities associated with user-specified host characteristics.

INTERNATIONAL SYMPOSIUM ON RUMINANT PHYSIOLOGY: Rumen fungi, archaea and their interactions

Anaerobic gut fungi (AGF) were the last phylum to be identified within the rumen microbiome and account for 7-9% of microbial biomass. They produce potent lignocellulases that degrade recalcitrant plant cell walls, and rhizoids that can penetrate the cuticle of plant cells, exposing internal components to other microbiota. Interspecies H2 transfer between AGF and rumen methanogenic archaea is an essential metabolic process in the rumen that occurs during the reduction of CO2 to CH4 by methanogens. This symbiotic relationship is bolstered by hydrogensomes, fungal organelles that generate H2 and formate. Interspecies H2 transfer prevents the accumulation of reducing equivalents that would otherwise impede fermentation. The extent to which hydrogenosomes serve as a conduit for H2 flow to methanogens is unknown, but it is likely greater with low quality forages. Strategies that alter the production of CH4 could also have implications for H2 transfer by anaerobic fungi. Understanding the factors that drive these interactions and H2 flow could provide insight into the effect of reducing CH4 production on the activity of ruminal fungi and the digestion of low-quality feeds.

The Holobiont concept in ruminant physiology - more of the same, or something new and meaningful to food quality, food security, and animal health?

The holobiont concept has emerged as an attempt to recognize and describe the myriad interactions and physiological signatures inherent to a host organism, as impacted by the microbial communities that colonize and/or co-inhabit the environment within which the host resides. The field acknowledges and draws upon principles from evolution, ecology, genetics, and biology, and in many respects has been "pushed" by the advent of high throughput DNA sequencing and, to a lesser extent, other "omics"-based technologies. Despite the explosion in data generation and analyses, much of our current understanding of the human and ruminant "holobiont" is based on compositional forms of data and thereby, restricted to describing host phenotypes via associative or correlative studies. So, where to from here? We will discuss some past findings arising from ruminant and human gut microbiota research and seek to evaluate the rationale, progress, and opportunities that might arise from the "holobiont" approach to the ruminant and human host. In particular, we will consider what is a "good" or "bad" host gastrointestinalmicrobiome in different scenarios, as well as potential avenues to sustain or alter the holobiont. While the holobiont approach might improve food quality, food security and animal health, these benefits will be most likely achieved via a judicious and pragmatic compromise in data generation, both in terms of its scale, as well as its generation in context with the "forgotten" knowledge of ruminant and human physiology.

Gallic and Ellagic Acids Differentially Affect Microbial Community Structures and Methane Emission When Using a Rumen Simulation Technique

Dietary tannins can affect rumen microbiota and enteric fermentation to mitigate methane emissions, although such effects have not yet been fully elucidated. We tested two subunits of hydrolyzable tannins named gallic acid (GA) and ellagic acid (EA), alone (75 mg/g DM each) or combined (150 mg/g DM in total), using the Rusitec system. EA and EA+GA treatments decreased methane production, volatile fatty acids, nutrient degradation, relative abundance of Butyrivibrio fibrisolvens, Fibrobacter succinogenes, Ruminococcus flavefaciens but increased Selenomonas ruminantium. EA and EA+GA increased urolithins A and B. Also, EA and EA+GA reduced bacterial richness, with limited effects on archaeal richness. For bacteria, Megasphaera elsdenii was more abundant after EA and EA+GA, while Methanomethylophilaceae dominated archaea in all treatments. EA was more effective than GA in altering rumen microbiota and fermentation but GA did not reduce VFA and nutrient degradation. Thus, dietary supplementation of EA-plant extracts for ruminants may be considered to mitigate enteric methane, although a suitable dosage must be ensured to minimize the negative effects on fermentation.

Connecting the ruminant microbiome to climate change: insights from current ecological and evolutionary concepts

Ruminant livestock provide meat, milk, wool, and other products required for human subsistence. Within the digestive tract of ruminant animals, the rumen houses a complex and diverse microbial ecosystem. These microbes generate many of the nutrients that are needed by the host animal for maintenance and production. However, enteric methane (CH4) is also produced during the final stage of anaerobic digestion. Growing public concern for global climate change has driven the agriculture sector to enhance its investigation into CH4 mitigation. Many CH4 mitigation methods have been explored, with varying outcomes. With the advent of new sequencing technologies, the host-microbe interactions that mediate fermentation processes have been examined to enhance ruminant enteric CH4 mitigation strategies. In this review, we describe current knowledge of the factors driving ruminant microbial assembly, how this relates to functionality, and how CH4 mitigation approaches influence ecological and evolutionary gradients. Through the current literature, we elucidated that many ecological and evolutionary properties are working in tandem in the assembly of ruminant microbes and in the functionality of these microbes in methanogenesis. Additionally, we provide a conceptual framework for future research wherein ecological and evolutionary dynamics account for CH4 mitigation in ruminant microbial composition. Thus, preparation of future research should incorporate this framework to address the roles ecology and evolution have in anthropogenic climate change.

The roles of phytogenic feed additives, trees, shrubs, and forages on mitigating ruminant methane emission

Ruminant animals naturally emit methane gas owing to anaerobic microbial fermentation in the rumen, and these gases are considered major contributors to global warming. Scientists worldwide are attempting to minimize methane emissions from ruminant animals. Some of these attempts include the manipulation of rumen microbes using antibiotics, synthetic chemicals, dietary interventions, probiotics, propionate enhancers, stimulation of acetogens, manipulation of rumination time, vaccination, and genetic selection of animals that produce low methane (CH4). The majority of synthetic additives are harmful to both beneficial rumen microbes and the host or only temporarily affect methanogenesis. Phytogenic feed additives (PFAs) have recently emerged as the best alternatives to antibiotics and synthetic chemicals because of growing public concerns regarding drug resistance and the negative impacts of antibiotics and synthetic chemicals on humans, livestock, and the environment. These additives reduce methane production and improve the volatile fatty acid profile. In this review, we provide an overview of PFA sources and how their bioactive components affect the rumen microbiome to reduce methane emissions. Additionally, we highlight the mechanisms of action of PFAs as a whole, as well as some of their bioactive components. We also review some selected trees, herbs, shrubs, and forages and their roles in reducing methane emissions.

Multiomics of yaks reveals significant contribution of microbiome into host metabolism

An intensive feeding system might improve the production cycle of yaks. However, how intensive feeding system contributes to yak growth is unclear. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the regulatory mechanisms of intensive feeding system on yaks. Increased growth performance were observed. Rumen metagenomics revealed that Clostridium, Methanobrevibacter, Piromyces and Anaeromyces increased in the intensively fed yaks, contributing to amino acid and carbohydrate metabolism. The grazing yaks had more cellulolytic microbes. These microbiomes were correlated with the pathways of "Alanine aspartate and glutamate metabolism" and "Pyruvate metabolism". Intensive feeding increased methane degradation functions, while grazing yaks had higher methyl metabolites associated with methane production. These rumen microbiomes and their metabolites resulted in changes in plasma metabolome, finally influencing yaks' growth. Thus, an intensive feeding system altered the rumen microbiome and metabolism as well as host metabolism, resulting in improvements of yak growth.

Harnessing meta-omics to unveil and mitigate methane emissions in ruminants: Integrative approaches and future directions

Methane emissions from enteric fermentation present a dual challenge globally: they not only contribute significantly to atmospheric greenhouse gases but also represent a considerable energy loss for ruminant animals. Utilizing high-throughput omics technologies to analyze rumen microbiome samples (meta-omics, i.e., metagenomics, metatranscriptomics, metaproteomics, metabolomics) holds vast potential for uncovering the intricate interplay between diet, microbiota, and methane emissions in these animals. The primary obstacle is the effective integration of diverse meta-omic approaches and their broader application across different ruminant species. Genetic variability significantly impacts methane production in ruminants, suggesting that genomic selection could be a viable strategy to reduce emissions. While substantial research has been conducted on the microbiological aspects of methane production, there remains a critical need to delineate the specific genetic interactions between the host and its microbiome. Advancements in meta-omics technologies are poised to shed light on these interactions, enhancing our understanding of the genetic factors that govern methane output. This review explores the potential of meta-omics to accelerate genetic advancements that could lead to reduced methane emissions in ruminants. By employing a systems biology approach, the integration of various omics technologies allows for the identification of key genomic regions and genetic markers linked to methane production. These markers can then be leveraged in selective breeding programs to cultivate traits associated with lower emissions. Moreover, the review addresses current challenges in applying genomic selection for this purpose and discusses how omics technologies can overcome these obstacles. The systematic integration and analysis of diverse biological data provide deeper insights into the genetic underpinnings and overall biology of methane production traits in ruminants. Ultimately, this comprehensive approach not only aids in reducing the environmental impact of agriculture but also contributes to the sustainability and efficiency of livestock management.

Screening and Functional Prediction of Rumen Microbiota Associated with Methane Emissions in Dairy Cows

Agricultural activities are a significant contributor to global greenhouse gas emissions, accounting for 14.5% of total anthropogenic emissions. Specifically, greenhouse gas emissions from beef cattle and dairy cattle constitute 35% and 30% of total global livestock emissions, respectively. This study focuses on dairy cattle, exploring the complex relationships between rumen microbiota and methane emission. The methane emissions of 968 lactating Holstein cows were measured using a laser methane detector (LMD, Shanghai Hesai Technology Co., Ltd., Shanghai, China). Among the measured cows, 107 individuals were further selected into high (HME) and low methane-emitting (LME) groups, including 50 cows in the HME group and 57 in the LME group. This study analyzed differences in rumen microbiota and microbial functions between cows with varying levels of methane emissions. The results showed significant differences in the Simpson and Pielou indices of rumen bacterial communities between the HME and LME groups. Beta diversity analysis revealed significant differences in microbial community structure between the two groups. It was found that the abundance of Bacteroidales and Prevotellaceae in the rumen of cows in the HME group cows was significantly higher than that of cows in the LME group (LDA > 3, p < 0.05). Additionally, bacterial functions related to biosynthesis and carbohydrate metabolism were more active in the HME group. This study revealed distinct differences in the rumen bacterial communities between HME and LME cow in Chinese Holstein cattle, and identified specific bacteria and their functional differences in the HME group. The microbial characteristics and metabolic pathways provide new insights for developing strategies to reduce methane emissions, supporting the sustainable development of the dairy industry.

The effect of Asparagopsis taxiformis, Ascophyllum nodosum, and Fucus vesiculosus on ruminal methanogenesis and metagenomic functional profiles in vitro

The ruminant-microorganism symbiosis is unique by providing high-quality food from fibrous materials but also contributes to the production of one of the most potent greenhouse gases-methane. Mitigating methanogenesis in ruminants has been a focus of interest in the past decades. One of the promising strategies to combat methane production is the use of feed supplements, such as seaweeds, that might mitigate methanogenesis via microbiome modulation and direct chemical inhibition. We conducted in vitro investigations of the effect of three seaweeds (Ascophyllum nodosum, Asparagopsis taxiformis, and Fucus vesiculosus) harvested at different locations (Iceland, Scotland, and Portugal) on methane production. We applied metataxonomics (16S rRNA gene amplicons) and metagenomics (shotgun) methods to uncover the interplay between the microbiome's taxonomical and functional states, methanogenesis rates, and seaweed supplementations. Methane concentration was reduced by A. nodosum and F. vesiculosus, both harvested in Scotland and A. taxiformis, with the greatest effect of the latter. A. taxiformis acted through the reduction of archaea-to-bacteria ratios but not eukaryotes-to-bacteria. Moreover, A. taxiformis application was accompanied by shifts in both taxonomic and functional profiles of the microbial communities, decreasing not only archaeal ratios but also abundances of methanogenesis-associated functions. Methanobrevibacter "SGMT" (M. smithii, M. gottschalkii, M. millerae or M. thaueri; high methane yield) to "RO" (M. ruminantium and M. olleyae; low methane yield) clades ratios were also decreased, indicating that A. taxiformis application favored Methanobrevibacter species that produce less methane. Most of the functions directly involved in methanogenesis were less abundant, while the abundances of the small subset of functions that participate in methane assimilation were increased.

IMPORTANCE

The application of A. taxiformis significantly reduced methane production in vitro. We showed that this reduction was linked to changes in microbial function profiles, the decline in the overall archaeal community counts, and shifts in ratios of Methanobrevibacter "SGMT" and "RO" clades. A. nodosum and F. vesiculosus, obtained from Scotland, also decreased methane concentration in the total gas, while the same seaweed species from Iceland did not.

Feed efficiency and enteric methane emissions indices are inconsistent with the outcomes of the rumen microbiome composition

The correlation between enteric methane emissions (eME) and feed efficiency (FE) in cattle is linked to the anaerobic fermentation of feedstuffs that occurs in the rumen. Several mathematical indices have been developed to predict feed efficiency and identify low methane emitters in herds. To investigate this, the current study aimed to evaluate the rumen microbial composition in the same group of animals ranked according to six different indices (three indices for FE and three for eME). Thirty-three heifers were ranked into three groups, each consisting of 11 animals, based on FE (feed conversion efficiency - FCE, residual weight gain - RG, and residual feed intake - RFI) and eME indices (production, yield, and intensity). Rumen fluids were collected using a stomach tube and analyzed using 16S rRNA and 18S rRNA, targeting rumen bacteria, archaea, and protozoa. The sequencing analysis revealed that the presence of unique microbial species in the rumen varies across animals ranked by the FE and eME indices. The High RG group harbored 17 unique prokaryotic taxa, while the High FCE group contained only seven. Significant differences existed in the microbial profiles of the animals based on the FE and eME indices. For instance, Raoultibacter was more abundant in the Intermediate RFI group but less so in the Intermediate RG and Intermediate FCE groups. The abundance of Entodinium was higher while Diplodinium was lower in the High FCE group, in contrast to the High RG and High RFI groups. Methanobrevibacter exhibited similar abundances across eME indices. However, the heifers did not demonstrate the same production, yield, and intensity of eME. The present findings underscore the importance of standardizing the FE and eME indices. This standardization is crucial for ensuring consistent and reliable assessments of the composition and function of the rumen microbiome across different herds.

Unraveling the genetic basis of methane emission in dairy cattle: a comprehensive exploration and breeding approach to lower methane emissions

Ruminant animals, such as dairy cattle, produce CH4, which contributes to global warming emissions and reduces dietary energy for the cows. While the carbon foot print of milk production varies based on production systems, milk yield and farm management practices, enteric fermentation, and manure management are major contributors togreenhouse gas emissions from dairy cattle. Recent emerging evidence has revealed the existence of genetic variation for CH4 emission traits among dairy cattle, suggests their potential inclusion in breeding goals and genetic selection programs. Advancements in high-throughput sequencing technologies and analytical techniques have enabled the identification of potential metabolic biomarkers, candidate genes, and SNPs linked to methane emissions. Indeed, this review critically examines our current understanding of carbon foot print in milk production, major emission sources, rumen microbial community and enteric fermentation, and the genetic architecture of methane emission traits in dairy cattle. It also emphasizes important implications for breeding strategies aimed at halting methane emissions through selective breeding, microbiome driven breeding, breeding for feed efficiency, and breeding by gene editing.

Integrating genome- and transcriptome-wide association studies to uncover the host-microbiome interactions in bovine rumen methanogenesis

The ruminal microbiota generates biogenic methane in ruminants. However, the role of host genetics in modifying ruminal microbiota-mediated methane emissions remains mysterious, which has severely hindered the emission control of this notorious greenhouse gas. Here, we uncover the host genetic basis of rumen microorganisms by genome- and transcriptome-wide association studies with matched genome, rumen transcriptome, and microbiome data from a cohort of 574 Holstein cattle. Heritability estimation revealed that approximately 70% of microbial taxa had significant heritability, but only 43 genetic variants with significant association with 22 microbial taxa were identified through a genome-wide association study (GWAS). In contrast, the transcriptome-wide association study (TWAS) of rumen microbiota detected 28,260 significant gene-microbe associations, involving 210 taxa and 4652 unique genes. On average, host genetic factors explained approximately 28% of the microbial abundance variance, while rumen gene expression explained 43%. In addition, we highlighted that TWAS exhibits a strong advantage in detecting gene expression and phenotypic trait associations in direct effector organs. For methanogenic archaea, only one significant signal was detected by GWAS, whereas the TWAS obtained 1703 significant associated host genes. By combining multiple correlation analyses based on these host TWAS genes, rumen microbiota, and volatile fatty acids, we observed that substrate hydrogen metabolism is an essential factor linking host-microbe interactions in methanogenesis. Overall, these findings provide valuable guidelines for mitigating methane emissions through genetic regulation and microbial management strategies in ruminants.

Designing host-associated microbiomes using the consumer/resource model

A key step towards rational microbiome engineering is in silico sampling of realistic microbial communities that correspond to desired host phenotypes, and vice versa. This remains challenging due to a lack of generative models that simultaneously capture compositions of host-associated microbiomes and host phenotypes. To that end, we present a generative model based on the mechanistic consumer/resource (C/R) framework. In the model, variation in microbial ecosystem composition arises due to differences in the availability of effective resources (inferred latent variables) while species' resource preferences remain conserved. The same latent variables are used to model phenotypic states of hosts. In silico microbiomes generated by our model accurately reproduce universal and dataset-specific statistics of bacterial communities. The model allows us to address three salient questions in host-associated microbial ecologies: (1) which host phenotypes maximally constrain the composition of the host-associated microbiomes? (2) how context-specific are phenotype/microbiome associations, and (3) what are plausible microbiome compositions that correspond to desired host phenotypes? Our approach aids the analysis and design of microbial communities associated with host phenotypes of interest.

Editing microbes to mitigate enteric methane emissions in livestock

Livestock production significantly contributes to greenhouse gas (GHG) emissions particularly methane (CH4) emissions thereby influencing climate change. To address this issue further, it is crucial to establish strategies that simultaneously increase ruminant productivity while minimizing GHG emissions, particularly from cattle, sheep, and goats. Recent advancements have revealed the potential for modulating the rumen microbial ecosystem through genetic selection to reduce methane (CH4) production, and by microbial genome editing including CRISPR/Cas9, TALENs (Transcription Activator-Like Effector Nucleases), ZFNs (Zinc Finger Nucleases), RNA interference (RNAi), Pime editing, Base editing and double-stranded break-free (DSB-free). These technologies enable precise genetic modifications, offering opportunities to enhance traits that reduce environmental impact and optimize metabolic pathways. Additionally, various nutrition-related measures have shown promise in mitigating methane emissions to varying extents. This review aims to present a future-oriented viewpoint on reducing methane emissions from ruminants by leveraging CRISPR/Cas9 technology to engineer the microbial consortia within the rumen. The ultimate objective is to develop sustainable livestock production methods that effectively decrease methane emissions, while maintaining animal health and productivity.

Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses

Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.

Effect of Padina gymnospora biowaste inclusion on in vitro methane production, feed fermentation, and microbial diversity

In vitro studies were undertaken aiming to study the methane (CH4) mitigation potential of biowaste (BW) of Padina gymnospora at the graded inclusion of 0% (C), 2% (A2), 5% (A5), and 10% (A10) of the diet composed of straw and concentrate in 40:60 ratio. The chemical composition analysis revealed that the BW contained higher crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), and ether extract (EE) than the PF (fresh seaweed, P. gymnospora). The concentration of cinnamic acid, sinapic acid, kaempferol, fisetin p-coumaric acid, ellagic acid, and luteolin in BW was 1.5-6-folds less than the PF. Inclusion of BW decreased (P < 0.0001) CH4 production by 34%, 38%, and 45% in A2, A5, and A10 treatments, respectively. A decrease (P < 0.0001) of 7.5%-8% in dry matter (DM) and organic matter (OM) digestibility was also recorded with the BW supplementation. The BW inclusion also decreased the numbers of total (P = 0.007), Entodinomorphs (P = 0.011), and Holotrichs (P = 0.004) protozoa. Metagenome data revealed the dominance of Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Fibrobacter microbial phyla. At the phylum level, Euryarchaeota dominated the archaeal community, whereas Methanobrevibacter was most abundant at the genus level. It can be concluded that the inclusion of BW in straw and concentrate based diet by affecting rumen fermentation, protozoal numbers, and compositional shift in the archaeal community significantly decreased CH4 production. Utilization of biowaste of P. gymnospora as a CH4 mitigating agent will ensure its efficient utilization rather than dumping, which shall cause environmental pollution and health hazards.

How much can performance measures explain of the between-cow variation in enteric methane?

Enteric CH4 produced from dairy cows contributes to the emission of greenhouse gases from anthropogenic sources. Recent studies have shown that the selection of lower CH4-emitting cows is possible, but doing so would be simpler if performance measures already recorded on farm could be used, instead of measuring gas emissions from individual cows. These performance measures could be used for selection of low emitting cows. The aim of this analysis was to quantify how much of the between-cow variation in CH4 production can be explained by variation in performance measures. A dataset with 3 experiments and a total of 149 lactating dairy cows with repeated measures was used to estimate the between-cow variation (the variation between cow estimates) for performance and gas measures from GreenFeed (C-Lock, Rapid City, SD). The cow estimates were obtained with a linear mixed model with the diet within period effect as a fixed effect and the cow within experiment as a random effect. The cow estimates for CH4 production were first regressed on the performance and gas measures individually, and then performance and CO2 production measures were grouped in 3 subsets for principal component analysis and principal component regression. The variables that explained most of the between-cow variation in CH4 production were DMI (R2 = 0.44), among the performance measures, and CO2 production (R2 = 0.61), among gas measures. Grouping the measures increased the R2 to 0.53 when only performance measures were used, and to 0.66 when CO2 production was added to the significant performance measures. We found the marginal improvement to be insufficient to justify the use of grouped measures rather than an individual measure because the latter simplifies the model and avoids over-fitting. Investigation of other measures that can be explored to increase explanatory power of between-cow variation in CH4 production is briefly discussed. Finally, the use of residual CH4 as a measure for CH4 efficiency could be considered by using either DMI or CO2 production as the sole predicting variables.

Interpretation of the effects of rumen acidosis on the gut microbiota and serum metabolites in calves based on 16S rDNA sequencing and non-target metabolomics

Introduction

Rumen acidosis is one of the most common diseases in beef cattle. It severely affects the normal development of calves and poses a significant threat to the farming industry. However, the influence of rumen acidosis on the gut microbiota and serum metabolites of calves is currently unclear.

Objective

The aim of this study is to investigate the changes in the gut microbiota and serum metabolites in calves after rumen acidosis and analyse the correlation.

Methods

Eight calves were selected as the rumen acidosis group, and eight health calves were selected as the healthy group. The faecal gut microbiota and serum metabolites of calves were detected respectively using 16S rDNA high-throughput sequencing and non-target metabolomics. The correlation between gut microbiota and serum metabolites was analyzed by Spearman correlation analysis.

Results

Differential analysis of the diversity and composition of gut microbiota between eight male healthy (Health) and eight male rumen acidosis (Disease) calves revealed that rumen acidosis increased the abundance of the gut microbiota in calves. At the phylum level, compared to the Healthy group, the relative abundance of Proteobacteria in the Disease group significantly decreased (P<0.05), while the relative abundance of Desulfobacterota significantly increased in the Disease group (P<0.05). At the genus level, compared to the Disease group, the relative abundance of Alloprevotella, Muribaculaceae, Succinivibrio, Prevotella, Agathobacter and Parabacteroides significantly increased in the Healthy group (P<0.05), while the relative abundance of Christensenellaceae_R-7 and Monoglobus significantly decreased in the Healthy group (P<0.05). Differential analysis results showed the Healthy group had 23 genera with higher abundance, while the Disease group had 47 genera with higher abundance. Serum metabolomics results revealed the differential metabolites associated with rumen acidosis, including nicotinamide, niacin, L-glutamic acid and carnosine, were mainly enriched in the nicotinate and nicotinamide pathway and the histidine pathway.

Conclusion

The occurrence of rumen acidosis can induce changes in the gut microbiota of calves, with a significant increase of the Christensenellaceae_R-7 genus and a significant decrease of Prevotella and Succinivibrio genera. In addition, the occurrence of rumen acidosis can also induce changes in serum metabolites including niacin, niacinamide, L-glutamine, and carnosine, which may serve as the diagnostic biomarkers of rumen acidosis of calves.

Characteristics of rumen microbiota and Prevotella isolates found in high propionate and low methane-producing dairy cows

Ruminal methane production is the main sink for metabolic hydrogen generated during rumen fermentation, and is a major contributor to greenhouse gas (GHG) emission. Individual ruminants exhibit varying methane production efficiency; therefore, understanding the microbial characteristics of low-methane-emitting animals could offer opportunities for mitigating enteric methane. Here, we investigated the association between rumen fermentation and rumen microbiota, focusing on methane production, and elucidated the physiological characteristics of bacteria found in low methane-producing cows. Thirteen Holstein cows in the late lactation stage were fed a corn silage-based total mixed ration (TMR), and feed digestion, milk production, rumen fermentation products, methane production, and rumen microbial composition were examined. Cows were classified into two ruminal fermentation groups using Principal component analysis: low and high methane-producing cows (36.9 vs. 43.2 L/DMI digested) with different ruminal short chain fatty acid ratio [(C2+C4)/C3] (3.54 vs. 5.03) and dry matter (DM) digestibility (67.7% vs. 65.3%). However, there were no significant differences in dry matter intake (DMI) and milk production between both groups. Additionally, there were differences in the abundance of OTUs assigned to uncultured Prevotella sp., Succinivibrio, and other 12 bacterial phylotypes between both groups. Specifically, a previously uncultured novel Prevotella sp. with lactate-producing phenotype was detected, with higher abundance in low methane-producing cows. These findings provide evidence that Prevotella may be associated with low methane and high propionate production. However, further research is required to improve the understanding of microbial relationships and metabolic processes involved in the mitigation of enteric methane.

Dietary fat and carbohydrate-balancing the lactation performance and methane emissions in the dairy cow industry: A meta-analysis

For the agroecosystems of the dairy cow industry, dietary carbohydrate (starch, neutral detergent fiber [NDF]) and fat could directly affect rumen methane emissions and host energy utilization. However, the relationships among diet, lactation performance, and methane emissions need to be further determined to assist dairy farms to adjust diet formulations and feeding strategies for environmental and production management. A meta-analysis was conducted in the current study to explore quantitative patterns of dietary fat and carbohydrate at different levels in balancing lactation performance and environment sustainability of dairy cows, and to establish a methane emission prediction model using the artificial neural network (ANN) model. The results showed that the regression relationship between dietary fat, carbohydrate and methane emissions could be shown by the following models: methane = 106.78 + (14.86 × DMI), R2 = 0.80; methane = 443.17 - (46.41 × starch/NDF), R2 = 0.76; and methane = 388.91 + (31.40 × fat) - (5.42 × fat2), R2 = 0.80. The regression relationships between dietary fat, carbohydrate and lactation performance could be shown by the following models: milk fat yield = 1.08 + (0.43 × starch/NDF) - [0.34 × (starch/NDF)2], R2 = 0.79; milk protein yield = 0.68 + (0.15 × fat) - (0.016 × fat2), R2 = 0.82. In the structural equation model, we found that when formulating dietary carbohydrates and fats, it was necessary to balance the relationship between methane emissions and lactation performance. Specifically, dietary starch/NDF was lower than 0.63 (extremum point) and dietary fat was between 2.89% and 4.69% (extremum point), it could ensure that the aim of methane emission reduction (methane emissions decrease with increasing dietary starch/NDF and fat) was achieved without losing lactation performance of dairy cows (lactation performance increase with increasing dietary starch/NDF and fat). Finally, we established the ANN model to predict methane emissions (training set: R2 = 0.62; validation set: R2 = 0.61).

A meta-analysis of probiotic interventions to mitigate ruminal methane emissions in cattle: implications for sustainable livestock farming

In recent years, the significant impact of ruminants on methane emissions has garnered international attention. While dietary strategies have been implemented to solve this issue, probiotics gained the attention of researchers due to their sustainability. However, it is challenging to ascertain their effectiveness as an extensive range of strains and doses have been reported in the literature. Hence, the objective of this experiment was to perform a meta-analysis of probiotic interventions aiming to reduce ruminal methane emissions from cattle. From 362 articles retrieved from scientific databases, 85 articles were assessed independently by two reviewers, and 20 articles representing 49 comparisons were found eligible for meta-analysis. In each study, data such as mean, SD, and sample sizes of both the control and probiotic intervention groups were extracted. The outcomes of interest were methane emission, methane yield, and methane intensity. For the meta-analysis, effect sizes were pooled using a fixed effect or a random effect model depending on the heterogeneity. Afterward, sensitivity analyses were conducted to confirm the robustness of the findings. Overall pooled standardized mean differences (SMDs) with their confidence intervals (CIs) did not detect significant differences in methane emission (SMD = -0.04; 95% CI = -0.18-0.11; P = 0.632), methane yield (SMD = -0.08; 95% CI = -0.24-0.07; P = 0.291), and methane intensity (SMD = -0.22; 95% CI = -0.50-0.07; P = 0.129) between cattle supplemented with probiotics and the control group. However, subgroup analyses revealed that multiple-strain bacterial probiotics (SMD = -0.36; 95% CI = -0.62 to -0.11; P = 0.005), specifically the combination of bacteria involved in reductive acetogenesis and propionate production (SMD = -0.71; 95% CI = -1.04 to -0.36; P = 0.001), emerged as better interventions. Likewise, crossbreeds (SMD = -0.48; 95% CI = -0.78 to -0.18; P = 0.001) exhibited a more favorable response to the treatments. Furthermore, meta-regression demonstrated that longer periods of supplementation led to significant reductions in methane emissions (P = 0.001), yield (P = 0.032), and intensity (P = 0.012) effect sizes. Overall, the results of the current study suggest that cattle responses to probiotic interventions are highly dependent on the probiotic category. Therefore, extended trials performed with probiotics containing multiple bacterial strains are showing the most promising results. Ideally, further trials focusing on the use of probiotics to reduce ruminal methane in cattle should be conducted to complete the available literature.

Insights into Effects of Combined Capric and Lauric Acid on Rumen Bacterial Composition

This study used next-generation sequencing to assess the impact of combined capric acid (C10) and lauric acid (C12) on the ruminal bacterial composition. Eight Holstein cows were randomly assigned to two groups using a cross-over design. The cows were fed two silage-based diets with the addition of either 100 g of stearic acid per cow per day (control), or 50 g of capric acid and 50 g of lauric acid per cow per day (C10 + C12). On day 18, 250 mL of rumen fluid was collected from each cow, and DNA was isolated, amplified, and sequenced. Treatment did not alter bacterial diversity indices, the relative abundance of archaea, nor the fiber-degrading microorganisms, except for a decrease in Fibrobacter (from 2.9% to 0.7%; p = 0.04). The relative abundance of Prevotellaceae decreased (from 39.9% to 29.6%; p = 0.009), which is notable because some members help to efficiently utilize ammonia by releasing it slowly into the rumen. Furthermore, the relative abundance of Clostridia increased (from 28.4% to 41.5%; p = 0.008), which may have aided the increased ammonia-nitrogen levels in the rumen, as this class contains hyperammonia-producing members. Our study reveals alterations in bacterial abundances with implications for rumen ammonia levels, offering insights into potential strategies for modulating rumen fermentation processes and methane production in ruminant livestock.

Alfalfa supplementation timing changes the rumen archaeal and fungal community composition and colonization in pre-weaning lambs

The establishment of the rumen microbiota plays an important role in the rumen development. However, little is known about the effects of alfalfa supplementation time on rumen microbiota establishment. Here, a total of 42 Hu lambs, seven-day-old, were chosen for the study. After a week of adjustment, six lambs were sacrificed to establish a baseline. The remaining 36 lambs were randomly split into two groups: one receiving alfalfa hay at 14 days (EAF), the other at 42 days (LAF), both groups received milk replacer and starter pellets. Introducing alfalfa at 14 days of age significantly improved total dry matter intake between 28 and 42 days (p = 0.04) and average daily gain from both 14 to 28 days (p = 0.04) and 28 to 42 days (p < 0.01), but this effect disappears from 56 to 70 days (p > 0.05). At 42 days, the abundances of Naganishia, Ascochyta, and Neosetophoma in the EAF group were significantly higher (p < 0.05) than those in the LAF group (17.8% vs. 3.97, 10.89% vs. 1.77, and 1.27% vs. 0.09%, respectively). At 56 days, the abundances of Ascochyta, Wallemia, and Aspergillus in the EAF group were significantly lower (p < 0.05) than in the LAF group (3.53% vs. 16.40, 8.78% vs. 18.89, and 2.14% vs. 4.69%). At 70 days, Aspergillus abundance in the EAF group was significantly higher (p < 0.05) than in the LAF group (2.69% vs. 0.85%). The LEfSe analysis showed that Methanobrevibacter_smithii was the archaeal biomarker at 14 days in both groups. Methanobrevibacter_sp_AbM4 was enriched at 56 days in the LAF group. Compared to the LAF group, the specific fungal biomarkers in the EAF group included Sporobolomyces and Bullera at 14 days, Naganishia, Didymella, Cleistothelebolus, and Alloleptosphaeria at 42 days, Ascochyta, Neoascochyta, and Alfaria at 70 days. Correlation analysis results showed strong patterns of association both within and between archaea and fungi, which were influenced by alfalfa supplementation time. In summary, alfalfa supplementation at 14 days of age promotes the growth performance of lambs before weaning, and alfalfa supplementation timing significantly affects rumen archaeal and fungal communities and dynamical changes.

Evanescent wave quartz-enhanced photoacoustic spectroscopy employing a side-polished fiber for methane sensing

We present an all-fiber-based laser gas analyzer (LGA) employing quartz-enhanced photoacoustic spectroscopy (QEPAS) and a side-polished fiber (SPF). The LGA comprises a custom quartz tuning fork (QTF) with 0.8 mm prong spacing, two acoustic micro-resonators (mR) located on either side of the prong spacing, and a single-mode fiber containing a 17 mm polished section passing through both mRs and QTF. The SPF polished face is positioned to enable the evanescent wave (EW) to create a photoacoustic wave and excite the fundamental flexural mode of the QTF. Sensor performance was demonstrated using methane in nitrogen gas mixtures, with CH4 mixing ratios ranging from 75 ppmv to 1% (by volume), measured with an accumulation time of 300 ms, and a minimum detection limit of 34 ppmv subsequently determined. The EW-QEPAS sensor is ideal for miniaturization, as it does not contain any free-space optics and is suitable for gas sensing in harsh environments and where mobility is required.

Exploiting Agri-Food Waste as Feed for Tenebrio molitor Larvae Rearing: A Review

The agri-food industry generates substantial amounts of waste, including by-products and residues. The increasing demand for sustainable and eco-friendly practices in the agri-food sector has sparked an interest in finding alternative uses for such waste materials. One promising approach is the utilization of waste from the agri-food industry as feed for the rearing of mealworms (Tenebrio molitor). Since agri-food waste is rich in proteins, carbohydrates, lipids, and vitamins, as well as other bioactive compounds, all of which are essential for insect growth and development, incorporating such waste into the diet of mealworms promotes sustainable insect production, reducing the economic and environmental problems associated with waste disposal. This practice can also be beneficial for the rearing of mealworms since their nutritional value can also be enhanced. To this end, various waste materials, such as fruit and vegetable peels, spent grains, and food processing residues, have been investigated as potential feed sources, leading to increased mass production, lower cost, and enhanced nutritional value. This review aims to highlight the potential of agri-food waste as a feed source for mealworms, as well as their potential to enhance their nutritional value. Furthermore, the potential applications of mealworms reared on agri-food waste are highlighted, including their potential as a sustainable protein source for human consumption and as feed ingredients in the livestock and aquaculture sectors.

Composition of the rumen microbiome and its association with methane yield in dairy cattle raised in tropical conditions

BACKGROUND

Methane (CH4) emissions from rumen fermentation are a significant contributor to global warming. Cattle with high CH4 emissions tend to exhibit lower efficiency in milk and meat production, as CH4 production represents a loss of the gross energy ingested by the animal. The objective of this study was to investigate the taxonomic and functional composition of the rumen microbiome associated with methane yield phenotype in dairy cattle raised in tropical areas.

METHODS AND RESULTS

Twenty-two Girolando (F1 Holstein x Gyr) heifers were classified based on their methane yield (g CH4 / kg dry matter intake (DMI)) as High CH4 yield and Low CH4 yield. Rumen contents were collected and analyzed using amplicon sequencing targeting the 16 and 18S rRNA genes. The diversity indexes showed no differences for the rumen microbiota associated with the high and low methane yield groups. However, the sparse partial least squares discriminant analysis (sPLS-DA) revealed different taxonomic profiles of prokaryotes related to High and Low CH4, but no difference was found for protozoa. The predicted functional profile of both prokaryotes and protozoa differed between High- and Low CH4 groups.

CONCLUSIONS

Our results suggest differences in rumen microbial composition between CH4 yield groups, with specific microorganisms being strongly associated with the Low (e.g. Veillonellaceae_UCG - 001) and High (e.g., Entodinium) CH4 groups. Additionally, specific microbial functions were found to be differentially more abundant in the Low CH4 group, such as K19341, as opposed to the High CH4 group, where K05352 was more prevalent. This study reinforces that identifying the key functional niches within the rumen is vital to understanding the ecological interplay that drives methane production.

Can freshwater plants and algae act as an effective feed supplement to reduce methane emissions from ruminant livestock?

Methane production by livestock is a substantial component of greenhouse gas emissions worldwide. The marine red algae, Asparagopsis taxiformis, has been identified as a possible supplement in livestock feeds due to its potent inhibition of methane production but currently is unable to be produced at scale. Finding additional taxa that inhibit methane production is therefore desirable. Here we provide foundational evidence of methanogenesis-inhibiting properties in Australian freshwater plants and algae, reviewing candidate species and testing species' chemical composition and efficacy in vitro. Candidate plant species and naturally-occurring algal mixes were collected and assessed for ability to reduce methane in batch testing and characterised for biochemical composition, lipids and fatty acids, minerals and DNA. We identified three algal mixes and one plant (Montia australasica) with potential to reduce methane yield in in vitro batch assay trials. All three algal mixes contained Spirogyra, although additional testing would be needed to confirm this alga was responsible for the observed activity. For the two samples that underwent multiple dose testing, Algal mix 1 (predominantly Spirogyra maxima) and M. australasica, there seems to be an optimum dose but sources, harvesting and storage conditions potentially determine their methanogenesis-inhibiting activity. Based on their compositions, fatty acids are likely to be acting to reduce methane in Algal mix 1 while M. australasica likely contains substantial amounts of the flavonoids apigenin and kaempferol, which are associated with methane reduction. Based on their mineral composition, the samples tested would be safe for livestock consumption at an inclusion rate of 20%. Thus, we identified multiple Australian species that have potential to be used as a feed supplement to reduce methane yield in livestock which may be suitable for individual farmers to grow and feed, reducing complexities of supply associated with marine alternatives and suggesting avenues for investigation for similar species elsewhere.

Understanding the Diversity and Roles of the Ruminal Microbiome

The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.

Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species

Ruminant livestock, including cattle, sheep, goats, and camels, possess a distinctive digestive system with complex microbiota communities critical for feed conversion and secondary metabolite production, including greenhouse gases. Yet, there is limited knowledge regarding the diversity of rumen microbes and metabolites benefiting livestock physiology, productivity, climate impact, and defense mechanisms across ruminant species. In this study, we utilized metataxonomics and metabolomics data from four evolutionarily distinct livestock species, which had fed on diverse plant materials like grass, shrubs, and acacia trees, to uncover the unique signature microbes and secondary metabolites. We established the presence of a distinctive anaerobic fungus called Oontomyces in camels, while cattle exhibited a higher prevalence of unique microbes like Psychrobacter, Anaeromyces, Cyllamyces, and Orpinomyces. Goats hosted Cleistothelebolus, and Liebetanzomyces was unique to sheep. Furthermore, we identified a set of conserved core microbes, including Prevotella, Rickenellaceae, Cladosporium, and Pecoramyces, present in all the ruminants, irrespective of host genetics and dietary composition. This underscores their indispensable role in maintaining crucial physiological functions. Regarding secondary metabolites, camel's rumen is rich in organic acids, goat's rumen is rich in alcohols and hydrocarbons, sheep's rumen is rich in indoles, and cattle's rumen is rich in sesquiterpenes. Additionally, linalool propionate and terpinolene were uniquely found in sheep rumen, while valencene was exclusive to cattle. This may suggest the existence of species-specific microbes and metabolites that require host rumen-microbes' environment balance. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry.IMPORTANCERumen fermentation, which depends on feed components and rumen microbes, plays a crucial role in feed conversion and the production of various metabolites important for the physiological functions, health, and environmental smartness of ruminant livestock, in addition to providing food for humans. However, given the complexity and variation of the rumen ecosystem and feed of these various livestock species, combined with inter-individual differences between gut microbial communities, how they influence the rumen secondary metabolites remains elusive. Using metagenomics and metabolomics approaches, we show that each livestock species has a signature microbe(s) and secondary metabolites. These findings may contribute toward understanding the rumen ecosystem, microbiome and metabolite networks, which may provide a gateway to manipulating rumen ecosystem pathways toward making livestock production efficient, sustainable, and environmentally friendly.

Recent Advances in Enteric Methane Mitigation and the Long Road to Sustainable Ruminant Production

Mitigation of methane emission, a potent greenhouse gas, is a worldwide priority to limit global warming. A substantial part of anthropogenic methane is emitted by the livestock sector, as methane is a normal product of ruminant digestion. We present the latest developments and challenges ahead of the main efficient mitigation strategies of enteric methane production in ruminants. Numerous mitigation strategies have been developed in the last decades, from dietary manipulation and breeding to targeting of methanogens, the microbes that produce methane. The most recent advances focus on specific inhibition of key enzymes involved in methanogenesis. But these inhibitors, although efficient, are not affordable and not adapted to the extensive farming systems prevalent in low- and middle-income countries. Effective global mitigation of methane emissions from livestock should be based not only on scientific progress but also on the feasibility and accessibility of mitigation strategies.

Effect of nutmeg essential oil (Myristica fragrans Houtt.) on methane production, rumen fermentation, and nutrient digestibility in vitro

The study evaluated the effect of adding of nutmeg (Myristica fragrans Houtt.) essential oil (NEO) as a feed additive on methane production, rumen fermentation parameters, rumen enzyme activity, and nutrient digestibility in vitro. This study was divided into three treatments based on the level of NEO addition, which included 0 µL/L (T0), 100 µL/L (T1), and 200 µL/L (T2). The feed substrate composition consisted of king grass as forage and concentrate in a 60:40 ratio. Feed fermentation was conducted using the Menke and Steingass gas production and two-step Tilley and Terry in-vitro digestibility technique. The data obtained from the study were analyzed using one-way ANOVA and if there were differences between means, they were further assessed using DMRT. The results showed that T2 treatment significantly decreased (P < 0.05) ammonia (NH3) levels, total VFA, acetate, propionate, butyrate, and microbial protein (P < 0.05). Methane production and the activity of rumen protease enzyme significantly decreased (P < 0.05) at T1 and T2 treatment. The T2 treatment significantly reduced (P < 0.05) protein digestibility (IVCPD) at 48 h, while IVCPD at 96 h significantly increased (P < 0.05). On the other hand, the addition of nutmeg essential oil did not effect the activity of the amylase, carboxymethyl cellulase, and β-glucosidase enzymes, as well as the in-vitro digestibility of dry matter (IVDMD), crude fiber (IVCFD), and organic matter (IVOMD). The conclusion drawn from this study is that the optimum level for NEO is 200 µL/L, which can reduce methane production and increase crude protein digestibility at 96 h without any negative effect on rumen fermentation and nutrient digestibility.

- Invited Review - The role of rumen microbiota in enteric methane mitigation for sustainable ruminant production

Ruminal methane production functions as the main sink for metabolic hydrogen generated through rumen fermentation and is recognized as a considerable source of greenhouse gas emissions. Methane production is a complex trait affected by dry matter intake, feed composition, rumen microbiota and their fermentation, lactation stage, host genetics, and environmental factors. Various mitigation approaches have been proposed. Because individual ruminants exhibit different methane conversion efficiencies, the microbial characteristics of low-methane-emitting animals can be essential for successful rumen manipulation and environment-friendly methane mitigation. Several bacterial species, including Sharpea, uncharacterized Succinivibrionaceae, and certain Prevotella phylotypes have been listed as key players in low-methane-emitting sheep and cows. The functional characteristics of the unclassified bacteria remain unclear, as they are yet to be cultured. Here, we review ruminal methane production and mitigation strategies, focusing on rumen fermentation and the functional role of rumen microbiota, and describe the phylogenetic and physiological characteristics of a novel Prevotella species recently isolated from low methane-emitting and high propionate-producing cows. This review may help to provide a better understanding of the ruminal digestion process and rumen function to identify holistic and environmentally friendly methane mitigation approaches for sustainable ruminant production.

Rumen fermentation and microbiota in Shami goats fed on condensed tannins or herbal mixture

BACKGROUND

Phytochemical compounds can modify the rumen microbiome and improve rumen fermentation. This study evaluated the impact of supplementation with tannin and an herbal mixture containing ginger (Zingiber officinale), garlic (Allium sativum), Artemisia (Artemisia vulgaris), and turmeric (Curcuma longa) on the rumen fermentation and microbiota, and histology of rumen tissue of goats. Eighteen Shami male goats were divided into three groups (n = 6): non-supplemented animals fed the basal diet (C, control); animals fed basal diet and supplemented with condensed tannin (T); and animals fed basal diet and supplemented with herbal mixture (HM). Each animal received a basal diet composed of Alfalfa hay and a concentrate feed mixture.

RESULTS

Group HM revealed higher (P < 0.05) rumen pH, total volatile fatty acids (VFA), acetic, propionic, isobutyric, butyric, isovaleric, and valeric. Principal Co-ordinate analysis (PCoA) showed that rumen microbial communities in the control group and supplemented groups were distinct. The supplementation increased (P < 0.05) the relative abundances of phylum Bacteroidota and Proteobacteria and declined (P < 0.05) Firmicutes and Fibrobacterota. Additionally, the dominant genus Prevotella and Rikenellaceae RC9 gut group were increased (P < 0.05) and the family Ruminococcaceae was declined (P < 0.05) due to the supplementation. The supplementation decreased (P < 0.05) the archaeal genus Methanobrevibacter and increased (P < 0.05) Candidatus Methanomethylophilus. Tannin supplementation in T group shortened the rumen papillae.

CONCLUSIONS

The results revealed that the herbal mixture might be used to alter the rumen microbiota to improve rumen fermentation.

Application of fenugreek in ruminant feed: implications for methane emissions and productivity

Background

Human demand for meat and dairy products will increase as a result of economic development and population growth, and the farming of ruminants, such as cattle and sheep, will also increase. Methane (CH4) emission from the enteric fermentation of ruminant livestock is a major source of greenhouse gas emissions and a significant contributor to global warming. Meanwhile, growth performance is often limited and animals are more vulnerable to diseases in high-density, intensive farming, greatly reducing livestock productivity, so developing ways to reduce CH4 emissions and improve ruminant productivity has become a research hotspot. Studies have reported that fenugreek (Trigonella foenum-graecum L.) as feed additives have the potential to reduce ruminant methane and improve the productivity. However, systematic reviews of such studies are lacking.

Methodology

In this review, databases of Google Scholar, Web of Science, PubMed, Scopus and Science Direct were used for the literature search. The initial keywords search was fenugreek or Trigonella foenum-graecum L. For more focused search, we added terms such as methane, rumen fermentation, growth, milk production and antioxidants. All were done for ruminants. The literature that conforms to the theme of this article is selected, summarized, and finally completed this article.

Results

By regulating the rumen microbiome (suppressing protozoans, methanogenic bacteria, and fungi), fenugreek can lower CH4 emissions according to many in vitro anaerobic fermentation experiments. Fenugreek secondary metabolites (saponins and tannins) are responsible for this impact, but it is still unclear exactly how they work. Therefore, more long-term in vivo experiments are needed to verify its efficacy. Fenugreek is also rich in alkaloids, amino acids, flavonoids, saponins and phenolic acids. These compounds have been shown to have beneficial effects on ruminant growth, lactation, and total antioxidant capacity. Therefore, fenugreek has a great opportunity to develop into a new green feed additive.

Conclusions

This review provides a summary of the effect of fenugreek and its bioactive compounds on rumen fermentation, CH4 emissions and production performance by ruminants. In addition, based on the available data, the possible biochemical pathway of fenugreek to reduce CH4 emissions in ruminants was described. Overall, the livestock feed industry has the opportunity to develop natural, environmentally-friendly feed additives based on fenugreek.

Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management

Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.

Characterization of the ruminal microbiota in sheep and goats fed different levels of tannin-rich Sericea lespedeza hay

Understanding ruminal microbiota and diet-host breed interactions under forage feeding conditions is essential for optimizing rumen fermentation and improving feed efficiency in small ruminants. This study aimed to investigate the effects of different ratios of condensed tannin-rich Sericea lespedeza (SL; Lespedeza cuneata) in the diets on changes and interactions of ruminal microbiota and host species (i.e., sheep and goats). Katahdin sheep (n = 12) and Alpine goats (n = 12) at approximately 10 to 12 mo of age were blocked by body weight (BW = 30.3 and 25.5 kg, respectively) and randomly assigned to one of the 3 treatments. Diets contained 75% coarsely ground forage and 25% concentrate. The forages were 1) 100% alfalfa hay (AL), 2) 100% SL, and 3) 50% AL + 50% SL (ASL). In the present study, the diversity and composition of ruminal microbiota differed between sheep and goats fed similar diets. Based on the taxonomic analysis, there was a distinct clustering pattern (P < 0.05) for sheep by diets, but such a pattern was not observed for goats (P > 0.1). The most predominant phyla were Firmicutes, Bacteroidetes, Ascomycota, and methanogen species of Methanobrevibactor sp. in the rumen of sheep and goats, regardless of diets. The Bacteroidetes and Ascomycota were enriched in sheep fed AL and ASL. In contrast, these microbial phyla were enhanced in goats fed tannin-rich SL diets, with the diet-by-host species interaction (P < 0.02) for the Bacteroidetes phylum. Sheep rumen fluid samples showed a higher degree of variability in microbial community composition compared to goat rumen fluid samples. The relative proportion of the Aspergillus fungi population was reduced to 90.7% in the SL group compared with the AL group, regardless of host species. The antimicrobial activity of tannins and greater sensitivities of selected microbiota species to these tannin compounds during SL feeding in sheep and goats perhaps caused this difference. The results from this study suggest that differences in the microbiota were associated with differences in diets and host species. Therefore, this study provides a better understanding of ruminal microbiota and diet-host species interactions under various tannin-rich diets, which could advance consolidative information on rumen microbiome community diversity changes and may improve sheep and goat production.

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 3 wk before the expected calving day until 10 wk 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 6 wk 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.

Sward type alters enteric methane emissions, nitrogen output and the relative abundance of the rumen microbial ecosystem in sheep

Observed improvements in animal and sward performance, coupled with a desire for more sustainable pasture-based feeding systems, has triggered a surge in the implementation of more botanically diverse pastures. However, thus far, there has been limited research investigating the effects of botanically diverse sward types on enteric methane (CH4) or nitrogen (N) excretion, alongside the ruminal microbiota and fermentation profile, in sheep. Hence, this study investigates the effect of sward type on CH4 production and N excretion, in addition to assessing the rumen microbiome, volatile fatty acid proportions, and ammonia nitrogen (NH3-N) concentration in sheep. A 5 × 5 Latin square design experiment was implemented to investigate 5 dietary treatments; perennial ryegrass (Lolium perenne L.; PRG) only or PRG plus white clover (Trifolium repens L.; PRG + WC), red clover (Trifolium pratense L.; PRG + RC), chicory (Chicorium intybus L.; PRG + Chic) or plantain (Plantago lanceolata L.; PRG + Plan). Diets were mixed at a ratio of 75% PRG and 25% of the respective companion forage and 100% PRG for the PRG treatment, on a dry matter basis. Twenty castrated male sheep were housed in metabolism crates across 5 feeding periods. Methane measurements were acquired utilizing portable accumulation chambers. Rumen fluid was harvested using a transoesophageal sampling device. Microbial rumen DNA was extracted and subjected to 16S rRNA amplicon sequencing and fermentation analysis. Data were analyzed using PROC MIXED in SAS. Results show that animals consuming PRG + WC ranked lower for CH4 production (g/d) than sheep offered PRG, PRG + Chic or PRG + Plan (P < 0.01) while the addition of any companion forage ranked CH4 yield (g/kg dry matter intake (DMI)) lower (P < 0.001) than PRG. There was a moderate positive correlation between DMI and CH4 (g/d; r = 0.51). Ruminal NH3-N was lowest in animals consuming the PRG diet (P < 0.01). There was a greater abundance of Methanobrevibacter and reduced abundance of Methanosphaera (P < 0.001) in sheep offered PRG, compared with any binary sward. On average, herb diets (PRG + Chic or PRG + Plan) reduced the urinary nitrogen concentration of sheep by 34% in comparison to legume diets (PRG + WC or PRG + RC) and 13% relative to the PRG diet (P < 0.001). Sheep offered PRG + Chic had a greater dietary nitrogen use efficiency than PRG + RC (P < 0.05). This study demonstrates the potential for sward type to influence rumen function and the microbial community, along with CH4 and N output from sheep.

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

Background

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.

Results

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.

Conclusion

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.