Gut microbiota and meat quality in ruminants: a review of mechanisms and microbiota-targeted interventions

Abstract

The quality of ruminant meat (e.g., beef and lamb) is a vital source of high-quality protein and essential nutrients for humans, and is gaining global consumer attention. As a crucial nexus in ruminant physiology, the complex gut microbiota plays a pivotal role in determining meat quality by driving nutrient conversion, controlling systemic signaling cascades, and acting as a key regulator of immune balance. Research shows a close association between gut microbiota and meat quality indicators, such as color, flavor, tenderness, pH value, and water-holding capacity (WHC). The underlying mechanisms involve modulating energy metabolism and fat deposition, regulating fatty acid synthesis, supporting protein turnover, and reducing oxidative stress. Moreover, multi-omics technologies are gradually revealing how gut microbes influence meat quality. These insights also help develop targeted intervention strategies, including feed formulation optimization (e.g., supplementation with prebiotics or functional additives), probiotic and enzyme inhibitor application, and targeted regulation of microbial metabolic pathways. This paper systematically reviews the compositional characteristics of the ruminant gut microbiota, evaluates key indicators of meat quality, and explores the mechanisms regulating meat quality alongside microbiota-targeting intervention strategies, providing theoretical references and practical approaches for the green, efficient production of high-quality ruminant meat.

Introduction

As a critical source of high-quality dietary animal protein, the meat quality of ruminants (e.g., cattle, sheep, goats) exerts a direct and profound influence on both consumer health and the economic sustainability of the global livestock industry (FAO 2022, Ding et al. 2024). Meat quality, a complex trait encompassing sensory attributes (e.g., tenderness, juiciness, flavor), nutritional composition (e.g., fatty acid profiles, amino acid content), and food safety, is a primary determinant of consumer acceptance and market competitiveness. With the escalating standards of living and growing consumer awareness of nutritional health, demand for ruminant meat has shifted towards pursuing superior sensory characteristics and balanced nutritional composition (Ding et al. 2024). Consequently, the optimization of meat quality has become a pivotal objective for advancing sustainable livestock production. Although conventional strategies, including genetic selection, dietary manipulation, and husbandry management, have achieved incremental improvements, inherent limitations such as prolonged regulatory cycles, inconsistent outcomes, and potential environmental trade-offs persist, underscoring the need for innovative, targeted approaches. In recent years, the field of research focusing on the gut microbiota has emerged as a promising area of research. The indispensable roles of the gut microbiota in the processes of nutrient digestion, absorption, and metabolite biosynthesis in ruminants offer novel mechanistic avenues for meat quality modulation.

The gut microbiota of ruminants constitutes a highly diverse and complex microbial ecosystem, which is widely referred to as an “invisible organ” due to its intimate symbiotic crosstalk with the host (Chen et al. 2025). The rumen, as the primary anaerobic fermentation compartment, is dominated by three core phyla, Bacteroidetes, Firmicutes, and Proteobacteria. These microbial communities are responsible for the degradation of indigestible dietary components into bioavailable nutrients, particularly through fibrous feed fermentation to produce volatile fatty acids (VFAs). Beyond nutritional metabolism, the gut microbiota generates a diverse array of bioactive metabolites, including short-chain fatty acids (SCFAs) and amino acid derivatives, which are systemically translocated via the circulatory system to modulate key physiological processes in skeletal muscle, such as intramuscular fat (IMF) deposition and myofibrillar protein synthesis (Zhang and Davies 2016). Decades of research have demonstrated the critical role of the gut microbiota in regulating meat quality-related traits in ruminants (Ding et al. 2024, He et al. 2025, Cao et al. 2021). Thus, dissecting the causal relationships between gut microbial community structure and meat quality, deciphering the underlying molecular regulatory mechanisms, and developing microbiota-targeted intervention strategies hold profound theoretical and practical significance for systematically improving ruminant meat quality.

The integration of multi-omics technologies, including microbiomics, metagenomics, metabolomics, and transcriptomics, coupled with advances in structural biology and in vitro fermentation models, has facilitated significant progress in elucidating the molecular pathways through which gut microbes modulate meat quality. While early research in ruminant gut microbiology primarily centered on improving feed conversion efficiency and promoting growth performance (Sousa et al. 2014), recent studies have progressively revealed the intricate associations between gut microbial community dynamics and meat quality traits (He et al. 2025). For instance, accumulating evidence indicates robust correlations between gut microbial diversity, taxonomic composition, and key meat quality indicators: alterations in the Bacteroidetes/Firmicutes ratio, for example, have been directly linked to changes in muscle fatty acid profiles (e.g., polyunsaturated fatty acid content) and tenderness by regulating lipid metabolism and extracellular matrix remodeling (Cao et al. 2021, Sha et al. 2023, Yue et al. 2024). Nevertheless, the precise functional roles of core microbial taxa in mediating meat quality traits remain poorly characterized, and the effects of environmental factors (e.g., diet, housing conditions) and host genotypes on microbial interventions further obscure regulatory mechanisms, necessitating further systematic investigation.

This review systematically summarizes the molecular mechanistic links between gut microbiota and ruminant meat quality based on current research advances. It comprehensively evaluates the efficacy of various targeted microbial intervention strategies, discusses existing challenges in the field, and proposes future research directions. The aim is to provide the latest breakthroughs and application prospects of gut microbiota in enhancing ruminant meat quality, thereby offering a reference for the in-depth development of sustainable livestock production systems.

Composition and characteristics of the gut microbiota in ruminants

The gastrointestinal microbiota of ruminants exhibits a high degree of compartmentalisation. The compositional and functional differences between the rumen and the hindgut (the small and large intestines) constitute the key biological basis that collectively influence host muscle metabolism and meat quality traits (Cholewińska et al. 2020). As the primary ‘metabolic engine’, the rumen’s vast bacterial community efficiently degrades crude fibre by secreting cellulases, hemicellulases, and other enzymes. This process generates SCFAs, predominantly acetate, propionate, and butyrate, which supply the majority of the host’s energy. Among these, propionate is converted into glucose via gluconeogenesis, directly fuelling muscle tissue, while acetate and butyrate participate in lipid synthesis and epithelial energy metabolism, respectively (Dixit et al. 2023, Huang et al. 2023, Shen et al. 2021). Meanwhile, rumen microbes degrade feed proteins and resynthesise them into microbial crude protein, which is subsequently digested and absorbed in the small intestine, and serves as the main source of amino acids for muscle protein synthesis (Ku et al. 2021). In contrast, the hindgut microbiota (e.g., Bifidobacterium, Lactobacillus, and yeast-like groups in the small intestine; and Bacteroides, Clostridium, and Lactobacillus in the large intestine) exhibit more specialised functions. For example, Bifidobacterium in the small intestine participates in protein and amino acid degradation, while Bacteroides in the caecum are the primary agents of cellulose degradation (Keum et al. 2024, Celi et al. 2017). They are responsible for further degrading nutrients incompletely digested in the rumen, supplementing energy and nitrogen sources. Furthermore, Bacteroides and Prevotella strains can synthesise B vitamins (e.g., vitamin B₁₂, which is involved in fatty acid β-oxidation) (González-Montaña et al. 2020, Liu et al. 2023, Akins et al. 2013) compensating for vitamin deficiencies in the diet. Additionally, the metabolite VFAs activate G protein-coupled receptors (GPR41/43) in host intestinal epithelial cells, thereby promoting the expression of tight junction proteins (Claudin-1, Occludin) to maintain the integrity of the intestinal mucosal barrier. At the same time, they regulate the nuclear factor-κB (NF-κB) signalling pathway, thereby suppressing inflammatory responses (Sina et al. 2009). This indirectly supports systemic nutritional homeostasis and an anti-inflammatory environment, providing essential metabolic and microbiotic safeguards for efficient muscle synthesis and superior meat quality (e.g., marbling, fatty acid composition).

In summary, the rumen and hindgut microbiota, through functional complementarity and synergy, jointly and differentially regulate ruminant muscle growth and development, as well as the ultimate formation of meat quality, across multiple dimensions including energy supply, protein synthesis, fat metabolism, and internal environmental homeostasis.

Meat quality indicators for ruminants

Sensory quality indicators

Sensory indicators directly influence consumer purchasing decisions and are the main criteria used for grading meat. These predominantly include color, tenderness, juiciness, and flavor, each with well-defined grading thresholds and standardized analytical methods (Table 1).

Table 1.

Sensory quality indicators and standards for evaluating ruminat meat quality

Indicator	Standard	Value
Colour	Standard colour chart: Grades 1–5	Quality threshold: Grade 3–4
	Myoglobin content: L* (lightness), a* (redness) and b* (yellowness)	Higher a* values Moderate L* values
Tenderness	WBSF	Very tender < 35 N Fairly tender 35–45 N Coarse and tough > 50 N
	Sensory evaluation: ease of fibre breakage during chewing, dental resistance	Can be swallowed after 3–5 chews with no noticeable fibrous residue
Juiciness	WHC	Higher WHC
	Drip loss (%) = [(W1 - W2) / W1] × 100%	Excellent: < 2% Good: 2% − 4% Fair: 4% − 6% Poor: > 6%
	Cooking loss (%) = [(C1 - C2) / C1] × 100%	Excellent: < 15% Good: 15% − 25% Fair: 25% − 30% Poor: > 30%
Flavour	Non-volatile compounds	Inosine monophosphate, guanosine monophosphate and free amino acids
	Fatty acid composition	UFAs proportion

WBSF: Warner-Bratzler shear force; W1, Initial weight; W2: Second weighing; C1, Initial weight; C2: Second weighing; WHC: water-holding capacity; UFAs: Unsaturated fatty acids

The colour of meat is a direct indicator of its freshness, enabling a simultaneous assessment of its freshness status and inherent quality. In accordance with the NY/T 676–2021 standard color chart (grades 1–5), grades 3–4 (bright red) are considered to represent the premium quality threshold, which corresponds to the myoglobin stability range at pH 5.8–6.2 (Suman and Joseph 2013). Myoglobin content and redox state are the core determinants of meat color: fresh meat typically exhibits a bright red appearance, while myoglobin oxidation during storage induces color darkening, potentially resulting in brown or gray hues. The objective quantification of meat color parameters, including lightness (L*), redness (a*), and yellowness (b*), can be achieved using a colorimeter (He et al. 2025). Accumulating evidence indicates that color stability is closely associated with gut microbial metabolism. Ruminant gut bacteria have been found to synthesize antioxidants such as vitamin E and anthocyanins, which inhibit myoglobin oxidation. The abundance of these antioxidant-producing bacteria demonstrates a strong positive correlation with meat color scores (R² = 0.68, p < 0.01), thereby extending the shelf-life during which fresh meat meets premium color standards by 2–3 days (Mancini and Hunt 2005).

Tenderness is a key parameter reflecting meat textural fineness, quantitatively evaluated via Warner-Bratzler shear force (WBSF). Industry-recognized grading criteria classify meat as follows: WBSF < 35 N (extremely tender), 35–45 N (moderately tender), and > 50 N (tough). At the sensory evaluation level, tenderness is further assessed by subjective indicators, including the ease of muscle fiber fragmentation during chewing and dental resistance. High-quality meat should meet the sensory standard of being swallowable after 3–5 chews without noticeable fibrous residues (Zulfiqar et al. 2025). Marbling, defined as the content and distribution density of IMF, serves as the core carrier of meat juiciness and flavor, directly modulating both sensory attributes.

Juiciness is closely associated with the muscle water-holding capacity (WHC), with drip loss and cooking loss widely recognized as quantitative indicators for WHC evaluation. Additionally, non-volatile compounds, such as inosine monophosphate (IMP), guanosine monophosphate (GMP), and free amino acids, have been identified as contributing to the umami taste of meat (Li et al. 2025). The flavor profile of ruminant meat is further influenced by the composition of intramuscular fatty acids, where a higher proportion of unsaturated fatty acids (UFAs) is generally associated with superior organoleptic quality.

Physicochemical and nutritional indicators

Physicochemical and nutritional indicators characterize the intrinsic properties of meat, correlating with freshness, WHC, and nutritional value. Their quantitative standards provide precise targets for quality optimization strategies. Freshness assessment of ruminant meat primarily focuses on pH value and drip loss, with premium quality thresholds defined as pH 5.6–6.6 and drip loss < 3%. Superior meat WHC is mediated by gut microbiota-regulated myosin synthesis: butyric acid produced during ruminal fermentation upregulates myosin expression in muscle cells, modulating cellular osmotic pressure and reducing drip loss (Abebe et al. 2024, Huang et al. 2021). High-quality ruminant meat is characterized by elevated protein content and optimal amino acid composition, typically with crude protein exceeding 20% and complete essential amino acid profiles (lysine ≥ 1.8%, methionine ≥ 0.5%). These essential amino acid levels serve as critical benchmarks for evaluating meat protein nutritional quality (Hwang et al. 2018). The fatty acid composition of meat is a key metric for assessing its nutritional value, with a primary objective of quality enhancement being to increase the proportion of UFAs while reducing the saturated-to-unsaturated fatty acid (SFA/UFA) ratio in ruminant meat. Unsaturated fatty acids, particularly conjugated linoleic acid (CLA) and omega-3 polyunsaturated fatty acids (n-3 PUFAs), have been demonstrated to alleviate inflammatory responses and improve cardiovascular function, conferring significant human health benefits (Simopoulos 2002). Furthermore, the nutritional value of ruminant meat is enriched by diverse functional components, including B vitamins, vitamin D, essential minerals (e.g., iron, zinc, selenium), and endogenous antioxidants (e.g., glutathione peroxidase, superoxide dismutase). Collectively, these components contribute to the overall nutritional quality and health-promoting properties of ruminant meat.

The mechanisms by which gut microbiota modulate meat quality in ruminants

Regulation of the formation and stability mechanisms of meat colour

The colour of meat is a key indicator for assessing meat quality, fundamentally determined by the content, form, and oxidation state of myoglobin within muscle tissue (Ding et al. 2024, Yue et al. 2024, Huang et al. 2021). Myoglobin synthesis relies on trace elements such as iron, copper, and zinc. Iron constitutes the central component of haem, while copper and zinc participate in iron absorption, transport, and the regulation of enzyme activity involved in myoglobin synthesis (Kondaiah et al. 2019). Lactic acid bacteria and bifidobacteria in the rumen generate organic acids, lowering intestinal pH to convert insoluble iron in feed into soluble forms, thereby enhancing iron absorption by intestinal epithelial cells. Certain microorganisms synthesise iron carriers that bind environmental iron ions for host utilisation. Concurrently, gut microbiota modulate the expression of iron transporters (DMT1, FPN1) in host intestinal epithelial cells, further regulating iron absorption and transport (Wang et al. 2020, Grace and Lee 1990, Huang et al. 2023). Moreover, the oxidative stability of myoglobin is crucial for maintaining bright red meat colour, and the body’s oxidative stress levels directly influence myoglobin oxidation rates. In sheep models, aflatoxin exposure has been shown to disrupt the gut microbiota, reducing the abundance of Clostridium butyricum, elevating oxidative stress markers, and decreasing meat redness values (a* values) (Cao et al. 2021). Conversely, a healthy gut microbiota has been shown to inhibit lipopolysaccharide translocation, alleviate systemic inflammation, and protect muscle tissue from inflammatory damage. Furthermore, some gut microbes can synthesise antioxidants such as vitamin E and glutathione. SCFAs, such as butyrate, have been shown to activate the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway, upregulating host endogenous antioxidant enzymes including superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) (Gao et al. 2025). Interestingly, studies have shown that feeding goats with iron sulphate-supplemented feed can reduce oxidative stress levels in muscles, thereby delaying lipid and myoglobin oxidation and maintaining a bright meat colour (Purba et al. 2022).

Mechanisms mediating muscle fibre remodelling and tenderness regulation

The key factors influencing meat tenderness are the composition of muscle fibres, connective tissue, and intramuscular fat within the muscle. Intramuscular fat, interwoven between muscle fibres in the form of adipose tissue, significantly enhances meat juiciness and tenderness. The resulting marbling pattern is considered the key manifestation determining the tenderness of ruminant meat (Ding et al. 2024). Research indicates that SCFAs influence meat tenderness by regulating intramuscular fat deposition (Yue et al. 2022). Butyrate has been demonstrated to activate the peroxisome proliferator-activated receptor gamma (PPARγ) signalling pathway, modulating adipocyte differentiation and proliferation to increase intramuscular fat content (Pan et al. 2025). Research indicates that meat sheep with a higher abundance of butyrate-producing bacteria in the gut exhibit increased intramuscular fat content, attributed to butyrate’s regulation of gene expression related to lipid synthesis (Dou et al. 2023). Furthermore, gut microbiota utilise non-protein nitrogen sources and feed amino acids to synthesise essential amino acids, while hydrolysing feed proteins into peptides and free amino acids. These nitrogenous substrates serve as precursors for microbial crude protein synthesis. Following absorption by the host, this microbial crude protein becomes a high-quality substrate for muscle protein synthesis, thereby increasing muscle protein content while enhancing meat nutritional value and tenderness (Firkins et al. 2007, Lee et al. 2025).

Mechanisms regulating the production of flavour compounds in muscle tissue

The formation of meat flavour is determined by the types and concentrations of volatile flavour compounds, fatty acid derivatives, nitrogen-containing compounds, and non-volatile flavour compounds within muscle tissue, including free amino acids and inosine monophosphate. Gut microbiota play a pivotal regulatory role in ruminant fatty acid metabolism, directly shaping the fatty acid composition of intramuscular fat and thereby influencing meat flavour. A higher proportion of unsaturated fatty acids (UFAs) has been shown to correlate with superior flavour. Biohydrogenation plays a central role in regulating fatty acid saturation, with anaerobic rumen bacteria and fibre-degrading bacteria such as Bifidobacterium soligradens mediating this process to control fatty acid saturation. Conjugated linoleic acid (CLA), an unsaturated fatty acid, is a functional fatty acid with anti-cancer and anti-obesity properties that impart distinctive flavour characteristics to meat. Rumenic diversity and abundance of anaerobic bacteria significantly enhance CLA content in meat (Schmid et al. 2006). Furthermore, acetic acid, propionic acid, and butyric acid produced by rumen microbial fermentation serve as key precursors for fatty acid synthesis. It has been demonstrated that the enrichment of Bacteroides and Prevotella-1 has a significant impact on propionic acid production. Propionic acid is a gluconeogenic precursor that has been shown to inhibit fatty acid synthase activity, thereby reducing fat deposition in bovine muscle and subcutaneous adipocytes (Wan et al. 2009). Meanwhile, acetate has been found to upregulate the expression of acetyl-CoA carboxylase and fatty acid synthase, promoting fatty acid synthesis in the liver and adipose tissue (Li et al. 2013). Butyrate activates PPARγ, regulating the expression of genes associated with lipid metabolism and facilitating the accumulation of unsaturated fatty acids (Zhang et al. 2025). In vitro studies have confirmed that treatment with 1 mmol/L butyrate regulates fatty acid metabolism-related genes via pathways including oxidative phosphorylation and mitogen-activated protein kinase (MAPK), thereby influencing the differentiation of bovine skeletal muscle satellite cells (Wang et al. 2025).

Mechanism mediating the optimisation of muscle nutrients

The nutritional value of meat is primarily linked to the proteins, fatty acids, and other functional components within the muscle tissue. The gut microbiota of ruminants optimises the composition of muscle nutrients by regulating the degradation, absorption, and conversion of these nutrients. It is estimated that approximately 70% of dietary protein requires degradation by rumen microbes before absorption and utilisation. Beneficial bacteria in the rumen, including Fibrobacter, Streptococcus, and Bifidobacterium, have been shown to degrade crude protein and non-protein nitrogen in the diet into peptides and amino acids, which are then synthesised into microbial protein (Putri et al. 2021). Dietary amino acid supplementation has been shown to have a significant impact on muscle formation and metabolism. Branched-chain amino acids (BCAAs) are a group of essential amino acids comprising leucine, isoleucine, and valine. It has been demonstrated that BCAAs are absorbed by nearly all tissues. Research indicates that low-BCAA diets increase fatty acid oxidation and reduce hepatic lipogenesis (Bai et al. 2015), whereas BCAA-rich diets promote fat deposition, thereby optimising the nutritional value of muscle proteins (Whon et al. 2021). Furthermore, the fatty acid composition of mutton and associated biological pathways have been successfully modified through strategic control of rumen bacterial communities (Wang et al. 2021). Research indicates that Angus cattle exhibit enhanced fatty acid synthesis capacity and higher IMF content, attributable to their greater production of butyrate-generating bacteria (Fan et al. 2019). Furthermore, rumen microbiota in ruminants have been shown to synthesise B vitamins, which participate in host energy metabolism and protein synthesis. A proportion of these vitamins may be accumulated within muscle tissue, thereby enriching the vitamin profile of meat (Jiang et al. 2022). Research has demonstrated that vitamin B12 (cobalamin) also stimulates propionic acid production by the predominant rumen bacterium Xylanibacter ruminicola. Propionic acid, a primary end product of rumen fermentation, contributes to enhancing the nutritional value of meat (Mahoney-Kurpe et al. 2024).

Signalling pathways and mechanisms by which SCFAs regulate meat quality

The regulation of meat quality in ruminants by SCFAs, metabolic products derived from the gut microbiota, is ultimately achieved through multi-tiered molecular mechanisms. These mechanisms exert their effects by modulating the expression of genes associated with muscle tissue (Fig. 1). SCFAs, which are produced by gut microbial fermentation, primarily acetate, propionate, and butyrate, can enter the liver via the portal vein for metabolism or be absorbed by the hindgut and directly enter the peripheral circulation (Huang et al. 2023, Besten et al. 2013). These SCFAs, acting as crucial signalling molecules and metabolic substrates, bind to specific receptors in skeletal muscle, GPR41/43 (Maruta and Yamashita 2020), regulating muscle metabolism and meat quality by activating two core signalling pathways: AMPK-PGC-1α and PPARs.

Fig. 1.

The signalling pathways and mechanisms by which short-chain fatty acids (SCFAs) influence meat quality

Research has demonstrated that acetic acid and butyric acid can directly enhance adenosine 5’-monophosphate (AMP)-activated protein kinase (AMPK) phosphorylation and activity in skeletal muscle and myotubes (Pan et al. 2015). Upon AMPK activation, it promotes the uptake and oxidation of fatty acids (Gao et al. 2009), while inhibiting lipogenesis, thereby directly reducing IMF deposition (Walsh et al. 2015). At the same time, there is an elevation in the expression of peroxisome proliferators-activated receptor gamma coactivator l alpha (PGC-1α). PGC-1α is a pivotal regulator of mitochondrial biogenesis and oxidative metabolism, driving the conversion of fast-twitch muscle fibres to oxidative slow-twitch fibres (Type I), thereby enhancing meat colour stability and water-holding capacity. It has also been demonstrated to increase mitochondrial content and function, supporting sustained fatty acid oxidation (Maruta and Yamashita 2020, Pan et al. 2015, Gao et al. 2009, Lin et al. 2002).

Concurrently, SCFAs have been observed to upregulate expression of the peroxisome proliferator-activated receptor (PPAR) family within skeletal muscle (Gao et al. 2009). Specifically, the participation of PPAR-α in lipid oxidation has been demonstrated to reduce IMF content, while PPAR-γ promotes IMF deposition and the formation of oxidative fibres (Wagner and Wagner 2010). This not only directly induces an increase in the proportion of type I muscle fibres but also forms synergistic effects with the AMPK pathway, further enhancing the formation of oxidative muscle fibres by upregulating PGC-1α expression (Wang et al. 2004). Furthermore, different SCFA subtypes and microbially derived SCFAs exhibit specific regulatory effects on PPAR subtypes. For instance, propionate modulates PPAR-γ expression to influence lipid metabolism (Lukovac et al. 2014), while butyrate significantly upregulates PPAR-δ expression (Gao et al. 2009). Furthermore, AMPK and PPAR-δ demonstrate reciprocal regulatory interactions, wherein PPAR-δ agonists activate AMPK (Narkar et al. 2008, Ji et al. 2023), thereby establishing a positive feedback loop. This process is pivotal in regulating meat tenderness, flavour, and nutritional value by balancing myofibre types and IMF content.

Microbial-targeted interventions for improving meat quality in ruminants

Microbiologically targeted interventions to enhance ruminant meat quality involve optimising dietary fibre and feeding regimes, employing probiotics and enzyme inhibitors to improve fermentation and nutrient utilisation, alongside targeted regulation of metabolic pathways to modulate the gut microbiota for meat quality improvement (Fig. 2).

Fig. 2.

Microbial-targeted interventions for improving meat quality in ruminants

Dietary regulation strategies

Dietary modulation is a well-established and effective approach to regulating gut microbiota and enhancing the quality of ruminant meat, primarily implemented through precision feed optimization (Wang et al. 2024, Zulfiqar et al. 2025). The differences between grain-fed and grass-fed systems directly determine meat quality and gut microbial composition. The grass-fed system, centred on natural forage and rich in slowly fermentable fibre, significantly enriches fibre-degrading microbial communities such as Fibrobacter and the Christensenellaceae R-7 group. This process enhances the content of n-3 polyunsaturated fatty acids, vitamin E, and antioxidants in the meat, resulting in leaner cuts with a natural flavour; however, it should be noted that the growth cycle is longer (Du et al. 2023). The grain-fed system relies primarily on concentrated grain feeds, with a high energy density in the diet, which increases the abundance of Prevotella, promotes fat deposition, and raises IMF content, resulting in meat that is more tender and juicy; however, it has a higher proportion of saturated fatty acids and is prone to causing an imbalance in the ruminal microflora (Ortiz-Chura et al. 2025). Research indicates that grass-fed beef contains significantly higher levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) than grain-fed beef, aligning with health-conscious consumer demands (Marino et al. 2025). A judicious combination of these two feeding regimes during the finishing phase can markedly enhance meat quality. It is important to note that, in the initial phase, sufficient roughage must be retained to maintain stable rumen pH and promote the establishment of the microbial community; in the middle phase, the concentrate ratio should be increased to boost energy intake and drive the synchronous deposition of muscle and fat; and in the late phase, further increasing the concentrate ratio can significantly improve IMF content, but the roughage ratio should not fall below 15%, otherwise ruminal acidosis is likely to occur (Griffith et al. 2016, Zhang et al. 2020). Research has demonstrated that a concentrate-to-roughage ratio of 70:30 during the fattening period can enhance the slaughter performance and meat tenderness of Tibetan sheep, while optimising ruminal fermentation patterns (Wang et al. 2024). Conversely, an excessively high concentrate ratio (80:20) has been shown to increase drip loss in the meat (Gou et al. 2025). When the daily energy intake of ruminants exceeds the levels of required for maintenance and growth, the excess energy is primarily converted into fat via two pathways. Firstly, VFAs produced by ruminal fermentation are transported via the bloodstream to adipose tissue, where they are synthesised into fatty acids under the action of acetyl-CoA carboxylase (ACC). Secondly, the liver converts propionate into glucose via gluconeogenesis, thereby stimulating insulin secretion and promoting the uptake of glucose into adipocytes for conversion into triglycerides. Of these, subcutaneous fat deposition takes precedence over intramuscular fat, as intramuscular fat cells have lower adipogenic potential and are regulated by anti-adipogenic genes; however, insufficient duration of energy surplus can lead to inadequate IMF deposition, affecting the marbling grade of the meat (Laliotis et al. 2010).

In addition, functional plant-derived compounds, including tannins, flavonoids, p-hydroxycinnamic acid (HoC), and plant essential oils, exhibit selective modulatory effects on gut microbial homeostasis. It is worth noting that continuous supplementation of 1 g/d of pine nut essential oil (PEO) for 17–20 days can reduce intestinal methane emissions in ruminants (Choi et al. 2023), optimizing meat quality through the regulation of hydrogen metabolism while aligning with sustainable livestock production goals. Research has shown that there are synergistic effects associated with the use of combined feed additives: the effect of sodium 2-bromoethanesulfonate (BES) combined with nitro compounds on rumen fermentation. It was found that the combination of BES and other inhibitors could reduce methane production by 95.2%-99.2%, and the production of volatile fatty acids increased in a dose-dependent manner, which could further optimize the rumen fermentation mode and improve the nutritional value of meat (Zhang and Yang 2012). Accumulating evidence indicates that combined supplementation of probiotics and plant extracts synergistically modulates microbial communities, significantly increasing IMF content and UFA ratios while improving meat flavor and tenderness (Ding et al. 2024, Yue et al. 2024, Yue et al. 2025).

Husbandry systems and environmental control techniques

Husbandry systems exert a significant impact on gut microbial structure and function by regulating animal activity levels, feeding behavior, and stress responses, thereby indirectly influencing meat quality. Exercise interventions have been shown to enhance host metabolism by improving gut morphology and promoting the proliferation of propionate-producing microbiota, exemplified by the Bacteroidetes phylum (Mika et al. 2015). Increased short-chain fatty acids, including propionate, not only act as signalling molecules to enhance systemic energy metabolism and insulin sensitivity but also reduce systemic inflammation by maintaining intestinal barrier health. This integrated action collectively improves animals’ nutritional efficiency (enhancing dressing percentage), stabilises muscle glycogen metabolism during ante-mortem stress, and maintains post-mortem muscle pH within the optimal range, ultimately elevating meat quality. However, excessive shear stress induced by intense exercise may have a negative effect on meat tenderness, highlighting the need for precisely tailored exercise protocols. Furthermore, stress management is paramount, as transport and crowding stress disrupt gut microbial balance, resulting in abnormal muscle pH and reduced WHC. Research has shown that mitigating transport stress in sheep, for example by shortening journey times, improving transportation conditions, and administering anti-stress agents such as gamma-aminobutyric acid and probiotic complexes, can alleviate gut microbial dysbiosis, thereby reducing meat drip loss and colour deterioration (Zhao et al. 2023). Furthermore, the judicious use of antibiotics in combination with alternative strategies (e.g., plant extracts, probiotics, prebiotics) helps to maintain gut microbial equilibrium, thereby safeguarding animal health and meat quality (Ding et al. 2024, Yue et al. 2025, Xu et al. 2025).

Targeted regulation of probiotic preparations and enzyme inhibitors

In recent years, there have been significant advancements in the discovery and functional validation of novel probiotic strains and enzyme inhibitors (Table 2). Probiotic screening has evolved from traditional functional speculation to precision selection based on multi-omics analysis. For example, Bacteroides distasonis F4, a novel probiotic isolated from the calf rumen, exhibits robust carbohydrate metabolic activity and organic acid production capabilities, as confirmed by whole-genome sequencing. Supplementation with this strain has been demonstrated to significantly alter the microbial community structure and enhance SCFA production (Feng et al. 2025, Ezeji et al. 2021). The supplementation of 1% Lactobacillus in Sunit sheep promoted muscle fiber type conversion and improved meat quality by regulating the AMPK signaling pathway (Wang et al. 2022). Enzyme inhibitors slow down urea degradation by specifically targeting the activity of key enzymes, thereby reducing ammonia nitrogen wastage, improving nitrogen utilisation and protein deposition, and consequently enhancing lean meat yield and improving meat flavour. Precision engineering has facilitated a transition from broad-spectrum inhibition to target-specific modulation. A research team from the Chinese Academy of Agricultural Sciences has identified dominant urease-encoding genes in bovine rumen microbiota via metagenomic analysis, revealing that these ureases originate from a novel genus within the family Acinetobacteraceae. They subsequently developed epiberberine, a novel plant-derived urease inhibitor with high efficacy (Zhao et al. 2025, Zhang et al. 2024). Advances have also been made in methanogenase inhibitors: BES, a specific inhibitor of methyl-coenzyme M reductase (MCR), reduces methane production in a dose-dependent manner (Grawert et al. 2014).

Table 2.

Probiotic preparations and enzyme inhibitors for targeted regulation of ruminant gut microbiota

Name	Types	Function	References
Probiotic preparations	Parabacteroides delbrueckii F4	Exceptional cellulose degradation capacity and volatile fatty acid production capability, with outstanding performance in propionic and butyric acid synthesis.	(Zhang et al. 2021)
	Lactobacillus plantarum N-1	Functional genes enhancing host antioxidant capacity and improving lipid metabolism.	(Zhou et al. 2023)
	Saccharomyces	Further optimisation of intestinal tissue morphology and rumen epithelial gene expression.	(Guimarães et al. 2020)
	Bacillus licheniformis B63	Produces multiple antimicrobial peptides and digestive enzymes.	(Zeng et al. 2022)
	Complex-probiotic-preparation	Functional complementarity, metabolic product synergy, spatial ecological niche complementarity, and immune regulation coordination.	(Reuben et al. 2022)
Enzyme inhibitors	Epiberberine	By binding to the active site of urease, it impedes urea entry, thereby reducing the rate of urea decomposition .	(Zhang et al. 2025)
	Acetohydroxamic acid	Enhance the digestibility of organic matter, crude protein and fibre.	(Reddy et al. 2023)
	Coptisine	The interaction between the nickel ion in the urease active centre and the amino acid residues at the active site exerts an inhibitory effect.	(Zhou et al. 2011)
	BES	Binds to the active site of methyl-Coenzyme M reductase, thereby inhibiting the final step in methane synthesis.	(Zhou et al. 2011)
	PEO	Reduce methane emissions without affecting dry matter intake.	(Choi et al. 2023)
	Asparagopsis taxiformis	Eliminate methanogenic bacteria, inhibit key fibre-degrading bacteria and volatile fatty acid-producing bacteria.	(O’Hara et al. 2023)

BES, Sodium 2-bromoethanesulfonate; PEO: Pine nut essential oil

Metabolic pathway-targeted regulation

Metabolic pathway-targeted regulation technology employs hydrogen metabolism reprogramming as its core strategy. By intervening in the metabolic flux of rumen microorganisms, it achieves two key objectives: reducing methane emissions and improving meat quality. Its mechanism revolves closely around the targeted optimisation of key meat quality indicators through the regulation of gut microbiota. The core determinants of meat quality in ruminants, intramuscular fat deposition, muscle glycogen reserves, and the synthesis of precursors for flavour compounds, are all closely linked to rumen microbial metabolism. The introduction of exogenous electron acceptors (e.g., PEO, DFS) allows hydrogen to be reallocated from methane synthesis to beneficial metabolic pathways for the production of propionate and other value-added metabolites. It significantly reduced methane emissions, accompanied by a significant increase in propionate production, feed conversion efficiency, muscle glycogen reserves, and intramuscular fat deposition (Choi et al. 2023, Zhang and Yang 2012). Dose-response studies emphasize the importance of precise modulator formulation in regulating the gut microbiota and improving meat quality. BES exhibits dose-dependent methane suppression within the range of 12 mmol/L. The combined use of multiple modulators can produce synergistic effects, further enhancing methane reduction rates whilst simultaneously optimising the ratio of intramuscular fat deposition to muscle glycogen synthesis through the coordinated regulation of gut microbial metabolic balance, thereby achieving precise improvements in meat quality (He et al. 2022). Ecological safety assessments indicate that such interventions have minimal impact on the stability of rumen microbial community structure and functional genes. They maintain the homeostasis of the intestinal microecosystem, preventing fluctuations in meat quality caused by microbial dysbiosis, and there is currently no evidence of associated long-term ecological risks (Li et al. 2022). Furthermore, multi-pathway synergistic strategies, integrating the regulation of hydrogen and nitrogen metabolism with energy and protein metabolic pathways, systematically optimize rumen fermentation patterns. Whilst reducing methane emissions, this approach regulates the efficiency with which gut microbiota utilise nitrogen, thereby minimising protein wastage and promoting the synergistic optimisation of muscle protein synthesis and intramuscular fat deposition. This further enhances the protein content and flavour quality of the meat, providing a viable pathway for the sustainable production of ruminant livestock (Yamada et al. 2024).

Challenges and future perspectives

In recent years, research into the link between ruminant gut microbiota and meat quality has made significant progress in terms of both mechanistic elucidation and technological development. The application of multi-omics technologies (e.g., metagenomics, metabolomics, transcriptomics) has clarified the roles of core metabolic pathways such as VFA metabolism and hydrogen metabolic reprogramming, as well as key signaling pathways including PPARγ and mTOR. Meanwhile, enzyme inhibitor screening based on structural biology and targeted metabolic pathway regulation technologies has enabled a transition from broad-spectrum interventions to precision control. From a methodological perspective, significant progress in 16 S rRNA gene sequencing, cryo-electron microscopy, and in vitro rumen simulation systems has provided robust support for microbial functional analysis and technical screening. Progress in microbial cultivationomics has further facilitated the discovery of novel functional strains such as Bacteroides fragilis F4. At the application level, products including palmitoyl-CoA-dependent protease inhibitors, probiotic formulations, and metabolic modulators have demonstrated strong industrialization potential, promising to drive the livestock industry toward high-quality, green, and efficient transformation.

However, several critical challenges persist. The relationship between gut microbiota and meat quality is complex and specific to the host, with universal regulatory principles yet to be fully elucidated. The specific molecular pathways and interaction mechanisms through which microbial metabolites regulate muscle cell function require further investigation. Despite the widespread application of high-throughput sequencing in gut microbiome research, inadequate integration and interpretation of multi-omics data, coupled with a lack of reliable causal validation models, constrain in-depth mechanistic analysis (Huang et al. 2024). Concurrently, insufficient long-term efficacy and safety assessments of existing intervention techniques, alongside technical bottlenecks such as probiotic stability and the precise delivery of metabolic modulators, hinder their industrialization and widespread adoption (Chen et al. 2025). Collectively, these limitations hinder the development and application of precision regulation strategies.

Future research in ruminant gut microbiota and meat quality will exhibit a trend toward interdisciplinary integration. At the mechanistic level, cutting-edge technologies such as single-cell sequencing and spatial metabolomics will be employed to precisely elucidate the molecular pathways governing interactions between region-specific gut microbiota, their metabolites (e.g., SCFAs), and muscle cell receptors. Multi-omics data integration will facilitate the construction of comprehensive regulatory networks spanning the entire chain from microbiota to host genes to meat quality, providing a basis for breed-specific regulation (He et al. 2025, Li et al. 2024, Huang et al. 2022, Koyama et al. 2024). Technological development will focus on precision and sustainability, encompassing: personalized probiotic selection based on host metagenomic profiles; synthetic biology-engineered functional strains; novel natural-source inhibitor design via structural biology; and Internet of Things (IoT)-enabled big data systems for dynamic microbial monitoring and precision feeding (Xu et al. 2025). A systematic evaluation framework is to be established to assess the short- and long-term impacts of targeted microbial interventions on meat quality, host health, and environmental sustainability. At the same time, we must be watchful for possible risks, such as the emergence of antibiotic resistance and pathogen transmission, to ensure the safe and sustainable application of these technologies. Finally, interdisciplinary collaboration will serve as a pivotal driver. By integrating expertise from animal science, microbiology, information science, and other fields, comprehensive green farming solutions will be developed to simultaneously enhance meat quality, reduce methane emissions, and safeguard food safety, thereby unifying economic benefits with environmental sustainability.

Conclusions

The ruminant gut microbiota exerts a significant regulatory influence on key meat quality traits including tenderness, flavor profiles, and nutritional value via multifaceted mechanisms: (i) modulation of host energy metabolism and nutrient partitioning; (ii) regulation of intramuscular fatty acid biosynthesis, desaturation, and accumulation (e.g., polyunsaturated fatty acid enrichment and conjugated linoleic acid isomer formation); (iii) mediation of myogenic differentiation and muscle fiber type transformation; and (iiii) maintenance of gut mucosal barrier integrity and systemic immune homeostasis, thereby mitigating oxidative stress-induced myopathy. Current research has shown that microbiota-targeted strategies, including dietary composition optimization, husbandry system modification, probiotic/prebiotic/enzyme inhibitor administration, and targeted metabolic pathway modulation, have demonstrated promising potential for improving meat quality parameters in controlled experimental settings. However, this research field faces several challenges. These include the high taxonomic and functional complexity of the gut microbiota, strong host genetic specificity, inconsistent intervention efficacy across production systems, and economic feasibility constraints for large-scale industrial application. With the rapid advancement of multi-omics technologies, artificial intelligence-driven microbial network analysis, and synthetic biology tools, future research will prioritize the precise delineation of core functional microbiota taxa and their mechanistic contributions to meat quality. This will facilitate the development of personalized, context-dependent intervention strategies tailored to specific ruminant species, production environments, and consumer demands.

Author contributions

Conceptualization, S.C.H.; writing-original draft preparation, Y.J. and K.L.L.; writing-review and editing, Y.J. and S.C.H. All authors have read and agreed to the published version of the manuscript.

Funding

This study was supported by the Xuzhou Cutting-Edge Technology Research Program (KC25119), the Xuzhou Vocational College of Bioengineering University-Level Project (XSZR202512), the Basic Research Project of the Natural Science Foundation of the Jiangsu Higher Education Institutions (23KJB360017), the Basic research program young talents in science and Technology project of Xuzhou (KC23037), and the General Program of Philosophy and Social Science Research in Jiangsu Universities (2025SJYB0894).

Data availability

The original contributions presented in this study are included in the article. Data sharing is not applicable to this article.

Declarations

Competing interests

The authors declare no competing interests.

Ethical approval

This article does not require IRB/IACUC approval because there are no human and animal participants.