High-Protein Diets: Characteristics of Bacterial Fermentation and Its Consequences on Intestinal Health

Abstract

Although high-protein diets are widespread, the fate of dietary protein, its fermentation by gut microbiota, and the resulting effects on intestinal health are not yet fully understood. This article provides a comprehensive overview of microbial protein fermentation and its impact on intestinal health. We focus on the bacterial anabolic and catabolic pathways involved in microbial protein metabolism and the generation of metabolites such as ammonia, biogenic amines (BAs), and short-chain fatty acids (SCFAs). This review also examines how excessive dietary protein affects intestinal health. Elevated protein levels may disrupt microbial homeostasis, promoting the proliferation of pathogenic bacteria while reducing beneficial microbiota. Furthermore, enhanced bacterial metabolic activity can lead to greater production of harmful compounds such as BAs. These alterations are associated with impaired intestinal barrier function, immune dysregulation, and elevated inflammatory responses. Further research is necessary to clarify the metabolism of high-protein diets and their consequences for intestinal health.

1. Introduction

Protein metabolism in the intestine is a critical area of research because of its essential role in nutrition, growth, and overall health [1]. This process involves complex enzymatic activities and microbial fermentation that enable the efficient breakdown and utilization of dietary proteins [2]. Understanding protein metabolism, the features of microbial protein fermentation, and their consequences for intestinal physiology are crucial for developing optimized nutritional strategies that support intestinal health.

The small intestine plays a central role in protein digestion and absorption, where host-derived proteases hydrolyze dietary proteins into amino acids (AAs) and peptides [3]. These compounds are necessary for host metabolism and also serve as key substrates for the gut microbiota, which convert them into bioactive molecules such as ammonia, biogenic amines (BAs), and short-chain fatty acids (SCFAs). SCFAs generally support intestinal barrier function and immune regulation, while excessive production of ammonia and BAs has been linked to gut dysbiosis, inflammation, and impaired barrier integrity [4]. Whereas some protein fermentation can take place in the distal ileum, the majority of proteolytic fermentation happens in the large intestine, particularly within the colon. Proteolytic bacteria in this area break down indigestible proteins and peptides, producing metabolites like branched-chain fatty acids (BCFAs) and BAs that affect gut health [5,6].

High-protein diets have attracted attention due to their associations with muscle growth and metabolic health [7]. Increased dietary protein can enhance digestion and nutrient utilization, modulate the gut microbiome composition and metabolism, and promote the production of beneficial metabolites that support tissue growth and overall gut function [8,9]. However, high protein intake markedly alters microbial composition and metabolism, often leading to dysbiosis characterized by an expansion of pathogenic species and a reduction in beneficial bacteria [10]. Moreover, high-protein diets can reduce intestinal barrier capacity, enhancing permeability, allowing harmful substances to cross, and triggering immune responses and chronic inflammation [11]. This review presents studies across multiple species, including humans, pigs, and rodents. Therefore, this review focused on integrate interspecies evidence regarding the impact of dietary protein levels on gut microbiota composition, metabolic outcomes, and gut health, while considering interspecies differences in response to dietary protein levels. In human nutrition, high-protein intake is often defined as 1.2–1.6 g/kg/day, with consumption exceeding 2.0 g/kg/day considered excessive [12,13]. In rodents, diets containing 30–40% protein are typically categorised as high-protein [14]. In pigs, dietary crude protein (CP) levels of 18–20% are often considered as high, whereas levels exceeding 20–21% are deemed excessive [15,16]. In this review, we summarize the characteristics of protein metabolism by digestive enzymes and microbiota in the small intestine and compile evidence on the effects of high-protein diets on gut health. This review highlights the importance of understanding high-protein metabolism and its systemic effects to develop nutritional strategies that maintain gut homeostasis and overall health.

2. Methods

This narrative review employed a systematic literature search strategy to ensure comprehensive coverage of the subject. Scientific publications were obtained from PubMed (https://pubmed.ncbi.nlm.nih.gov, accessed on 1 December 2025), Web of Science  (https://www.webofscience.com, accessed on 1 December 2025), and Google Scholar (https://scholar.google.com, accessed on 1 December 2025). The subsequent keywords and their combinations utilized include dietary protein, high-protein diet, protein fermentation, gut microbiota, SCFAs, BCFAs, biogenic amines, intestinal barrier, immunity, rodent model, swine nutrition, and human intervention study. The search encompassed studies published from 2000 to 2025. Both human and animal studies were incorporated to enable cross-species comparisons. Articles were selected based on their relevance to (i) dietary protein levels, (ii) microbial fermentation pathways and metabolites, and (iii) intestinal health outcomes (including barrier function, immune response, and inflammation). The review prioritized experimental, clinical, and mechanistic studies, and selected the latest cutting-edge research to ensure the quality and clarity of methodology.

3. Protein Metabolism in the Small Intestine

3.1. Protein Metabolism by Digestive Enzymes

Protein hydrolysis is catalyzed by digestive enzymes. Although comprehensive studies on human protein digestion and absorption are well-documented [17], “digestion” refers to the breakdown of proteins into peptides and AAs, while “absorption” refers to the uptake of these breakdown products by enterocytes from the gastrointestinal lumen.

The process begins in the mouth, where food is mechanically broken down through chewing and mixed with saliva before being swallowed. In the stomach, proteolysis is facilitated by peristaltic motions and is initiated by the action of gastric acid and pepsin. Gastric pH typically decreases due to secretory activity, but may temporarily rise after a meal as food buffers the acidity. Pepsin exhibits maximal activity at approximately pH 2 and retains partial functionality up to pH 6; thus, the postprandial buffering of gastric acidity only transiently reduces its proteolytic activity [18]. Gastric proteolysis is limited and mainly facilitates the release of peptides and aromatic AAs, which signal meal composition to intestinal sensory mechanisms [19].

Proteases secreted by the pancreas into the intestinal lumen further degrade dietary proteins into peptides and AAs. Physiological surfactants such as bile acids and phospholipids denature proteins, increasing their sensitivity to proteolytic enzymes [17]. Peptides and AAs may also interact with gastrointestinal receptors to exert bioactivities [20].

The intestinal lumen also contains endogenous proteins, including mucus, enzymes, and desquamated cells; thus, dietary protein is not the only source of AAs. Daily endogenous nitrogen loss from the ileum has been calculated at 2026 ± 441 mg/d. The AAs in endogenous proteins are partially recycled during digestion, so these proteins could be a major source of bioactive peptides [21].

In the small intestinal lumen, endogenous proteins mix with dietary proteins. Gastric and pancreatic secretions, desquamated intestinal epithelial cells, and mucous proteins are several sources of the endogenous luminal proteins [22,23]. Proteases and peptidases from the exocrine pancreas break down these proteins in the small intestine lumen. The resultant peptides can be further degraded by enterocyte enzymes. Then, transporters located in the brush border and basolateral membranes of enterocytes move oligopeptides and AAs from the lumen into the portal bloodstream [24,25].

3.2. Microbial Fermentation of Amino Acids

3.2.1. Catabolic Pathways of Amino Acids by Bacteria

Two main pathways drive AA degradation by gut bacteria: deamination and decarboxylation, which generate SCFAs and amines, respectively [26]. These two types of metabolites are essential, as summerized in Figure 1.

The three major SCFAs acetate, propionate and butyrate are the main end products from carbohydrate fermentation in the proximal colon. In contrast, AA fermentation in the distal colon produces a more complex mixture of metabolites, including ammonia, SCFAs (acetate, propionate, and butyrate), and branched-chain fatty acids (BCFAs; valerate, isobutyrate, 2-methylbutyrate, and isovalerate). BCFAs, which account for 5–10% of total SCFAs and originate exclusively from branched-chain AAs (BCAAs) [27,28]. Importantly, a shift in SCFA profiles, particularly a relative increase in AA-derived SCFAs and BCFAs, often reflects the displacement of carbohydrate fermentation due to reduced substrate availability, rather than a direct increase in protein fermentation per se. Though both carbohydrate- and amino acid-derived pathways can produce SCFAs, their physiological effects differ significantly [29]. Carbohydrate-derived SCFAs, specifically acetate, propionate, and butyrate, are typically linked to beneficial effects, including the enhancement of barrier integrity and the regulation of immune and anti-inflammatory responses [30]. In contrast, AA-derived BCFAs serve as indicators of proteolytic fermentation, frequently associated with intestinal irritation, elevated luminal pH, and heightened permeability or inflammation [31]. Distinguishing between these sources is essential for the analysis of fermentation outcomes and their health implications. These metabolites influence epithelial physiology by modulating the mucosal immune system and signaling pathways in epithelial cells [27,32]. They also regulate bacterial gene expression and the production of enzymes related to AAs metabolism [33]. In addition, microbial metabolism of AAs also produces BAs.

Decarboxylation of AAs produces BAs. Intestinal bacteria commonly generate cadaverine from lysine and agmatine from arginine [34]. These BAs can have notable physiological effects. Agmatine, for instance, raises tissue cAMP levels in rats, replicating caloric restriction-related metabolic reprogramming and reducing diet-induced weight gain [35].

AAs are generally utilized either for the synthesis of bacterial cellular components or catabolized via multiple metabolic pathways. Dietary proteins or AAs intake can shift AA metabolism by modulating microbial populations and metabolic pathways. Such shifts in microbial metabolism can have either beneficial or detrimental effects on the host. Thus, modifying dietary protein or AA intake could serve as a strategy to shape the composition and metabolic activity of gut bacteria, in turn, host metabolism [36].

3.2.2. Anabolic Pathway of Amino Acids by Bacteria

AAs can be directly incorporated into bacterial proteins. This process requires bacterial AA transporters, which can transport external AAs into bacterial cells, especially under nutrient-sufficient conditions. For example, the ABC-type methionine transporter (MetN) mediates the high-affinity uptake of methionine. In Escherichia coli, deletion of metN abolishes methionine transport, leading to decreased cellular viability [37]. Similarly, ArtJ, an ABC transporter that specifically binds arginine with high affinity, enhances arginine uptake when overproduced in Escherichia coli.

In addition to directly utilizing these external sources, gut microbiota also expands the AA pool through de novo biosynthesis [36] (Figure 1). In vitro studies have demonstrated that Streptococcus bovis, Selenomonas ruminantium, and Prevotella bryantii, isolated from ruminal bacteria, perform de novo synthesis of AAs in the presence of physiological levels of peptides [38]. Gut microbial genomes are enriched with multiple clusters of orthologous genes associated with critical AA synthesis [39]. These AAs are built from metabolic precursors derived from central metabolism, with thirteen of the twenty originating from pyruvate, oxaloacetate, and α-oxoglutarate. Among these AAs, glutamine and glutamate are key intermediaries in nitrogen metabolism [40]. Glutamate and aspartate are particularly abundant due to their roles in microbial nitrogen assimilation and cellular biosynthesis. These AAs are subsequently incorporated into bacterial proteins through ribosomal translation, whereby mRNA templates direct the stepwise assembly of polypeptides [38].

Within the complex gut environment, microbial communities exhibit remarkable metabolic flexibility, enabling them to assimilate available nutrients to support growth and maintain functional proteomes. In vitro experiments with ¹⁵N-labeled ammonia have revealed that a substantial portion of microbial AA nitrogen can be derived from ammonia through de novo biosynthesis pathways, especially under peptide-limiting conditions. As peptide availability increases, the relative contribution of de novo synthesis decreases, although it remains important for metabolism. In vivo studies further support the nutritional relevance of microbial AAs, showing that lysine produced by gut microbiota can be absorbed by the host and incorporated into host proteins [41,42]. These findings underscore the physiological importance of de novo synthesis of AAs by gut microbiota.

Taken together, these findings indicate that resident gut microbial species not only rely on dietary or host-derived AAs but are also capable of synthesizing nutritionally important AAs independently. This ability supplies essential building blocks for protein synthesis, enabling microbial communities to maintain proteomic and cellular function even under nutrient scarcity. The tight coupling between de novo AA production and protein translation underscores the metabolic adaptability that supports bacterial proliferation and functional resilience in the gut [43].

4. Effect of High Protein Levels on Gut Microbes

4.1. Dysbiosis

The intestine hosts a diverse colony of bacteria that tremendously facilitates protein metabolism. Recent studies suggest that more protein sources and AAs have different effects on the gut microbiome, and protein-rich diets are shown to dramatically change the composition of gut bacteria, leading to dysbiosis, as summerized in Figure 2. This imbalance is associated with altered intestinal morphology, permeability, and pro-inflammatory cytokines. Furthermore, pigs fed high-protein diets show a significantly increased occurrence of post-weaning diarrhea. Conversely, a high level of protein in the diet leads to increased body weight and average daily gain (ADG). High-protein diets can improve some aspects of growth, but also potentially impair gut health and microbial balance [44]. High-protein diets enhance proteolytic fermentation in the gut, leading to increased luminal concentrations of protein fermentation metabolites such as BAs that have been shown to increase gut permeability [45]. A high-protein diet has shown considerable feedback in some other studies. The concentration of lactate, succinate, and formate increased significantly in colonic luminal contents in rats fed a high-protein diet, which relates to an increase in substrate availability and a decrease in Faecalibacterium prausnitzii [46], Clostridium leptum groups and Clostridium coccoides counts observed in the cecum and colon. Moreover, high-protein diets result in a decrease in propionate- and butyrate-producing bacteria and consequently a decrease in propionate and butyrate production, which may contribute to a more favorable niche for pathogenic bacteria. Feeding rats with a high-protein diet resulted in an increase in some bacteria associated with diseases (e.g., Escherichia/Shigella, Enterococcus, and Streptococcus) and a decrease in beneficial bacteria (e.g., Ruminococcus, Akkermansia, and F. prausnitzii) [47].

A reduced abundance of carbohydrate utilizers including Lachnospiraceae, Ruminococcaceae, Akkermansia, Prevotella, Roseburia, Ruminococcus, Akkermansia muciniphila, Bifidobacterium animalis, F. prausnitzii, Roseburia/Eubacterium rectale, and Ruminococcus bromii is observed in high-protein diets [48]. This clearly highlights the importance of efficient dietary carbohydrate consumption in not only minimizing protein fermentation but also maintaining a healthy population of commensal bacteria capable of generating beneficial metabolites like SCFAs [49]. For example, the probiotic Akkermansia muciniphila degrades mucin, an important constituent of the mucus layer, which has been linked to host metabolism and immunity and also serves as a therapeutic target for several gastrointestinal, metabolic, immune, and neoplastic diseases [50]. Therefore, these findings partially align with the negative consequences of a high protein intake, particularly in the presence of low-carbohydrate diets.

4.2. Bacterial Metabolism

Protein-utilizing bacteria break down proteins, AAs, and oligopeptides through several metabolic pathways. These processes generate metabolites including SCFAs, BAs, and ammonia [2,51]. The microbiota-derived BAs are critical in intestinal health, which can be influenced by the dietary protein levels [52]. Availability of free AAs and the existence of decarboxylase-positive non-starter bacteria are key factors contributing to excessive BAs production [53]. High-protein diets can induce dysbiosis, an imbalance between pathogenic and beneficial bacteria. Although most nitrogenous compounds can be reabsorbed, a diet excessive in protein promotes the proliferation of proteolytic bacteria, thus increasing the synthesis of ammonia and BAs. These metabolites can affect gut health, including altering luminal pH and disrupting the overall microbial habitat [13,54]. Therefore, maintaining appropriate protein levels is essential for supporting a stable gut microbial ecology [8].

Though BAs play an essential role in various biological processes, elevated concentrations can be harmful, potentially contributing to disease development or toxic effects [55]. High levels of BAs have been linked to a variety of negative health consequences, including nausea, respiratory trouble, sweating, heart palpitations, headache, bright red rash, oral burning sensations, changes in blood pressure, diarrhea, and hypertension [56]. Establishing precise toxicity thresholds for BAs remains challenging due to significant interindividual variation in the efficiency of detoxification systems, which greatly influences the dose required to elicit harmful effects. This variability depends on factors such as personal sensitivity, alcohol consumption, and medication use, particularly substances that either interfere with amine oxidase enzymes responsible for detoxifying excess BAs or act as monoamine oxidase inhibitors [57,58].

5. Effect of High-Protein Diets on Intestinal Physiology

5.1. Barrier Function

Compromised gut barrier function is closely linked to many chronic illnesses and systemic inflammation. Gut microbiota break down undigested dietary proteins and produce nitrogenous metabolites that have been shown to impair barrier integrity in vitro [59]. Protein fermentation generates compounds that can compromise intestinal barrier integrity [60]. Proteolytic bacteria and their metabolites are influenced by dietary protein levels, playing a critical role in regulating the intestinal mucosal barrier through modulation of tight junction proteins (TJs) and Zonulin signaling. This dysregulation can lead to increased intestinal permeability, allowing harmful substances to pass from the gut lumen into the bloodstream [61].

Gut microorganisms influence the intestinal epithelial barrier by regulating the expression of TJs such as Zonula occludens-1 (ZO-1) and Zonula occludens-2 (ZO-2) [62]. High levels of wheat gliadin have been reported to cause intestinal mucosal damage in patients with celiac disease. However, supplementation with Bifidobacterium lactis under high levels of wheat gliadin can reduce buckling of the intestinal epithelial membrane and upregulate ZO-1 expression, thus ameliorating the injury exerted by celiac-toxic gliadin [63]. Conversely, low-protein diets or normal-protein diets reduce intestinal epithelial permeability through modulating ZO-1 expression [64]. Such dietary interventions can lower E. coli abundance, and inhibition of E. coli growth has been further associated with ZO-2 up-regulation, helping to protect enterocytes and restore epithelial barrier function [65]. Zonulin is a known physiological regulator of intercellular tight junctions. It triggers the disassembly of tight junctions and increases intestinal permeability upon binding to its receptor on epithelial cells. It has been reported that Zonulin could mediate interactions between gut bacteria and tight junction proteins [66], and its up-regulation in genetically susceptible individuals may contribute to immune-mediated illnesses [67]. Intestinal bacteria are capable of inducing Zonulin secretion, which can be influenced by nutrient levels. It has been reported that high-protein diets stimulate the growth of E. coli and Salmonella, which induces Zonulin release and increases paracellular permeability. These findings underscore the role of protein level intervention in modulating gut bacteria and intestinal barrier function. Recent human studies indicate that optimal intake of high-quality dietary protein or particular protein-derived peptides (such as whey or glutamine) can improve intestinal barrier integrity by raising the expression of tight junction proteins, including ZO-1 and Occludin, and reducing inflammatory markers such as CRP and Tumor necrosis factor-alpha (TNF-α) [68,69]. However, excessive protein intake, particularly when exceeding 30% of total energy or predominantly sourced from animal protein, has been associated with increased intestinal permeability, oxidative stress, and proinflammatory responses [70]. These findings suggest that balanced protein consumption is essential for maintaining epithelial stability and intestinal health, whereas overconsumption may compromise barrier function.

5.2. Immunity

Proteins are essential for supporting growth, cellular operation, and immune defense. The intestine, serving as the main site for protein digestion and absorption, is also a major immune organ. Numerous studies have demonstrated that the intestinal immune system is highly sensitive to protein levels.

High protein levels can modulate Toll-like receptor (TLRs) and cytokine production, therefore triggering immune cell activation and inflammation. AAs are necessary for the synthesis of immune proteins such as cytokines and antibodies that mediate immune responses [71]. Specific AAs such as tryptophan and arginine could be metabolized into bioactive compounds that participate in immune regulatory pathways [72]. Studies in pigs and Drosophila melanogaster models have shown that high dietary protein improves intestinal cellular and humoral immunity, which correlates with elevated expression of antimicrobial peptides [73]. An intervention study involving individuals with type 2 diabetes demonstrated that high-protein diets led to reduced levels of the proinflammatory adipokine chemerin [74]. Similarly, energy-restricted diets with either normal or high protein content result in weight loss accompanied by considerable decreases in proinflammatory monocyte subpopulations, plasma lipids, and lipoproteins in overweight and obese adults [75]. Human studies support these findings, indicating that protein consumption affects both systemic and intestinal immunity. Clinical interventions have shown that balanced protein intake (15–20% of total energy) supports immune homeostasis by maintaining anti-inflammatory cytokine profiles such as Interleukin-10 (IL-10) and reducing TNF-α and Interleukin-6 (IL-6) levels [76]. Conversely, high protein intake over 30% of total energy consumption may elevate oxidative stress and systemic inflammation in humans. The results indicate that sufficient protein intake, rather than excessive rates, is essential for maintaining immune equilibrium and mitigating inflammation-related risks [77]. A comprehensive understanding of the role and mechanisms of protein level intervention is crucial for refining nutritional recommendations and mitigating potential immune-related complications.

While adequate protein is indispensable for proper immune function, excessive protein intake may disrupt immune homeostasis, particularly in the gut. High protein consumption can lead to an imbalance in gut-associated lymphoid tissue, therefore compromising immune balance. High-protein diets have been shown to increase intestinal permeability and elevate cytokine secretion in response to lipopolysaccharide compared with normal-protein diets in piglets [78]. For instance, TNF-α is a typical proinflammatory cytokine. Diets high in protein (18–20%) significantly increased TNF-α levels compared to a 16% protein control, indicating that excessive protein intake may promote inflammation [15]. Moreover, it has been reported that high-protein diets induced intestinal inflammation via upregulation of Nuclear factor kappa B (NF-κB) signaling pathway, contributing to intestinal inflammation and diarrhea in piglets [79]. Several studies have indicated that high protein levels could increase pro-inflammatory factors and upregulate the expressions of Myeloid differentiation primary response 88 (MyD88), TLR-4, and NF-κB in the colon of piglets, ultimately leading to impaired immune function [80] (Figure 2).

6. Regulatory Strategies

6.1. Dietary Regulation

Recent research underscores that the level and type of dietary protein are crucial in modulating gut microbiota composition and intestinal health, notably through the nitrogen metabolism pathway [81]. The definitions of “low”, “moderate”, and “high” dietary protein levels varied among species due to variations in digestive physiology and nitrogen use efficiency. In humans, protein consumption above 2.0 g/kg body weight per day is typically regarded as elevated and has been linked to alterations in gut microbial fermentation pathways [13]. Diets for pigs above 18–20% CP are categorized as high-protein diets and have been demonstrated to elevate proteolytic fermentation and intestinal inflammation in piglets [15]. An appropriate balance of nitrogen nutrition, including hydrolyzed proteins, peptides, and plant-derived proteins, has demonstrated the ability to regulate gut microbial metabolism, diminish detrimental nitrogenous metabolites, and preserve epithelial integrity [82]. Moreover, it has been shown that optimizing the carbon-to-nitrogen (C/N) ratio through dietary intervention, particularly by adding resistant starch improves gut health and microbial nitrogen utilization [83]. This approach promotes the microbial production of SCFAs while limiting the generation of ammonia and other proteolytic byproducts [84] that are linked to inflammation and barrier impairment [85]. Research in both animals and humans indicates that a moderate dietary protein level, generally between 14–16% for monogastric animals, is optimal for maintaining a balanced microbiota and intestinal function [86,87]. Animal studies have also demonstrated that diets with approximately 17% crude protein can enhance intestinal barrier function without inducing excessive protein fermentation [88]. In human research, protein consumption of 1.2–1.6 g/kg/day has been linked to good immune regulation and gastrointestinal health, especially in elderly or sick groups [12]. Therefore, controlling the amount and quality of protein in the diet provides a comprehensive strategy for improving intestinal health.

6.2. Microbiome Modulation

One practical strategy to enhance host immunity and metabolism is to modify gut microbes. Adjusting fiber and protein intake can encourage the growth of advantageous microbes by identifying bacterial enterotypes, such as Prevotella-dominant or Bacteroides-dominant profiles. While those with Prevotella-rich microbiota often benefit from diets higher in fiber, Bacteroides-dominant individuals may respond better to diets high in protein [89,90]. Additionally, the identification of probiotics that overexpress proteolytic enzymes, such as Lactobacillus helveticus or Bacillus subtilis, may alleviate excessive protein fermentation and enhance nitrogen utilization in the gastrointestinal tract [91,92]. Such solutions provide a tailored nutritional strategy to enhance gut homeostasis and mitigate protein-related dysbiosis [93]. The inclusion of resistant starches and soluble fibers (such as inulin and arabinoxylan) can further decrease ammonia and biogenic amine accumulation [94]. Protein source and solubility also determine the extent of microbial degradation; for instance, plant-based proteins (soy, pea) are fermented more slowly than animal-derived or highly soluble proteins (casein, whey), leading to reduced putrefactive metabolites [95]. Additionally, probiotic strains such as Lactobacillus plantarum, Bifidobacterium longum, and Bacillus subtilis have shown species-specific benefits in mitigating intestinal inflammation and restoring barrier function [96]. Co-feeding fermentable carbohydrates with moderate protein diets effectively suppresses proteolytic pathways and supports gut homeostasis across host species [97,98] (Table 1).

Table 1. Summarizes practical strategies that can be applied to regulate proteolytic fermentation and improve intestinal health.

Condition	Specie	Recommended Intervention	Ref.
High protein diet (>17%)	Human	Add 3–5% resistant starch or soluble fiber to balance C/N ratio	[92]
shortage of feed protein sources	ruminant	replace with non-protein nitrogen (urea, ammonia solution), beneficial for microbial protein synthesis in ruminants	[99]
high fermentation crude protein (20.1%), damage the colonic barrier function	piglet	provide high level of fermentable carbohydrates (total dietary fibre 18.0%) to balance C/N ratio and improve barrier function.	[95]
excessive protein fermentation ↑ nitrogenous metabolites, ↓ epithelial integrity	human	An appropriate balance of nitrogen nutrition, including hydrolyzed proteins, peptides, and plant-derived proteins	[78]
↓ epithelial barrier integrity	human	Supplement Probiotics (Lactobacillus and Bifidobacterium genera)	[96,100]

up arrow ↑: increased; down arrow ↓: decreased

Table 1. Summarizes practical strategies that can be applied to regulate proteolytic fermentation and improve intestinal health.

Condition	Specie	Recommended Intervention	Ref.
High protein diet (>17%)	Human	Add 3–5% resistant starch or soluble fiber to balance C/N ratio	[92]
shortage of feed protein sources	ruminant	replace with non-protein nitrogen (urea, ammonia solution), beneficial for microbial protein synthesis in ruminants	[99]
high fermentation crude protein (20.1%), damage the colonic barrier function	piglet	provide high level of fermentable carbohydrates (total dietary fibre 18.0%) to balance C/N ratio and improve barrier function.	[95]
excessive protein fermentation ↑ nitrogenous metabolites, ↓ epithelial integrity	human	An appropriate balance of nitrogen nutrition, including hydrolyzed proteins, peptides, and plant-derived proteins	[78]
↓ epithelial barrier integrity	human	Supplement Probiotics (Lactobacillus and Bifidobacterium genera)	[96,100]

up arrow ↑: increased; down arrow ↓: decreased

7. Conclusions and Perspectives

Protein metabolism is a complex process involving host-derived enzymes as well as gut bacterial activity. Dietary proteins are primarily broken down into AAs and peptides by proteases, which are essential for nutrient absorption. Concurrently, protein-utilizing bacteria further degrade proteins, AAs, and oligopeptides through multiple pathways, generating metabolites such as ammonia, BAs, and SCFAs. These metabolites exert significant physiological effects that shape systemic metabolism and intestinal health. High dietary protein intake can significantly alter the gut ecology. It alters bacterial composition, leading to dysbiosis, an imbalance between pathogenic and beneficial bacteria. This imbalance is often accompanied by increased production of BAs, which may have detrimental health effects when accumulated at high levels. Furthermore, excessive protein consumption enhances bacterial metabolic activity that promotes the synthesis of harmful metabolites, which may exacerbate intestinal and systemic dysfunction.

High protein levels also play a role in intestinal health, primarily influencing inflammation, immunity, and barrier function. Excessive protein fermentation can damage the intestinal barrier, thus increasing its permeability and allowing harmful substances to enter the bloodstream. This impairment often triggers immune responses and inflammation, thereby contributing to gut-related disorders. Understanding the regulatory mechanisms underlying these effects is essential for developing strategies to mitigate the negative impacts of high-protein diets on gut health.

Future research should focus on elucidating the interactions between dietary protein and the gut microbiota, including the effects of different protein sources and structures on microbial ecology and metabolism. It is also essential to investigate the role of microbial metabolites, such as SCFAs, ammonia, and BAs, in regulating intestinal barrier integrity and immune responses. Integrating multi-omics technologies, in vitro models, and human intervention trials will be crucial to systematically decipher the molecular mechanisms and physiological effects along the “protein–microbiota–host” axis. The ultimate goal is to develop evidence-based, personalized dietary recommendations that can precisely modulate the gut microbial community and its metabolic outputs, thereby promoting intestinal health and overall well-being.