Nanoparticle-Driven Modulation of Mucosal Immunity and Interplay with the Microbiome

Abstract

Mucosal surfaces are dynamic immunological interfaces that play a critical role in maintaining host defense and microbial homeostasis. Disruptions in the interaction between the mucosal immune system and its commensal microbiota have been associated with the onset of several diseases, including inflammatory bowel disease, asthma, and bacterial vaginosis. This review examines recent advances in nanoparticle (NP)-based strategies aimed at modulating mucosal immunity and restructuring microbial communities. It highlights how organic and inorganic NPs such as polysaccharide-based carriers, lipid NPs, and metallic nanomaterials enhance the delivery and stability of probiotics, prebiotics, and synbiotics, and facilitate targeted immunomodulation across gastrointestinal, respiratory, and female reproductive mucosal tissues. NP-based strategies are particularly emphasized for their ability to penetrate mucus barriers, facilitate microbial colonization, modulate cytokine activity, and enhance the restoration of epithelial barrier function. Disease-specific applications, including NP-based therapies for colitis, respiratory inflammation, and vaginal dysbiosis, are also discussed. In addition, this review outlines current challenges related to biosafety, targeting specificity, and clinical translation, and suggests future directions for research. Altogether, NP platforms offer a promising avenue for the precise modulation of mucosal immunity and microbiota, with significant potential in the prevention and treatment of mucosal-associated diseases.

Introduction

Mucosal surfaces are fundamental interfaces between the host and its external environment, forming the first line of defense while facilitating essential physiological functions. Located in the gastrointestinal (GI), respiratory, and female reproductive tracts, these surfaces not only act as barriers against pathogens but also support symbiotic relationships with commensal microorganisms [1, 2]. The mucosal areas are equipped with complex networks of physical, chemical, and immune mechanisms that defend against pathogenic microbial threats while facilitating essential physiological functions [3].

The mucosal immune system is uniquely positioned to balance protective immunity with immune tolerance [4]. It relies on an intricate interplay of epithelial barriers, innate immune defenses, and adaptive immune responses to recognize and eliminate pathogens while maintaining tolerance to commensal microorganisms and dietary antigens [5]. Disruption of this delicate balance may result in immune dysfunction, contributing to the onset of inflammatory disorders, allergic reactions, and susceptibility to infections [6].

The mucosal microbiome encompasses groups of microbes and their genetic material forming a complex and dynamic ecosystem of microorganisms inhabiting mucosal surfaces that closely interact with the immune system [7]. Predominantly composed of bacteria, the microbial community plays a critical role in modulating immune responses, preserving epithelial barrier function, and regulating host metabolic pathways [8]. Interestingly, certain microbial taxa within the general microbiota have been shown to influence the regulation of mucosal immune systems including adaptive, innate, and cell-autonomous immune responses [7]. However, disruption of the balance of the microbiome composition known as dysbiosis, characterized by reduced microbial diversity or the over proliferation of pathogenic species, is increasingly implicated in the pathogenesis of mucosal and systemic disorders, including inflammatory bowel disease (IBD), asthma, and bacterial vaginosis (BV) [9, 10].

Recent advances in nanotechnology have provided novel tools to address the challenges associated with mucosal immunity and microbiome modulation [11]. Nanoparticles (NPs), characterized by their nanoscale dimensions and highly tunable physicochemical properties, demonstrate significant potential in targeting the mucosal microenvironment [12]. Owing to their unique physicochemical properties, NPs represent promising platforms for the design of drug delivery systems and the development of therapeutic strategies aimed at restoring microbial homeostasis [13]. Nevertheless, direct evidence for the role of nanoparticle-based strategies in mucosal microbiome regulation remains largely unexplored.

This review explores the distinct roles of mucosal immunity, the microbiome, and NPs, examining their individual contributions and interconnections. We suggest that NPs, by targeting microbial imbalances and modulating immune responses, offer promising avenues for supporting microbial homeostasis and mitigating the effects of dysbiosis-associated conditions.

Overview of Mucosal Immunity

Mucosal surfaces represent the first site of interaction between the host and its external surroundings [14]. The mucosal surfaces fulfill a dual role by both defending against pathogen invasion and fostering symbiotic interactions with commensal microorganisms that reside on mucosal sites [15]. The mucosal immune system relies on a coordinated network of physical, chemical, and immunological defenses to inhibit pathogen entry while ensuring the preservation of critical processes such as nutrient absorption, gas exchange and maintenance of reproductive tract integrity [16]. The major components of the mucosal immune system consist of diverse immune cell populations, epithelial cells, mucus layers, and a range of antimicrobial mediators [17]. Together, these elements form a dynamic barrier that ensures a balance between immune protection and tolerance to non-pathogenic antigens, maintaining microbial and tissue equilibrium [18].

Mucosal Epithelial Cells

Epithelial cells form a structurally continuous barrier maintained by tight junctions, which regulate selective permeability to support critical physiological functions while restricting pathogen entry [19]. In addition to their barrier function, epithelial cells actively interact with microbiota, which play a critical role in maintaining barrier integrity and modulating immune responses [20]. For instance, epithelial cells respond to microbial metabolites, such as SCFAs (short-chain fatty acids) including propionate, acetate, and butyrate, which are produced by microbiota, enhance tight junction integrity and promote anti-inflammatory pathways [21]. Beyond their structural role, epithelial cells produce antimicrobial peptides (AMPs) including defensins, cathelicidins, and lactoferrin, which exhibit potent antimicrobial activity against a broad spectrum of pathogens [22]. For instance, epithelial cells recognize bacteria through Toll-like receptors (TLRs) or NOD-like receptors, triggering signaling pathways that produce AMPs and cytokines while avoiding excessive inflammation to maintain homeostasis [23].

In contrast, pathogenic bacteria exploit epithelial cells to facilitate infection. Pathogens such as Helicobacter pylori, Escherichia coli, and Pseudomonas aeruginosa disrupt tight junctions by secreting virulence factors, weakening the epithelial barrier and allowing microbial translocation [24]. For instance, enterohemorrhagic E. coli produces Shiga toxin, which damages epithelial cells and disrupts the intestinal barrier [25]. Additionally, pathogens such as E. coli, Salmonella and Shigella, induce epithelial cell apoptosis or hijack endocytic pathways to gain intracellular access, further compromising barrier integrity [26].

Innate Immunity

Innate immune cells including dendritic cells (DCs), macrophages, innate lymphoid cells, and natural killer (NK) cells, are strategically distributed within mucosal tissues, each performing distinct and complementary roles in host defense [27].

Macrophages are abundant in mucosal tissues, playing key roles in pathogen clearance, apoptotic cell removal, and tissue repair [28]. They balance pro-inflammatory and anti-inflammatory responses to maintain immune homeostasis [29]. Within the GI tract, intestinal macrophages of the M2 phenotype secrete anti-inflammatory cytokines, such as IL (interleukin)-10, IL-4, and transforming growth factor beta (TGF-β) to mitigate excessive inflammatory responses and facilitate immune tolerance to commensal microbiota, thereby preserving the integrity of the gut barrier [30]. In the respiratory system, alveolar macrophages clear pathogens and particulates while producing IL-10 to prevent inflammation-induced damage to the lungs. Alveolar macrophages also coordinate tissue repair after injury or infection [31].

DCs, as the major antigen-presenting cells (APCs), capture mucosal antigens and migrate to lymph nodes to activate T cells and initiate adaptive immunity [32]. In the intestinal mucosa, they induce immune tolerance to dietary antigens and commensal microbes, preventing aberrant immune activation [33]. In the female reproductive mucosa, microbes such as Lactobacillus promote DC-induced regulatory T cell (T_reg) differentiation, suppressing excessive inflammation and maintaining immune homeostasis [34].

Adaptive Immunity

The adaptive immune system in mucosal tissues is highly specialized to provide long-term, pathogen-specific immunity while maintaining tolerance to non-pathogenic antigens [35]. This coordinated interaction shapes antigen-specific immune responses. This dual functionality enables the immune system to effectively combat infections while preserving tissue integrity by minimizing excessive or inappropriate inflammatory responses [36].

T cells in mucosal immunity encompass diverse subtypes, each specialized to address distinct immunological challenges [37]. These include CD4⁺ helper T cells, CD8⁺ cytotoxic T cells (CTLs), γδ T cells, and others [38]. Collectively, these subtypes coordinate a highly adaptive immune response tailored to the specific needs of mucosal tissues.

T helper cells, known as CD4⁺ T cells, comprise several subtypes, including T helper 1 (T_H1), T helper 2 (T_H2), T helper 17 (T_H17), and T_reg cells. These subsets contribute respectively to intracellular pathogen clearance, antiparasitic immunity, induction of antimicrobial peptides, and regulation of excessive immune responses [39].

CTLs are fundamental in targeting and eliminating infected or abnormal epithelial cells in mucosal tissue by recognizing pathogen-derived peptides on major histocompatibility complex (MHC) class I from DCs and releasing perforin and granzyme [40].

In conclusion, the mucosal immune system orchestrates a complex interplay of physical barriers, innate defenses, and adaptive responses to protect against pathogens while maintaining tolerance to commensals and non-threatening antigens [41]. This balance is critical for preserving tissue integrity across the GI, respiratory, and reproductive tracts [42], highlighting its central role in health and its potential as a target for advanced therapeutic strategies.

Mucosal Microbiome

Technological progress in metagenomics and 16S rRNA-based sequencing has greatly enhanced insights into the mucosal microbiome [43]. These methodologies have enabled the comprehensive identification and characterization of non-culturable microorganisms that were previously undetectable using conventional culture-based approaches [44]. Bacteria, the dominant members of the mucosal microbiome, coexist with diverse microorganisms such as archaea, fungi, viruses, and protozoa, residing on mucosal surfaces [45]. These microorganisms interact with microbial metabolites and the surrounding microenvironment to support critical host functions and microbial homeostasis [46]. The mucosal microbiome regulates key host physiological processes including nutrient metabolism, immune modulation, and epithelial barrier defense [4], thereby maintaining microbial equilibrium. Disruptions in this balance, referred to as dysbiosis, can lead to immune dysfunction and increase the risk of various mucosal and systemic diseases [47] (Fig. 1).

Fig. 1. Representative patterns of mucosal dysbiosis across disease conditions.

Site-specific microbial shifts observed in the gut, respiratory tract, and female reproductive tract under various disease conditions. Dysbiosis is represented by the relative enrichment or depletion of microbial taxa associated with obesity, type 2 diabetes, inflammatory bowel disease, asthma, chronic obstructive pulmonary disease, respiratory infections, and sexually transmitted infections.

The Gut Microbiome

The gut microbiome, hosting over a trillion microorganisms, is the most extensively studied mucosal microbiota [48]. A healthy gut microbiome is characterized by high microbial diversity, which confers resilience against environmental stressors such as dietary shifts, infections, and antibiotic exposure. In contrast, gut dysbiosis disrupts immune regulation, increases systemic inflammation, and contributes to metabolic dysfunction [49](Table 1).

Table 1.

Diseases associated with gut microbiome dysbiosis.

Disease	Microbiome change	Functional effect	Ref.
Obesity	Firmicutes/Bacteroidetes ratio ↑	Enhanced carbohydrate fermentation and nutrient absorption	[52]
	Porphyromonas, Campylobacter, Bacteroides, Staphylococcus, Parabacteroides, Dialister, Ruminococcus ↑	Associated with low microbial diversity, inflammation, and metabolic dysregulation	[53]
	Christensenellaceae, Methanobacteriales, Bifidobacteria, Akkermansia ↓	Reduced probiotics linked to inflammation and metabolic dysfunction	[54]
Type 2 Diabetes (T2D)	Firmicutes ↓ Betaproteobacteria, Lactobacillus ↑	Reduced glucose tolerance, systemic inflammation, and metabolic dysregulation	[56]
	F. prausnitzii, R. intestinalis ↓	Loss of butyrate producers linked to reduced insulin sensitivity and impaired glucose regulation	[57]
	Bifidobacterium, Bacteroides, Akkermansia ↓	Impaired gut barrier, immune dysfunction, and reduced insulin sensitivity	[58]
Inflammatory Bowel Disease (IBD)	F. prausnitzii, Bifidobacterium, Firmicutes ↓	Reduced butyrate production, impaired mucosal protection, and increased inflammation	[62]
	Clostridium leptum group, Firmicutes ↓	Reduced butyrate production and impaired mucosal immune regulation	[63]
	Bacteroides group, Bifidobacterium spp., Clostridium leptum group, Firmicutes ↓ Enterobacteria ↑	Pro-inflammatory potential and epithelial adhesion	[64]

Obesity

Obesity, defined by body mass index (BMI) greater than 30 kg/m² [50], is primarily driven by dietary and genetic factors, but is also increasingly recognized to be critically influenced by the gut microbiota [51]. Many studies have identified an increased Firmicutes-to-Bacteroidetes ratio in individuals with obesity [52]. For instance, studies have demonstrated that individuals with obesity exhibit higher abundances of bacterial genera such as Porphyromonas, Campylobacter, Bacteroides, Staphylococcus, Parabacteroides, Dialister, and Ruminococcus when compared to lean individuals [53]. On the other hand, the Christensenellaceae family, along with the genera Methanobacteriales, Lactobacillus, Bifidobacteria, and Akkermansia, are commonly recognized as probiotics, with their relative levels frequently showing an inverse correlation with obesity [54].

Type 2 Diabetes (T2D)

T2D is a chronic metabolic disorder characterized by insulin resistance and insufficient insulin production, leading to prolonged hyperglycemia [55]. Gut microbiome studies in T2D patients have revealed a decline in the phylum Firmicutes, alongside an increase in the class Betaproteobacteria and the genus Lactobacillus, associated with elevated plasma glucose [56]. Additionally, there is a notable decrease in beneficial commensals in the phylum Firmicutes such as Faecalibacterium prausnitzii and Roseburia intestinalis and frequent depletion of other beneficial microbes, including genera Bifidobacterium, Bacteroides, and Akkermansia [57, 58]. These alterations are associated with microbial oxidative stress, β-cell dysfunction, and impaired glucose tolerance [57, 59]. This dysbiotic shift weakens gut barrier integrity, increasing gut permeability and LPS translocation, which causes metabolic endotoxemia, intensifies chronic inflammation, reduces SCFA production, and disrupts insulin signaling, exacerbating T2D complications [60].

Inflammatory Bowel Disease (IBD)

IBD impacts around 1 million individuals in the United States, with a rising global prevalence, particularly in early adulthood [61]. IBD, which includes Crohn's disease (CD) and ulcerative colitis (UC), is linked with decreased microbial diversity and depletion of anti-inflammatory species such as F. prausnitzii and Roseburia [62, 63]. While the abundance of Enterobacteria, including species such as E. coli, has been shown to increase in IBD patients [64]. This dysbiosis exacerbates mucosal inflammation and weakens the epithelial barrier, leading to increased levels of pro-inflammatory cytokines such as tumor necrosis factor-α (TNF-α), IL-18 and IL-6 as well as reactive oxygen species (ROS), which further contribute to intestinal damage [65].

The Respiratory Microbiome

The respiratory microbiome, encompassing microbial communities across the upper and lower airways, plays a critical role in maintaining pulmonary health and regulating immune responses [47]. Traditionally considered a sterile environment, the respiratory tract is now understood to host a dynamic and metabolically active microbiome, albeit with lower biomass and diversity compared to the gut microbiome [66]. The balance between commensal and pathogenic microorganisms across the respiratory tract is essential for immune equilibrium, protection against airborne pathogens, and preservation of pulmonary function [67] (Table 2).

Table 2.

Diseases associated with respiratory microbiome dysbiosis.

Disease	Microbiome Change	Functional Effect	Ref.
Asthma	Bacteroides spp. ↓ Haemophilus, Moraxella, Streptococcus, Staphylococcus ↑	Loss of immune regulation, steroid resistance, neutrophilic inflammation, and increased risk of exacerbation	[69]
	Lactobacillales, Mogibacteriaceae, Veillonella, Prevotella ↓ M. catarrhalis, H. influenzae, Streptococcus spp. ↑	Neutrophilic inflammation, steroid resistance, impaired immune regulation (IL-5, IL-6, IL-13, IL-8, IL-17A ↑ )	[71, 72]
	Firmicutes, Bacteroidetes, Actinobacteria ↓ Proteobacteria ↑	Reduced microbial diversity, impaired lung function, and a shift toward a proinflammatory microbial profile	[73]
COPD	Prevotella, Veillonella, Gemella ↓ Haemophilus, Moraxella, S. pneumoniae, S. aureus, P. aeruginosa, gram-negative enteric bacteria ↑	Neutrophilic inflammation, reduced lung function, immune exhaustion, and decreased microbial diversity (IL-8, TNF, IL-1β ↑ )	[75]
	Prevotella, Veillonella ↓ H. influenzae, S. pneumoniae, M. catarrhalis ↑	Biofilm-mediated immune evasion, persistent neutrophilic inflammation, and reduced antibiotic responsiveness	[76]
Respiratory Infections	Prevotella, Veillonella, Rothia spp. ↓ H. influenzae, S. pneumoniae, M. catarrhalis ↑	Reduced diversity, immune imbalance, and increased susceptibility to symptomatic viral infection	[81]
	Prevotella, Veillonella ↓ H. influenzae, M. catarrhalis, S. pneumoniae ↑	Impaired mucosal immunity, increased susceptibility to viral and bacterial coinfection	[82, 83]
	Corynebacterium, Dolosigranulum ↓	Negative correlation with disease severity, IFN-γ, IL-33 ↓	[84]

Asthma

Asthma is a chronic inflammatory airway disease marked by bronchial hyperresponsiveness, episodic airflow obstruction, and persistent inflammation [68]. The condition is frequently accompanied by microbial dysbiosis, typified by reduced microbial diversity and an overabundance of pathogenic taxa, which exacerbates airway inflammation and promotes disease progression [68]. This dysbiosis is characterized by reduced microbial diversity and overabundance of pathogenic taxa including Proteobacteria and Firmicutes at the phylum level. Within Proteobacteria, genera such as Haemophilus, Moraxella, and Neisseria are frequently overrepresented, and within Firmicutes, species such as Streptococcus pneumoniae and Staphylococcus aureus are enriched [69, 70]. Severe asthma is often associated with pathogenic colonization in the lower airways by M.catarrhalis, H.influenzae, and Streptococcus spp., triggering increased IL-5, IL-13, IL-8 and eosinophils [71, 72]. Conversely, the depletion of commensal bacteria such as those from the phyla Firmicutes, Bacteroidetes, and Actinobacteria compromises immune regulation and epithelial barrier integrity, further exacerbating the inflammatory milieu [73].

Chronic Obstructive Pulmonary Disease (COPD)

COPD is a progressive and debilitating lung condition that ranks among the foremost contributors to the global disease burden, affecting over 300 million people worldwide [74]. In COPD, the lung microbiome undergoes significant alterations, with a notable loss of microbial diversity and a concurrent rise in pathogenic taxa. Predominant pathogens in COPD include S. pneumoniae, S. aureus, M. catarrhalis, P. aeruginosa, Haemophilus species and gram-negative enteric bacteria [75], which trigger neutrophilic inflammation, exacerbate symptoms, and accelerate lung damage. These bacteria form biofilms, enhancing persistent antibiotic resistance and impairing mucociliary clearance [76].

Respiratory Infections

The viruses disrupt immune homeostasis and damage the respiratory epithelium, progressing to secondary bacterial infections, which worsen disease severity and delay recovery [77]. Common pathogens include S. pneumoniae, S. aureus, M. catarrhalis, H. influenzae, K. pneumoniae, and P. aeruginosa are frequently isolated in severe patients [78]. S. pneumoniae and S. aureus release cytotoxins, increasing epithelial apoptosis and bacterial proliferation [79], while K. pneumoniae and M. catarrhalis contribute to airway inflammation, especially in coinfections [80]. Beyond secondary infections, viral respiratory infections induce lung dysbiosis. Commensal bacteria, such as Prevotella and Veillonella, are frequently diminished [81], whereas pathogenic taxa from the Proteobacteria phylum, including S. aureus, S. pneumoniae, H. influenzae, and M. catarrhalis tend to be overrepresented [82], weakening epithelial barriers and promoting inflammation [83]. However, Corynebacterium and Dolosigranulum show a negative correlation with disease severity, highlighting their potential protective role [84].

The Female Reproductive Tract Microbiome

The female reproductive tract microbiome is critical for immunity, reproduction, and infection resistance [85]. Once thought to be static, it is now recognized as highly dynamic, influenced by hormonal changes, age, lifestyle, and external factors [86]. In healthy women, Lactobacillus species including L. jensenii, L. crispatus and L. gasseri, secret lactic acid to maintain an acidic vaginal pH (3.5 to 4.5), [87] which inhibits the growth of pathogens, including Gardnerella vaginalis and Candida albicans [88]. Beyond acid production, Lactobacillus limits pathogen adherence through competitive exclusion, forms a protective biofilm, and enhances mucosal barrier integrity by stimulating epithelial tight junctions and producing immune-modulating cytokines [89]. Like other mucosal sites, dysbiosis in the vaginal microbiome disrupts the microbial balance and contributes to health issues [90](Table 3).

Table 3.

Diseases associated with female reproductive microbiome dysbiosis.

Disease	Microbiome Change	Functional Effect	Ref.
STI	Lactobacillus spp. ↓ BV-associated anaerobes (G. vaginalis, Prevotella) ↑	Reduced mucosal defense, Risk of asymptomatic STIs and complications (infertility, ectopic pregnancy)	[92, 93]
	Lactobacillus spp. ↓ BV-associated anaerobes (G. vaginalis, A. vaginae, Prevotella spp.) ↑	Increased vaginal pH, reduced lactic acid, elevated SCFAs, impaired barrier, increased proinflammatory cytokines	[94, 95]
	Lactobacillus spp. ↓ BV-associated anaerobes (G. vaginalis, A. vaginae, Prevotella, Megasphaera) ↑	Reduced lactic acid and H2O2; increased pH and SCFAs; elevated IL-1β, IL-6, IL-8; epithelial barrier disruption; enhanced STI pathogen adhesion and invasion	[97-99]

Sexually Transmitted Infections (STI)

STIs are highly prevalent among sexually active individuals, with over 2.5 million cases reported in the United States [91]. Chlamydia trachomatis and Neisseria gonorrhoeae are common bacterial STIs and are often asymptomatic, leading to delayed diagnosis and complications such as infertility, and ectopic pregnancy [92, 93]. STI patients exhibit significant alterations in the vaginal microbiota, including reduced Lactobacillus levels and an increase in anaerobic bacteria such as G. vaginalis, A. vaginae [87, 94]. These microbial shifts raise vaginal pH and increase metabolites such as SCFAs, creating a favorable environment for pathogen colonization [95]. The loss of Lactobacillus reduces lactic acid and hydrogen peroxide production [96], weakening antimicrobial defenses and allowing N. gonorrhoeae and C. trachomatis to adhere to epithelial cells [97, 98]. Additionally, dysbiosis-associated anaerobes release inflammatory metabolites, stimulating the secretion of cytokines such as IL-1, IL-6, IL-12, and TNF-α. This exacerbates local inflammation, recruits immune cells, and weakens epithelial barriers, paradoxically facilitating pathogen survival and tissue damage [99]. The resulting inflammatory state sustains infection and increases susceptibility to other STIs, including human immunodeficiency virus (HIV) [100].

The Functionality of NPs in the Mucosal System

Organic NPs

Protein-based NPs. Protein-based NPs have emerged as a promising platform for modulating mucosal microbiota and immune responses due to their biocompatibility, biodegradability, and functional versatility [101]. These NPs are synthesized from natural or recombinant proteins, enabling the controlled delivery of bioactive compounds such as probiotics, antimicrobial peptides, and immunomodulatory agents [102]. Their ability to form stable nanostructures through self-assembly or engineered fabrication enhances their therapeutic potential in mucosal environments [101].

Protein-based NPs exert significant effects on the mucosal microbiota by selectively modulating microbial communities and enhancing probiotic viability. Encapsulation of Lactobacillus species in whey protein and zein protein NPs protects them from acidic degradation and improves their colonization efficiency within the GI tract [103]. Casein- and gelatin-based NPs have attracted considerable attention for their ability to protect probiotic viability and facilitate targeted delivery to the intestinal mucosa. These systems allow for efficient encapsulation and enable safe delivery without inducing cytotoxicity [104].

Beyond microbiota modulation, protein-based NPs influence mucosal immunity by enhancing the immune response and disease resistance as well as reinforcing epithelial barriers [105]. Albumin NPs loaded with bacterial lysates promote antigen presentation within mucosa-associated lymphoid tissue (MALT), leading to increased secretory immunoglobulin A (sIgA) production and enhanced mucosal immune responses [106]. Additionally, gelatin-based NPs have been shown to regulate inflammation by reducing pro-inflammatory cytokines such as TNF-α, IL-1 and IL-6 while promoting regulatory cytokines such as IL-10 and TGF-β [107, 108]. These immunomodulatory effects contribute to maintaining mucosal immune balance, which is critical in conditions such as IBD and allergic airway inflammation such as COPD [109, 110]. Moreover, protein-based NPs modulate mucosal barrier function by transiently opening epithelial tight junctions and interacting with goblet cells to influence mucin production, thereby facilitating drug transport while maintaining epithelial homeostasis [111].

The multifunctionality of protein-based NPs underscores their potential utility in mucosal-targeted applications. By modulating microbial composition, regulating local immune responses, and enhancing mucosal barrier integrity, these systems offer a promising framework for microbiome-centered therapeutic strategies. Nonetheless, further investigations are needed to refine their formulations, evaluate long-term safety, and establish reproducible clinical outcomes [112].

Lipid-based NPs. Lipid-based NPs are among the most established nanocarriers for mucosal delivery, owing to their biocompatibility, structural flexibility, and ability to encapsulate both hydrophilic and hydrophobic bioactive agents [113]. Common forms include liposomes, solid lipid nanoparticles (SLNs), nanostructured lipid carriers (NLCs), and lipid–polymer hybrid systems [114]. These systems are particularly suited for modulating mucosal microbiota and immune responses, as they can facilitate localized delivery to epithelial surfaces, enhance epithelial permeability, and protect labile compounds from enzymatic degradation in mucosal environments [115].

In mucosal systems, lipid-based NPs, such as curcumin-loaded liposomes combined with chitosan/gelatin multilayer coatings, have been used to enhance probiotic delivery. This strategy improves probiotic survival and adhesion while modulating gut microbiota—specifically increasing beneficial Lactobacillus and Ruminococcaceae and reducing inflammation-associated Marinifilaceae [116]. Lipid-based NPs contribute to mucosal immune modulation by facilitating the uptake of antigens and immunomodulators by APCs, such as DCs and macrophages [117]. Intranasal or oral mucosal delivery of lipid NPs has been shown to enhance local immune responses, including IgA secretion, and modulate T cell responses [118, 119].

At the epithelial barrier level, lipid-based NPs do not disrupt tight junction integrity, ensuring the preservation of mucosal barrier function. For example, in intestinal models, siRNA-loaded lipid NPs maintained transepithelial electrical resistance and the localization of tight junction proteins such as zonula occludens-1 (ZO-1), indicating no adverse effect on epithelial cohesion [120]. In contrast, pathological conditions such as IBD and colorectal cancer are associated with increased epithelial permeability due to tight junction disruption and immune cell infiltration. This so-called epithelial enhanced permeability and retention (EPR) effect facilitates the passive accumulation of NPs at inflamed sites, improving their potential for targeted delivery [121].

Collectively, these findings highlight the potential of lipid-based NPs as safe and efficient mucosal delivery platforms capable of modulating the microbiota, enhancing immune responses, and enabling targeted therapeutic action in both healthy and inflamed mucosal environments.

Polysaccharide-based NPs. Polysaccharide-based NPs have gained significant attention as mucosal delivery systems due to their biocompatibility, biodegradability, low immunogenicity, and intrinsic mucoadhesive properties [122]. In addition to these favorable characteristics, many of these NPs can selectively promote the growth of beneficial microbes, thereby modulating the gut environment. For instance, Bifidobacterium growth is promoted by octenyl succinic anhydride–modified starch NPs [123], and alginate hydrogel microspheres encapsulating Bifidobacterium enhance delivery to the colon and support proliferation while suppressing inflammation [124]. Lactobacillus populations are significantly enhanced by nanocrystalline cellulose [125], and alginate-based microspheres, which improve inflammatory gene expression, acid resistance, intestinal adhesion and SCFA expression [124].

In mucosal immunity, polysaccharide-based NPs influence immune responses by engaging pattern recognition receptors (PRRs), such as TLRs and C-type lectin receptors, found on mucosal DCs and macrophages [126]. Chitosan-based NPs have been shown to function as effective adjuvants by enhancing antigen uptake, promoting antigen presentation, and stimulating both humoral and cellular immune responses [126, 127].

Overall, the versatility of polysaccharide-based NPs—encompassing microbial modulation, immune regulation, and epithelial protection—underscores their therapeutic potential in mucosal-targeted interventions. Future innovations in surface engineering, stimuli-responsive release systems, and combinatorial delivery of microbiome modulators will further strengthen their role in next-generation mucosal nanomedicine (Fig. 2).

Fig. 2. Functional properties of organic nanoparticles in the mucosal system.

Key immunological and microbiological effects of protein-based, lipid-based, and polysaccharide-based nanoparticles at mucosal surfaces, including enhanced probiotic delivery, antigen uptake, immune modulation, and epithelial barrier support.

Inorganic NPs

Titanium dioxide (TiO₂) NPs. TiO₂ NPs are extensively utilized in diverse fields such as food processing, cosmetics, and pharmaceuticals due to their exceptional stability, biocompatibility, and photocatalytic properties [128]. These NPs have gained attention for their potential to influence the gut microbiome, particularly by targeting and eliminating pathogenic microorganisms that contribute to microbial imbalances [129].

TiO₂ NPs exert their antimicrobial effects primarily by disrupting bacterial biofilms, which are complex extracellular matrices composed of polysaccharides, proteins, and DNA. These biofilms serve as protective barriers for various pathogens, including P. aeruginosa, Proteus vulgaris, Acinetobacter baumannii, Serratia marcescens, and E. coli [130, 131]. Furthermore, TiO₂ NPs show the capability to generate ROS under physiological conditions such as neutral pH and body temperature. This ROS production effectively degrades key biofilm components including polysaccharides, proteins, and extracellular DNA, thereby compromising biofilm structural integrity and increasing pathogen susceptibility [132]. Furthermore, TiO₂ NPs have been reported to influence the mucus layer within the gut, modulating its thickness and composition [133]. These effects, particularly on acidic and neutral mucins, may enhance mucosal defenses by reducing pathogen adherence and invasion, thereby bolstering the intestinal barrier against microbial stressors [134].

Despite their potential, the application of TiO₂ NPs in gut microbiome modulation remains controversial due to challenges related to their long-term safety, potential bioaccumulation, and unintended effects on microbial communities [135]. For instance, experimental studies have indicated that exposure to TiO₂ NPs can inadvertently disrupt beneficial microbial populations such as Lactobacillus [136]. Additionally, TiO₂ NPs have been observed to stimulate host cells to produce pro-inflammatory cytokines, including IL-6 and IL-8, which may exacerbate gut inflammation under certain conditions such as high NP concentrations in the presence of pre-dispersed formulations, or depending on specific physicochemical properties such as surface area, crystallinity, and dispersion state [137, 138]. This highlights the need for careful nanoparticle design to minimize unintended immune responses in both gut and lung microbiomes.

Such findings emphasize the need for surface modifications and dosage optimization of TiO₂ NPs to balance their antimicrobial benefits while minimizing inflammatory and microbial disruption risks [139]. Moreover, evidence from oral toxicity studies comparing surface-treated and untreated TiO₂ particles indicates no adverse impact on toxicity, even at very high doses, highlighting the importance of carefully designing nanoparticle interventions [140]. Further research is essential to elucidate the long-term interactions between TiO₂ NPs, host immune responses, and the gut microbiome.

Silver (Ag) NPs. Ag NPs have emerged as a potent antimicrobial agent, with significant efficacy against a wide range of pathogenic microorganisms, including multidrug-resistant strains [141]. Their antimicrobial properties are largely attributed to the generation of ROS, which induce oxidative stress and cause structural disruption in the bacterial membrane, such as membrane perforation or pore formation [142]. In addition to inducing the generation of ROS, the toxicity of Ag NPs compounds arises mainly from the release of ions that compromise the cell envelope’s integrity by destabilizing the membrane [143]. These ions also interact with nucleic acids and proteins, interfering with replication and synthesis processes [144], and inhibiting essential metabolic pathways [145]. Additionally, by dismantling biofilm structures, Ag NPs effectively enhance the susceptibility of embedded bacteria to antimicrobial agents, thereby addressing one of the most challenging aspects of infection management [146].

Although Ag NPs demonstrate considerable antimicrobial potential, their application presents notable challenges and limitations. While they exhibit antimicrobial effects under certain conditions, Ag NPs may decrease the Firmicutes/Bacteroidetes ratio, including Lactobacillus [147]. Notably, silver and its compounds are broadly effective against both Gram-positive and Gram-negative bacteria [148]. However, some in vivo findings suggest that Ag NP exposure can shift gut microbiota composition toward greater proportions of Gram-negative bacteria, whereas others report no significant alterations in these bacterial phyla [149].

Additionally, the interaction of Ag NPs with host cells presents both opportunities and challenges. On one hand, their ability to modulate inflammatory responses, including the reduction of pro-inflammatory cytokines, offers therapeutic potential for conditions characterized by excessive gut inflammation [150]. On the other hand, Ag NPs induce the release of cytokines such as TNF-α, macrophage inhibitory protein (MIP-2) and IL-1β in a size-dependent manner, potentially exacerbating inflammation [151]. However, recent evidence suggests that prophylactic administration of Ag NPs to the lungs can reduce viral loads and virus-induced cytokines, partly by recruiting and regulating lymphoid cells, including NK cells, activated through their interaction with alveolar macrophages [152]. These dual actions underscore the importance of a comprehensive understanding of how Ag NPs interact with both the microbiota and the host immune system.

The long-term safety of Ag NPs remains an area of active research. Concerns about bioaccumulation and the potential for inducing microbial resistance necessitate comprehensive toxicological evaluations. An in vitro study revealed that prolonged exposure of BEAS-2B cells to Ag NPs leads to the upregulation of TGFβ1 and promotes epithelial-mesenchymal transition and cellular transformation, as demonstrated by RNA sequencing analysis [153].

Although emerging evidence supports their potential for gut microbiome modulation, achieving an optimal balance between therapeutic efficacy and safety remains essential. Advances in nanoparticle engineering, particularly through surface functionalization and controlled release mechanisms, hold the potential to address these challenges and unlock the full therapeutic potential of Ag NPs [154] (Fig. 3).

Fig. 3. Functional properties of inorganic nanoparticles in the mucosal system.

Immunologically and microbiologically relevant actions of titanium dioxide (TiO₂) and silver (Ag) nanoparticles at mucosal surfaces, including ROS-driven antimicrobial activity, biofilm disruption, regulation of immune signaling, and modulation of mucus characteristics and microbial community structure.

Application of NPs as a Direct Modulator of Mucosal Microbiota Dynamics

Probiotics, which are live microorganisms that provide health benefits to the host when consumed in sufficient quantities, and prebiotics, which are indigestible dietary components that selectively enhance the growth and activity of beneficial microorganisms in the GI tract, have gained significant interest in the areas of functional foods, nutraceuticals, and therapeutic applications [155]. Both probiotics and prebiotics play pivotal roles in maintaining gut health, modulating immune responses, and preventing dysbiosis—a microbial imbalance associated with various health conditions [156]. However, conventional formulations of probiotics and prebiotics often face significant limitations, including low survival rates during storage and transit through the harsh acidic environment of the stomach, inadequate colonization in the host’s gut, and premature degradation or nonspecific utilization of prebiotics before reaching their target sites [157]. The integration of nanoparticle-based delivery systems into probiotics and prebiotics research has introduced a transformative approach to addressing dysbiosis across diverse mucosal environments. Probiotic and prebiotic NPs leverage nanotechnology to overcome inherent limitations such as low stability, inefficient delivery, and limited therapeutic efficacy in conventional formulations [158].

The encapsulation techniques enhance survival, target site specificity, and bioavailability, paving the way for innovative strategies to restore microbial balance and support host health [159]. Various encapsulation strategies have been employed to optimize delivery efficiency. Polysaccharide-based encapsulation, using materials such as alginate, chitosan, and pectin, provides a protective matrix that enhances probiotic survival under harsh gastric conditions while enabling controlled intestinal release and low immunogenicity [160-162]. Protein-based encapsulation, utilizing carriers such as whey protein, casein, and gelatin, offers structural stability and gradual degradation, making it suitable for sustained probiotic and prebiotic release [163-165]. Lipid-based encapsulation, such as liposomes and solid lipid NPs, enhances probiotic efficiency while providing a protective barrier against gastric conditions, but is prone to oxidation and thermal instability [158, 166]. Polymer-based encapsulation, employing biocompatible materials such as hydrogels, chitosan derivatives, and gelatin scaffolds, enables enhanced protection and stimuli-responsive targeted release [167, 168].

Probiotics can modify gut microbiota by promoting the production of SCFAs and lactic acid, while also enhancing the generation of AMPs such as lactobin A, curvacin A, enterocin, and pediocin [169-173]. Several probiotic strains, including Lactobacillus spp. (L. acidophilus, L. amylovorus, L. brevis, L. bulgaricus, L. casei, L. curvatus, L. helveticus, L. lactis, and L. plantarum), Leuconostoc gelidum, Enterococcus faecium (E. faecium CTC492, E. faecium T136, and E. faecium P13), and Pediococcus spp. (P. acidilactici and P. pentosaceus), are well known for their ability to produce these AMPs, contributing to gut homeostasis and pathogen inhibition [174]. Additionally, these systems regulate the activity of DCs, T cells, and B cells, suppressing inflammatory responses and modulating the immune system [175, 176]. On the other hand, prebiotic NPs encapsulate substrates such as inulin, fructooligosaccharides (FOS), and galactooligosaccharides (GOS) within nano-size carriers made of biocompatible materials [177-179]. Inulin-based NPs effectively regulate gut microbiota, enhance SCFA production, and improve anti-inflammatory immune responses, showing potential in colorectal cancer therapy by increasing regorafenib accumulation in tumors and polarizing tumor-associated macrophages toward an M1 phenotype [180]. Additionally, GOS-loaded PLGA NPs have been shown to enhance gut barrier integrity, promote SCFA production, and activate T-regulatory cells, thereby improving gut permeability and modulating gut-associated immune responses in models of intestinal inflammation [181].

The co-encapsulation of probiotics and prebiotics into a single nanoparticle delivery system introduces the concept of synbiotic NPs. These systems enable simultaneous and localized delivery of both components, amplifying their synergistic effects [182]. For instance, prebiotics such as chitosan, protein, cellulose and inulin within the nanoparticles act as a nutrient source for co-delivered probiotics such as Lactobacillus, enhancing their colonization and metabolic activity and overall therapeutic efficacy [183-187]. In the Drosophila model, Lactobacillus fermentum was encapsulated with chitosan, a prebiotic, to create a synbiotic nanoparticle system. This approach not only stabilized the probiotics during gut transit but also enhanced their immunomodulatory effects, mitigating acrylamide-induced toxicity by modulating gut microbiota and reducing oxidative stress [184]. This integrated approach maximizes SCFA production, strengthens mucosal defenses, and accelerates the restoration of microbial equilibrium. Encapsulating probiotics such as Bacillus amyloliquefaciens, L. acidophilus, and Bifidobacterium bifidum in chitosan NPs improves their survival in acidic and intestinal conditions, effectively delivering them to the colon [188]. This encapsulation reduces inflammation, enhances anti-inflammatory cytokine expression, and restores epithelial integrity in colitis models, highlighting their utility in treating IBD [189].

Furthermore, other advanced nanoparticle formulations have demonstrated notable benefits. Chitosan-coated PLGA NPs loaded with lyophilized probiotic extract have demonstrated targeted delivery to inflamed colon tissues, significantly reducing pro-inflammatory cytokines, lipid peroxidation, and myeloperoxidase activity, as well as improving colonic histopathological conditions in murine colitis models [187]. Additionally, lipid NP based delivery systems, such as SLNs loaded with rosiglitazone and probiotics, enhance the stability and viability of probiotics, offering antioxidant activity and sustained release properties, and demonstrating potential for diverse applications [190]. Ag and TiO₂ NPs exhibit antimicrobial activity against beneficial bacteria such as L. casei, L. plantarum, and L. fermentum. However, the presence of prebiotics such as raffinose, lactulose, and inulin significantly mitigates their decline, suggesting a protective role of prebiotics in buffering the antimicrobial effects of NPs and supporting the survival of beneficial bacteria [191]. Additionally, studies on Ag NP exposure in gut microbiota models indicate that while core bacterial communities remain stable, rare species exhibit significant fluctuations, and Firmicutes to Bacteroidetes ratios shift. The co-administration of probiotics such as Bacillus subtilis alleviated these effects by maintaining microbial homeostasis and preventing metabolic disruptions [192]. Similarly, TiO₂ NP exposure disrupts gut microbiota, depletes Lactobacillus, and induces colonic inflammation via NF-κB activation. While Lactobacillus rhamnosus GG offers protective effects, further research is needed to assess long-term risks and refine probiotic interventions [193].

In the respiratory tract, various strategies using probiotic, prebiotic and synbiotic NPs offer an innovative approach to enhance the effectiveness of respiratory treatments. L. rhamnosus encapsulated in oleic acid–substituted chitosan-linoleic acid–retinol (OASCLR) NPs enable targeted respiratory delivery via intratracheal administration, enhancing stability and probiotic activity. These NPs facilitated the macrophage transition from M1 to M2 through CD44-hyaluronic acid (HA) interaction, mitigating excessive immune response in bacterial pneumonia. Additionally, OASCLR NPs modulate inflammation by reducing TNF-α and increasing IL-10 levels [194]. In the female reproductive tract, maintaining a Lactobacillus-dominant microbiome is crucial for preventing infections such as BV and candidiasis. HA hydrogel offers an innovative solution by ensuring the delivery and survival of Lactobacillus species, which produce lactic acid and hydrogen peroxide to inhibit pathogens such as G. vaginalis and C. albicans [195, 196]. In addition, L. rhamnosus and L. gasseri immobilized in electrospun polymeric nanofibers exhibited potent inhibitory effects against pathogens such as G. vaginalis and C. albicans, while maintaining high survival rates and stability during long-term storage, suggesting a promising strategy for enhancing vaginal health through innovative delivery systems [197]. However, despite these promising findings, the continuous turnover of vaginal mucus poses a significant challenge to the retention and effectiveness of NPs potentially limiting their therapeutic impact [198, 199]. Thus, further research is needed to provide consistent and robust evidence supporting the efficacy of these interventions [200] (Fig. 4).

Fig. 4. Functions and mucosal effects of probiotic, prebiotic, and synbiotic NPs.

(Left) Functions of each NP type. Probiotic NPs enhance gastrointestinal survival, immune modulation, and microbial balance. Prebiotic NPs promote shortchain fatty acid (SCFA) production, anti-inflammatory activity, and gut barrier function. Synbiotic NPs co-deliver both components, resulting in synergistic effects, including improved colonization, metabolism, and mucosal protection. (Right) Combined mucosal effects. In the GI tract, NPs reduce inflammation, restore microbiota balance, enhance barrier integrity, and increase SCFA levels. In the respiratory tract, they modulate immune responses and enhance IgA production. In the female reproductive tract, they contribute to infection prevention, pH regulation, and pathogen exclusion.

Conclusion and Future Directions

NPs have emerged as transformative tools in the modulation of mucosal immunity and microbiome dynamics. This review highlights the intricate interplay between the immune system, microbial ecosystems, and nanoparticle technologies within the mucosal environment. NPs influence the mucosal immune response both directly through interactions with epithelial and immune cells, and indirectly by modulating the composition and metabolic activity of microbiota. Such modulation of the microbiome plays a crucial role in restoring the balance between innate and adaptive immune responses, maintaining immune tolerance, and alleviating inflammation. Consequently, NP-mediated microbiome regulation holds substantial potential for the prevention and treatment of various mucosal-associated diseases, including IBD, airway disorders, and infectious diseases. By leveraging these interactions, NPs demonstrate significant potential in restoring microbial homeostasis and mitigating inflammation. Notably, NPs offer promising strategies for addressing dysbiosis through precise modifications of the mucosal microbiome, thereby contributing to the treatment of related disorders (Fig. 5).

Fig. 5. Overview of nanoparticle-mediated modulation of the mucosal immune system and microbiota.

Within the mucosal environment, NPs enhance probiotic viability, suppress pro-inflammatory cytokines (e.g., TNF-α, IL-1, IL-6), promote sIgA production, maintain epithelial barrier integrity, and modulate local immune cell activity. NPs can accumulate at inflamed sites via the enhanced permeability and retention (EPR) effect, thereby facilitating targeted therapeutic delivery.

However, several critical limitations must be addressed to fully realize this potential. First, while the short-term efficacy of nanoparticle-based therapies has been well-documented in preclinical studies, data on their long-term safety, effectiveness, and potential adverse effects remain limited. The long-term interactions between NPs and host-microbial communities, as well as the immune system, are not yet fully understood, underscoring the need for comprehensive and longitudinal studies. Furthermore, although preclinical research has provided valuable insights, clinical trials involving human subjects remain sparse. Robust, large-scale, and long-term clinical trials are essential to validate the safety and efficacy of nanoparticle-based interventions and establish their translational viability.

Additionally, the risk of off-target effects represents a significant challenge in the application of nanoparticle technologies. Despite their high specificity, NPs may inadvertently interact with commensal microorganisms or host tissues, potentially disrupting microbial homeostasis or impairing immune regulation. Such unintended effects could diminish therapeutic outcomes or even exacerbate existing conditions. To mitigate these risks, advancements in nanoparticle design and functionalization are required to enhance their selectivity and minimize off-target interactions. In this context, some NPs hold particular promise for probiotic delivery. By promoting survival and targeted delivery of beneficial microorganisms, these systems can stabilize the mucosal environment and restore microbial balance, thereby amplifying therapeutic efficacy.

In conclusion, NPs represent a powerful and versatile platform for the modulation of mucosal immunity and the microbiome. However, addressing key limitations, such as the lack of long-term data, limited clinical trials, and the potential for off-target effects, is critical for advancing this field. Overcoming these challenges will pave the way for NPs to serve as innovative solutions in the treatment of mucosal immune-related disorders and microbiome-associated diseases.