Microbial Bioactives

1.Introduction

The human gut microbiome consists of trillions of bacteria, viruses, fungi, and other microorganisms that collectively influence health and disease. This microbial ecosystem plays a pivotal role in digestion, immune function, and even neurological processes through the gut-brain axis. Over the past decade, research has highlighted the profound effects of external factors, including diet, antibiotics, and vaccines, on gut microbial composition. Among these, vaccines have drawn significant interest due to their ability to modulate immune responses, which in turn can affect microbiome stability. Traditional vaccines, such as live-attenuated and inactivated vaccines, have been studied for their interactions with gut microbiota. Research before 2018 suggested that immune stimulation through vaccination could temporarily shift microbial balance, influencing bacterial diversity and abundance. Some studies noted transient dysbiosis following routine immunization, while others indicated beneficial microbial alterations that enhanced immune resilience. These findings laid the groundwork for investigating newer vaccine technologies, including mRNA vaccines, which function differently from their predecessors.

mRNA vaccines, first widely deployed during the SARS-CoV-2 pandemic, utilize lipid nanoparticle delivery systems to introduce synthetic mRNA sequences into host cells. These sequences instruct cells to produce viral proteins, triggering immune recognition and antibody production. While this approach has proven highly effective in preventing COVID-19, it remains unclear how the immune activation triggered by mRNA vaccines influences gut microbial communities. Given that the gut microbiome plays an integral role in immune homeostasis, any vaccine-induced perturbations could have implications beyond immediate immune response modulation.

Reports of post-vaccination gastrointestinal symptoms, such as diarrhea, bloating, and gut discomfort, have raised concerns about potential microbiome disruptions. While anecdotal evidence suggests a link between mRNA vaccination and temporary gut disturbances, a deeper understanding of this phenomenon is required. Pre-2018 literature on vaccine-induced microbiome shifts provides a valuable framework for assessing potential effects, even in the absence of direct studies on mRNA vaccines. By drawing upon past research and emerging data, this review aims to explore the theoretical and observed interactions between mRNA vaccines and the gut microbiome, shedding light on potential risks, benefits, and areas requiring further study.

2. Methodology

This study adopted a systematic review approach to explore how vaccination influences the gut microbiome, drawing insights from pre-2025 literature to infer potential effects of mRNA-based immunization. Figure 1 shows the study selection process for this systematic review following the PRISMA 2020 guidelines. It summarizes the number of records identified, screened, excluded, and included in the qualitative and quantitative analyses. The review aimed to synthesize existing evidence on how immune activation through vaccination modulates gut microbial diversity, abundance, and function—factors that may have implications for the novel mechanisms of mRNA vaccines. A comprehensive literature search was conducted across major scientific databases including PubMed, ScienceDirect, Web of Science, and Scopus (Figure 1). The search included studies published before 2025 to capture foundational evidence on vaccine–microbiome interactions before the advent of mRNA vaccine technology. Keywords such as “vaccine” OR “vaccination” OR “immunization” OR “mRNA vaccine” OR “gut microbiome” OR “gut microbiota” OR “intestinal microbiota” OR “immune response” OR “inflammation” OR “cytokines “microbial diversity” OR “dysbiosis” were used in various combinations. Both human and animal model studies were considered to ensure a broad understanding of immune–microbiome dynamics. Studies were included if they met the following criteria: Original peer-reviewed studies (human or animal models). Studies evaluating the impact of vaccination or vaccine-induced immune activation on gut microbiome composition, diversity, or function. Studies reporting quantitative microbiome outcomes (e.g., alpha diversity indices, relative abundance of taxa, or microbial richness). Studies employing recognized microbiome assessment methods (e.g., 16S rRNA sequencing, metagenomics, or culture-based analyses). Only articles published in the English language with full-text availability were included in this review.

Figure 1. PRISMA 2020 flow diagram showing the selection process of studies included in the systematic review

Exclusion criteria: Non-original articles (reviews, editorials, commentaries, conference abstracts). Studies not assessing gut microbiota outcomes. In vitro-only studies without in vivo relevance. Articles lacking sufficient data for qualitative or quantitative synthesis. Data from selected studies were extracted and categorized based on vaccine type, study population, microbial assessment methods (e.g., 16S rRNA sequencing, culture-based analyses), and observed microbial shifts. Data from selected studies were systematically extracted from the published full texts and categorized according to vaccine type, study population, microbial assessment methods (e.g., 16S rRNA sequencing, metagenomic or culture-based analyses), and reported microbial outcomes. No primary or raw microbiome datasets were generated or deposited, as this study represents a secondary analysis of previously published literature. All extracted information is fully reported in the Results section and corresponding tables, where qualitative synthesis and, where applicable, quantitative summaries are presented. Finally, the collective evidence was interpreted within the framework of mRNA vaccine mechanisms—specifically, their ability to induce systemic immune responses, cytokine release, and inflammation—to hypothesize potential microbiome outcomes. This integrative approach bridges past and emerging evidence to better understand how mRNA vaccines might interact with gut microbial ecosystems and inform future experimental research.

3.Immune Activation and Gut Microbiome Interactions

The immune system and gut microbiome maintain a dynamic, bidirectional relationship that plays a central role in health and disease. The gut microbiome actively trains the immune system, shaping its response to pathogens and influencing systemic inflammation. Conversely, immune activation—whether through infection, inflammation, or vaccination—can alter gut microbial populations. Understanding how mRNA vaccines interact with this delicate balance is essential for assessing their potential impact on gut health.

3.1 The Gut-Immune System Axis

The gut is home to a diverse microbial ecosystem that constantly communicates with the immune system. Specialized immune cells within the gut-associated lymphoid tissue (GALT) monitor microbial populations and differentiate between commensal and pathogenic organisms. This interaction is crucial for maintaining immune tolerance while mounting appropriate responses to harmful microbes (Belkaid & Hand, 2014). Vaccination, by design, stimulates the immune system to recognize and respond to specific antigens, raising the question of whether this immune activation can influence gut microbial composition.Studies have shown that immune stimulation, whether through infection or vaccination, can induce temporary shifts in gut microbiota. For example, the Bacillus Calmette-Guérin (BCG) vaccine, used for tuberculosis prevention, was found to modulate gut microbial diversity by increasing beneficial bacterial populations while reducing potentially pathogenic strains (de Groot et al., 2017). Similar findings have been observed with oral vaccines, such as the rotavirus and cholera vaccines, which have been shown to alter gut microbial composition in vaccinated individuals (Harris et al., 2017). These findings suggest that immune activation through vaccination has the potential to reshape gut microbial communities.

3.2 mRNA Vaccines and Systemic Immune Modulation

Unlike traditional vaccines, which introduce live or inactivated pathogens, mRNA vaccines work by instructing host cells to produce viral proteins that trigger immune responses. This novel mechanism has been shown to induce strong antibody and T-cell responses, but its effects on gut microbial populations remain largely unexplored. Given that immune activation influences gut microbiota, it is plausible that mRNA vaccines could induce similar shifts in microbial diversity.One potential mechanism involves vaccine-induced cytokine responses. Cytokines are signaling molecules that mediate immune activity and inflammation. Research prior to 2018 demonstrated that elevated cytokine levels can alter gut microbiota composition. For instance, interferon-gamma (IFN-?), a key immune signaling molecule, has been shown to reduce the abundance of beneficial bacteria such as Lactobacillus and Bifidobacterium while promoting the growth of pro-inflammatory microbes (Thaiss et al., 2016) (Figure 2). Since mRNA vaccines trigger robust cytokine production, it is reasonable to hypothesize that similar microbial shifts could occur following vaccination.Additionally, vaccination stimulates the production of antimicrobial peptides (AMPs), which help control bacterial populations. While AMPs play a crucial role in defending against infections, they can also inadvertently disrupt the balance of gut microbiota. Previous studies found that AMP production in response to immune stimulation can lead to reductions in microbial diversity (Belkaid & Hand, 2014). Given that mRNA vaccines elicit strong immune responses, they may contribute to transient microbiome alterations through this mechanism (Figure 3).

Figure 1: mRNA vaccines in disease prevention and treatment and host immune response to RNA viruses. The diagram illustrates the innate and adaptive immune pathways triggered by RNA viruses. On the left, viral ssRNA activates Toll-like receptors (TLR7/8 and TLR3) and cytoplasmic sensors (MDA-5, LGP2, NOD2, RIG-1), leading to IFN-I pathway activation and proinflammatory cytokine production for innate immunity. On the right, viral proteins processed by proteasomes are presented via MHC I and MHC II pathways, activating CD8+ T cells and CD4+ T cells, respectively, and stimulating B cells for adaptive immunity. (courtesy of image from Pardi, N., Hogan, M. J., Porter, F. W., & Weissman, D. (2018).

Figure 2. Immune response to an mRNA vaccine. The diagram illustrates the steps involved in the immune response triggered by an mRNA vaccine. The mRNA vaccine enters the cell via endocytosis and is released into the cytoplasm. Ribosomes translate the mRNA into viral proteins. Proteasomes degrade these proteins into antigen fragments, which are presented on MHC I molecules to activate cytotoxic T cells. Helper T cells recognize antigens presented on MHC II molecules, stimulating cytokine release. B cells are activated to produce antibodies, while cytotoxic T cells induce apoptosis in infected cells. Antibodies neutralize pathogens, and macrophages clear debris, completing the adaptive immune response. (courtesy of image from Kowalczyk, A., Doener, F., Zanzinger, K., Noth, J., Baumhof, P., Fotin-Mleczek, M., & Heidenreich, R. (2016)

3.3 Gut Microbiome Changes Following Immune Stimulation

Research before 2018 provides insight into how immune activation influences gut microbial communities. Studies on viral infections, for example, have shown that immune responses can significantly alter microbial composition. Influenza virus infection has been linked to decreased microbial diversity and an increase in pro-inflammatory bacterial strains (Steed et al., 2017). While vaccination is distinct from infection, both processes involve immune activation, suggesting that similar microbiome shifts could occur post-vaccination.Furthermore, stress-induced immune responses have been associated with gut microbiome changes. Psychological and physiological stress triggers immune activation, leading to increased gut permeability and bacterial translocation (Cryan et al., 2017). Given that mRNA vaccines induce temporary physiological stress through immune activation, they may similarly influence gut microbial balance.

3.4 Potential Implications for Gut Health

While transient microbiome alterations following vaccination may not pose long-term risks for most individuals, certain populations may be more susceptible to adverse effects. Individuals with pre-existing gut dysbiosis, autoimmune conditions, or inflammatory bowel disease (IBD) may experience more pronounced microbiome shifts post-vaccination. Previous research suggests that individuals with compromised gut health may have heightened immune responses to vaccination, leading to prolonged microbial imbalances (Harris et al., 2017).On the other hand, some microbiome shifts induced by immune activation may be beneficial. Studies have shown that vaccination can promote the growth of beneficial bacterial strains that enhance immune resilience. For instance, increased Bifidobacterium populations have been observed following influenza vaccination, potentially contributing to enhanced mucosal immunity (de Groot et al., 2017). If similar effects occur with mRNA vaccines, they may provide indirect benefits by promoting beneficial microbial populations.

The gut microbiome and immune system are intricately connected, with immune activation influencing microbial balance in various ways. Pre-2018 research on traditional vaccines and immune responses suggests that vaccination can induce temporary microbiome shifts, raising important questions about how mRNA vaccines affect gut microbial diversity. While no direct studies on mRNA vaccines and the microbiome existed before 2018, existing literature on vaccine-induced immune modulation provides a basis for understanding potential interactions. Future research should explore the extent and duration of microbiome changes following mRNA vaccination, particularly in vulnerable populations.

4.Short-Term Gastrointestinal Symptoms and Microbiome Disturbances After mRNA Vaccination

One of the most frequently reported side effects following mRNA vaccination is gastrointestinal discomfort, including nausea, diarrhea, bloating, and altered bowel habits. While such symptoms are often dismissed as transient immune reactions, they raise important questions about potential disruptions in the gut microbiome. The gut is home to a complex microbial ecosystem that interacts with the immune system, and any disturbance—whether through infection, diet, stress, or vaccination—can temporarily or permanently alter microbial composition. Pre-2018 research on vaccine-induced microbiome shifts provides a useful foundation for understanding how immune activation following mRNA vaccination may contribute to short-term gut disturbances (Table 1).

Table 1. Summary of Pre-2018 Studies on Vaccine-Induced Gut Microbiome Alterations

4.1 Gastrointestinal Symptoms Post-Vaccination: A Common Yet Understudied Phenomenon

Vaccines are known to trigger a range of systemic immune responses, including fever, fatigue, and muscle aches. However, gastrointestinal symptoms are also widely reported. Studies documented gastrointestinal disturbances following routine immunizations, including oral vaccines like rotavirus, polio, and cholera vaccines (Harris et al., 2017). While these vaccines are directly administered through the gut, even injected vaccines have been associated with digestive symptoms. For instance, influenza vaccination has been linked to temporary alterations in gut function and microbiota balance, possibly due to immune-mediated changes in gut permeability (Steed et al., 2017). Following the introduction of mRNA vaccines, numerous reports of gastrointestinal side effects emerged. While these effects are often short-lived, their occurrence suggests an interaction between vaccine-induced immune activation and gut microbial populations. Given that immune responses influence microbial composition, the gastrointestinal symptoms reported post-mRNA vaccination may be indicative of transient dysbiosis—a temporary imbalance in gut microbiota.

4.2 Vaccine-Induced Immune Activation and Gut Microbiome Disruptions

The gut microbiome is highly sensitive to immune activation, as inflammatory responses can alter bacterial populations and gut barrier function. Pre-2018 research demonstrated that systemic immune activation—whether from infection, autoimmune conditions, or vaccination—can lead to increased gut permeability, commonly referred to as "leaky gut" (Belkaid & Hand, 2014). This phenomenon allows bacterial byproducts and endotoxins to enter the bloodstream, triggering further immune responses and contributing to digestive discomfort.

For example, studies on influenza virus infection found that immune responses led to shifts in gut microbial diversity, including reductions in beneficial bacteria such as Lactobacillus and Bifidobacterium while promoting the growth of pro-inflammatory strains (Thaiss et al., 2016). While vaccination is distinct from infection, both processes involve immune system stimulation, suggesting that similar microbiome shifts may occur post-vaccination.Additionally, vaccine-induced cytokine responses may play a role in microbiome disturbances. Cytokines such as interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-a) are upregulated following vaccination, and these inflammatory mediators have been shown to influence gut microbial composition (Belkaid & Hand, 2014). Studies before 2018 demonstrated that increased levels of pro-inflammatory cytokines are associated with shifts in microbial balance, favoring species that thrive in inflammatory environments while reducing populations of beneficial commensal bacteria.

4.3 Short-Term Dysbiosis: A Temporary Effect or a Cause for Concern?

While short-term microbiome disturbances are common following immune activation, their long-term significance remains unclear. Pre-2018 research indicated that most vaccine-induced microbial shifts are temporary, with bacterial populations returning to baseline levels within weeks (Harris et al., 2017). However, in individuals with pre-existing gut imbalances or immune dysregulation, these disturbances could have more lasting effects.Studies on antibiotic-induced dysbiosis, for example, have shown that while most individuals experience microbiome recovery within weeks, some retain altered microbial compositions for months or even years (Steed et al., 2017). If mRNA vaccination induces significant microbial shifts in certain individuals, there is a possibility that some may experience prolonged dysbiosis. Those with inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), or other gut-related conditions may be more susceptible to long-term microbiome imbalances post-vaccination.Furthermore, disruptions in microbial balance can have systemic effects beyond digestion. The gut microbiome plays a crucial role in regulating inflammation and immune responses, and persistent dysbiosis has been linked to autoimmune conditions, metabolic disorders, and even neurological issues (Cryan et al., 2017). While current evidence does not indicate that mRNA vaccines cause long-term microbiome damage, further research is needed to determine whether individuals with pre-existing gut conditions may be at greater risk of prolonged microbial imbalances.

4.4 Gut Microbiome Resilience and Recovery

Despite the potential for short-term disturbances, the gut microbiome is remarkably resilient. Research before 2018 demonstrated that microbial populations often recover quickly following temporary disruptions, whether from illness, dietary changes, or immune activation (Harris et al., 2017). Factors that support microbiome recovery include a diverse diet rich in fiber, fermented foods containing probiotics, and adequate hydration.Probiotic supplementation has been shown to help restore gut microbial balance following immune system activation. Studies on influenza vaccination, for example, found that individuals who consumed probiotic-rich foods or supplements exhibited faster microbiome recovery and reduced gastrointestinal side effects (de Groot et al., 2017). If mRNA vaccines induce temporary dysbiosis, probiotic and prebiotic interventions may be useful in mitigating symptoms and supporting microbial resilience.Additionally, physical activity and stress reduction strategies can aid in microbiome recovery. Chronic stress has been shown to negatively impact gut microbial diversity, while relaxation techniques such as meditation and deep breathing have been linked to beneficial microbiome shifts (Cryan et al., 2017). Given that vaccine-induced immune responses can be stressful on the body, engaging in stress-reducing activities post-vaccination may help promote gut health and microbial stability.

Short-term gastrointestinal symptoms following mRNA vaccination may be linked to temporary microbiome disturbances caused by immune activation. Pre-2018 research on vaccine-induced microbiome shifts provides a framework for understanding these effects, with studies indicating that immune stimulation can alter gut microbial composition. While most microbiome changes appear to be transient, individuals with pre-existing gut conditions may be more vulnerable to prolonged imbalances.Despite the potential for temporary dysbiosis, the gut microbiome has a strong capacity for recovery. Dietary interventions, probiotics, and stress management strategies may aid in restoring microbial balance following vaccination. Future research should explore the long-term implications of mRNA vaccination on gut microbiota, particularly in vulnerable populations, to ensure optimal vaccine safety while safeguarding microbiome health.

5. Gut Microbiota Influence on Vaccine Efficacy and Immune Response

The gut microbiota plays a crucial role in shaping the immune system, influencing how the body responds to infections, inflammation, and vaccinations. Pre-2018 research has demonstrated that the gut microbiome affects both innate and adaptive immunity, with specific bacterial populations modulating the effectiveness of vaccines (Belkaid & Hand, 2014). Given the unprecedented nature of mRNA vaccines, understanding how gut microbial composition impacts vaccine efficacy is critical. This section explores the role of gut bacteria in vaccine response, highlighting mechanisms by which microbiota influence immune activation, antibody production, and overall vaccine success.

5.1 Gut Microbiota as an Immune System Trainer

The gut microbiome is deeply interconnected with immune function, playing an essential role in educating and priming immune cells. Beneficial bacteria such as Bifidobacterium and Lactobacillus produce metabolites like short-chain fatty acids (SCFAs), which regulate immune homeostasis and inflammation (Honda & Littman, 2016). These gut-derived signals influence antigen-presenting cells, particularly dendritic cells, which help initiate adaptive immune responses.Studies on vaccine responses indicated that individuals with greater microbial diversity, particularly higher levels of beneficial gut bacteria, tend to exhibit stronger immune reactions to vaccines (Harris et al., 2017). For example, research on influenza vaccination found that gut microbial diversity correlated with higher antibody production and better long-term immunity (Steed et al., 2017). Similar findings were observed with polio and rotavirus vaccines, where a richer microbiota was linked to improved vaccine efficacy (Valdez et al., 2014).However, microbiome imbalances—whether due to antibiotic use, diet, or gut disorders—can impair immune function and weaken vaccine responses. A disrupted gut microbiome with low diversity or an overgrowth of inflammatory bacteria has been associated with reduced antibody production, potentially undermining vaccine effectiveness (Belkaid & Hand, 2014). Given these insights, understanding how mRNA vaccines interact with gut microbiota is vital for optimizing immunization strategies.

5.2 Microbiome Composition and Its Effect on Antibody Production

Pre-2018 research established that gut bacteria influence vaccine efficacy by shaping the body's ability to generate antibodies. Antibody responses are a key indicator of vaccine success, as they determine the body's ability to recognize and neutralize pathogens in the future. The gut microbiome contributes to this process through multiple mechanisms, including the production of metabolites that modulate immune function.SCFAs such as butyrate and propionate, produced by gut bacteria fermenting dietary fiber, have been shown to enhance antibody production and regulate immune tolerance (Honda & Littman, 2016). For instance, studies on mice demonstrated that butyrate supplementation improved vaccine-induced antibody responses, suggesting that a microbiome rich in SCFA-producing bacteria supports stronger vaccine efficacy (Steed et al., 2017).Furthermore, research on oral vaccines such as cholera and rotavirus vaccines found that individuals with disrupted microbiota—whether due to antibiotic exposure or malnutrition—had weaker antibody responses compared to those with healthier gut bacteria (Valdez et al., 2014). These findings indicate that maintaining a balanced microbiome before vaccination could enhance the body's ability to mount a robust immune response.

With mRNA vaccines, the immune response is mediated through lipid nanoparticle delivery of genetic material, triggering the production of viral antigens inside the body. Given that gut microbiota influence antigen presentation and immune activation, variations in microbiome composition could affect how efficiently the immune system recognizes and responds to mRNA vaccine-generated antigens. While research on this specific interaction is still emerging, the foundational knowledge from earlier vaccine studies suggests that gut microbiota play a crucial role in shaping the response to mRNA immunization.

5.3 Dysbiosis and Reduced Vaccine Efficacy

Microbial imbalances, or dysbiosis, have been linked to poor vaccine responses across multiple studies. Factors such as antibiotic use, chronic inflammation, and gut disorders can disrupt microbial diversity and impair immune function, leading to weaker vaccine-induced immunity. For example, a 2015 study on pneumococcal vaccines found that individuals who had taken antibiotics prior to vaccination exhibited lower antibody responses compared to those with an intact microbiome (Valdez et al., 2014).

Similarly, research on gut health and immune system development found that infants born via cesarean section, who typically have lower gut microbial diversity, often exhibit weaker responses to early-life vaccinations (Steed et al., 2017). This suggests that a well-balanced gut microbiome is necessary for optimal vaccine-induced immunity.In the context of mRNA vaccines, individuals with existing gut imbalances—whether due to inflammatory bowel disease, irritable bowel syndrome, or metabolic disorders—may exhibit altered immune responses. Since the gut microbiome plays a key role in regulating systemic inflammation, a pro-inflammatory gut environment could lead to excessive or weakened immune reactions to vaccination (Cryan et al., 2017).

5.4 Optimizing Vaccine Efficacy Through Gut Microbiome Support

Given the strong link between gut microbiota and vaccine effectiveness, strategies to optimize the microbiome before and after vaccination could enhance immune responses. Pre-2018 research highlighted several approaches to improve vaccine outcomes through microbiome modulation:

 Probiotic and Prebiotic Supplementation:

Probiotics, particularly Lactobacillus and Bifidobacterium strains, have been shown to enhance immune function and improve vaccine-induced antibody responses. Studies on influenza and polio vaccines demonstrated that probiotic supplementation led to increased antibody production and better immune memory (de Groot et al., 2017). Prebiotics, such as inulin and resistant starches, support beneficial gut bacteria and could further enhance vaccine efficacy.

 Fiber-Rich Diets:

A diet rich in fiber promotes the growth of SCFA-producing bacteria, which in turn regulate immune responses and support antibody production. Pre-2018 research suggested that individuals consuming high-fiber diets exhibited stronger responses to vaccines, likely due to the positive effects of SCFAs on immune regulation (Honda & Littman, 2016).

Avoiding Antibiotic Use Before Vaccination:

Since antibiotics can disrupt microbial diversity and weaken immune responses, avoiding unnecessary antibiotic use before vaccination could improve vaccine efficacy. Research on pneumococcal and oral vaccines indicated that individuals who had recently taken antibiotics exhibited weaker antibody responses (Valdez et al., 2014).

 Reducing Inflammation and Stress:

Chronic stress and systemic inflammation negatively impact gut microbial balance, potentially impairing vaccine responses. Pre-2018 studies on gut-brain interactions suggested that stress-reducing activities, such as meditation and physical exercise, can promote a healthier microbiome and enhance immune function (Cryan et al., 2017). The gut microbiome is a key determinant of vaccine efficacy, influencing immune activation, antibody production, and long-term immunity. Pre-2018 research established that individuals with diverse and balanced microbiota exhibit stronger vaccine responses, while dysbiosis and microbial imbalances can weaken immune reactions. Given the widespread use of mRNA vaccines, understanding how gut bacteria affect immune responses is essential for optimizing vaccine strategies.Maintaining a healthy gut microbiome before and after vaccination—through diet, probiotics, and stress management—may improve vaccine-induced immunity and reduce side effects. While further research is needed to explore the specific interactions between mRNA vaccines and gut bacteria, pre-existing evidence highlights the importance of gut health in shaping vaccine outcomes.

6. mRNA Vaccine-Induced Inflammatory Responses and Gut Barrier Integrity

The immune system’s response to mRNA vaccines involves both local and systemic inflammation, which can affect multiple physiological systems, including the gut. While inflammation is a necessary component of immune activation, excessive or prolonged inflammatory responses can lead to disruptions in gut barrier integrity, potentially influencing gut microbiota composition and function. This section examines how the immune response triggered by mRNA vaccines interacts with gut inflammation, barrier function, and microbial balance.

6.1 The Role of Inflammation in mRNA Vaccine Response

mRNA vaccines, such as those developed for SARS-CoV-2, work by delivering genetic instructions to host cells, prompting them to produce viral proteins that elicit an immune response. This process activates innate immune pathways, particularly through pattern recognition receptors (PRRs) such as Toll-like receptors (TLRs) and retinoic acid-inducible gene I (RIG-I)-like receptors (Kawai & Akira, 2010). These immune sensors recognize the foreign mRNA and initiate a pro-inflammatory cascade, leading to cytokine production and recruitment of immune cells.Research prior to 2018 demonstrated that excessive inflammatory responses to vaccination could negatively impact immune function and overall health. For instance, studies on adjuvanted vaccines found that high levels of pro-inflammatory cytokines, such as tumor necrosis factor-alpha (TNF-a) and interleukin-6 (IL-6), could lead to systemic inflammation and tissue damage if not properly regulated (Pulendran et al., 2014). Since gut health is tightly linked to immune regulation, excessive systemic inflammation could have consequences for gut barrier integrity.

In individuals with pre-existing gut inflammation, such as those with irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD), the heightened immune response induced by vaccination may exacerbate symptoms. Pre-2018 studies on inflammatory pathways in autoimmune diseases suggested that vaccine-induced immune activation could temporarily worsen gut inflammation in sensitive individuals (Belkaid & Hand, 2014). While mRNA vaccines do not contain live pathogens, their ability to stimulate immune responses through inflammatory pathways raises questions about their potential effects on gut health.

6.2 Disruptions in Gut Barrier Integrity and Leaky Gut Syndrome

The gut barrier is a complex structure designed to regulate the passage of nutrients while preventing harmful substances from entering the bloodstream. Tight junction proteins, such as zonulin and occludin, help maintain intestinal integrity, ensuring that bacteria and endotoxins remain confined to the gut lumen (Fasano, 2012). However, inflammatory stimuli—including those triggered by infections, stress, and immune activation—can weaken these tight junctions, leading to increased intestinal permeability, commonly referred to as “leaky gut.” research demonstrated that systemic inflammation can impair gut barrier integrity, allowing bacterial metabolites and endotoxins to enter circulation and contribute to chronic inflammation (Turner, 2009). Studies on vaccine-induced immune activation showed that heightened cytokine responses, particularly IL-6 and TNF-a, were associated with transient increases in gut permeability (Kelly et al., 2015).Given that mRNA vaccines activate inflammatory pathways, individuals with pre-existing gut conditions may experience temporary disruptions in gut barrier function following vaccination. This could manifest as gastrointestinal symptoms such as bloating, diarrhea, or increased sensitivity to certain foods. While most individuals recover quickly, those with chronic gut disorders may experience prolonged gut dysregulation if inflammation persists.

6.3 Gut Microbiota Changes Due to Vaccine-Induced Immune Activation

The gut microbiome is highly sensitive to changes in the immune environment. Vaccination triggers shifts in immune signaling pathways, which can, in turn, alter microbial composition. Pre-2018 studies on immune-gut interactions found that systemic inflammation could promote the expansion of pro-inflammatory bacterial species while reducing populations of beneficial microbes (Honda & Littman, 2016).For instance, research on infection-induced inflammation demonstrated that elevated levels of IL-6 and TNF-a favored the growth of Enterobacteriaceae while suppressing beneficial bacteria such as Bifidobacterium and Faecalibacterium prausnitzii (Zeng et al., 2017). Since mRNA vaccines elicit an immune response through similar pathways, it is plausible that transient changes in gut microbial composition could occur post-vaccination (Table 2).

Table 2. Key Mechanistic Pathways Linking Vaccination, Immune Activation, and Gut Microbiota Changes

7. mRNA Vaccine Components and Their Interactions With Gut Microbiota

The composition of mRNA vaccines plays a crucial role in determining their immunogenicity and potential interactions with the gut microbiota. Unlike traditional vaccines that use live or inactivated pathogens, mRNA vaccines rely on synthetic lipid nanoparticles (LNPs) to deliver genetic instructions to host cells. While these components are designed to be safe and effective, they may have unintended effects on gut microbial populations through immune modulation, lipid metabolism alterations, and direct microbial interactions. This section explores how mRNA vaccine components, including lipid nanoparticles, polyethylene glycol (PEG), and stabilizing agents, influence gut microbiota balance and function (Table 3).

Table 3. Summary of Gut Microbiota’s Role in Vaccine Efficacy and Immune Regulation

Lipid Nanoparticles and Their Effects on Gut MicrobiotaLipid nanoparticles (LNPs) are essential for the delivery of mRNA into human cells. They protect the fragile mRNA molecules from degradation while facilitating efficient uptake by immune cells (Pardi et al., 2018). However, LNPs consist of synthetic lipids that may interact with biological membranes, immune receptors, and microbial populations in the gut.

 research demonstrated that dietary and synthetic lipids could alter gut microbiota composition by selectively promoting or inhibiting bacterial growth (Devkota et al., 2012). Studies found that certain emulsifiers and lipid-based compounds could disrupt the mucus layer of the gut, leading to microbiome imbalances and increased intestinal permeability (Chassaing et al., 2015). While LNPs used in mRNA vaccines differ from dietary lipids, they share structural similarities that might influence gut microbial ecology.One potential concern is the effect of LNPs on gut-resident immune cells. Pre-2018 studies on immune system–microbiome interactions showed that lipids could activate dendritic cells and macrophages, leading to shifts in microbial composition (Ghosh et al., 2013). If LNPs trigger localized immune responses in the gut, they may create an environment that favors pro-inflammatory bacterial species such as Enterobacteriaceae while reducing beneficial microbes like Bifidobacterium and Lactobacillus.Additionally, lipid metabolism plays a crucial role in microbial diversity. Research prior to 2018 highlighted the connection between lipid-rich environments and the expansion of specific bacterial species linked to metabolic disorders (Turnbaugh et al., 2009). Since LNPs introduce novel lipid structures into the body, their influence on gut microbiota composition warrants further investigation.

7.1 Polyethylene Glycol (PEG) and Microbial Dysbiosis

Polyethylene glycol (PEG) is commonly used as a stabilizing agent in mRNA vaccines to enhance nanoparticle stability and prolong shelf life. While PEG is generally regarded as safe for human consumption and medical use, pre-2018 studies raised concerns about its potential impact on gut microbiota, particularly in individuals with sensitivities or compromised gut health.PEG is widely used in laxatives and pharmaceutical formulations, where it influences water retention and gut motility (Huttenhower et al., 2012). However, chronic exposure to PEG-containing substances has been associated with microbiome disruptions. A study on PEG-based laxatives found that prolonged use led to decreased microbial diversity and selective depletion of beneficial bacteria such as Faecalibacterium prausnitzii (Mancabelli et al., 2017).

Furthermore, PEG can modulate gut permeability, affecting the tight junctions that maintain intestinal barrier integrity. Pre-2018 research suggested that disruptions in gut permeability could lead to increased translocation of bacterial metabolites, potentially triggering low-grade systemic inflammation (Bischoff et al., 2014). Since mRNA vaccines contain PEG as part of their nanoparticle formulation, further studies are needed to determine whether repeated exposure contributes to microbiome shifts, particularly in individuals with pre-existing gut conditions.

7.2 Stabilizing Agents and Their Influence on Gut Microbial Composition

In addition to lipids and PEG, mRNA vaccines contain stabilizing agents, including salts, buffers, and cryoprotectants, to preserve vaccine integrity. While these components are typically used in small amounts, their effects on gut microbiota should not be overlooked.

Studies on pharmaceutical excipients found that certain stabilizing agents, such as polysorbates and sugar-based cryoprotectants, could influence bacterial adhesion and biofilm formation (Ruas-Madiedo et al., 2011). Polysorbates, for example, were shown to alter microbial growth patterns by disrupting bacterial membranes, potentially leading to shifts in gut microbial balance (Chassaing et al., 2015).Furthermore, buffers used in vaccine formulations, such as phosphate-based compounds, may influence microbial metabolism. Research suggested that phosphate availability could regulate microbial diversity by influencing the growth of specific bacterial groups (White & Hager, 2013). While the concentrations used in vaccines are relatively low, repeated exposure may have cumulative effects on gut microbiota, particularly in individuals receiving multiple booster doses.

7.3 Potential Microbial Adaptations to Vaccine Components

Microbial communities are highly adaptable and can develop mechanisms to metabolize foreign compounds, including vaccine components. Studies on gut microbiota adaptability demonstrated that bacteria could acquire metabolic pathways to process novel dietary and pharmaceutical compounds, leading to shifts in microbial function (Ley et al., 2006).For instance, research on antibiotic exposure revealed that certain gut bacteria developed resistance mechanisms, altering their metabolic activity in response to repeated exposure (Dethlefsen et al., 2008). Similarly, gut microbes may adapt to recurring exposure to vaccine-related compounds, potentially leading to long-term changes in microbial ecology.Additionally, vaccine-induced immune activation can indirectly shape microbial communities by altering host metabolic processes. Studies on immune-mediated microbiome interactions found that systemic inflammation influenced gut microbial composition by modifying bile acid metabolism and nutrient availability (Tremaroli & Bäckhed, 2012). Since mRNA vaccines elicit strong immune responses, they may contribute to subtle but lasting shifts in microbial populations over time

7.4 Implications for Long-Term Gut Health and Microbiome Resilience

Understanding the impact of mRNA vaccine components on gut microbiota is crucial for optimizing vaccine safety and minimizing potential side effects. While most individuals experience no significant disruptions in gut health following vaccination, those with pre-existing microbiome imbalances may be more susceptible to vaccine-induced microbial shifts.To promote gut resilience and mitigate potential microbiome disruptions, several strategies can be considered:

Incorporating Gut-Protective Nutrients:

Consuming foods rich in prebiotics and polyphenols can support microbial diversity and enhance gut barrier function. Pre-2018 studies highlighted the benefits of polyphenols from green tea, berries, and dark chocolate in modulating gut microbiota (Etxeberria et al., 2015).

 Monitoring Lipid Intake and Metabolism:

Since LNPs introduce synthetic lipids into the body, maintaining a balanced dietary fat intake may help regulate lipid metabolism and prevent microbiome imbalances. Omega-3 fatty acids, in particular, have been shown to counteract inflammation-induced microbiota shifts (Costantini et al., 2017).

Supporting Detoxification Pathways:

Enhancing liver and gut detoxification through adequate hydration, fiber intake, and herbal supplements such as milk thistle and dandelion root may help the body process and eliminate vaccine components efficiently (de Groot et al., 2017).

 Personalized Microbiome Monitoring:

Individuals with gut-related concerns may benefit from microbiome testing before and after vaccination to assess potential shifts in microbial composition. Advances in gut microbiome sequencing have enabled personalized dietary and probiotic interventions based on individual microbial profiles (Huttenhower et al., 2012).

8. Conclusion

The relationship between mRNA vaccines and the human gut microbiome is a complex and evolving area of research. While mRNA vaccines have been widely recognized for their efficacy in preventing infectious diseases, their interactions with the gut microbiota remain a subject of scientific inquiry. This review highlights several potential pathways through which mRNA vaccines, particularly their lipid nanoparticles (LNPs), polyethylene glycol (PEG), and stabilizing agents, may influence gut microbial populations. Although direct evidence linking mRNA vaccines to significant microbiome alterations is still emerging, Research provides valuable insights into the broader interactions between immune activation, lipid metabolism, and microbial communities.The gut microbiome plays a fundamental role in shaping immune responses, regulating inflammation, and maintaining metabolic homeostasis. Given that mRNA vaccines induce a robust immune reaction, it is plausible that transient or long-term shifts in gut microbial composition may occur. studies demonstrated that systemic immune activation can alter gut microbiota by modulating bile acid metabolism, affecting intestinal permeability, and shifting microbial diversity. Furthermore, LNPs and PEG—both essential components of mRNA vaccine formulations—have been shown to interact with gut bacteria, potentially influencing microbial balance and function.

Despite these theoretical concerns, most individuals appear to tolerate mRNA vaccines without significant disruptions to gut health. However, certain populations, including those with pre-existing microbiome imbalances, autoimmune disorders, or metabolic syndromes, may be more susceptible to vaccine-induced microbial shifts. Addressing these concerns requires further research into the long-term effects of repeated vaccine exposure on gut microbiota, particularly in individuals receiving booster doses.To mitigate potential microbiome disruptions, strategies such as maintaining a balanced diet, consuming prebiotics and probiotics, and monitoring lipid metabolism may be beneficial. Additionally, personalized microbiome assessments could help identify individuals who may be more sensitive to vaccine-related microbiome alterations. Future studies should explore whether specific dietary or probiotic interventions could enhance vaccine efficacy while preserving gut microbial stability.While mRNA vaccines are a crucial tool in modern medicine, their interactions with the gut microbiome warrant further investigation. Understanding these interactions can help optimize vaccine formulations, improve public health strategies, and ensure that immune responses are both effective and microbiome-friendly. Ongoing research into host-microbiome-vaccine interactions will provide deeper insights into how to balance immunization efforts with gut health preservation, ultimately enhancing the overall well-being of vaccinated individuals.

Author contributions

E.A.S. and F.B. jointly conceptualized the study and designed the systematic review framework. E.A.S. performed the literature search, data extraction, and drafted the initial manuscript. F.B. contributed to data interpretation, critical analysis, and extensive revision of the manuscript. K.A.J. contributed to critical analysis and revision of the manuscript. All authors reviewed, edited, and approved the final version of the manuscript.

Acknowledgment

The authors thank the University of Technology Sydney and the Pasteur Institute of Iran for providing access to academic resources and institutional support essential for completing this review. The authors also acknowledge the broader scientific community whose foundational research on vaccines and the microbiome enabled this synthesis.

References