Cross-kingdom dialogs in the gut: Integrating bacterial pathogens, helminths, and microbiota interactions for immune homeostasis

Abstract

The interactions between bacterial pathogens, helminths, and commensal microbiota in the gut form a complex ecological network that profoundly impacts host immunity and health. Pathogens employ strategies such as type VI secretion systems (T6SS) and inflammation induction to evade colonization resistance, disrupt microbial balance, and establish self-benefit ecological niches. These interactions involve competition with commensal bacteria and helminths, which play a critical role in maintaining gut homeostasis by occupying ecological niches, competing for nutrient, and supporting the mucus barrier. Meanwhile, helminths can modulate commensal bacterial gene expression, metabolic activity, and survival by secreting excretory–secretory products. In addition, by inducing a Th2 immune response, helminths can enhance the intestinal mucosal barrier, alter the gut microbiota composition, and thereby inhibit bacterial pathogen colonization. Interestingly, helminths and pathogens can exhibit synergistic or competitive relationships. For instance, Ascaris lumbricoides may provide a survival niche for Vibrio cholerae, while helminths can also indirectly inhibit pathogenic bacteria through immune modulation. These intricate interactions influence gut microbial composition, digestion, and immune function, and are closely associated with diseases. Future research should focus on elucidating the molecular mechanisms underlying these interactions. Understanding the interactions between pathogens, helminths, and commensal microbiota not only provides novel insights into maintaining host immune homeostasis but also establishes a theoretical foundation for future development of gut health intervention strategies.

1. Introduction

The intestinal tract is a complex ecological environment where host and microbial inhabitants have coevolved over millennia, leading to mutually beneficial or competitive interactions [1]. Research reports have indicated that the gut microbiota plays a role in supporting nutrient acquisition and metabolism, pathogen defense, as well as shaping the development and responses of immune cells [2].

Bacterial pathogen infections significantly disrupt the balances and functions of intestinal commensal microbiota through various mechanisms. For example, pathogens impair the growth of commensal bacteria by competing for essential nutrients such as short-chain fatty acids (SCFAs) and occupying ecological niches [3,4]. Pathogens can also eliminate commensal bacteria through the type VI secretion system (T6SS) or modify the intestinal environment by inducing host inflammation, thereby creating conditions favorable to themselves but detrimental to commensal bacterium [5]. Moreover, bacterial pathogens degrade intestinal barriers and interfere with the metabolic activities of commensal bacteria, weakening their protective roles in the host. These combined mechanisms disrupt intestinal homeostasis, potentially leading to microbiota-related diseases [6,7].

Furthermore, studies have confirmed that specific microbiota are essential for the hatching of Trichuris muris eggs and enhance the infection of Heligmosomoides polygyrus in mice [8,9]. Helminth infections can alter the composition and abundance of gut bacteria in their hosts. For instance, the excretory–secretory (ES) products of Ascaris suum and H. polygyrus exhibit diverse antibacterial activities, such as bacterial growth inhibition, biofilm disruption, and agglutination [10,11]. Additionally, Ascaris has evolved counter-regulatory mechanisms that prevent excessive inflammatory responses caused by bacterial translocation and tissue damage during larval migration [12]. Interestingly, helminths and pathogenic bacteria may also have symbiotic relationships. For example, the free-living Caenorhabditis elegans can derive nutrition from microbial components [13]. Moreover, Ascaris lumbricoides has been colonized by V. cholerae isolated from cholera patients, suggesting that the nematode intestine could act as a survival niche for bacterial pathogens [12,14]. These interactions between pathogenic bacteria and helminths contribute to the creation of an optimal ecological niche for survival.

The intestinal tissue consists primarily of immune cells, epithelial cells, and stromal cells, which together maintain the gut barrier, preventing pathogen invasion and stabilizing the intestinal environment [15–17]. Immune defense against microbial pathogens is referred to as type 1 immunity, which primarily relies on the direct killing of pathogens or infected host cells. The adaptive component of this immunity is mediated by type 1 and th17 cells, cytotoxic T cells, as well as IgM, IgA, and several IgG antibody classes. This type of immunity is characterized by elevated levels of the cytokines IL-12, IL-22, IL-23, IFN-γ, and IL-17. [18]. In contrast, helminths primarily mediate type 2 immunity for defense, relying on barrier defenses and IgG1 antibodies, along with multiple components of the innate immune system, including epithelial barriers, innate lymphoid cells (ILCs), eosinophils, mast cells, basophils, and alternatively activated macrophages (AAMs) [18,19]. To ensure long-term coexistence with their hosts, helminths modulate inflammatory responses by inducing regulatory T cells, AAMs, and releasing anti-inflammatory cytokines such as IL-10 and TGF-β [20–22]. Interestingly, intestinal stromal cells interact with various epithelial cell populations through the basement membrane, playing a crucial role in supporting epithelial cell proliferation and functional maintenance [17]. This regulatory process is primarily mediated by soluble mediators, including specific communication between stromal cells and epithelial stem cells [23]. Recent research data demonstrate that Wnt signaling derived from stromal cells plays a dominant role in maintaining epithelial stem cell homeostasis [24]. Notably, stromal cell support for intestinal epithelial differentiation and function is not merely a stationary, passive process. Sophisticated mouse colitis models have revealed that during inflammatory responses, stromal cells actively redistribute to the peri-cryptal region and initiate epithelial barrier repair through prostaglandin E2 secretion [25].

This review primarily explores the intricate interactions in the intestine, focusing on the mutualistic and competitive relationships between intestinal commensal microbiota, bacterial pathogens, and helminths. It highlights the mechanisms by which intestinal pathogens disrupt the balance and functions of commensal microbiota, as well as the interactions between helminths and commensal bacteria, including how helminths regulate commensal microbiota composition and influence host immune response. This review analyzes the interactions between bacterial pathogens, helminths, and commensal bacteria in the gut immune ecosystem. It offers insights for studying gut balance and developing treatments for related diseases.

2. The intestinal ecosystem: A stable niche for microbial crosstalk

The intestine is a complex organ consisting of specialized epithelium, nerves, immune cells, blood, lymphatic vessels, smooth muscle, and provides nutrients and a hospitable niche for the trillions of microorganisms. The gastrointestinal tract comprises two main regions: the small and large intestines, with the innermost mucosal layer playing a pivotal role. This mucosa, made of a single cohesive layer of columnar epithelial cells, is responsible for secreting mucus and absorbing nutrients [26]. Embedded within this layer is the lamina propria, which contains blood vessels, lymphatics, nerves, and lymphoid tissue, as well as numerous intestinal glands [1]. These glands secrete intestinal fluids that aid in digestion and nutrient absorption. Supporting the mucosal layer is the submucosa, composed of loose connective tissue enriched with blood vessels, lymphatics, and nerve fibers, crucial for maintaining the digestive, absorptive, motility, and sensory functions of the intestine. The outermost layer, the muscularis externa, is divided into inner circular and outer longitudinal muscle layers, facilitating intestinal peristalsis and food propulsion.

In the intricate and sophisticated microecological system of the intestine, different types of cells play crucial roles in maintaining intestinal homeostasis. When microbial pathogens invade, intestinal epithelial cells (IECs) upregulate the expression of defensins immediately [27]. These defensins act like frontline warriors that directly combat invading pathogens. At the same time, alarm signals serve as signaling molecules, sending emergency alerts to nearby IECs and the immune system, triggering a more extensive defense response. For example, in the case of Salmonella infection, IECs can induce a substantial production of antimicrobial peptides (AMPs) and express pattern recognition receptors such as NLRP6, further enhancing intestinal defense capabilities [28]. It is noteworthy that ISCs also demonstrate remarkable adaptability in the face of infection. In certain situations, ISCs can change their fate determination and differentiate into more specialized defensive effector cells, such as enterocytes and Paneth cells. When Salmonella strikes, ISCs execute specific transcriptional programs to increase the number of enterocytes and Paneth cells, thus enhancing the effectiveness of infection resistance [28]. However, when faced with different pathogens, such as Clostridioides difficile, IECs may choose to self-sacrifice through apoptosis to prevent the spread of infection and protect the surrounding tissues [29]. In summary, different types of cells in the intestine collaboratively maintain the integrity of the intestinal epithelial barrier through complex interactions, thereby ensuring the homeostasis of the intestinal microecological system.

The unique cellular architecture of the intestine establishes a stable niche for commensal microorganisms. The major commensal bacterial communities in mammals consist of Gram-negative bacteria, such as those from the phylum Pseudomonadota and Bacteroidota, as well as Gram-positive bacteria from the phylum Bacillota [30]. Over millions of years of co-evolution, a mutualistic relationship has developed between the host and its commensal microbiota. Within the gut, commensal bacteria adapt to local niches to obtain nutrients and space while regulating the microbial community through resource competition, limiting invasive pathogens. [31]. In return, gut commensal bacteria provide a range of critical functions for the host, including promoting the integrity of the intestinal epithelial barrier and maintaining immune homeostasis [5]. However, when invasive pathogens (bacterium, virus, and helminth) enter the gut, this delicate balance may be disrupted, triggering host immune responses, which play a pivotal role in the development of gut health and disease.

3. Bacterial pathogen-induced immunity via intestinal epithelium

Intestinal homeostasis is maintained by a complex interplay among the epithelium, immune factors, and microbial flora, including bacteria, fungi, viruses, archaea, and protozoans [16]. During bacterial invasion, a cascade of signals is initiated that leads to the release of cytokines, chemokines, acute-phase proteins, and other immune effectors.

Cytokines from the IL-1 family, particularly IL-18, play a pivotal role in maintaining intestinal homeostasis during bacterial challenges (Fig 1). Released by intestinal epithelium, IL-18 relies on the activation of the inflammasome complex [32,33]. It is crucial for pathogen clearance, such as Salmonella Typhimurium, by inducing enterocytes to produce AMPs and goblet cells to secrete mucus [16]. Furthermore, IL-18 can influence CD4+ Th17 cells and Foxp3+ Tregs directly that express the IL-18R1 receptor, modulating their differentiation both in homeostasis and inflammatory states [34].

Fig 1. Immune responses to pathogens in intestinal epithelium.

This diagram illustrates the immune responses initiated by pathogens in the intestinal epithelium, including interactions between microbiota, epithelial receptors (e.g., TLRs, NLRs), immune cells (e.g., ILCs, T cells, and macrophages), and cytokines (e.g., IL-22, IL-18, and IL-12). It highlights the coordination of innate and adaptive immunity in maintaining intestinal homeostasis and combating infections.

IL-22 plays an essential role in both innate and adaptive immune responses (Fig 1) [35]. It is secreted by T cells (Th1, Th17, Th22, CD8+ T cells, and γδ T cells), natural killer (NK) cells, and ILCs [36]. Induced by IL-6 and IL-23, Th1 and Th17 cells secrete IL-22, while TGF-β can inhibit its production [37–39]. Additionally, IL-12 and IL-17 can induce Th1 cells to produce IL-22 [36]. The accumulation of IL-22 activates the STAT3 signaling pathway, and then promoting the proliferation of IECs and stimulating the secretion of RegIIIβ and RegIIIγ [4]. Salmonella gastroenteritis infection induces the release of IL-1β and IL-12. Notably, IL-12 not only stimulates ILC1 to secrete IFN-γ but also promotes antibody production through a B-cell intrinsic IL-12/IFN-γ feed-forward loop. Meanwhile, IL-1β functions synergistically to enhance IFN-γ production by ILC1 [40–42].

While species from the Clostridiales family, such as C. difficile, invade IECs and induce goblet cells and CD103+ dendritic cells (DCs) to secrete TGF-β and IL-10, consequently promoting Treg proliferation. However, direct evidence demonstrating this mechanism’s contribution to immune evasion remains lacking [43–45]. Additionally, Clostridium-derived bioactive molecules, such as SCFAs and tryptophan, can activate DCs and T cells to induce Treg proliferation (Fig 1) [43]. However, in Rag1^−/− mice lacking T and B lymphocytes, ILC3s serve as the dominant immune responders during Clostridium difficile infection, showing upregulated expression of IL-22, IL-17a, and RegIIIγ. [41]. Citrobacter rodentium is a mouse-specific pathogen. In the initial stages of infection, ILC3s are activated through ligand-activated transcription factors, including aryl hydrocarbon receptor (AHR), RORγt, and Vitamin A and D receptors or bacteria-derived metabolites (SCFAs, Butyrate) [46–49]. The interaction among myeloid cells, such as CX3CR1+ DCs, TL1A+ macrophages, and ILC3s, mediates the secretion of the chemokine CXCL16, controlling the production of IL-22 and AMPs [50–52]. Mechanistically, STAT5a, STAT5b, and STAT3 signaling are initiated by IL-2 or IL-23, respectively [53]. Subsequently, IL-22 interacts with epithelial cells through the STAT3 signaling pathway to regulate immune responses, eliminate pathogens, and maintain intestinal homeostasis [4] (Fig 1).

4. Helminth-induced immunity via intestinal epithelium

Helminths can directly damage or activate IECs either through larval invasion or feeding [54,55]. Although the mechanisms by which the host sensing helminths are still not fully understood. The activation of type 2 immune responses is correlated with the release of alarmins, such as ATP, IL-25, IL-33, and thymic stromal lymphopoietin (TSLP), by epithelial cells [1,56].

Interleukin-33 (IL-33) plays an important role in regulating immune responses in epithelial cells (Fig 2). It helps maintain immune homeostasis and enhances defense against pathogens through promoting the release of Th2 cytokines, mediating tissue repair, and triggering inflammation [57]. IL-33 is produced by activated mast cells during H. polygyrus infection in response to ATP released from apoptotic epithelial cells [58]. In addition, IL-33 can induce ILC2 and Th2 cells to secret IL-13, which enhances the populations of tuft and goblet cells [59,60]. IL-33-deficient mice show defective type 2 responses and inefficient expulsion of Nippostrongylus brasiliensis, highlighting the importance of IL-33 in parasite clearance [61].

Fig 2. Immune responses to helminth in intestinal epithelium.

This illustration depicts the immune response triggered by helminth infection in the intestinal epithelium. It highlights the role of tuft cells (producing IL-25), dendritic cells, and innate lymphoid cells (ILC2) in inducing Type 2 immunity. Key cytokines, including IL-4, IL-5, IL-13, and IL-33, drive the activation of Th2 cells, mast cells, and B-cells, leading to antibody production (IgG1/IgE) and helminth expulsion. Proliferative responses involving stem cells and communication with epithelial cells are also shown to maintain intestinal integrity.

IL-25 (also known as IL-17E) is a unique cytokine within the IL-17 family, essential for inducing type 2 immune responses, maintaining tissue homeostasis, and stimulating injury repair (Fig 2) [62,63]. Produced by various immune cells such as T cells, DCs, and ILC2s, a significant source of IL-25 is tuft cells [59]. Tuft cells are crucial for recognizing helminth infections, and their absence in Pou2f3-deficient mice leads to reduced IL-25 production and defective type 2 responses [60]. During infection with N. brasiliensis, tuft cells significantly increase IL-25 production, recruiting CD4+ T cells and BATF-dependent ILC2s to the lamina propria [64]. The resulting production of IL-4 and IL-13 promotes the differentiation of tuft and goblet cells, facilitating mucus secretion and helminth expulsion [59,60].

TSLP was initially identified in mouse thymic stromal cells, and it plays an important role in the development and differentiation of lymphocytes (Fig 2) [65]. TSLP is produced by epithelial cells in response to helminth infections and binds to receptors on both intraepithelial immune cells and DCs. Upon activation by TSLP, DCs drive the polarization of Th2 responses, enhancing the expulsion of T. muris [1]. TSLP preferentially activates Th2 and Th9 cells, promoting the production of T2 cytokines while limiting pro-inflammatory cytokines, such as TNF-α, IL-1b, and IL-6, as well as Th1-polarizing cytokines (IL-12 and interferons). In addition, TSLP has been shown to suppress Th17-driven mucosal inflammation after bacterial colonization [66]. TSLP also stimulates NKT cells to produce IL-4 and IL-13, enhancing the type 2 immune response [67]. In the adaptive immune response, TSLP signaling directly influences naive T cells in the presence of T cell receptor stimulation, promoting the proliferation and differentiation of Th2 cells through the induction of IL-4 gene transcription [68–70]. Additionally, TSLP mediates the proliferation and differentiation of Tregs induced by DCs [71,72]. It also promotes B-cell lymphopoiesis by inducing the proliferation and differentiation of B-cell progenitors [73–75]. In the presence of TSLP, multilineage-committed CD34+ progenitor cells, pro B-cells, and pre B-cells differentiate and proliferate [76]. TSLP also induces the release of chemokines that attract T cells, including thymus and activation-regulated chemokine (TARC)/CCL17, DC-CK1/pulmonary and activation-regulated chemokine (PARC)/CCL18, macrophage-derived chemokine (MDC)/CCL22, and macrophage inflammatory protein (MIP3β)/CCL19.

5. Bacterial pathogen and commensal bacteria interactions

In the gut microbial ecosystem, commensal and pathogenic bacteria shape the host’s health-disease balance through complex ecological interactions involving nutrient competition, modulation of host immunity, and coexistence strategies [5]. Colonization resistance is a mechanism by which the gut microbiota prevents the colonization of pathogens through resource competition, niche occupation, and immune modulation [77]. Between the bacteria, colonization resistance can be influenced through producing inhibitory compounds or competing for resources. Additionally, commensal bacterial have indirect defensive mechanisms in the gut that restrict the invasion or expansion of pathogens. These include the microbiota-induced or microbiota-maintained mucus layer, oxygen levels, and both innate and adaptive immune responses [5].

5.1 Direct mechanisms

The gut microbiota can restrict the expansion of pathogens by depleting the majority of available nutrients (Fig 3). For example, in germ-free (GF) mice or antibiotic-treated mice, the levels of sugars, amino acids, and other nutrients in the intestinal lumen increase, accompanied by a decline in colonization resistance [78–80]. Studies have shown that microbial consumption of dietary amino acids is a key factor in limiting the colonization of S. Typhimurium. Additionally, commensal bacteria mediate resistance to S. Typhimurium through the consumption of oxygen, iron, zinc, manganese, and anaerobic respiratory electron acceptors [81,82]. Beyond nutrient competition, certain active growth inhibition or infection mechanisms also promote colonization resistance. Bacteriocins are a heterogeneous class of peptides produced by bacteria, enhance colonization resistance by specifically inhibiting or killing targeted bacteria, typically those closely related to the producer, such as pathogenic Enterococci and other gram-positive bacteria [83–85]. In contrast, pheromones are small peptides secreted by Enterococci that specifically target pathogenic strains, such as virulent Enterococcus faecalis, to facilitate colonization resistance [86].

Fig 3. Competition and cooperation between bacterial pathogens and commensals.

The illustration highlights the interplay between pathogens and commensals in the gut, involving nutrient competition, effector molecules, and metabolites. Commensals secrete bacteriocins, SCFAs, and metabolites to inhibit pathogens and strengthen the gut barrier. Pathogens, meanwhile, employ T3SS, T6SS, and induce reactive oxygen/nitrogen species (ROS/RNS) to invade host tissues. Additionally, the involvement of trace element chelation, antimicrobial peptides (AMPs), and the regulation of signaling molecules further contributes to the balance and resistance mechanisms of the microbial community.

Gut bacteria employ contact-dependent growth inhibition system and secreted metabolites to compete and restrict pathogen colonization (Fig 3). A cell contact-dependent inhibition (CDI) system, termed CDI, was discovered in E. coli and later in other Pseudomonadota. CDI requires a specific receptor protein to recognize target cell and encode different toxic effector domains with various modes of inhibition. In addition, toxic effector genes are usually accompanied by a protective protein that neutralizes the toxin to protect the producing cell [87,88]. Another CDI system, the T6SS, can spear neighboring cells and inject toxic proteins without the need for a receptor. The system is widely present in Gram-negative bacteria, especially Pseudomonadota and Bacteroidota [88]. Beyond contact-dependent mechanisms, bacterial metabolites are also critical for colonization resistance. Secondary bile acids, generated through 7α/β-dehydroxylation by rare bacteria such as Clostridium scindens, inhibit Gram-positive bacteria like C. difficile and enhance resistance to infection [89–93]. Similarly, SCFAs, including acetate, propionate, and butyrate, can serve as an energy source for IECs and contribute to colonization resistance [94]. For example, SCFAs can suppress the growth of pathogenic E. coli, C. rodentium, and C. difficile, as well as limit the colonization of S. Typhimurium in the murine gut [95–98].

5.2 Indirect mechanisms

Besides directly inhibiting pathogen colonization, gut microbiota indirectly strengthen colonization resistance by preserving mucus layer, regulating oxygen levels, and modulating innate and adaptive immune responses.

The mucus layer forms a physical barrier that prevents pathogens from invading the underlying epithelium. For certain pathogens, such as C. rodentium, Salmonella species, and pathogenic E. coli strains, which rely on attachment to the epithelium to initiate infection and colonization, the mucus layer is particularly crucial in enhancing colonization resistance [5]. So far, studies have confirmed that a varied microbiota is important to promote mucus barrier function and colonization resistance in the presence of a disrupted mucus layer. For example, comparing the mucus layer between GF animals and conventionally raised mice reveals that GF animals have a thinner mucus layer, suggesting that microbial symbionts may enhance the mucosal barrier to limit pathogen colonization [99,100]. Similarly, mice lacking mucin 2 exhibit increased pathogen burden and greater disease severity following infection with C. rodentium, S. Typhimurium, and Listeria monocytogenes [101–103].

The gut microbiota also regulates oxygen levels within the intestine to inhibit pathogen expansion. For instance, members of the Clostridia class produce butyrate through β-oxidation, which enhances aerobic respiration in IECs, thereby depleting oxygen levels at the epithelial surface and restricting the growth of facultative anaerobes such as S. Typhimurium [104–107]. A depletion of Clostridia or a reduction in butyrate levels, often observed during inflammation and microbiota dysbiosis, elevates oxygen levels and facilitates pathogen proliferation. Additionally, commensal bacteria can compete for residual oxygen to limit pathogen colonization, such as by suppressing the expression of oxygen-dependent virulence genes in Shigella flexneri or restricting aerobic respiration in C. rodentium and S. Typhimurium [108–110]. Under anaerobic conditions, commensal bacteria such as Mucispirillum schaedleri further inhibit pathogen growth by competing for anaerobic respiratory substrates like nitrate, thereby limiting the expansion of pathogens that rely on nitrate respiration in the inflamed intestine [111–113]. This intricate regulation of oxygen levels and substrate competition underscores the pivotal role of gut microbiota in maintaining ecological balance and promoting colonization resistance against pathogens.

The gut microbiota inhibits pathogen colonization by stimulating the secretion of AMPs and proteins from host epithelial cells, exerting both antimicrobial effects and regulation of microbial balance. AMPs such as RegIIIβ and RegIIIγ, secreted by Paneth cells, maintain spatial segregation between commensals and IECs [114,115]. A reduction in these AMPs increases susceptibility to pathogen infection. For instance, microbial depletion by antibiotic administration reduces RegIIIγ expression, impairing the clearance of vancomycin-resistant Enterococcus [116]. Stimulation with Toll-like receptor 7 agonists or activation of the NOD1/2 signaling pathway can restore AMP production and limit pathogen colonization [117,118]. Lipocalin-2 (LCN2), another antimicrobial protein, inhibits pathogen growth by sequestering bacterial iron acquisition systems, and LCN2-deficient mice exhibit dysregulated gut microbiota composition [119–121]. Similarly, related proteins such as calprotectin demonstrate antimicrobial activity by chelating metal ions like iron, zinc, calcium, and manganese, although the relationship between calprotectin and the gut microbiota requires further investigation [122]. Collectively, these AMPs and proteins play critical roles in maintaining intestinal ecological balance and resisting pathogen colonization.

The gut microbiota also restricts pathogen colonization by inducing cytokines and adaptive immune responses. Microbiota-induced IL-22 enhances intestinal barrier function, alters microbiota composition, and promotes the growth of commensals like Phascolarctobacterium, which compete with pathogens, such as C. rodentium and C. difficile [123–125]. Additionally, IL-1β contributes to pathogen clearance, such as S. Typhimurium and Pseudomonas aeruginosa, by rapidly recruiting immune cells and neutrophils. In terms of adaptive immunity, certain commensals induce the production of polyreactive, low-affinity IgA antibodies, which cross-react with antigens expressed by gut pathogens and other bacterial species. Furthermore, IgA supports commensal expansion and maintains a favorable ecological niche, thereby limiting pathogen colonization [126–128]. Through these mechanisms, the gut microbiota collaborates with the immune system to provide resistance against intestinal pathogens and prevent their colonization.

5.3 Bacterial pathogen-driven counterattack

While being regulated by the gut microbiota, bacterial pathogens have evolved various strategies to evade colonization resistance (Fig 3). First, they employ virulence mechanisms to modify the intestinal environment for their own growth. For example, S. Typhimurium induces inflammation to produce reactive oxygen and nitrogen species, creating byproducts that can be utilized for respiration, while also exploiting the increased oxygen levels caused by inflammation to gain a growth advantage [3,129,130]. Additionally, S. Typhimurium uses high-affinity iron and zinc transport systems to outcompete other microbes for scarce metal resources. Second, pathogens directly antagonize the resident microbial community to establish ecological niches. The T6SS is a common competitive tool used by pathogens, which injects toxic effector molecules to kill neighboring bacteria [131]. For instance, V. cholerae leverages its T6SS to kill competing E. coli, enhancing its infectivity. Similarly, S. Typhimurium uses its T6SS to eliminate Klebsiella oxytoca, promoting its colonization. Shigella sonnei employs its T6SS to kill related species, such as Shigella flexneri and E. coli, thereby improving its ability to colonize. In addition, C. rodentium has been shown to utilize its T6SS during the early invasion stage to kill commensal E. coli or evade killing by other T6SS-bearing E. coli, enabling its successful colonization [132–134]. In addition, through the type III secretion system (T3SS), pathogens can inject effectors to alter the host’s physiological environment and promote their own growth. C. rodentium uses T3SS to adhere to IECs and inject effectors, inducing excessive epithelial proliferation, which releases oxygen for its respiration while metabolizing hydrogen peroxide (H₂O₂) to sustain growth [135]. S. Typhimurium employs T3SS effectors to trigger inflammatory responses, releasing reactive oxygen species and reactive nitrogen species that generate respiratory electron acceptors, such as tetrathionate (SO₄O₆²⁻) and nitrate (NO₃⁻), providing essential energy sources for its growth [5]. These mechanisms demonstrate that pathogens effectively overcome colonization resistance by altering the host environment and directly competing with the resident microbiota.

6. Helminth and commensal bacteria interactions

The influence of helminth infection on gut microbiota is intricate and multifaceted, occurring through diverse mechanisms (Fig 4). Helminth infections can affect the gene expression of intestinal bacteria, modulating their metabolic activities and survival capabilities [45]. While residing within the gut, helminths secrete various metabolic products that interact with gut bacteria, impacting bacterial growth and community structure [10]. Furthermore, there exists a competitive relationship between helminths and gut bacteria for nutritional resources, where the presence of helminths alters the nutrient environment within the gut, consequently influencing bacterial survival and reproduction [45]. In addition, helminth infection induces immune responses in the host, particularly Th2-type immune responses, which regulate the balance of the gut bacterial community. Helminth infection may also alter the physical and chemical environment of the gut, affecting microbial composition [56].

Fig 4. Competition and cooperation between helminths and commensals.

Helminths modulate gut microbiota by consuming nutrients and secreting excretory–secretory products (ES), while also stimulating goblet cells to produce mucus and antimicrobial peptides. They suppress pathogenic bacteria by competing for nutrients, whereas pathogens may inhibit helminth development by limiting fatty acids and ethanolamine. Meanwhile, commensal bacteria secrete short-chain fatty acids (SCFAs) to regulate Th2 immunity and restrict helminth infections. These interactions collectively shape and maintain gut microbial balance.So far, specific mechanisms of helminth and bacterial interactions are being elucidated. Continuous production and shedding of mucus play a significant role in blocking both helminth and bacterial infections. Beyond its defensive function, mucus also provides nutrition for certain commensal microorganisms [136]. The composition of mucus is regulated by glycosylation patterns, including the addition of sialic acid and sulfate residues [137]. Helminth infections induce Th2 immune responses that may regulate mucus modification through glycosylation and sulfation [138–140]. Additionally, the mucus-rich environment effectively prevents commensals, pathogens, and other large particulates from penetrating the intestinal epithelial monolayer into the mucosal and submucosal, while also serving as an anchor point for AMPs, including RegIIIγ and Relm-β to synergistically suppress pathogenic colonization. [1,141]. Numerous antimicrobial proteins (AMPs) have been identified, including a new one named small proline-rich protein 2A (SPRR2A), discovered during H. polygyrus infection in mice. SPRR2A is phylogenetically distinct from previously known AMPs [142]. Another intestinal bactericidal protein, resistin-like molecule β (RELMβ), primarily targets gram-negative bacteria and is dependent on type 2 cytokines [143]. Nutritional interactions are another significant aspect of helminth-bacterial dynamics. For instance, Venzon reported that E. coli mutants infected in gnotobiotic mice affected the proper development of T. muris parasites due to nutritional defects in fatty acid biosynthesis and ethanolamine utilization [144]. Helminth-induced intestinal epithelial damage caused by tissue-migrating larvae or adult worms can also modify bacterial communities by altering the intestinal environment [56]. In addition, the immune responses elicited by helminth infections can lead to various physiological alterations, influencing bacterial communities in the gut, including modifications in digesta transit time, which alters food digestion dynamics [145]. This altered digestion process is crucial for shaping both the composition and metabolic capabilities of the bacterial community.

The relationship between helminths and gut microbiota, shaped by evolution, is bidirectional. Recent studies have explored interactions between helminths and bacteria. In the case of T. muris infection in mice, diverse microbes are necessary for the optimal hatching of T. muris larvae from ingested eggs [8]. Conversely, structural changes in the cecal microbiome during infection can suppress subsequent parasite egg hatching, protecting the host from overcrowding [146]. Interestingly, many bacteria identified in animal studies modify the intestinal microbiota in both mice and pigs, utilizing chitin-based parasite egg shells as an energy source [147,148]. Additionally, Intestinal helminth larvae hatch in the soil and are known to carry bacteria into the host. Once inside, helminths may compete with intestinal bacteria for available nutrients (e.g., acetate and lactate) and/or secrete products (e.g., proteins and peptides) that alter bacterial growth [149,150]. Interestingly, it has been reported that protective bifidobacteria can also produce acetate, which in turn enhances epithelial cell-mediated intestinal defense, thereby protecting the host from fatal infections [6]. The presence or absence of the microbiota can also influence the colonization of helminths. For example, in animals treated with antibiotics or maintained in sterile environments, both larval and adult worms of H. polygyrus tend to reside closer to the duodenum, leading to reduced intestinal motility [151]. This significantly impedes the host’s critical role in the “weep and sweep” response against helminths [152]. Ultimately, both helminths and bacterial communities strive to establish long-term residence in the intestine without evoking inflammation [45].

7. Conclusions and perspectives

This article highlights the complex interactions among pathogenic bacteria, commensal microbiota, and helminths within the gut ecosystem. Commensal bacteria provide colonization resistance against pathogens through direct mechanisms, such as nutrient competition, production of inhibitory compounds, and secretion of metabolites like SCFAs and secondary bile acids. These metabolites not only inhibit pathogen growth but also support intestinal epithelial health. Indirectly, commensal bacteria regulate the gut environment by maintaining the mucus barrier, modulating oxygen levels, and inducing immune responses. However, pathogenic bacteria have evolved sophisticated strategies to counter colonization resistance, including the use of T6SS to kill commensal bacteria, inducing inflammation to alter the gut environment, and competing for resources such as iron and oxygen to establish ecological niches.

Meanwhile, helminths interact with commensal bacteria through both direct and indirect mechanisms, further complicating the gut ecosystem. Helminths secrete ES products that regulate bacterial gene expression, metabolic activity, and survival, while competing with bacteria for nutritional resources, thereby altering the composition and functionality of the microbiota. Indirectly, helminth infections elicit Th2 immune responses that regulate microbial balance through cytokines (e.g., IL-18 and IL-22) and antimicrobial proteins (e.g., SPRR2A and RELMβ). These immune responses reshape the gut environment, promoting the expansion of anti-inflammatory bacterial populations and enhancing the mucus barrier to support the growth of beneficial bacteria. Interestingly, helminths and pathogenic bacteria may exhibit either synergistic or competitive relationships. For example, helminths may provide a survival niche for pathogenic bacteria, as observed in the colonization of V. cholerae within the intestines of Ascaris lumbricoides. Conversely, helminths may indirectly inhibit pathogenic bacteria through immune modulation.

Currently, studies on the mechanisms underlying interactions among commensal bacteria, pathogens, and helminths remain limited. This raises several important questions worth exploring. For instance, does the disruption of intestinal epithelial tight junctions by pathogenic bacteria via the T3SS facilitate helminth infection? If so, what are the specific mechanisms? Furthermore, how do pathogenic bacteria sense changes in the gut microbiota or metabolite composition through two-component systems? How does this sensing regulate gene expression to promote infection and colonization? During helminth infections, do changes in gut commensal bacterial metabolites influence the virulence of pathogens? If so, through which metabolic or signaling pathways? In addition, bacterial T6SS can kill competing bacteria within the same niche by secreting toxins. Could helminths exploit certain gut bacteria to utilize T6SS, eliminating competitors and obtaining resources to establish ecological dominance?

Helminth infections also impact the gut environment, but whether these effects are beneficial or detrimental remains unclear. What mechanisms mediate these outcomes? For example, helminth infection induces a Th2-skewed immune response, including cytokines such as IL-4 and IL-10. This suppresses Th1 responses, including IFN-γ, thereby weakening host cellular immunity and reducing resistance to intracellular pathogens like Salmonella and Mycobacterium. On the other hand, helminths may regulate gut microbiota by increasing beneficial bacterial populations or reducing the colonization of pathogens such as E. coli. Additionally, helminths secrete anti-inflammatory molecules, which alleviate inflammation and restore gut homeostasis. These mechanisms may interact with one another, further complicating the dynamic relationships within this system.

Understanding how commensal bacteria, pathogens, and helminths interact to orchestrate intestinal homeostasis is crucial (Fig 5). Such insights could deepen our understanding of microecological regulation within the host and provide a theoretical foundation for developing effective strategies to prevent and manage intestinal diseases.

Fig 5. The balance among bacterial pathogens, helminths, and commensal bacteria.

Funding Statement

This work was supported by the National Natural Science Foundation of China (32302898 to HSH) and the Earmarked Fund for Doctoral Research Start-Up Fund of Henan University of Science and Technology (13480105 to HSH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.