Living within: endosymbiosis in parasites of medical importance—profits, expenses, and implications for host–parasite interactions

1 Introduction

Human parasitic infections have long represented an intractable problem in global public health. Although significant progress has been achieved in the treatment and control of medically important parasites, they continue to have considerable morbidity impacts and socioeconomic burden especially in developing countries (Ung et al., 2021). Meanwhile, knowledge and gaps on parasite biology, virulence factors, vulnerabilities, and pathogenicity remain to be elucidated.

Endosymbiosis is a biological relationship, where one organism lives within the body of another. The concept of endosymbiosis was first introduced relevant to the origin and development of organelles in eukaryotes, mainly mitochondria and plastids, which were contemplated to be acquired from bacterial endosymbionts (Taylor et al., 2012; Manoj et al., 2021). Then, evidence of endosymbiotic bacteria and fungi within arthropods was established, and later microorganisms were reported to be associated with different eukaryotes, including parasitic helminths and protozoa (Afzelius et al., 1989; Taylor et al., 2012). Virus-like particles (VLPs) were observed in parasites in the 1960s, and a molecular proof of viruses within protozoa was documented in the late 1980s, leading to the uncovering of double-stranded RNA (dsRNA) viruses in a number of parasitic protists (Molyneux, 1974; Benchimol et al., 2002; Barrow et al., 2020). Over the past years, an increasing array of microorganisms has been identified within parasites (Figure 1).

It is important to note that symbiosis is a complex phenomenon where the biological relationships span over a continuum ranging broadly from parasitism to commensalism and to mutualism. However, modern consensus has highlighted the overlap between these distinct terms and their highly dynamic context-dependent nature, as microbial behavior can shift according to ecological composition and environmental conditions within the host, as well as evolutionary time (Raina et al., 2018; Wiles and Guillemin, 2019). In fact, studies on the parasite–endosymbiont association were first of evolutionary concerns. More recently, researchers have paid attention to the role of this association in parasite biology and parasite–human host interactions. Research on parasitic helminth microbiomes remains scarce, and knowledge on the incidence and the impacts of the harbored microorganisms is still being developed (Jenkins et al., 2019; Gobert et al., 2022). Many pathogenic bacteria have been found to be infected with lysogenic bacteriophages that markedly affect their virulence, while information regarding protozoan endoviruses is lagging far behind (Janssen et al., 2015; Lafleur and Olivier, 2022).

Within the scope of this review, the term “symbiosis” is used to describe the association between the parasite and the microorganisms residing within it, whereby neither partner is harmed and one or both may benefit from the association (Martin and Schwab, 2013). This narrative review synthesizes current knowledge of parasite microbiome across medically important protozoa, helminths, and arthropods, with particular emphasis on its role within the host–parasite–endosymbiont triad. The objective is to provide a framework for understanding parasite–microbial interactions and their impact on host–parasite interactions, while highlighting their potential as therapeutic targets.

2 Methodology

To construct this narrative review, we systematically searched multiple databases: PubMed, Scopus, and Google Scholar. No date limit was applied on the literature search to retrieve all relevant studies including early foundational publications. We focused on endosymbiotic associations in key parasites infecting humans. Search terms included the following: “Acanthamoeba”, “Entamoeba”, “Giardia”, “Leishmania”, “Trypanosoma”, “Trichomonas”, “Cryptosporidium”, “Plasmodium”, “Toxoplasma”, “Blastocystis”, “filarial nematodes”, “Wuchereria”, “Onchocerca”, “intestinal nematodes”, “Fasciola”, “Schistosoma”, “Opisthorchis”, “Flat worms”, “Cestodes”, “Echinococcus”, “Taenia”, “Hymenolepis”, “Sarcoptes”, “Demodex”, “Pediculus”, and “Wohlfahrtia”, as well as “Endosymbiont”, “Endosymbiosis”, “Endosymbiotic bacteria”, “Bacterial endosymbiont”, “Endosymbiotic virus”, “Viral endosymbiont”, and “Viral-like particles”. We incorporated the Boolean queries “AND” and “OR” as appropriate to the above terms to generate the search strategy. The scope of this review encompassed primary and secondary research of heterogenous evidence types, focusing on endosymbionts or microbiota harbored within medically important parasites and exploring their potential impact on the parasite biology and the host–parasite interactions. Studies investigating endosymbiosis in parasite species that do not infect humans; studies involving hyperparasites, endosymbiont organelles, and evolutionary symbiosis; and non-peer-reviewed preprints were excluded.

Literature selection followed a standardized two-stage screening process: title/abstract screening followed by full-text evaluation. Extracted data points included taxonomic classification of the parasite species and the associated endosymbiont, technique employed, endosymbiont impact on the parasite biology, and host–parasite–endosymbiont crosstalk. Findings were organized according to parasite taxonomy integrating data from review articles, human observational studies, and experimental studies. Given the narrative nature of this review, we acknowledge that the scope of the search was non-exhaustive. Nevertheless, studies were curated through the authors’ judgment to provide a representative and significant overview of the relevant literature.

3 Endosymbionts of parasitic protozoa

3.1 Amoebozoan parasites

Acanthamoeba (Lobosa) is a free-living amoeba that can act as an opportunistic human pathogen. It has been identified from different environmental sources and can cause fatal granulomatous encephalitis and blinding keratitis [“Acanthamoeba keratitis” (AK)] (Siddiqui and Khan, 2012; Hajialilo et al., 2019). Among Acanthamoeba genotypes (T1–T23), T4 is the most prevalent in environmental samples and the most commonly involved in human infections (Hajialilo et al., 2019; Rayamajhee et al., 2022). The amoebae have been reported to host a variety of organisms comprising bacteria, viruses, protists, and yeasts (Siddiqui and Khan, 2012). Acanthamoeba has been described as the “Trojan horse” of microorganisms; trophozoites and cysts can maintain microorganisms and act as reservoir of human pathogens. Various bacterial groups were found to be carried by Acanthamoeba spp., including Legionella pneumophila, Aeromonas spp., Escherichia coli, Pseudomonas aeruginosa, and Shigella spp., Vibrio cholerae (Mungroo et al., 2021), as well as Mycobacteria, Chlamydia spp., Rickettsia spp., Coxiella spp., and Bartonella spp. (Price et al., 2024). The majority of Acanthamoeba clinical isolates from patients with AK were found to carry one or more bacterial endosymbionts that were recorded to affect corneal pathology and disease outcome (Rayamajhee et al., 2022). Mungroo et al. (2021) revealed that Acanthamoeba-associated microorganisms use amoeba as a shield to resist stressful conditions and evade the human host immune response, while multiplying safely and adapting and exchanging genes within, thus leading to potentiated pathogenicity. Furthermore, Price et al. (2024) proposed that phagocytic predatory amoebae serve as “training ground” where evolution and selection of microorganisms occur, thus potentiating their pathogenic capabilities. In the early 2000s, a new virus called Acanthamoeba polyphaga Mimivirus (APMV) was isolated. The virus has a large and complex double-stranded DNA (dsDNA) genome, exceeding the size of many bacteria, and a new family was created—the Mimiviridae (Colson et al., 2013). Later, numerous giant viruses (phylum Nucleocytoviricota) associated with Acanthamoeba spp. were identified (Queiroz et al., 2022). The detection of giant viruses of amoebae in humans and the study of their possible virulence are emerging research areas (Colson et al., 2017). APMV is an assumed pneumonia agent detected in sputum and bronchoalveolar lavage samples (Sakhaee et al., 2022); its role in nosocomial infections is still under investigation (Bousbia et al., 2013). Regarding amoeba–giant virus interaction, the virus can prevent amoebal encystation through inhibition of serine proteinase expression, a protein essential for the process. Meanwhile, Acanthamoeba cysts are reported to be resistant to APMV infection as long as the stimulus for cell encystment started before the viral infection (Boratto et al., 2015; Queiroz et al., 2022).

Entamoeba histolytica (Conosa) is the causative agent of amoebiasis, a parasitic infection of great public health concern in developing countries. Approximately 10% of infected individuals develop an invasive disease. Details regarding the pathobiological aspects of tissue invasion by the parasite in intestinal and extraintestinal diseases are still not clear (Guillén, 2023). Protozoal endoviruses were demonstrated for the first time in E. histolytica, following electron microscopy observation of VLPs that caused parasite lysis in axenic cell cultures (Diamond et al., 1972). A series of studies then described the morphogenesis of the amoeba viral particles, but the taxonomy of the virus had not been determined (Mattern et al., 1977; Hruska et al., 1974). No further investigation on the subject of Entamoeba virus genome sequences was accomplished as reported by Lafleur and Olivier (2022). Fifty years later, Kinsella et al. (2020) implicated Entamoeba and Giardia parasites as hosts of CRESS viruses. CRESS viruses are a group of small single-stranded DNA (ssDNA) viruses having a circular conserved replication-associated protein (REP) and a diverse host range (Zhao et al., 2019). Unclassified CRESS viruses are frequently detected in human stool samples, raising questions regarding host specificity and clinical significance (Phan et al., 2015). Using metagenomic sequencing, two CRESS virus families, Naryaviridae and Nenyaviridae, were reported to infect Entamoeba, while Giardia was infected by the Vilyaviridae family (Kinsella et al., 2020). The CRESS virus family Redondoviridae was reported to be linked to human periodontal disease and critical illness. Redondovirus and the oral commensal amoeba Entamoeba gingivalis coexist in metagenomic data from oral disease and healthy human subjects (Abbas et al., 2019). Keeler et al. (2023) investigated the cell niche of the Redondovirus in oro-respiratory specimens and recorded E. gingivalis as the potential host supporting its replication.

3.2 Excavata parasites

Leishmania spp. (Discoba) are intracellular trypanosomatid parasites, occurring in two subgenera Leishmania and Viannia, and are transmitted by phlebotomine sandflies (de Almeida et al., 2017). Depending on the Leishmania spp., three main clinical forms of leishmaniasis occur: visceral (VL), cutaneous (CL), and mucocutaneous (MCL). Worldwide, over 12 million individuals are infected with Leishmania spp. (Lockard et al., 2019). VLPs were first detected in L. hertigi (a lizard parasite), and later Leishmania dsRNA viruses (LRVs) were reported to inhabit the parasite as a natural host (Saberi et al., 2019). LRVs (family Totiviridae/genus Leishmaniavirus) are non-enveloped dsRNA viruses classified into two main types: LRV1 and LRV2. The LRV1 type comprises the New World (NW) strains (L.V. guyanensis and L.V. braziliensis) and is divided into 14 subtypes. The Old World (OW) strains (L. major, L. tropica, and L. aethiopica) belong to the LRV2 type (Zangger et al., 2014; Ginouvès et al., 2016; Cantanhede et al., 2018; Barrow et al., 2020). LRV is transmitted vertically in the parasite during multiplication, and as VLPs were detected in Leishmania exosomes, it may also be horizontally conveyed (Atayde et al., 2019). LRV was noted to promote parasite-infected mammalian cell survival through AKT1 prosurvival kinase phosphorylation (Eren et al., 2016). LRVs were found not to directly affect the parasite growth. The release of the virus from the degraded parasite impairs the innate immune response by inducing hyperinflammation via Toll-like receptor (TLR3) signaling activation. Thus, the virus can induce increased parasite burden, disease exacerbation, metastatic disease, and parasite persistence (Hartley et al., 2012; 2016; Parmentier et al., 2016; Rossi and Fasel, 2018). Furthermore, LRV was proposed to enhance expression of the parasite key virulence factors GP63 and MPI, allowing Leishmania to evade digestion in macrophages (Mirabedini et al., 2023; Sabeti et al., 2025). A new non-LRV Leishmania endosymbiont virus has been discovered that is hosted by L. martiniquensis, a species that can cause severe visceral disease in humans. The virus was found to have several features of the Bunyaviridae, which are enveloped, negative-sense ssRNA viruses, and this Leishbunyavirus was termed LmarLBV1 (Grybchuk et al., 2020). Leptomonas spp. (monoxenous trypanosomatids) are regarded nonpathogenic to man; meanwhile, Leptomonas seymouri was reported as a co-infectant in clinical specimens from VL and PKDL cases (Singh et al., 2013). Thakur et al. (2020) proclaimed that Leptomonas spp. can act as opportunistic human pathogens. A L. seymouri narna-like virus, the Lepsey NLV1 naked positive ssRNA virus, was demonstrated in Indian VL cultured isolates, raising the question of its possible role in disease pathogenicity (Sukla et al., 2022). In contrast to their relatives within the same clade, the human-infecting Trypanosoma brucei and Trypanosoma cruzi, responsible for Human African Trypanosomiasis and Chagas disease, respectively, are described as endosymbionts lacking trypanosomatids (Alves et al., 2013). However, in a study by Fernández-Presas et al. (2017), clusters of enveloped and non-enveloped VLPs were observed within T. cruzi epimastigotes using electron microscopy, though reported to be absent from the amastigotes and trypomastigotes. Their acquisition, characterization, and biological significance require further investigation.

Trichomonas vaginalis (Metamonada) is an obligate parabasalid flagellated parasite of the human genitourinary tract and the agent of a widespread sexually transmitted inflammatory disease (Zhang et al., 2023). T. vaginalis has a remarkable ability to establish symbiotic relationships with other microorganisms (Mercer and Johnson, 2018; de Aquino and Simoes-Barbosa, 2022). In 1985, a dsRNA virus of the Totiviridae family was found to live within T. vaginalis, the first virus discovered in a protozoan organism (Graves et al., 2019a). Trichomonas vaginalis virus (TVV) has four distinct species and is closely associated with the parasite Golgi complex (Barrow et al., 2020). Manny et al. (2022) reported a new TVV species using transcriptome mining (TVV5). Approximately 40% to 100% of T. vaginalis isolates shelter the virus, with TVV1 being the most commonly encountered (Fichorova et al., 2017). TVV endosymbiont has been demonstrated to upregulate the expression of T. vaginalis major immunogenic proteins, the cysteine proteinases that are linked to cytotoxicity, cytoadherence, and host immune evasion. Additionally, TVV has been associated with varying compartmental expression of P270, another T. vaginalis immunogenic protein, yet its role in pathogenicity remains unclear (Fichorova et al., 2013; He et al., 2017; Rada et al., 2022; Graves et al., 2025). TVV particles are liberated from the parasite within secretory extracellular vesicles (sECVs), which are reported to stimulate a higher proinflammatory response compared to non-infected T. vaginalis strains (Rada et al., 2022). TVV1 and TVV2 have been linked to trichomoniasis severity, whereas TVV2 and TVV3 have been associated with parasite virulence factor expression (Graves et al., 2019b). In addition to TVV, Mycoplasma hominis was identified in T. vaginalis clinical isolates by PCR in 1998. Most T. vaginalis isolates were found later to harbor M. hominis, and a novel species called Candidatus Mycoplasma girerdii. Mycoplasma is a member of the bacterial class Mollicutes, very small bacteria that lack a cell wall; M. hominis is a potential pathogen involved in bacterial vaginosis, and its strict symbiosis with T. vaginalis has been reported to be a unique association of two obligate human parasites (Dessì et al., 2019). M. hominis multiplies readily within the trichomonad, which provides a safe environment for the bacterium and plays a role in its transmission. In return, Mycoplasma can affect T. vaginalis growth rate, and its biochemical metabolic pathways promote a mutual benefit. T. vaginalis–Mycoplasma alliance can interfere with nitric oxide production by macrophages by competing for arginine, the key substrate during the immune reaction (Margarita et al., 2016; Fichorova et al., 2017). The bacteria were also shown to modulate T. vaginalis gene expression and to enhance its cytoadherence and hemolytic activity in vitro (de Aquino and Simoes-Barbosa, 2022). T. vaginalis–Mycoplasma endosymbiosis potentiates the trichomonad vaginal pathogenesis by upregulation of the human host proinflammatory response to the parasite, and predisposing to the outcomes associated with severe inflammation (Dessì et al., 2019). More recently, T. vaginalis–Mycoplasma endosymbiosis has been shown to modulate host immune signaling pathways; the presence of M. hominis drives type 1 IFN responses mediated by IFN-ϵ, which protect against cytoadherence and host cell death. This protective effect is disrupted by T. vaginalis sECVs that downregulate type 1 IFN gene expression, promoting host cell lysis and increasing parasite burden (Kochanowsky et al., 2025).

Giardia lamblia (Metamonada) is a diplomonad flagellate designated among the most prevalent intestinal protozoan pathogen in humans worldwide (Adam, 2021). Eight different genetic assemblages of the parasite species complex, A through H, are recognized. Assemblages A and B are infectious to humans, while assemblages C to H are related to infections in animals (Caccio et al., 2018). G. lamblia was reported to be a niche for an endosymbiotic dsRNA virus in the 1980s, the Giardiavirus (GLV) classified as Totiviridae (Janssen et al., 2015). Unlike other Totiviridae, GLV is more thermoresistant, has a different capsid protein translation site, and can be extracellularly transmitted (Garlapati and Wang, 2004). GLV seems to infect the trophozoite through receptor-mediated endocytosis and to leave it without cell lysis. The growth of the parasite was found to be arrested when GLV reaches a high titer, approximately 500,000 viruses per trophozoite (Lagunas-Rangel et al., 2021). A Giardia chaperone protein (GdDnaJ) has been suggested as a potential regulator of G. lamblia proliferation and GLV replication (Zhang et al., 2023). Several studies have revealed a virus infection rate of approximately 30% in Giardia isolates of different assemblages (Miska et al., 2009; Barrow et al., 2020). Marucci et al. (2021) indicated the occurrence of at least two GLV subtypes, which display distinct phenotypes and transmissibility in experimental infections of a GLV naïve Giardia isolate. The biological significance of parasite–GLV endosymbiosis and its impact on refractory giardiasis and treatment failure remain to be elucidated.

3.3 Alveolata parasites

Cryptosporidium (Apicomplexa) is a coccidian parasite causing severe diarrhea in children and immunocompromised patients (Gerace et al., 2019). The parasite has over 35 species with various host specificities, with C. hominis and C. parvum primarily infecting humans (Mkandawire and Sateriale, 2022). On the basis of gp60 gene, the most polymorphic marker in the Cryptosporidium genome, C. hominis and C. parvum sequences have been subtyped (Ia–Ig for C. hominis and IIa–IIo for C. parvum) (Rojas-Lopez et al., 2020; Lebbad et al., 2021). Cryptosporidium initiates frequent outbreaks around the world, and meanwhile, there is no effective treatment for the infection, mainly due to research impediments including efficient in vivo and in vitro models (Marzook and Sateriale, 2020). Cryspovirus (CspV1), a new genus in the family Partitiviridae non-enveloped dsRNA viruses, was first found to infect C. parvum in 1997 (Adjou et al., 2023). More than one species of the virus is speculated, as sequence-based divergence between CspV1 from C. parvum and viruses from C. hominis, C. felis, and C. meleagridis has been revealed (Jenkins et al., 2015). CspV1 can positively affect parasite fecundity with higher multiplication rates interpreted in culture studies (Jenkins et al., 2008; Lafleur and Olivier, 2022). The virus is transmitted intracellularly within the oocyst stage during cell division. CspV1 sequence detection was deduced to have a great potential as a tracing marker for Cryptosporidium infection sources (Adjou et al., 2023). Cryptosporidium can exploit the virus–endosymbiont association for evasion of the host immune response, through activation of type 1 IFN response and attenuation of IFN-γ-mediated epithelial antiparasitic defense (Deng et al., 2023). Graham et al. (2023) reported that C. parvum abducts a host long noncoding RNA (LncRNA) U90926 to evade the intestinal epithelial immune reaction, and CspV1 was found to upregulate U90926 during the infection.

Toxoplasma gondii (Apicomplexa) is a ubiquitous coccidian parasite in the family Sarcocystidae. T. gondii displays great genetic diversity, and strains have been classified into archetypal (I, II, and III genotypes) and non-archetypal strains (Bastilho et al., 2025). T. gondii infection persists as a hazardous opportunist to immunocompromised patients and pregnant women; moreover, it is a leading infectious cause of uveitis (Goh et al., 2023). From a computational viral screen of human neuronal datasets, Gupta et al. (2024) reported a novel narnavirus (Apocryptovirus odysseus Ao) associated with two hypervirulent strains of T. gondii—RUB and COUGAR. The narnavirus Ao is a member of the highly divergent Narnaviridae group of naked positive-sense RNA viruses. The authors presented an in silico evidence that Ao is a plausible proinflammatory inducer in human and mouse cells infected with T. gondii and suggested that Ao could function as a hypervirulence factor.

Plasmodium vivax (Apicomplexa) is a haemosporidian parasite, which is the main Plasmodium species causing malaria outside of sub-Saharan Africa (Mazhari et al., 2023). P. vivax has a strict host tropism for reticulocytes (Gruszczyk et al., 2018). The parasite can form a latent liver stage, the hypnozoite, which later activates and triggers a disease relapse (Schäfer et al., 2021). Through a metatranscriptomic investigation of blood samples from patients with malaria infected with P. vivax, P. falciparum, and P. knowlesi, a Narnavirus-like sequence was discovered in P. vivax-infected patients and not in other patients with malaria. A new single-stranded RNA virus, termed Matryoshka RNA virus 1 (MaRNAV-1), was identified. As the virus was found to be prevalent in geographically diverse P. vivax isolates obtained from humans and mosquitoes, a strong association of MaRNAV-1 and P. vivax was speculated (Charon et al., 2019). Currently, ongoing research aims to answer unresolved questions regarding the emergence and evolution of this specific virus–parasite association, which is absent in other Plasmodium species infecting humans including the hypnozoite-forming species P. ovale. In addition, the role of MaRNAV-1 in P. vivax transmission potential, pathobiology, and disease severity is still being investigated (Petrone et al., 2026).

3.4 Stramenopiles parasite

Blastocystis spp. is considered one of the most common intestinal protozoa detected in humans, mammals, and birds, encompassing at least 40 subtypes (ST) based on SSU-rRNA analysis (Zhang et al., 2025). Blastocystis ST1 to ST9 are found in human colon and regarded as dynamic yet enigmatic elements in the human gut microbial community. Despite the wide spread of Blastocystis infection and the advances in subtype identification, literature on Blastocystis spp. clinical significance is often contradictory. There were subtype-specific variations regarding the effect of Blastocystis on gut functions, where both beneficial and harmful modulations of the intestinal microenvironment have been reported. Regarded as having a context-dependent dual effect, Blastocystis spp. have been reported to disrupt the intestinal epithelial barrier and induce gut dysbiosis, thereby augmenting GIT inflammation. Conversely, they have also been found to exert anti-inflammatory effects by maintaining a balanced microbial composition and preserving intestinal barrier integrity (Deng and Tan, 2025). Shaw et al. (2026) proposed the possible presence of bacterial and VLP endosymbionts in Blastocystis spp. after reviewing the limited reports published over the past 50 years, which paves the way for further testing and confirmation.

4 Endosymbionts of parasitic helminths

4.1 Filarial nematodes

Nematodes of the family Onchocercidae (Spirurida/Filarioidea) are the causative agents of lymphatic filariasis (LF) and onchocerciasis, two diseases representing major health issues. They are mainly found in tropical and subtropical regions of the developing world and are transmitted by blood-feeding insects (Ramaiah and Ottesen, 2014). Late in the 1960s and early 1970s, rickettsia-like intracellular particles were first detected in filarial nematodes, and later identified as Wolbachia bacteria (Ferri et al., 2011). Onchocercid worms have a striking dependence on the endosymbiotic bacterium Wolbachia (Taylor et al., 2005).

Wolbachia is a Gram-negative alphaproteobacterium belonging to the order Rickettsiales. The bacteria infect two groups of organisms: arthropods, where they are widespread, infecting approximately 40% of terrestrial arthropods, and a single family of nematodes, the Onchocercidae (Zug and Hammerstein, 2012; Bouchery et al., 2013). Wolbachia has been classified into different molecularly identified supergroups, all attributed to one species, W. pipientis; supergroups C and D are limited to filariae while supergroup F encloses both arthropod and filarial hosts (Casiraghi et al., 2005). The bacteria were found in the filarial species causing LF: Wuchereria bancrofti, Brugia malayi, and B. timori; onchocerciasis: Onchocerca volvulus; mansonellosis: Mansonella perstans and M. ozzardi; and zoonotic dirofilariasis: Dirofilaria immitis and D. repens, but not in Loa loa (Hübner et al., 2022). Wolbachia has a wide range of symbiotic relations with its hosts. Its symbiosis spectrum extends from mutualistic and essential associations in filariae, where Wolbachia contributes to biosynthesis of molecules necessary for host fertility and viability such as heme, riboflavin, and nucleotide synthesis, to facultative and parasitic associations in the majority of infected arthropods (Manoj et al., 2021). Wolbachia is localized mainly in the female reproductive system and the hypodermal lateral cord in the infected onchocercid worms, it is found in all larval stages and is transmitted through the worm germ line to the next progeny (Ferri et al., 2011). The bacteria vary in density within the tissues of different onchocercids, and between life cycle stages and adult male and female of the same species (Fenn and Blaxter, 2004; Manoj et al., 2021). Wolbachia endosymbionts are reported to be involved in filarial worm embryogenesis, molting, and growth. Wolbachia was reported to provoke innate and adaptive TH1 inflammation responses, which can either be involved in filarial disease pathogenesis or promote infectivity through recruitment of mast cells that alter the blood flow and help infective larvae entry (Turner et al., 2006; Setegn et al., 2024). The concept of using anti-Wolbachia drugs as a treatment option of filarial diseases has been adopted due to its several advantages. The antibiotic treatment eliminates the bacteria and interrupts embryogenesis and microfilariae (MF) production, leading to permanent sterilization of female worms; meanwhile, the drugs achieve significant macrofilaricidal effect. In addition, as the anti-Wolbachia drugs do not induce rapid clearing of MF from the circulation or skin, they do not bear the risk of serious adverse incidents (Hübner et al., 2022). Breaking the nematode–bacterium association, by targeting either the bacteria or their molecular interactions, was claimed to reduce the risk of antibiotic resistance (Wangwiwatsin et al., 2023) and might achieve filarial infection elimination through downregulation of MF chitinase enzyme essential for its exsheathment and subsequent development in the vector (Quek et al., 2022).

4.2 Intestinal nematodes

Intestinal nematodes that commonly infect humans include the soil-transmitted helminths, the hookworms, Ascaris lumbricoides, Trichuris trichiura, and Strongyloides stercoralis, in addition to Enterobius vermicularis. The soil-transmitted helminths are part of the neglected tropical diseases that are prevalent in the disadvantaged communities causing chronic debilitation and impaired development in children (Stepek et al., 2006; Hassan et al., 2022). In contrast to the well-established Wolbachia spp. endosymbiont model in filarial nematodes, microbiome within intestinal nematodes has not been extensively investigated. Recent research explored A. lumbricoides gut microbiota and compared it to human gut microbiota using a metagenomic approach. A. lumbricoides gut microbiome was found to be distinct from human host gut microbiome; furthermore, A. lumbricoides microbiome population was demonstrated to differ according to worm burden within the host (Klomkliew et al., 2022; Muslim et al., 2024).

4.3 Platyhelminth parasites

4.3.1 Trematoda/Neodermata/Digenea

Fasciola hepatica is an increasingly reported zoonotic foodborne pathogen in Asia, Africa, and South America. The parasite has a large genome that is highly polymorphic, permitting adaptation and invasion of a broad range of hosts (Lalor et al., 2021). The sequencing of F. hepatica isolates led the way to the first discovery of Neorickettsia endobacterium (nFh) in a prevalent human trematode pathogen (McNulty et al., 2017). Neorickettsia (Alphaproteobacteria, Rickettsiales/Anaplasmataceae) are obligate intracellular bacterial pathogens that were found to colonize some digenean trematodes. The bacteria can be transmitted from the infected trematode to the mammalian host tissues, invading and multiplying intracellularly, leading to a severe disease (Greiman et al., 2016; Fischer et al., 2017). The exact nature of Neorickettsia–digenean flukes association is not clear, but it is suggested that the bacteria are not essential for flukes’ survival (Formenti et al., 2020). In F. hepatica, nFh bacterium was detected in the female reproductive tract, Mehlis gland, eggs, seminal vesicle, and oral sucker. The location of the bacteria in reproductive tissues and eggs suggests a vertical propagation route, and their presence in the oral sucker that fixes the worm to the biliary epithelium may indicate a method of infection of the mammalian host (McNulty et al., 2017).

Schistosoma mansoni is an intravascular blood fluke, which is the cause of intestinal schistosomiasis, a common neglected tropical parasitic disease (Mawa et al., 2021). Worldwide, approximately 236.6 million people have schistosomiasis, mostly attributed to S. mansoni. The parasite is found in Africa, Middle East, the Caribbean, Brazil, Venezuela, and Suriname. In spite of the large-scale mass drug administration programs using praziquantel as preventive chemotherapy since 2003, schistosomiasis continues to be prevalent (Kittur et al., 2019; Levecke et al., 2020). Mawa et al. (2021) elucidated that schistosomes are highly complex multihost parasitic organisms, for which several features of the biology, virulence, worm–host interactions, and epidemiology remain largely unknown. Formenti et al. (2023) explored S. mansoni microbiome throughout the fluke life cycle stages, using fluorescence in situ hybridization employing a pan bacterial 16S rRNA gene-specific probe. The research group reported bacteria in the gut and tegument of adult worms, the apical and lateral glands of the eggs and miracidia, and the oral and ventral suckers of the cercariae, which required further characterization of the harbored bacteria. Similarly, a previous study has demonstrated the colonization of the tegument and gastrodermis of adult S. japonicum by bacterial communities (Gobert et al., 2022). Formenti et al. (2020) clarified that worm core microbiome is an intrinsic part of the parasite and affects its biology, especially if associated with worm gonads, and is vertically transmitted to the next progeny, and is therefore detected across parasite life cycle stages. Alternatively, transiently harbored bacteria coating the surface of free-living larval stages or carried within the alimentary tract of the parasite do not seem to affect the parasite biology and its biochemical pathways but perhaps the disease it produced. Opisthorchis viverrini juveniles in the duodenum of the infected host have been demonstrated to ingest Helicobacter pylori and to carry the bacilli to the bile ducts where the flukes reside. The combined action of the parasite and bacillus has been suggested in the etiology of opisthorchiasis-associated cholangiocarcinoma (Deenonpoe et al., 2017).

4.3.2 Cestoda/Neodermata/Eucestoda

Cestodes (tapeworms) are distinctive among all helminths as they are perfectly specialized for the parasitic life (Tsai et al., 2013). The two most prevalent cestodes, Echinococcus and Taenia, present a major challenge to public health in various communities. Larval cestode infections are difficult to treat, with only few available antiparasitic chemotherapeutics (Hemphill et al., 2014). Research on these tapeworms remains limited, and the associated diseases have been added to the list of neglected tropical diseases (Mahanty, 2016; Ríos-Valencia et al., 2023). Tapeworms are defective in the piRNA pathway, one of the key mechanisms for silencing mobile genetic elements (MGE), which is important for preserving genome integrity between generations (Skinner et al., 2014). Herz and Brehm (2019) are the first to demonstrate the integration of densoviruses (ssDNA viruses) classified as Parvoviridae into the genome of different parasitic cestodes (Echinococcus spp., Taenia spp., and Hymenolepis spp.). The authors reported that further investigation into virus–cestode endogenization can assist in clearing up MGE silencing mechanisms in tapeworms. Dheilly et al. (2022) revealed an extensive diversity of viruses in parasitic Neodermata worms and reported that their role in flatworm-associated diseases must be focused on.

5 Endosymbionts of parasitic arthropods

Sarcoptes scabiei (Arachnida/Acariformes/Astigmata) is a parasitic mite that is the causative agent of an important human skin infectious disease—scabies. It is estimated that more than 300 million people are infected each year (Martin et al., 2018). The association between the mite infestation and secondary bacterial infections is increasingly reported and can lead to serious complications, including life-threatening Staphylococcus aureus bacteremia and severe post-streptococcal sequelae (Bowen et al., 2014; Thornley et al., 2018). Treatment and control of scabies are still arduous, as the available acaricides do not kill the eggs, which is the crucial life cycle stage for infection establishment (Wang et al., 2022). Swe et al. (2019) employed metagenome sequencing to clarify the internal microbial composition of S. scabiei adult females and eggs. Streptomyces spp., a Gram-positive, multicellular, spore-forming bacteria, was identified in both mite stages, with higher density in the adult female, especially in the gut. The authors reported that the bacteria may have an essential symbiotic role in the mite gut and may provide it with a survival advantage.

Demodex folliculorum (Arachnida/Acariformes/Prostigmata) is a mite that inhabits the pilosebaceous unit of the human skin. D. folliculorum and D. brevis, which are the most complex of the human skin microbiome, dwell mainly as commensals but can also trigger skin diseases such as rosacea, pityriasis folliculorum, and blepharitis (Forton, 2020; Wei et al., 2024). A number of Bacillus spp. (oleronius, cereus, and simplex), mainly Gram-positive bacteria, have been recorded to be associated with D. folliculorum, particularly the exoskeleton (Lacey et al., 2007; Tatu et al., 2017; Kubiak et al., 2018). Clanner‐Engelshofen et al. (2020) described, for the first time, the Gram-positive bacterium Corynebacterium kroppenstedtii demodicis as the endosymbiont of D. folliculorum mites. They reported that the bacteria that help the mite in the digestion of the lipid-rich sebum can be vertically transmitted to the progeny and appear to be essential for its survival.

Pediculus humanus (Insecta/Phthiraptera/Anoplura) is a hematophagous ectoparasite intimately connected to its human host. Two ecotypes of Pediculus infest humans: P. humanus humanus, the body louse, and P. humanus capitis, the head louse. Pediculus has been classified into six divergent mitochondrial clades from A to E, with clade A being the most prevalent. The head louse encloses the full genetic diversity of the clades, while the body louse belongs to clades A and D (Amanzougaghene et al., 2019). Body lice are known to transmit bacterial pathogens, mainly Rickettsia prowazekii, Borrelia recurrentis, and B. quintana, while the vector capacity of P. h. capitis is still subject to debate (Feldmeier, 2023). Acinetobacter spp., a Gram-negative gamma-proteobacteria, have been detected with high prevalence in head louse, suggesting its potential role for transmission of the bacteria (Sunantaraporn et al., 2015). P. humanus harbors a primary endosymbiotic bacterium Candidatus Reisia pediculicola, which is a Gram-negative gamma-proteobacterium that is transovarially transmitted to the progeny and located in the mycetome on the ventral side of the midgut (Kirkness et al., 2010). The bacteria are fundamental for lice development and survival, complementing their unbalanced diet and synthesizing missing elements (Hammoud et al., 2022). Agany et al. (2020) described the microbiome differences between the head and body lice. They reported a higher load of vertically transmitted bacterial endosymbiont in the head louse and distinct harbored non-endosymbiotic bacterial groups between the two ecotypes. The endosymbiotic bacteria have been proposed as a novel target for lice control, since control measures are challenged by the recent spread of insecticide resistance alleles (Hammoud et al., 2022).

Wohlfahrtia magnifica (Insecta/Diptera/Sarcophagidae) is an obligate parasite, as the fly is dependent on a vertebrate host to complete its life cycle. It is an important cause of myiasis in animals and humans (Schröttner et al., 2017; Wakid et al., 2022). Cutaneous myiasis usually occurs accidentally in humans through the infestation of non-healing wounds in high-risk groups by parasitic larvae. Bacteria have been isolated from the different developmental stages and larval organs of W. magnifica and were later identified as Wohlfahrtiimonas chitiniclastica and Ignatzscheneria spp., which are Gram-negative rods classified as Gammaproteobacteria (Toth et al., 2008; Reed et al., 2021). The relationship between the fly and the hosted bacteria may be symbiotic, as the bacteria are suggested to play a role in fly metamorphosis due to their strong chitinase activity. These bacteria have been detected in other parasitic flies (Schröttner et al., 2017; Maleki-Ravasan et al., 2020) as well. Wohlfahrtimonas and Ignatzscheneria spp. have been associated with rare human infections and sepsis, typically related to wound infestation by maggots of flesh flies (Connelly et al., 2019; Ahmad et al., 2022; Kozyk et al., 2023).

6 Discussion

6.1 Comparative analysis of immune modulation by endosymbionts and clinical implications

The tripartite relation of host–parasite–endosymbiont is multidimensional, where the human is considered the macro-host and the parasite is the micro-host. Since the existence of the endosymbiont can be directly linked to its micro-host, their survival can be mutually dependent, and the endosymbiont may influence the macro-host immune response in favor of parasite persistence. This work presents an overview from data collected regarding endosymbiosis in more than 20 species of parasites of medical importance (Table 1) to understand the endosymbiont-driven immunomodulatory effects.

Table 1. Summary of findings across various parasite–endosymbiont systems.

Across the parasite–endosymbiont systems reviewed above, only three systems were extensively studied, involving Leishmania, Trichomonas, and filarial nematodes. The Leishmania–LRV and Trichomonas–TVV demonstrate a common theme; both exacerbate the proinflammatory response, which can lead to host-damaging hyperinflammation and, at the same time, allow evasion and persistence. These dsRNA viral endosymbionts provide clear examples of endosymbiont-mediated modulation of immune response and disease phenotype. In patients infected with L. guyanensis and suffering from American tegumentary leishmaniasis, LRV-1 was shown to be associated with higher levels of intralesional inflammatory markers, resistance to pentamidine therapy, and relapsing symptoms (Bourreau et al., 2016). In parallel research including patients infected with L. guyanensis, LRV-1 was linked to higher levels of the pro-inflammatory cytokine interleukin-17A (IL-17A) and lower levels of the protective IFN-γ. In addition, chronic disease was observed more frequently among LRV1-positive patients than among LRV1-negative patients. Furthermore, in murine models, LRV1-associated Leishmania infection resulted in metastatic lesions in the presence of IL-17A and in the absence of IFN-γ (Hartley et al., 2016). A similar interaction was reported in T. vaginalis, with exaggerated symptomatology in infected females in the presence of TVV. However, the clinical spectrum observed showed variability and inconsistency between the different studies, probably due to the small sample sizes included (Fichorova et al., 2017). In vitro models demonstrated the TVV-driven robust inflammatory response mediated by the increased expression of IL-8 and RANTES, especially in the presence of pathogenic vaginal bacteria rather than the commensal Lactobacillus. Notably, parasite treatment with metronidazole was reported to increase the release of TVV, thus enhancing the inflammatory response, highlighting the effect of treatment on endosymbiont-associated immunopathology (Fichorova et al., 2012; 2013).

The second theme is the endosymbiont bacteria as the primary immunogen in the filaria–Wolbachia system. Remarkably, among all the endosymbionts described in parasites, Wolbachia is the one clearly established example of obligate mutual stable endosymbiont indispensable for parasite survival. Wolbachia is recently regarded as the dominant culprit in filariasis, not the worm itself; it stimulates a potent inflammatory and TH-1 immune response, resulting in disease pathogenesis and tissue damage. Similar to T. vaginalis–TVV, antiparasitic treatment and death of worms is associated with the release of Wolbachia into the blood, inducing systemic hyperinflammation (Turner et al., 2006; Setegn et al., 2024). The third theme is the endosymbiont as an immunologically silent partner, which can be revealed in the ectoparasite–endosymbiont systems, namely, the P. humanus–Riesia system, the S. scabiei–Streptomyces system, and the D. folliculorum–Corynebacterium system. These bacterial endosymbionts are described to play a primary role in parasite nutrition and development without evident immunological consequences. In contrast, immune response and disease complications that may arise are indirectly caused by the secondary bacterial infections rather than the endosymbiont (Kirkness et al., 2010; Swe et al., 2019; Clanner-Engelshofen et al., 2020). The fourth theme is the parasite as a replicative reservoir for the endosymbiont, for which the Acanthamoeba is the best example as it provides a protective niche for the microorganisms harbored within it—such as Legionella, Mycobacteria, and Chlamydia—and furthermore allows selection and evolution of virulent and immune evasion traits before exposure to the macro-host. A final note, Acanthamoeba-APMV interaction, in which the virus suppresses the expression of encystation-associated serine proteinase shares a broader functional similarity with the Leishmania–LRV interaction, in which the virus promotes infected macrophage survival through phosphorylation of AKT1; these interactions illustrate how virus-associated processes can manipulate the hosting cell (Boratto et al., 2015; Queiroz et al., 2022; Price et al., 2024).

6.2 Therapeutic opportunities

Obligate mutual symbiotic relations are mainly based on metabolic complementation and biochemical pathway potentiation in one or both hosts (Manoj et al., 2021). This obligate dependence of parasites on their endosymbionts offers therapeutic opportunities either by directly targeting the endosymbiont, by altering host pathways in parasite–symbiont interaction, or by exploiting endosymbiotic virus for efficient drug delivery. Distinguishing between transient microbial invaders, organisms sheltering inside more resilient parasites, and true endosymbionts is a pivotal step in understanding immunomodulatory impacts and therapeutic targets. Differentiating criteria involve several aspects such as location of microorganism within the parasite, transmission mode, stability of the association, genome characteristics, and functional dependence; these aspects are still unresolved in the majority of parasite–endosymbionts systems. The Parasite Microbiome Project highlighted the challenges in parasite endosymbiosis research including low-biomass microbial nucleic acid recovery and emphasized the need for standardized approach and metagenomic protocol to identify true endosymbionts from transient environmental microbes (Dheilly et al., 2019).

The strongest proof of concept is the filaria–Wolbachia system where endosymbiont targeting efficiently curtails the pathogenicity of the parasite. Wolbachia is vertically transmitted, stable, and indispensable for the survival of its filarial nematode host. Molecular studies have revealed that parasites such as B. malayi and O. volvulus have lost the ability to synthesize important biomolecules including heme, nucleotides, riboflavin, and certain lipids. This extensive metabolic interdependence creates a therapeutic opportunity, making their biosynthesis pathways potential targets for anti-Wolbachia drug design, thus impairing the parasite viability and development (Slatko et al., 2010). Doxycycline is established as an effective and safe anti-Wolbachia drug, is recommended as a treatment option for human filarial infections, is given as a prolonged regimen (ranging from 4 to 6 weeks), and is contraindicated in children and pregnant women. Therefore, doxycycline is typically prescribed for individual cases but not for mass drug administration. In their comprehensive review, Risch et al. (2024) discussed potential antifilarial drugs in development, including anti-Wolbachia candidates flubentylosin—a macrolide antibiotic, AWZ1066S compound, and rifampicin. The trials on the first two candidates were discontinued for weak efficacy and safety concerns, respectively, while rifampicin studies are ongoing, but its wide use can negatively impact its effect as an anti-tuberculous agent.

In addition to the well-established filaria–Wolbachia model for taking advantage of the parasite–endosymbiont relation in anti-parasitic therapeutics, the study of the potential value of viral endosymbionts to combat their hosting parasite has gained increasing attention, but remain largely experimental. The exploitation of the cytopathic effect of viruses against their sheltering host is a strategy under active investigation. The G. lamblia GLV virus stands out as the most promising candidate due to the inhibitory effect of increased viral load on parasite growth. Li et al. (2025) demonstrated that GLV can alleviate intestinal pathology in G. lamblia-infected mice, where GLV was found to disperse into the extracellular space to infect G. lamblia trophozoites by hijacking the parasites’ own vesicular system. The more selective the virus is to its host, and the simpler the life cycle of the parasite facilitating coordinated multiplication peaks in both agents, the more promising is the viral agent as a potential pharmaceutical tool in parasite control (Barrow et al., 2020). Another tactic in the use of viral endosymbionts in antiparasitic management involves exploiting VLPs. Candidate therapeutic agents can be delivered either inside the empty viral protein shells or attached to the surface of VLPs. This approach has provided promising results in the field of plant parasitology and is still under investigation for medically important parasites (Cao et al., 2015). VLPs can also be used as molecular vehicles to deliver genetic tools that can block the translation of essential parasite genes involved in vital metabolic processes (Zhang et al., 2018; Dan et al., 2000). Antisense sequences, DNA oligomers modified with methylenemorpholine rings (morpholinos), hammerhead ribozymes, and CRISPR-Cas are all promising techniques that were shown to induce at least transient modulation of parasite gene expression (Barrow et al, 2020). Finally, host-directed approaches are an important strategy in targeting components of the host immune system activated by the parasite–endosymbiont interactions. Viral agents hijack components of the host immune system to favor parasite survival for their own benefit. TLR3, type I interferon signaling, and pathways implicated in pro-inflammatory cytokine release are all potential therapeutic targets to dampen immunopathology associated with parasitic infections (Barrow et al., 2020; Mirabedini et al., 2023).

7 Conclusion

The endosymbiotic relationships documented across the presented array of medically important parasites revealed a diversity of microbial partners that, in many instances, shape parasite fitness and virulence, and consequently impact the human host immune response to the parasitic infection and the natural history of the disease. This review examined nearly 20 parasite–endosymbiont systems, focusing on their impact on host–parasite interactions and highlighting their potential as therapeutic targets. Within this context, the filaria–Wolbachia, Leishmania–LRV, and Trichomonas–TVV models demonstrate a significant proof that endosymbionts can directly drive immunomodulation in the human host, such as innate immune hyperresponsiveness, inflammatory cascades, and cytokine dysregulation, thus worsening the clinical outcome. Understanding these relationships introduced the concept of endosymbiotic-directed treatment, which became concrete in Wolbachia-targeted therapy in LF and onchocerciasis. Besides the bacterial endosymbiont-directed treatment, exploiting the viral endosymbiont and virus-derived delivery systems for the biological control of the protozoal host is an emerging therapeutic approach under investigation. Amid this landscape, the Acanthamoeba–endosymbionts model stands out as a hub for a remarkable diversity of bacteria that can cause disease independent of the parasite. This characterizes Acanthamoeba as a reservoir and environmental training ground that allows bacterial virulence evolution. Reciprocally, the bacteria influence Acanthamoeba encystment and pathogenic potential. Finally, it is worth mentioning that the depth of characterization of endosymbionts across parasite taxa is markedly uneven. Extensively studied systems such as filaria–Wolbachia and Leishmania–LRV contrast sharply with other parasites such as Blastocystis, Sarcoptes, Schistosoma, and the cestodes, where microbiome data remain limited, fragmentary, and inconclusive.

Disclosing the world of microorganisms living within parasites, especially with the advanced metagenomic analysis, represents a research frontier of immense biomedical significance. It can provide fundamental data concerning parasite biology, host–parasite interactions, and vulnerabilities that could be targeted for efficient treatment and control measures.

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Footnotes

Edited by: Arpit Kumar Shrivastava, Independent researcher, Indore, India

Reviewed by: Sarmistha Saha, GLA University, India

Bahareh Basirpour, Mazandaran University of Medical Sciences Faculty of Paramedical Science, Iran