Innate Immunity and Microbial Recognition in Reproduction: From Barrier Defense to Maternal-Fetal Tolerance.

Xianlin Rao, Yao Yao, and Changling Liu: writing – original draft, writing – review and editing. Li Zou: software, validation, visualization, and writing – review and editing.

The maternal–fetal interface is a specialized site in which the decidua and placenta must maintain antimicrobial defense without provoking fetal rejection. This balance depends on layered physical barriers, dense innate‐cell niches, and tightly regulated cytokine and chemokine networks [ 55 , 56 ]. Single‐cell studies show that decidual NK cells, macrophages, dendritic cells, and ILCs occupy defined positions around glands, vessels, and invading trophoblast, where they support implantation, vascular remodeling, and placental development [ 57 ]. When these regulatory circuits fail, the same pathways contribute to recurrent pregnancy loss, preeclampsia, fetal growth restriction, and infection‐driven preterm birth [ 56 ]. The following subsections focus on niche‐specific cell programs and disease links rather than restating the broader defense–tolerance framework. Structurally, the maternal–fetal interface includes the decidua basalis, villous placenta, and fetal membranes, each with distinct innate‐cell communities. Early decidua is leukocyte rich, with dNK cells and macrophages clustering around spiral arteries and extravillous trophoblasts [ 55 , 57 ]. The villous placenta adds serial barriers—syncytiotrophoblast, villous stroma, fetal capillary endothelium, and membranes—that restrict microbial invasion while still permitting exchange of gases, nutrients, hormones, antibodies, and cytokines [ 58 ]. Within these compartments, Hofbauer cells, decidual macrophages, and dNK cells continuously sample stress signals and remodel extracellular matrix, coupling architecture directly to surveillance and tolerance [ 58 , 59 ]. A schematic overview of the cellular and vascular organization of the human maternal–fetal interface, including decidual immune niches and villous placental layers as well as potential routes of vertical viral transmission (exemplified by Zika virus), is shown in Figure  1 . Human maternal–fetal interface and routes of pathogen transmission. This schematic summarizes the cellular and anatomical organization of the human maternal–fetal interface, highlighting key decidual immune and stromal compartments and the layered structure of the chorionic villus. It also illustrates representative routes of vertical transmission, using Zika virus (ZIKV) as an example of hematogenous spread and replication within decidual/placental cell types before fetal infection. dNK, decidual natural killer cells; dMφ, decidual (Maternal) macrophages; Ms., mesenchymal cells; Fb, fibroblasts; MG, maternal glands; iCTBs, invasive extravillous cytotrophoblasts; HBCs, Hofbauer cells; STB, syncytiotrophoblast; ZIKV, Zika Virus. In the first‐trimester human decidua, decidual innate cells are central to fetal tolerance and host defense [ 58 , 59 ]. dNK cells dominate early decidua and are highly secretory rather than strongly cytotoxic; through VEGF, placental growth factor, angiopoietins, and receptor interactions with fetal HLA‐C and HLA‐G, they guide trophoblast invasion and spiral artery transformation while retaining the ability to recognize stressed or infected cells. Decidual macrophages usually adopt an M2‐like regulatory phenotype that supports phagocytosis of apoptotic trophoblasts, matrix remodeling, and IL‐10/TGF‐β–mediated tolerance, but they can rapidly switch toward inflammatory programs during infection [ 60 , 61 , 62 , 63 , 64 ]. Decidual dendritic cells are fewer in number and often remain semi‐mature, favoring regulatory or Th2‐skewed responses unless strongly activated. ILC subsets add further plasticity, particularly in fetal membranes and decidua, where altered type 2 or type 3 ILC profiles have been linked to preterm birth. The multi‐layered mechanisms by which the maternal–fetal interface simultaneously limits fetal antigen transfer, reprograms maternal leukocytes toward regulatory phenotypes, and exploits placental glycosylation to dampen immune activation are summarized in Figure  2 . The emphasis here is on how each subset contributes to coordinated tolerance and defense. Core immune‐tolerance mechanisms at the maternal–fetal interface. This figure provides an overview of how a tolerant immune milieu is established despite continuous maternal exposure to semi‐allogeneic fetal cells and antigens. It emphasizes barrier‐limited antigen transfer, pregnancy‐associated acquisition of regulatory phenotypes by maternal immune cells, and tolerance reinforcement via reduced immune‐activating signals and placental glycosylation. dNK, decidual natural killer cells; MHC, major histocompatibility complex. In human placenta and fetal membranes, placental and membrane cells express a wide PRR repertoire, enabling cell‐intrinsic responses to both microbes and sterile stress [ 65 , 66 ]. Trophoblasts, decidual stromal cells, Hofbauer cells, and fetal‐membrane cells express multiple TLRs whose engagement by bacterial lipoproteins, LPS, flagellin, or viral nucleic acids activates NF‐κB and IRF pathways, inducing interferons, chemokines, and antimicrobial peptides [ 67 ]. These antiviral programs can be protective, but in early trophoblast, they may also trigger apoptosis when excessive [ 68 ]. Cytosolic sensors add another layer: NOD1/2, NLRP3‐related inflammasomes, and cGAS–STING pathways respond to peptidoglycan motifs, ATP, oxidative stress, or cytosolic nucleic acids and help defend against viral invasion [ 41 , 65 , 69 , 70 ]. The fetal membranes are particularly important as a second defensive boundary against ascending infection, but strong activation there can weaken membranes and precipitate preterm rupture [ 65 , 66 ]. In human placental tissues, placental homeostasis requires innate signaling that is active but restrained. Syncytiotrophoblasts constitutively express antiviral interferons and restriction factors, while trophoblast and decidual stromal cells display complement regulators and nonclassical HLA molecules that limit bystander immune injury [ 55 ]. dNK cells and decidual macrophages then translate this controlled signaling into vascular homeostasis by promoting extravillous trophoblast invasion, spiral artery remodeling, apoptotic‐cell clearance, and extracellular‐matrix turnover [ 58 , 59 , 71 , 72 ]. Sex steroids further modulate these programs by reinforcing mucosal and decidual tolerance, whereas endocrine disruption or metabolic stress can lower the threshold for inflammatory injury [ 49 , 73 ]. Figure  3 illustrates the bidirectional crosstalk between trophoblasts and immune cells, highlighting how distinct macrophage phenotypes, NK‐cell–derived mediators, immune checkpoint pathways, and Th17‐derived cytokines jointly shape trophoblast invasion, spiral artery remodeling, and the acquisition of a tolerant dNK phenotype. Bidirectional trophoblast–immune crosstalk shaping invasion, vascular remodeling, and tolerance. This schematic depicts coordinated signaling between trophoblasts and decidual immune cells that govern trophoblast invasion, spiral artery remodeling, and local immune tolerance. Pro‐inflammatory cues (e.g., M1‐associated IL‐1β and G‐CSF) can support invasion, whereas trophoblast‐derived mediators and immune‐checkpoint interactions promote M2‐like polarization, IDO induction, and suppression of effector T‐cell activity. In parallel, dNK‐derived angiogenic factors facilitate vascular remodeling, while Th17‐derived IFN‐γ can restrain dNK function. dNK, decidual natural killer cells; NK, natural killer cells; M1, classically activated macrophages; M2, alternatively activated macrophages; IL‐1β, interleukin 1 beta; G‐CSF, granulocyte colony‐stimulating factor; IDO, indoleamine 2,3‐dioxygenase; TGF‐β, transforming growth factor beta; M‐CSF, macrophage colony‐stimulating factor; IL‐10, interleukin 10; IL‐34, interleukin 34; Tim‐3, T Cell immunoglobulin and mucin domain‐containing protein 3; CD132, Common Gamma Chain (IL‐2 Receptor Gamma); Gal‐9, galectin 9; PD‐L1, programmed death‐ligand 1; RANKL, receptor activator of nuclear factor‐κB ligand; HA, hyaluronan; Th2, T Helper 2 cells; Treg, Regulatory T cells; VEGF, vascular endothelial growth factor; VEGF‐C, vascular endothelial growth factor C; IL‐8, interleukin 8; OGN, osteoglycin; PTN, pleiotrophin; Th17, T Helper 17 cells; IFN‐γ, Interferon gamma; MMP9, matrix metalloproteinase 9; HLA, human leukocyte antigen. Across human pregnancy cohorts, placental samples, and complementary experimental systems, many pregnancy complications can be interpreted as failures of innate immune control at the maternal–fetal interface. Placental ischemia, oxidative stress, infection, or danger‐associated ligands can convert physiologic inflammation into pathologic activation dominated by TLR and inflammasome signaling [ 56 , 66 ]. In preeclampsia, placental and circulating markers of NLRP3 activation are increased, linking sterile DAMP sensing to endothelial dysfunction and hypertension [ 74 , 75 ]. In preterm birth, ascending microbes and sterile mediators such as HMGB1 or extracellular DNA activate decidual and membrane PRRs, driving prostaglandin production, cervical ripening, contraction, and membrane rupture [ 56 , 65 , 66 ]. Defects in dNK‐mediated arterial remodeling, macrophage polarization, or ILC composition have likewise been associated with fetal growth restriction and other placental insufficiency states [ 64 , 71 , 72 ].

The authors have nothing to report.

Pattern recognition is engaged from the earliest reproductive stages. Gametes, reproductive epithelia, and preimplantation embryos all express innate sensors that detect microbial products or endogenous danger signals and convert them into cytokine, chemokine, and interferon responses. When tightly controlled, this activation appears to support fertilization and implantation; when excessive or mistimed, it can reduce gamete fitness, disrupt endometrial receptivity, and increase the risk of early pregnancy loss [ 46 , 47 , 48 ]. Although IVF can bypass part of natural sperm transport and tubal selection, downstream immune and microbial constraints on semen handling, endometrial receptivity, implantation, and placentation remain highly relevant to reproductive success [ 5 , 7 ]. The following subsections therefore distinguish gamete‐, implantation‐, and interferon‐centered contexts without repeating this shared logic. In human reproductive tissues and gametes, oocytes, embryos, and sperm are not immunologically inert. Human oocytes and granulosa cells express several TLRs, especially receptors linked to viral RNA and bacterial products, suggesting that follicular infection or stress can affect oocyte competence [ 46 ]. Preimplantation embryos also express multiple TLRs and downstream signaling molecules from the zygote to blastocyst stage and can respond functionally to ligands such as poly(I:C) and flagellin by inducing TLR‐pathway genes and secreting chemokines [ 47 ]. Spermatozoa likewise express TLR2 and TLR4; exposure to bacterial peptidoglycan or lipopolysaccharide reduces motility, promotes apoptosis, and impairs fertilization in experimental systems [ 48 ]. These findings indicate that innate sensing begins before implantation and may serve as both a defense mechanism and a quality‐control system for gametes and embryos. During sperm transit in humans and experimental mammalian systems, innate sensing helps balance host defense with reproductive efficiency. Bacterial ligands engaging sperm TLR2 and TLR4 can selectively reduce the viability of damaged or contaminated sperm, potentially limiting pathogen transfer to the female tract and conceptus [ 48 ]. At the same time, excessive exposure to microbial products can shrink the pool of fertilization‐competent sperm and thereby impair conception [ 48 ]. Beyond sperm‐autonomous sensing, capacitation and the acrosome reaction expose endogenous signals that stimulate uterine and tubal epithelial cells, which then recruit neutrophils and macrophages to remove excess sperm. Thus, innate pathways during sperm migration participate in microbial defense, gamete selection, and postcoital tissue homeostasis. In human endometrial tissues and cultured cells, implantation occurs in an endometrium equipped with broad PRR capacity [ 13 , 49 ]. Epithelial cells, stromal fibroblasts, and resident leukocytes express TLRs and NOD‐like receptors whose levels vary across the cycle under hormonal control [ 50 ]. Activation by microbial ligands induces NF‐κB and MAPK signaling, with production of IL‐6, IL‐8, TNF, and interferons that reshape the peri‐implantation cytokine milieu [ 51 ]. Limited activation contributes to the transient leukocyte influx, vascular permeability, and matrix remodeling needed for implantation and early decidualization [ 51 ]. Once stromal cells decidualize, however, innate signaling is more tightly restrained, and uterine NK cells and decidual stromal cells upregulate inhibitory mechanisms that preserve tolerance [ 14 ]. When microbial burden is high or regulation breaks down, TLR and inflammasome activation can shift the decidua toward pathogenic inflammation and impair trophoblast invasion [ 14 , 52 ]. The emphasis below is therefore on how signaling thresholds shape implantation outcomes, not on repeating receptor catalogs. Interferon pathways provide a major antiviral arm of reproductive innate immunity [ 33 , 49 ]. In both female and male tissues, ligands sensed by TLR3, TLR7/8, RLRs, and cytosolic DNA sensors activate IRF‐dependent transcription of interferon‐stimulated genes that limit viral replication and shape downstream leukocyte responses [ 53 ]. Female reproductive epithelia mount strong antiviral responses but are hormonally tuned to avoid excessive inflammation that would compromise fertility [ 29 , 49 ]. In the testis, Sertoli and Leydig cells maintain basal interferon activity that contributes to local immune privilege by suppressing viral spread behind the blood–testis barrier [ 33 , 54 ]. Yet excessive type I interferon signaling can also disrupt barrier integrity and spermatogenesis, illustrating the narrow therapeutic window between protection and damage [ 33 ]. Implantation is best understood as controlled, spatially restricted inflammation [ 51 ]. Physiologic activation of endometrial innate pathways recruits uterine NK cells, macrophages, and regulatory T cells, promotes vascular remodeling, and facilitates trophoblast invasion; importantly, these responses resolve as the decidua and early placenta become established [ 14 , 51 ]. Pathologic activation differs in magnitude, duration, or trigger. Intrauterine infection, dysbiosis, or sterile tissue damage can drive excessive TLR, inflammasome, TNF, IL‐1β, and interferon signaling, leading to impaired angiogenesis, abnormal leukocyte cytotoxicity, implantation failure, miscarriage, or defective placentation [ 14 , 52 ]. Whether innate activation is beneficial or harmful therefore depends on timing, cellular context, and the strength of local negative feedback [ 14 , 49 ].

Effector programs downstream of reproductive innate sensing extend well beyond leukocyte recruitment. Antimicrobial peptides, inflammasomes, regulated cell death, extracellular vesicles, complement, and lectin pathways all operate within reproductive tissues and together determine whether sensing translates into pathogen clearance, tissue remodeling, or inflammatory injury [ 28 , 82 ]. These nonclassical mediators are especially important because they act at epithelial and trophoblast surfaces that must remain functional for fertilization, implantation, placentation, and sperm preservation [ 83 , 84 ]. The following subsections focus on mechanism‐specific effector modules and their pathological thresholds rather than repeating this general point. Antimicrobial peptides are core effectors of reproductive mucosal defense. In the female tract, defensins, LL‐37, secretory leukocyte protease inhibitor, lactoferrin, and related peptides directly limit bacterial, viral, and fungal invasion while also modulating chemokine gradients, dendritic‐cell recruitment, and epithelial repair [ 28 ]. Their expression is shaped by sex steroids, microbiota, and inflammatory cues, and pregnancy further changes AMP production in cervical mucus, decidua, and fetal membranes [ 28 , 82 ]. Male tissues also use AMP‐rich secretions, particularly in the epididymis and accessory glands, to protect stored sperm and control microbes without provoking overt inflammatory damage. These properties make AMPs both direct antimicrobial agents and broader regulators of reproductive immune tone [ 28 , 82 ]. Inflammasomes and regulated cell death must be precisely controlled in reproduction. NLRP3, NLRC4, AIM2, and related complexes are expressed in trophoblasts, decidua, membranes, and myometrium, where they process IL‐1β and IL‐18 in response to infection or tissue stress and contribute to implantation‐associated inflammation and the normal inflammatory cascade of term labor [ 83 , 84 ]. Premature or excessive activation, however, is linked to placental lesions and preterm birth [ 83 , 84 ]. These pathways intersect with apoptosis, autophagy, necroptosis, ferroptosis, and pyroptosis, which influence trophoblast differentiation, invasion, vascular remodeling, and decidual renewal [ 84 ]. Similar inflammatory cell‐death programs are increasingly implicated in orchitis, testicular injury, and sperm dysfunction, indicating that regulated cell death is a shared but vulnerable component of reproductive homeostasis. The key issue is thus not their presence per se but the threshold at which these programs shift from remodeling to injury. Extracellular vesicles provide a mobile communication system for reproductive innate immunity. EVs released by trophoblasts, decidual stromal cells, endothelial cells, leukocytes, and endometrium transport cytokines, lipids, HLA molecules, and small RNAs that reprogram recipient cells, thereby shaping implantation, maternal immune adaptation, and antimicrobial defense. Seminal EVs, including prostasomes, add a complementary male signal: they carry complement‐regulatory molecules such as CD59, suppress phagocyte activity, and influence cytokine production in ways that can protect sperm while altering susceptibility to infection in the female tract [ 85 , 86 ]. Complement and soluble lectin systems add humoral pattern recognition to reproductive defense. Complement components are synthesized locally by uterine epithelium, decidua, trophoblasts, and testicular tissues, supplementing circulating proteins that enter through the microvasculature [ 35 , 87 ]. Limited activation supports opsonization and clearance of microbes and apoptotic debris, and complement fragments can also recruit and condition macrophages and NK cells [ 87 ]. Because uncontrolled activation would damage trophoblasts, endothelium, or sperm, these sites express strong regulatory mechanisms. Lectin‐pathway molecules such as mannose‐binding lectin and ficolins further sense glycans on microbes and dying cells, and low lectin activity has been associated in some cohorts with recurrent pregnancy loss [ 88 , 89 ]. In the male tract, complement regulators on sperm and prostasomes are especially important for preventing inflammatory lysis of gametes [ 35 ]. These effector systems form an interconnected network downstream of PRR activation [ 90 ]. Danger or microbial ligands can induce antimicrobial peptides, trigger inflammasome activity, generate extracellular vesicles carrying inflammatory cargo, and activate complement, with each pathway feeding forward on the others [ 88 , 91 , 92 , 93 ]. In successful reproduction, this network remains spatially confined and time limited, so pathogens are controlled without compromising sperm integrity, implantation, or placental function [ 93 ]. When negative regulation fails, however, the same circuits can reinforce one another and drive chronic inflammation, barrier breakdown, and adverse reproductive outcomes [ 88 , 92 , 93 ]. Mapping these interactions is therefore essential for designing targeted therapies that preserve both defense and tolerance [ 93 ].

Microbiota are active components of reproductive immunity in some compartments and candidate modulators in others rather than passive colonizers. Cervicovaginal communities have the strongest evidence for effects on epithelial barrier quality, tonic PRR signaling, and leukocyte recruitment, whereas microbial signals detected at endometrial, placental, and male genital interfaces require more cautious interpretation because these are low‐biomass niches. Gut‐derived metabolites further shape systemic immune set‐points and mucosal responsiveness [ 24 , 25 ]. Evidence quality is uneven across niches: cervicovaginal findings are supported by larger and more reproducible datasets, whereas endometrial, placental, and male upper‐tract signals come from low‐biomass specimens that are especially vulnerable to reagent contamination, environmental carryover, sampling bias, batch effects, and variable bioinformatic filtering. Claims for a resident placental microbiota therefore remain particularly debated, and microbial detection in these compartments should not be equated automatically with stable colonization or causal relevance. In healthy reproductive‐age women, Lactobacillus‐dominant vaginal communities generally support low pH and a lower inflammatory tone, whereas high‐diversity dysbiotic states and altered endometrial or male genital microbiota are associated with infertility, implantation failure, miscarriage, preterm birth, and sperm dysfunction [ 5 , 76 ]. Gut microbial products such as short‐chain fatty acids, bile acids, and tryptophan metabolites further connect diet and intestinal ecology to reproductive immune programming [ 77 , 78 ]. The following subsections therefore separate local niche effects from distal gut‐derived regulation and emphasize where the evidence is strongest. Cervicovaginal homeostasis is most consistently associated with Lactobacillus dominance, especially L. crispatus . These organisms maintain acidic pH through lactic acid production and contribute additional antimicrobial activities that suppress anaerobic overgrowth [ 24 ]. Cohort and meta‐analysis data link L. crispatus –dominant states with lower risk of preterm birth, whereas reduced Lactobacillus abundance and enrichment of taxa such as BVAB1, Sneathia, or Prevotella track with earlier delivery [ 24 , 25 ]. Mechanistically, cervicovaginal epithelial cells sense microbial patterns through TLRs, NLRs, and RLRs; Gardnerella‐rich communities provoke stronger NF‐κB activation and pro‐inflammatory cytokine release than Lactobacillus‐rich communities, while Lactobacillus metabolites tend to preserve barrier integrity and dampen excessive inflammatory signaling [ 79 ]. Vaginal dysbiosis is increasingly linked to adverse reproductive outcomes, whereas endometrial associations should be regarded as more preliminary and method‐sensitive. Bacterial vaginosis‐like communities, characterized by Lactobacillus depletion and anaerobic expansion, are associated with spontaneous preterm birth and preterm premature rupture of membranes, likely through chronic IL‐1β‐, IL‐6‐, and IL‐8‐rich inflammation, heightened TLR2/4 signaling, and recruitment of neutrophils and macrophages that weaken membranes and prime cervical ripening [ 5 , 24 , 25 , 79 ]. Upper‐tract dysbiosis may also impair implantation: infertile women with endometrial communities enriched in Gardnerella, Streptococcus, Atopobium, or related taxa tend to have lower implantation, ongoing pregnancy, and live‐birth rates than women with Lactobacillus‐dominant profiles [ 5 ]. Compared with vaginal data, the endometrial literature remains methodologically less settled. Because the endometrium is a low‐biomass site and many studies rely on transcervical sampling, reported taxa and effect sizes can be influenced by carryover from the cervix or vagina, inconsistent negative‐control practice, and differences in sequencing workflows. At present, the strongest inference is that some endometrial microbial patterns correlate with implantation‐related outcomes, whereas the existence, composition, and functional stability of a resident endometrial microbiota remain unresolved. Although causality is still being defined, current data support vaginal and endometrial microecology as linked determinants of receptivity, early pregnancy maintenance, and parturition timing [ 5 , 23 , 80 ]. This subsection therefore emphasizes outcome‐linked patterns rather than repeating descriptive microbiota surveys. Human semen and male genital‐tract studies detect microbial signals consistent with low‐biomass communities or transient microbial exposure that may interact with innate defense pathways. Associations between semen, urethral, epididymal, or prostatic dysbiosis and reduced sperm count, motility, and morphology are intriguing, but they remain largely associative and potentially confounded by inflammation, collection method, and contamination [ 76 ]. These findings are informative but should be interpreted cautiously. Semen and upper male tract samples are likewise low biomass, and results can vary with collection method, abstinence interval, inflammatory cell burden, culture‐versus‐sequencing workflows, and background contamination. Accordingly, current male genital microbiota data are stronger as associative markers of inflammatory or oxidative stress states than as proof of a conserved resident microbiota with uniform effects on fertility. Testicular and accessory‐gland tissues express TLRs and inflammasome components that help control infection but can also perpetuate sterile inflammation. In men with severe infertility, higher oxidative stress in seminal plasma correlates with poorer sperm retrieval, and inflammasome‐related mediators are increasingly being explored as markers of reproductive tract injury [ 76 , 81 ]. A gut–reproductive axis is now apparent. Gut microbial communities influence implantation, pregnancy maintenance, and birth timing by shaping systemic immune tolerance, estrogen metabolism, and epithelial integrity at the uterine interface [ 78 ]. Their metabolites, including short‐chain fatty acids, bile acids, and tryptophan derivatives, act through GPCRs and PRR‐linked pathways to regulate dendritic‐cell activation, Th17/Treg balance, and local cytokine production [ 77 , 78 ]. Conversely, gut dysbiosis can increase β‐glucuronidase‐driven estrogen recirculation and intestinal permeability, promoting translocation of LPS and other inflammatory products that lower the threshold for innate activation in reproductive tissues. These mechanisms may help explain links between intestinal dysbiosis and endometriosis, polycystic ovary syndrome, recurrent implantation failure, and preeclampsia. The emphasis below is on immune consequences of this axis rather than reiterating the existence of gut–reproductive crosstalk. An interaction‐centered view is therefore useful. Infertility is rarely explained by vaginal dysbiosis alone or host immunity alone; rather, it often emerges from the chemistry among sperm, seminal plasma, cervical mucus, epithelial glycans, microbial metabolites, PRR tone, and leukocyte responses across both partners. In a recent human observational study of infertile couples, genital niches remained distinct yet showed evidence of inter‐partner coupling, supporting the idea that reproductive success reflects a coupled male–female ecosystem rather than isolated compartments. Human and animal studies of seminal‐fluid signaling similarly indicate that sperm function, leukocyte recruitment, and endometrial conditioning are co‐determined by exposure history and mucosal context. This systems perspective argues against overly reductionist single‐target models and instead supports network‐based interventions that restore barrier integrity, microbial balance, and immune resolution together [ 8 , 9 , 10 , 11 ]. Microbial metabolites and microbial patterns jointly determine whether innate responses support barrier repair or trigger tissue damage. SCFAs can regulate phagocytosis, chemokine production, epithelial survival pathways, histone acetylation, and receptor signaling, thereby shaping antimicrobial‐peptide production and inflammatory thresholds [ 77 ]. In contrast, PAMPs released by dysbiotic vaginal or endometrial communities provide strong activating signals for TLR2/4, NOD‐like receptors, and related pathways, inducing cytokines and disrupting tight junctions [ 79 ]. Reproductive immunity is therefore governed not simply by the presence of pathogens, but by the broader chemical context in which commensal metabolites either buffer or amplify PRR‐triggered inflammation [ 77 , 78 ]. The way intestinal epithelial cells integrate PRR signaling with microbiota‐derived metabolites such as SCFAs, polyamines, and amino acid derivatives to coordinate antimicrobial peptide production, circadian and hormonal outputs, and barrier integrity at the gut–microbiota interface is depicted in Figure  4 . Intestinal epithelial sensing integrates PRR signaling with microbiota‐derived metabolites. This figure summarizes how intestinal epithelial cells integrate microbial components and metabolites through PRRs to coordinate mucus and antimicrobial peptide programs, coupled to IL‐18–centered feedback control. It highlights the requirement for transcriptional priming (via TLRs or GPR109a) and inflammasome‐dependent processing (via NLRP6), alongside contributions from immune‐derived cytokines and epithelial chemokines that shape lymphoid tissue and barrier dynamics. It also depicts how key microbiota‐regulated metabolites (e.g., SCFAs and indole) modulate inflammasome tone, epithelial tight‐junction integrity, and metabolic homeostasis. PRR, pattern recognition receptor; PRRs, pattern recognition receptors; TLRs, toll‐like receptors; NOD1, nucleotide‐binding oligomerization domain‐containing protein 1; NOD2, nucleotide‐binding oligomerization domain‐containing protein 2; RegIIIγ, regenerating islet‐derived protein 3 gamma; RegIIIβ, regenerating islet‐derived protein 3 beta; Ang4, angiogenin 4; Itln1, intelectin 1; IL‐18, interleukin 18; GPR109a, G Protein–coupled receptor 109A; NLRP6, NLR family pyrin domain‐containing 6; IFNs, interferons; DHX15, DEAH‐Box Helicase 15; IL‐22, interleukin 22; CCL20, C‐C motif chemokine ligand 20; NLRC4, NLR family CARD domain‐containing 4; SCFAs, short‐chain fatty acids; PXR, pregnane X receptor; HIF, hypoxia‐inducible factor; ASC, apoptosis‐associated speck‐like protein containing a CARD; CARD, caspase activation and recruitment domain; R, receptor.

Reproductive innate immunity is rooted in tissue architecture. Epithelia, mucus, stromal matrices, vascular interfaces, and resident leukocytes form layered barriers that must remain permeable to gametes and, during pregnancy, compatible with implantation and placentation while still detecting and containing microbes. Although these programs are organized differently in female and male tissues, both are linked to region‐specific PRR expression, endocrine regulation, and metabolic inputs. The following subsections therefore compare how these shared principles are deployed across compartments rather than repeating structural details. The female reproductive tract is divided into lower and upper compartments with distinct epithelial organization, permeability, and immune exposure. Stratified squamous epithelium dominates the vagina and ectocervix, whereas the endocervix, uterus, and fallopian tubes are lined by columnar epithelium; tight junctions, adherens junctions, and the glycocalyx restrict microbial passage and provide a scaffold for immune surveillance [ 26 , 27 ]. Cervical and endometrial mucus adds a dynamic biochemical barrier whose viscosity and pore structure change across the cycle and pregnancy, thereby influencing both sperm passage and microbial ascent. Cervicovaginal secretions also contain immunoglobulins, complement, lactoferrin, lysozyme, and multiple antimicrobial peptides that act directly on microbes and secondarily modulate chemokine production and leukocyte recruitment [ 28 ]. IFN‐ε adds a constitutive epithelial antiviral program that is hormonally regulated and particularly important for protection against genital viral and bacterial infection [ 29 , 30 ]. Key compartment‐specific epithelial and secreted innate barrier effectors are summarized in Table  1 . Key innate barrier components in the female reproductive tract. In the male tract, innate barrier design must protect highly immunogenic post‐meiotic germ cells without abolishing antimicrobial defense. The blood–testis barrier, created largely by Sertoli‐cell junctional complexes, partitions basal and adluminal compartments and supports an immune‐privileged environment enriched in local regulatory cytokines, complement control, and androgen signaling [ 33 ]. Distal segments are more overtly defensive: the epididymis uses tight epithelial barriers, region‐specific PRR expression, and antimicrobial peptides to support sperm maturation while limiting ascending infection, and the prostate contributes zinc‐rich secretions, proteases, and additional antimicrobial factors [ 1 ]. This architecture permits rapid responses in the epididymis and prostate but also makes those sites more vulnerable to chronic inflammatory injury when regulation fails [ 1 , 33 ]. Major innate immunoregulatory mechanisms that underpin immune privilege across male reproductive tissues, and their implications for infection and fertility, are summarized in Table  2 . Innate immune regulation and immune privilege in the male reproductive tract. Reproductive tissues contain dense, anatomically specialized innate‐cell networks [ 36 ]. In the female tract, leukocytes constitute a substantial stromal fraction, and the abundance of macrophages, dendritic cells, neutrophils, mast cells, NK cells, and tissue‐resident lymphocytes varies by site and cycle stage [ 26 , 36 ]. Macrophages and dendritic cells sample luminal antigens and clear apoptotic material, helping distinguish tolerance to sperm and the conceptus from inflammatory responses to pathogens, whereas neutrophils provide rapid antimicrobial defense but can also injure tissue through proteases, reactive oxygen species, and extracellular traps [ 26 ]. Uterine and decidual NK cells form a distinctive CD56bright population that expands during the secretory phase and early pregnancy and supports spiral artery remodeling, trophoblast invasion, and local tolerance; uterine ILCs provide additional cytokine control [ 26 ]. In the male tract, interstitial and peritubular macrophages, dendritic cells, and mast cells support steroidogenesis and immune privilege in the testis, while epididymal and prostatic myeloid cells coordinate with epithelium during ascending infection [ 1 , 26 , 33 , 36 ]. This subsection therefore emphasizes functional specialization across compartments rather than repeating basic leukocyte inventories. PRRs connect reproductive barriers to microbial and sterile danger signals. Across female tissues, epithelial and stromal cells express multiple TLRs, NOD1/2, and related adaptors, and receptor engagement induces chemokines such as CXCL8, demonstrating that reproductive mucosa is immunologically active rather than passive [ 37 ]. Their distribution is region‐specific: for example, TLR4 is relatively restricted in the lower tract, likely reflecting the need to tolerate abundant commensal Gram‐negative organisms [ 38 ]. More broadly, TLRs, NLRs, RLRs, and cGAS–STING detect extracellular, endosomal, and cytosolic ligands and converge on NF‐κB, MAPK, and IRF pathways to induce inflammatory cytokines and interferons [ 39 , 40 ]. Reproductive tissues tune these pathways according to physiological context; trophoblasts and decidual cells, for instance, preserve antimicrobial competence while limiting inflammation that would damage placental function, whereas the testis maintains lower basal PRR tone than the epididymis or prostate [ 1 , 33 , 41 , 42 ]. Endocrine signals continuously reshape reproductive innate immunity. Estradiol and progesterone alter epithelial integrity, mucus composition, antimicrobial peptide production, immunoglobulin content, and chemokine gradients across the menstrual cycle, thereby changing both susceptibility to infection and the timing of immune tolerance [ 27 , 43 ]. Leukocyte abundance also fluctuates, particularly in the endometrium, where NK cells, macrophages, and dendritic cells expand during the secretory phase and early pregnancy to support implantation and decidual remodeling [ 26 ]. In male tissues, androgens help maintain blood–testis barrier integrity and restrain excessive inflammatory signaling, preserving spermatogenesis [ 33 ]. Metabolic disturbances such as obesity or insulin resistance likely modify these hormonally regulated programs by shifting systemic cytokines, adipokines, and mucosal microbiota, although mechanistic evidence in reproductive tissues remains incomplete. Sex bias in innate immunity is evident systemically and is accentuated in reproductive organs. Women usually mount stronger innate and adaptive responses, including heightened TLR7/8 signaling, interferon production, and neutrophil activation, which can improve pathogen control but also increase inflammatory risk [ 44 , 45 ]. In the reproductive tract this translates into higher baseline leukocyte density, abundant resident NK cells, macrophages, and tissue‐resident T cells, and dynamic epithelial antimicrobial programs [ 26 , 27 ]. Men, by contrast, display a more strongly compartmentalized architecture: the testis is profoundly immune privileged, whereas the epididymis and prostate mount more conventional inflammatory responses and are therefore more prone to chronic infection‐related damage [ 1 , 33 ]. Understanding these sex‐specific architectures is essential for interpreting how infection, dysbiosis, and sterile injury influence fertility and pregnancy outcomes.

Reproductive success depends on innate immune systems that can do two seemingly incompatible jobs at once: defend against microbes and sustain tolerance to sperm, embryo, and fetus. Across male and female tissues, this balance is created by coordinated interactions among epithelial barriers, mucus, antimicrobial peptides, complement, PRRs, tissue‐resident leukocytes, and microbial communities, all of which are further shaped by endocrine and metabolic signals. The central conceptual advance of this review is a unified barrier defense–tolerance framework for reproductive biology. Within this framework, reproductive success and failure are interpreted as systems‐level outcomes of coordinated interactions among barrier architecture, innate sensing thresholds, microbial ecology, and endocrine–metabolic cues across male and female tissues and the maternal–fetal interface. Early innate sensing influences gamete quality, embryo competence, implantation, placentation, and parturition; when these pathways are excessive, mistimed, or poorly resolved, they contribute to infertility, recurrent pregnancy loss, preeclampsia, fetal growth restriction, and preterm birth. This perspective implies that infertility often emerges from the coupled chemistry of sperm, seminal plasma, mucosal barriers, host immunity, and partner microbiota, and therefore may be only partially bypassed—not nullified—by IVF‐based strategies [ 7 , 8 , 11 ]. However, evidentiary strength is not uniform across compartments: support is strongest for cervicovaginal communities, whereas endometrial, placental, and male genital microbiota data remain more heterogeneous because low‐biomass sampling increases susceptibility to contamination and reduces reproducibility across cohorts, and claims for stable placental colonization remain especially controversial. Carrying this framework forward, future progress will depend on combining mechanistic models with longitudinal multi‐omics and microbiome‐informed clinical studies so that protective innate immunity can be strengthened without compromising reproductive tolerance. From a translational perspective, the most clinically mature evidence currently comes from human microbiome‐based risk stratification and selected vaginal microbiome interventions, whereas many inflammasome‐, interferon‐, extracellular‐vesicle‐, and omics‐guided strategies remain anchored primarily in animal or engineered human systems.

Reproduction imposes an unusual immunological task: reproductive tissues must block sexually transmitted and ascending pathogens while simultaneously permitting exposure to paternal antigens and supporting a semi‐allogeneic conceptus [ 1 , 2 ]. Innate immunity is central to this balance because it provides rapid front‐line defense and shapes subsequent adaptive responses. When this equilibrium is lost, infertility, recurrent pregnancy loss, preterm birth, and other adverse outcomes become more likely [ 3 , 4 ]. Assisted reproductive technologies, particularly IVF and ICSI, bypass parts of coital sperm transport and selection, but they do not reduce the importance of innate immunity and microbial ecology because semen quality, endometrial receptivity, embryo transfer conditions, implantation, and placentation remain shaped by these pathways [ 5 , 6 , 7 ]. Accordingly, infertility is better viewed as an emergent property of interactions among sperm, seminal plasma, male and female microbiota, cervical mucus, epithelial barriers, and mucosal immunity than as a defect in dysbiosis alone or host response alone [ 8 , 9 , 10 , 11 ]. For clarity, representative examples are identified below as human, animal, or engineered in vitro when that distinction materially affects interpretation. This balancing function is executed largely through pattern‐recognition receptors, including Toll‐like receptors, NOD‐like receptors, RIG‐I‐like receptors, and cytosolic DNA sensors such as cGAS–STING [ 12 , 13 ]. In reproductive tissues, these sensors are expressed not only by leukocytes but also by epithelial, stromal, endothelial, trophoblast, and germ‐cell–supporting cells, allowing mucosal and parenchymal barriers to integrate microbial, hormonal, and metabolic cues [ 14 , 15 ]. In the female tract, compartment‐specific epithelia, mucus, soluble antimicrobials, complement, and resident innate cells are continuously remodeled across the menstrual cycle and pregnancy [ 1 , 14 , 16 , 17 ]. The male tract couples innate sensing with immune privilege through the blood–testis barrier and specialized somatic‐cell niches, but excessive activation can still impair spermatogenesis and steroidogenesis [ 15 , 18 ]. Local microbiota and distal microbial metabolites add another regulatory layer: Lactobacillus‐dominant vaginal communities generally support barrier stability and low inflammatory tone, whereas microbiota‐associated reproductive risk is most consistently supported in the vaginal compartment and should be interpreted more cautiously in low‐biomass endometrial, placental, and male genital niches [ 14 , 17 , 19 , 20 , 21 , 22 , 23 , 24 , 25 ]. This review advances the central conceptual framework of the article: reproductive innate immunity is best understood as a unified barrier defense–tolerance system in which barrier architecture, innate sensing thresholds, microbial ecology, and endocrine–metabolic context are functionally coupled across the male and female reproductive tracts and the maternal–fetal interface [ 1 , 2 , 22 ].

The authors declare no conflicts of interest.

Growing mechanistic resolution has made reproductive innate immunity an increasingly translational field. Microbiome states, soluble innate mediators, oxidative‐stress markers, and extracellular‐vesicle cargoes can now be profiled in reproductive tissues and fluids with greater precision, raising the prospect of earlier risk stratification for infertility, recurrent pregnancy loss, preterm birth, and male‐factor infertility. The next challenge is to convert these signatures into interventions that restore barrier competence without disrupting reproductive tolerance. The following subsections therefore focus on biomarker classes and intervention strategies with clearer clinical traction. For translational interpretation, the evidence discussed below is separated explicitly by source. Human clinical and cohort studies provide the strongest support for biomarker performance and near‐term clinical feasibility; animal models are used primarily for causal testing and in vivo safety or efficacy assessment; engineered in vitro systems are used mainly for cell‐specific mechanism, target validation, and hypothesis generation. Selected translational strategies targeting microbiota‐innate immune axes and related innate effector pathways in reproductive medicine are summarized in Table  3 . Translational strategies targeting microbiota–innate immune axes in reproductive medicine. Microbiome‐informed biomarkers are among the more clinically advanced translational tools, although their robustness differs substantially by reproductive niche. Non‐Lactobacillus, high‐diversity vaginal communities repeatedly associate with spontaneous preterm birth, and similar dysbiotic patterns predict poorer IVF outcomes [ 24 , 96 ]. Endometrial microbiota profiling after failed IVF also suggests that non–Lactobacillus‐dominant states are linked to lower subsequent live‐birth rates [ 80 , 97 ]. Beyond the female tract, altered gut, vaginal, semen, penile, and testicular microbiota have been reported in recurrent implantation failure, unexplained infertility, and idiopathic male infertility [ 23 , 76 ]. Combining these microbial signatures with soluble cytokines, leukocyte phenotypes, and oxidative‐stress measures may yield more robust multiparameter risk models than any single biomarker alone. Representative cervicovaginal and endometrial microbiota signatures associated with preterm birth and assisted reproduction outcomes are compiled in Table  4 . Female reproductive tract microbiota as biomarkers of reproductive outcomes. Accordingly, the biomarker evidence is currently strongest for human vaginal datasets, where repeated cohort‐level associations support risk stratification, whereas endometrial and male genital signatures remain less mature as clinical biomarkers. Animal studies can strengthen causal inference and define longitudinal dynamics, but they do not replace human validation, and in vitro assays are most useful for clarifying which microbial or innate signals are being captured by a candidate biomarker. Microbiome restoration and AMP‐based approaches are attractive because they act directly at mucosal barriers. In randomized clinical and follow‐up human studies, vaginal Lactobacillus crispatus CTV‐05 (LACTIN‐V) has reduced recurrence of bacterial vaginosis after antibiotic therapy and promoted durable recolonization, providing proof of principle that the vaginal ecosystem can be therapeutically shifted [ 94 ]. Follow‐up studies also show reduced genital inflammatory markers after LACTIN‐V, and early pregnancy studies support feasibility and tolerability, although efficacy for preventing preterm birth or improving ART outcomes remains unproven [ 98 , 99 ]. In parallel, endogenous AMPs and topical lectin‐based or synthetic peptide microbicides offer a route to suppress pathogens while preserving mucosal integrity [ 28 , 100 ]. Future clinical strategies may combine microbiome restoration with AMP‐supportive therapies to lower genital tract inflammation before conception or ART [ 28 , 94 , 100 ]. In translational terms, direct human interventional evidence in this space currently comes mainly from vaginal microbiome restoration, whereas most AMP‐based or broader mucosal immunomodulatory strategies remain preclinical, ex vivo, or formulation‐stage concepts. These approaches are therefore best interpreted as promising therapeutic directions rather than established ART adjuncts. Inflammasome, interferon, and oxidative‐stress pathways are promising but still early therapeutic targets [ 75 ]. In human placental tissue, primary trophoblast systems, and related experimental models, placental and systemic NLRP3 activation has been repeatedly documented, and experimental inhibition of upstream regulators such as TBK1 can dampen trophoblast inflammasome signaling [ 101 ]. Similar inflammasome signatures are present in some forms of male infertility, including varicocele, where NLRP3‐related mediators accompany poorer sperm quality [ 74 ]. Oxidative stress is also a recurring feature of recurrent pregnancy loss and male reproductive dysfunction, supporting the idea that redox and inflammasome markers could be used together for patient stratification [ 102 ]. What remains uncertain is which immunomodulators can safely rebalance these pathways during pregnancy or fertility treatment without impairing antimicrobial defense or fetal development [ 102 ]. The translational question is therefore which patients can be stratified for safe pathway modulation. Here, the therapeutic signal is driven largely by human placental specimens, primary‐cell systems, and complementary experimental models rather than by pregnancy intervention trials. For that reason, inflammasome‐, interferon‐, and redox‐directed strategies are presently more useful for patient stratification and target nomination than for immediate clinical implementation. Human meta‐analysis and mechanistic studies suggest that seminal plasma and reproductive‐fluid EVs may provide a more physiological route to immune preconditioning. Seminal plasma contains TGF‐β, prostaglandins, cytokines, and vesicles that can induce a more tolerogenic uterine environment, and meta‐analysis suggests that exposure around oocyte retrieval or embryo transfer modestly improves clinical pregnancy rates [ 103 ]. Prostasomes and other seminal EVs regulate complement, influence sperm function, and can directly drive T‐cell differentiation toward regulatory phenotypes, while endometrial and placental EVs also reshape local immune signaling [ 104 , 105 , 106 ]. These observations support the concept of using selected reproductive‐fluid fractions or engineered vesicles to condition implantation, although clinical evidence is still limited. For immune‐preconditioning approaches, human data presently support biological plausibility and modest clinical association, but mechanistic confidence still depends heavily on in vitro EV studies and other experimental systems. Translation will therefore require clearer separation between clinically observed benefit, which remains limited, and mechanism‐oriented preclinical support. Systems immunology is redefining reproductive immune phenotyping, with human single‐cell and spatial datasets now providing much of the core atlas‐level evidence in this area. Single‐cell atlases of the early maternal–fetal interface, term and preterm placenta, and cycling endometrium have resolved diverse trophoblast, macrophage, dendritic‐cell, NK‐cell, and interferon‐responsive states that were previously invisible in bulk assays [ 107 , 108 , 109 ]. Integrating these data with proteomics, metabolomics, and microbiome profiles should allow researchers to define composite immune states that predict implantation success, placental vascular remodeling, or preterm labor more accurately than single markers [ 110 , 111 , 112 ]. Such datasets also provide a foundation for data‐driven models and eventually digital‐twin approaches that could personalize monitoring and intervention across pregnancy and infertility care. Human studies offer direct clinical relevance because they capture natural microbial exposure, endocrine context, partner‐specific variability, and real pregnancy outcomes; they are therefore indispensable for biomarker validation and therapeutic prioritization. Their main limitations are ethical constraints, limited access to peri‐implantation and early placental tissues, and restricted scope for causal intervention. By contrast, mouse and other animal models allow timed mating, controlled microbial or genetic perturbation, lineage tracing, and mechanistic testing that are impossible in humans, making them essential for establishing causality. However, species differences in implantation strategy, placental architecture, seminal signaling, and pathogen susceptibility constrain direct translation. Emerging human organoid, assembloid, placenta‐on‐a‐chip, and ex vivo systems help bridge this gap by preserving human cell identity while allowing experimental control, but they still do not fully reproduce whole‐organism endocrine, vascular, and immune feedback. The strongest pipeline is therefore iterative: hypotheses generated in patients, tested mechanistically in animal or engineered human systems, and then returned to carefully phenotyped human cohorts for validation [ 55 , 113 , 114 , 115 ]. In practice, a robust translational pathway should move biomarkers from human discovery to external clinical validation, while therapeutic candidates move from mechanistic testing in engineered systems to in vivo animal studies and only then to carefully staged human trials. Several priorities now stand out. First, the field needs quantitative definitions of when physiological inflammation required for ovulation, implantation, or parturition shifts into pathological activation [ 107 , 108 , 116 ]. Second, local genital microbiota must be integrated with distal ecosystems, especially the gut and oral microbiota, in longitudinal multi‐omics studies that also capture endocrine and metabolic context [ 111 ]. Third, causal testing will require advanced organoids, organ‐on‐chip platforms, and humanized in vivo models capable of reproducing trophoblast–decidual and mucosal barrier interactions [ 70 ]. Finally, any intervention that deliberately modifies microbiota or immune signaling in reproduction must be evaluated not only for short‐term efficacy but also for offspring safety and long‐term immune consequences [ 111 ].