Natural sex reversal imparts permanent compositional changes to the swamp eel gonadal microbiome

Microbiome (2025) 13:217 Meng et al. Microbiome https://doi.org/10.1186/s40168-025-02187-7 Open Access RESEARCH Natural sex reversal imparts permanent compositional changes to the swamp eel gonadal microbiome Kaifeng Meng1,2, Meidi Hu1,3, Yuanyuan Chen1,4, Xing Lin1,4, Chaolin Jiang1, Jiarui Song1,4, Yifan Bai1,4, Yuanli Zhao1, Fei Liu1,4 and Daji Luo1,2,3,4* Abstract Background Microbial communities are increasingly recognized for their essential roles in the reproductive system. However, the microbial communities in healthy gonads—neither in the ovary nor the testis—have not been extensively explored, particularly with respect to sex differentiation. Sex reversal is a unique mode of sex differentiation that is a well-documented phenomenon in various animal species, with the swamp eel (Monopterus albus) being a notable example of a hermaphroditic species that undergoes natural female-to-male sex reversal. Thus, swamp eel offers a robust system for exploring gonad microbial communities and their biological and functional significance. Results Our study revealed a living microbial community in the gonads of healthy swamp eel, with microbial loads comparable to those found in three distinct niches: gut, skin, and blood. The gonad microbial communities shared > 55% of their diversity with those in the gut and blood. We focused on the niche-specific differences in microbial communities, particularly between the ovary and testis. After isolating and injecting the ovarian-dominant bacteria Bacillus, we observed significant microbial dysbiosis and metabolic responses in the ovary. These changes were primarily reflected in the altered abundance of the ovarian microbiota involved in amino acid and lipid metabolism, which may contribute to ovarian function in swamp eel. Additionally, Bacillus inhibited sperm motility, reduced sperm count, and induced inflammatory responses in the testes of male swamp eel. These findings highlight the crucial role of bacteria in the sexual transition from the ovary to the testis and in gametogenesis. Conclusions Characterizing the microbial composition and distribution in the gonads is crucial for understanding the role of the reproductive microbiome in hermaphroditic species and during sex reversal. Our findings first indicate that ovarian-dominant bacterial communities contribute to maintaining ovarian function while inhibiting testicular function in swamp eel, further suggesting that microbial communities are involved in the process of sex reversal. Highlights 1. Gonadal microbial communities at homeostasis are partially derived from the gut and blood microbiomes. 2. The dominant ovarian bacteria Bacillus leads to ovarian dysbiosis. 3. Prostaglandin E3 may serve as a metabolic biomarker in response to Bacillus. 4. Bacillus induces testicular inflammation and reduces sperm motility in hermaphroditic swamp eel. *Correspondence: Daji Luo Full list of author information is available at the end of the article © The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Meng et al. Microbiome (2025) 13:217 Page 2 of 18 Keywords Microbial community, Gonad, Hermaphroditic fish, Bacillus, Sex differentiation Graphical Abstract Background Distinct microbial communities have been identified in both sexes at multiple locations along the reproductive tract, exhibiting variations in bacterial diversity and composition [1, 2]. Microbiomes are increasingly acknowledged for their significant roles in the reproductive system [3]. Although some microorganisms are directly transferred from the reproductive tract of the mother to the baby during birth [4, 5], the microbial communities in healthy gonads—neither the ovary nor the testis—have not been extensively characterized, particularly in relation to sex differentiation and gonadal development. Teleosts, in particular, seem to be especially receptive to the presence of bacteria in their internal organs [6, 7]. While evidence is accumulating for the presence of microorganisms in the gonad [8], the question of whether gonadal microbiomes maintain homeostasis remains unanswered. Sex reversal, an extraordinary form of sexual plasticity that occurs during the life cycle, has been studied in fish, reptiles, birds, amphibians, and even mammals [9]. The swamp eel (Monopterus albus), a typical protogynous hermaphrodite fish, undergoes natural sex reversal, where an ovary transforms into a testis through ovotestis differentiation during its life cycle [6, 10]. While reproductive tract microbiomes are well characterized in female vertebrates, particularly the vaginal and cervical microbiota dominated by Lactobacillus species, emerging evidence suggests that even low-biomass ovarian microbial communities may influence reproductive health [11, 12]. In addition to the female system, gut-resident microbes such as Bacillus enhance reproductive performance through immunomodulation and metabolic regulation, improving folliculogenesis and fetal development [13]. Similarly, the seminal microbiota critically regulates physiological and pathological processes in male models [14, 15]. However, the presence of microbial communities in the vertebrate testis remains highly controversial, with reported associations limited to disease states [16], heat stress [17], and teleost-specific adaptations [6, 18]. Microbial communication via metabolites and signaling Meng et al. Microbiome (2025) 13:217 molecules is known to maintain tissue homeostasis [19]; however, its role in orchestrating gonad plasticity remains entirely unexplored. We hypothesize that dynamic microbiota-gonad communication facilitates sex reversal in teleosts, with microbial-derived cues potentially acting as modulators of this extraordinary sex differentiation. To investigate microbiota-gonad communications in hermaphroditic swamp eel, we integrated multi-omics analyses to resolve functional interactions between the symbiotic microbiota and gonadal development. Here, we demonstrated that sexually dimorphic bacterial communities colonize healthy ovaries and testes, with partial transmission from the gut and blood microbiota. Strikingly, functional analyses reve (...truncated)