The upper reproductive tract comprises the fallopian tubes, ovaries, and uterus, including the endocervix, and the lower tract consists of the ectocervix and vagina. The microbiome of the female genital tract varies between the lower and upper tracts, with the lower tract having a bacterial burden of 100–10,000-fold more than the upper tract (Chen et al., 2017; Baker et al., 2018). In 2011, Ravel et al. (2011) described five community state types (CSTs) in the vagina of healthy women, determined mainly by the dominant species of Lactobacillus and pH value, with CSTs I, II, III, and V involving dominant L. crispatus, L. gasseri, L. iners, and L. jensenii, respectively. CST IV has a low abundance of Lactobacillus and higher abundances of specific anaerobic genera (Atopobium, Dialister, Gardnerella, Prevotella, and Sneathia) (Ravel et al., 2011). Lactobacillus (i.e., L. crispatus and L. iners) was abundant in 92% of cervical specimens from healthy women (Ravel et al., 2011). Another study confirmed that the microbiome is strongly altered from the lower to the upper genital tract, with decreased Lactobacillus in the upper genital tract compared to that in the lower genital tract (Chen et al., 2017). The female reproductive tract microbiome is not fixed but changes with age, physiological conditions, lifestyle, and environmental factors.

The gut microbiome is a complex ecosystem of microbes acting upon and changing in response to the host environment (Gilbert et al., 2018; Chambers et al., 2021). The gut microbiome is dominated by five bacterial phyla: phylum Firmicutes (Clostridium, Lactobacillus, Eubacterium, Ruminococcus, Butyrivibrio, Anaerostipes, Roseburia, Faecalibacterium, etc.; Gram-positive species), phylum Bacteroidetes (Bacteroides, Porphyromonas, Prevotella, etc.; Gram-negative species), phylum Proteobacteria (Enterobacteriaceae, etc.; Gram-negative species), phylum Actinobacteria (Bifidobacterium; Gram-negative species), and phylum Verrucomicrobia (Akkermansia, etc.; Gram-negative species) (Doaa et al., 2016). Regarding the gut microbiota, almost 90% are Firmicutes and Bacteroidetes, while the rest are Actinobacteria and Proteobacteria. Verrucomicrobia is the least abundant (Yurtdaş and Akdevelioğlu, 2020; Sędzikowska and Szablewski, 2021). The gut microbiome’s structure is developed from birth and modulated by delivery mode and the maternal skin and gut microbiomes (Dominguez-Bello et al., 2010).

The gut microbiota influences the intestinal milieu, which acts on other organs and pathways. A healthy gut microbiota improves digestion, metabolism, and immune response; the symbiotic relationship between the host’s gut and the microbiota that maintains homeostasis is known as normobiosis (Rea et al., 2018).

Gut microbiomes are responsible for metabolizing estrogen; estrogens are metabolized by microbe-secreted β-glucuronidase, which converts estrogen from a conjugated form to a deconjugated form (Plottel and Blaser, 2011; Williams et al., 2020). Deconjugated and unbound (active and free) estrogens circulate in the bloodstream and bind to estrogen receptors alpha (ERα) and beta (ERβ) (Baker et al., 2017). Phytoestrogens are similarly metabolized and act via ERα and ERβ (Baker et al., 2017). The binding of estrogens and phytoestrogens to ERs initiates downstream signaling (Rietjens et al., 2017). This ultimately alters physiological conditioning, affecting reproductive health and neural development (Dewi et al., 2012).

The estrobolome refers to the gut microbiota genes involved in the metabolism of estrogen (Plottel and Blaser, 2011; Graham et al., 2021), while the endobolome refers to the gut microbiota genes and pathways involved in the metabolism of steroid hormones (including estrogen) and EDCs (Aguilera et al., 2020). EDCs have been defined by the US Environmental Protection Agency as “exogenous chemicals that interfere with the synthesis, secretion, metabolism, binding activity, or elimination of natural blood-borne hormones that are present in the body and are responsible for homeostasis, reproduction, and developmental function” (Diamanti-Kandarakis et al., 2009; Zoeller et al., 2016; Aguilera et al., 2020). EDCs include natural chemicals found in nature (phytoestrogens, genistein, and coumestrol) and artificial chemicals utilized in industrial solvents/lubricants and their by-products [polychlorinated biphenyls (PCBs), polybrominated biphenyls (PBBs), and dioxins], plasticizers (phthalates), pesticides [methoxychlor, chlorpyrifos, and dichlorodiphenyltrichloroethane (DDT)], antibacterials (triclosan), fungicides (vinclozolin), diethylstilbestrol (DES), and bisphenol A (BPA) (Diamanti-Kandarakis et al., 2009; Darbre, 2017; Aguilera et al., 2020). EDC exposure can cause marked gut dysbiosis, which can lead to disorders in many organ systems (Rosenfeld, 2017).

PCOS is a hormonal disease caused by an imbalance between estrogen and androgen. Tremellen and Pearce (2012) studied the role of gut dysbiosis in PCOS development due to poor diet. Dysbiosis increases gut mucosal permeability, resulting in the entry of lipopolysaccharide from Gram-negative colonic bacteria into the circulation. The resultant activation of the immune system interrupts insulin receptor function, increasing serum insulin levels, raising the ovaries’ production of androgens, and interfering with regular follicle production (Tremellen and Pearce, 2012). Studies have shown that lower circulating unconjugated estrogen and increased testosterone in PCOS patients may alter the gut microbiome (Tremellen and Pearce, 2012; Liu et al., 2017). Regarding the role of gut microbiota on PCOS, studies done by Guo et al. (2016) in 2016 showed that treatment of female Sprague–Dawley rats with letrozole (a nonsteroidal aromatase inhibitor) promoted PCOS and gut dysbiosis and altered the sex hormone levels, estrous cycles, and ovarian morphology. Lactobacillus, Ruminococcus, and Clostridium were downregulated while Prevotella was upregulated in PCOS rats compared to control rats (Guo et al., 2016). The same group showed that after treating PCOS rats with Lactobacillus and fecal microbiota transplantation (FMT) from healthy rats, the estrous cycles were enhanced in all animals in the FMT study group and 75% of rats in the Lactobacillus transplantation group had diminished androgen biosynthesis and normalized ovarian morphologies. The bacterial composition of gut microbiota was fixed in both FMT and Lactobacillus-treated groups, raising Lactobacillus and Clostridium and reducing Prevotella (Guo et al., 2016). A study indicated that the gut dysbiosis related to PCOS involved decreased bacterial diversity and an altered Firmicutes/Bacteroidetes ratio (Thackray, 2019). The role of the lower genital tract microbiota in PCOS has also been investigated. A study of vaginal and cervical biopsies showed that there were increased pathogens (such as Gardnerella vaginalis, Mycoplasma hominis, and Prevotella) and reduced Lactobacillus in both the vagina and cervix in PCOS patients compared to healthy controls (Tu et al., 2020). These findings were consistent with another study showing increased Mycoplasma and Prevotella and decreased L. crispatus in vaginal and cervical samples from PCOS patients compared to healthy controls (Hong et al., 2020). Thus, the estrobolome may affect sex hormone-driven disorders involving estrogen, such as PCOS.

Menopause is the permanent stop of menstrual cycle resulting in the loss of folliculogenesis and reduction in estrogen levels resulting in modifications impacting all body functions (Dalal and Agarwal, 2015). The gut microbiota may be important in regulating estrogen levels and estrogen metabolism during and after menopause. In postmenopausal women, gut microbiota diversity is linked to higher estrogen metabolite levels relative to parent estrogen levels in urine (Fuhrman et al., 2014). The gut microbiota also metabolizes estrogen-like compounds in food (such as soy isoflavones) and stimulates specific bacterial growth. Supplementation with soy isoflavones in postmenopausal women increases Bifidobacterium and reduces unclassified Clostridiaceae (Qi et al., 2021). Bifidobacterium has a beneficial role in stimulating absorption and immunity and inhibiting intestinal infection, while Clostridiaceae is involved in inflammatory diseases and is associated with obesity. These effects suggest that this host–microbiome estrogen-related interaction contributes to a broad spectrum of pathways influencing women’s health and illness (Nakatsu et al., 2014; Qi et al., 2021).

During dysbiosis, invasion of the vagina by many anaerobic bacteria as the abundance of Lactobacillus decreases leads to inflammatory reactions that promote tumor growth, thus causing diseases such as cervical intraepithelial neoplasia, which can develop into cervical cancer (Champer et al., 2018). Endometrial cancer is the fourth most common cancer in women and the fifth most common cause of cancer death in the United States (Brooks et al., 2019). In endometrial cancer, estrogens are essential for increasing inflammation by upregulating the production of pro-inflammatory mediators such as IL-6 and TNF-α, which can in turn synergistically upregulate the expression of enzymes involved in ovarian steroidogenesis (aromatase, 17β-hydroxysteroid dehydrogenase, and estrone sulfatase), thus producing a feedback loop (Wallace et al., 2010; Borella et al., 2021). Moreover, high estrogen can change the vaginal microbiome, indirectly sustaining the development of endometrial cancer by interfering with the gut and vaginal microbiomes (Nakamura et al., 2019; Borella et al., 2021). A cross-sectional study analyzed the microbiomes of the vagina, cervix, fallopian tubes, and ovaries and found that the bacterial taxa in the genital tract of patients with endometrial cancer are characterized by the predominance of Firmicutes (Anaerostipes, Dialister, Peptoniphilus, Ruminococcus, and Anaerotruncus), Spirochaetes (such as Treponema), Actinobacteria (Atopobium), Bacteroidetes (Bacteroides and Porphyromonas), and Proteobacteria (Arthrospira) (Walther-António et al., 2016; Borella et al., 2021). Another study examined the influence of Atopobium vaginae and Porphyromonas somera on endometrial cells in vitro, revealing that these bacteria increase the release of inflammatory cytokines and chemokines (IL-1α, IL-1β, IL-17α, and TNF-α) by endometrial cells, indicating their role in maintaining inflammation and in neoplastic initiation (Caselli et al., 2019). This was supported by another study demonstrating a link between genital tract dysbiosis, high inflammatory cytokine expression, and endometrial cancer (Lu et al., 2021).

Endometriosis is characterized by chronic inflammation in which the endometriotic cells promote the synthesis of ILs, TNF-α, and vascular endothelial growth factor (VEGF), generating the conditions for tumor transformation (Kokcu, 2011; Jiang et al., 2021). Endometritis is an infectious and inflammatory disorder of the endometrium (Kitaya et al., 2018).

Estrogen promotes epithelial cell proliferation throughout the female genital tract, and estrogen dysregulation is associated with proliferative disorders such as endometriosis (Zhang et al., 2009; Anderson, 2019). Endometriosis is common in premenopausal women and is associated with a hyperproliferative state secondary to elevated estrogen levels (Laschke and Menger, 2016). In 2002, Bailey and Coe (2002) showed that monkeys with endometriosis had a low abundance of Lactobacillus and a high abundance of Gram-negative bacteria. Recently, research has shown that endometriosis is accompanied by gut microbial dysbiosis; however, the exact findings vary among studies. For instance, Ata et al. (2019) showed that patients with moderate-to-severe endometriosis (n = 14) have more Shigella/Escherichia in their colon than healthy individuals (n = 14). In contrast, Shan et al. (2021) showed that patients with stage 3–4 endometriosis (n = 12) had lower gut microbiota alpha diversity and a higher Firmicutes/Bacteroidetes ratio than healthy participants. A recent large study by Svensson et al. (2021) on stool samples reported that the abundance of 12 bacteria in the classes Bacilli, Bacteroidia, Clostridia, Coriobacteriia, and Gammaproteobacteria strongly varied between endometriosis patients (n = 66) and healthy individuals (n = 198). The discrepancy between these studies necessitates more extensive studies of how endometriosis stage, age, race, medical history, medication use, and diet affect the bacteria involved in endometriosis (Chadchan et al., 2022). An animal study reported that at 42 days after mice were intraperitoneally injected with endometrial tissue to trigger endometriosis, there was a significant elevation in the Firmicutes/Bacteroidetes ratio between the endometriotic and control mice (Yuan et al., 2018).

Several studies have examined the relationship between hormone dysregulation, the uterine microbiota, and gynecological disorders such as endometriosis (Khan et al., 2014; Walther-António et al., 2016; Hernandes et al., 2020; Schreurs et al., 2021). Investigated the intrauterine microbiome colonization and occurrence of endometritis in women with endometriosis and controls (fertile women with no evidence of endometriosis), without significant clinical differences between the two groups. A subset of women from both groups was treated with a gonadotropin-releasing hormone agonist (GnRHa) for 4–6 months before collecting uterine and vaginal samples. Both groups, with or without endometriosis, had 16 types of anaerobic and aerobic bacteria and yeast colonizing the vagina. However, notably, subclinical uterus infection was more common in endometriosis patients than controls and much more common in those treated with GnRHa than in those who did not receive GnRHa (Khan et al., 2014). This was attributed to the presumption that GnRHa alters the intrauterine environment, thus increasing uterine infection in women with endometriosis. There was a significant increase in the diagnosis of endometritis in the GnRHa-treated women than untreated women, with or without endometriosis, due to the increased endometrial colonization rate caused by GnRHa. Higher abundances of multiple bacteria (including Staphylococcaceae, Moraxellaceae, Lactobacillacae, Streptococcaceae, and Enterobacteriaceae) were detected in endometrial swabs from GnRHa-treated women than untreated women, with or without endometriosis. Streptococcaceae and Staphylococcaceae increased and Lactobacillacae decreased in GnRHa-treated compared to untreated endometriosis patients, indicating that low estrogen due to GnRHa increases intrauterine infection, thus causing endometrial dysbiosis (Khan et al., 2014). Microbes from the vaginal area can move to and colonize the endometrium (where they are usually exposed to a different environment) (Khan et al., 2014). The increased intrauterine colonization in endometriosis patients was hypothesized to be attributable to increased prostaglandin E2 (PGE2), which caused immunosuppression that enabled bacterial survival and replication. In support of this hypothesis, PGE2-mediated immunosuppression of lymphocytes is higher in women with endometriosis than those without endometriosis (Khan et al., 2014). Notably, the presence of pathogenic bacteria (such as Escherichia coli) and enhanced bacterial colonization in women with endometriosis caused subclinical endometritis and further promoted endometriosis severity and/or complications (Khan et al., 2014). As sex steroids (such as estrogen) modulate the number of antimicrobial agents [such as defensins and secretory leukocyte protease inhibitor (SLPI)] in the endometrium and fallopian tubes ( Figure 3A ) (Khan et al., 2014), altering estrogen levels can lead to intrauterine microbial infection and/or tissue inflammation, leading to dysbiosis ( Figure 3B ). These studies concluded that altering estrogen levels triggers inflammatory responses in the endometrial tissues, leading to microbial colonization of the uterus, endometriosis, and endometritis (Khan et al., 2014).

UFs or leiomyomas are benign monoclonal tumors of the uterus derived from uterine smooth muscle (myometrium). They affect >70% of women of reproductive age worldwide, especially women of color (Wise and Laughlin-Tommaso, 2016; Al-Hendy et al., 2017). UFs significantly impact patients’ health, fertility, and economic status. In the United States, the annual financial burden of UF treatment is estimated to have reached $34.4 billion (Giuliani et al., 2020). There is a wide range of invasive and noninvasive treatment options, from short-term pharmacotherapies to laparoscopic or open myomectomy or hysterectomy (Istre, 2008; Yang et al., 2022). The treatment depends on the tumor size, tumor location, age, and reproductive plans. Epidemiological studies indicate that African American women develop UFs more frequently and at an earlier age, and the tumors tend to be more aggressive, growing larger and causing more significant symptoms than in Caucasian women (Al-Hendy and Salama, 2006; Eltoukhi et al., 2014; Stewart et al., 2016).

A characteristic feature of UFs is their dependence on the ovarian steroid hormones estrogen and progesterone (Elkafas et al., 2017). These hormones stimulate complex paracrine signals, which allow UF cells to secrete mitogenic stimuli and thereby influence adjacent immature UF cells, thus providing UF cells with undifferentiated cells that can support tumor growth (Ono et al., 2013; Reis et al., 2016). Estradiol increases the sensitivity of tissues to progesterone by increasing the availability of progesterone receptors (PRs) (McGuire et al., 1977; Mote et al., 2002; Elkafas et al., 2017). Selective PR modulators (SPRMs) are synthetic steroid ligands designed to modulate the PR site in a tissue-specific way; binding of SPRMs to PRs can cause agonistic effects, antagonistic effects [e.g., they can compete with agonists or enhance the effects of co-repressors to cause antagonistic effects (Islam et al., 2020)], or mixed effects. They can induce receptor dimerization and DNA binding and coordinate with co-activators and/or co-repressors (Madauss et al., 2007). Asoprisnil and ulipristal acetate are SPRMs, while raloxifene is a selective ER modulator that suppresses UF growth (ElKafas et al., 2018). Research using these compounds can help to study estrogen- and progesterone-dependent gynecological disorders.

In recent years, high-throughput sequencing has been used to study the gut microbiome diversity in UF patients. A case–control study examined the differences in follicle-stimulating hormone (FSH), estradiol (E2), and anti-Mullerian hormone (AMH) before and after transabdominal hysterectomy for UF patients and the effect of transabdominal hysterectomy on the gut microbiome (Wang et al., 2020). The results indicated that FSH increased after surgery, while E2 and AMH decreased. The ovaries are involved in hormone secretion and ovulation, and the study concluded that transabdominal hysterectomy altered ovary function, leading to decreased E2 and AMH and increased FSH. This decreased estrogen affected the gut microbiome diversity, with increased Proteobacteria and Firmicutes and decreased Bacteroidetes (Wang et al., 2020; Yang et al., 2022).