• Vaginal

• Urinary

• Endometrial

• Can be viewed independently and as part of an intricate network of crosstalk, systemic interactions and influences.

• Holistic understanding of how these microbiome systems relate to each other and body systems is integral to patient management and care.

• Reasons for not speaking to anyone about (vaginal) discomfort included:

 “It makes me uncomfortable/embarrassed” (60 %).

 “I do not think other people want to hear about my vaginal problems” (52 %).

 “It is private and does not concern others” (52 %).

 “It’s just part of growing older” (49 %).

• A substantial number of women with vaginal discomfort who did not discuss it with anyone also expressed a preference for someone else to initiate the conversation (20 %).

• Not every patient will report issues with their genitourinary microbiome/health.

 As clinicians, being alert for key “clues” is important. Integrating the information, prompting patients for associated information and then using the information in therapy choice completes a holistic picture.

Lactobacilli Taxonomy Phylum: Firmicutes Class: Bacilli Family: Lactobacillaceae Genus*: Lactobacilli Gram positive microbes Taxonomically: 170 species.

99.9% of the bacteria are Lactobacillus( they create a healthy state by maintaining  a  vaginal PH of 3.6 to 4.5. due to the build-up  of Lactic Acid).

When this population decreases, the different species of non-dominant bacteria will change the PH beyond 4.5 and allow candida, bacterial infections to develop, impact on fertility and contribute to bladder infections, aggravation or possibly trigger the endometrioses among other contributing factors. 

Vaginal microbes are the most studied and characteristics overlap with other microbiome sites.

What Does the Vagina Have to Do With It?

Defining the relationship between the vagina and the urinary microbiomes:

• Sampling of both the endometrium and bladder is difficult without possible contamination.

• Vaginal and urinary microbiome investigations indicated that 60 of the 100 most abundant operational taxonomic units in the samples largely overlapped.

 Composed of 5 Community State Types :

High levels of Lactic Acid: CST-I: L. crispatus dominated CST-II: L. gasseri dominated CST-III: L. iners dominated.

Lowered levels of Lactic Acid : CST-IV: Lactobacilli not dominant CST-IVA: higher abundance of Peptoniphulus, Anaeococcus, Corynebacterium, Finegoldia, Gardnerella, Prevotella, Sneathia… CST-IVB: Higher abundance of Atopobium CST-V: L. jensenii dominated.

The vaginal microbiome.

Most of what is known about fungi in the human vagina has come from culture-based studies and phenotypic characterisation of single organisms which mask the complexity.

• Though vastly outnumbered by its bacterial counterparts, fungi are important constituents of the vaginal ecosystem in many healthy women.

• Candida albicans has been the focus of decades of culture-based work and so is at the forefront of what we currently know about the microbiome of the vagina (and the other body sites).

Vaginal disbiosis.

• Symptoms are associated with shifts in the dominance of certain microbes and their effect on:

• Epithelial cells and cervix.

• Changes to Short Chain Fatty Acids production.

• LPS (lipopolysaccharides originated from the gut and either by direct contamination or via the blood circulation)  production modulating cytokine expression (inflammation).

• Reduction of antimicrobial peptides (bacteriocins).

• Homeostatic mechanisms: pH out of range and higher than 4.6.

It is important to note that the vaginal disbiosis either being bacterial or fungal can impact on the general health (leaky vagina).

Bacteria vaginosis:

• Vaginal discharge, thin white/grey.

• Fish like odour: biogenic amines.

• Vaginal pH > 4.5 (Litmus paper is a bedside test).

• Presence of clue cells on laboratory examination.

Endometrial and urinary microbiome:

 • The endometrium of healthy and asymptomatic women will be dominated by Lactobacilli.

• Lactobacillus-deficient communities have been identified in the genital tract of otherwise healthy and asymptomatic women.

• Lactobacillus can be present in the human endometrium, but without being a part of the core microbiota.

The urinary microbiome:

• Until relatively recently, there was no definitive proof of the existence of a microbiome above the lower urogenital tract (vagina and distal urethra).

• Still in the discovery phase of understanding the urinary microbiome (UMB).

• Males and females have different microbiomes, influenced through ascension from the lower genital tract and hormonal status.

• Like the vagina there is a urinary microbiome.

Factors that will impact on the vagina, Bladder and Uterus:


Neurological  status

Cardiovascular status

Musculoskeletal status


Urinary habits ( hygiene)

Dietary habits

Environmental issues


Lymphatic drainage

Endocrine status

Reproductive Health

Clinical clues:

• There are many clues in an endocrine review that could suggest a tendency or history of multi-site disbiosis.

• Associated disorders: fibroids, endometriosis, pelvic inflammatory disease, diabetes, dysmenorrhea, oligo menorrhoea, menorrhagia, infertility, miscarriage, preterm labour, cervical shortening in pregnancy, prior vaginal infections, genital herpes.

• Clinical tip: any of the above disorders should prompt questioning around the genitourinary health.

Hormonal Influences on Vaginal Tissues & Microbes:

Epithelial layers: depending on hormonal fluctuations the epithelial surface can contain up to 40 layers.

There is a proliferation of epithelial cells along with an increase in the number of cell layers in response to the menstrual cycle & oestrogen levels.

 As cellular density increases there is an associated increase in glycogen levels. In addition compared to other epithelial cells, vaginal epithelium contains high levels of glycogen.

Hormonal Changes Influence Microbes:

• Stage of life.

• Menstruating.

• Pregnancy.

• Puberty.

• Menopause.

• Different assumptions can be made about stage of life and vagina and endometrial microbe (EMB).

 • This is inferred to influence the UMB and EMB.


• Pre-puberty/childhood: anaerobic/aerobic mix, similar to menopause.

• Less outside impact, risk associated with hygiene, respiratory health, self-touch.

• Puberty: hormonal surges even before menarche, microbiome shifts to resemble that of a menstruating female.

• New discharges, different infection risk.

Clinical tip: vaginal microbes in young children are different from menstruating adults.

Infection tendencies need to be examined for hygiene, tissue trauma, and microbe translocation from respiratory system.

Discharges may appear different.

Changes through Adulthood:

• Menses: Lactobacilli dominance, oestrogen and progesterone fluctuations with menstrual bleed will affect the microbial profiles.

• Pregnancy: more stable hormones, high levels of oestrogen and progesterone, decreased immune function. Less diversity.

• Menopause: loss of oestrogen, microbial change, vaginal atrophy, less lubrication, pH shifts correlate with FSH.


• Oestrogen containing medications considered to be protective of eubiosis: consider impact of cessation.

• Some oestrogen medications associated with higher incidences of vulvovaginal candidiasis (VVC) (still requires opportunity).

• Intra Uterine Device: associated with increased bacterial vaginosis (BV) initiator microbes and VVC (due to biofilm).

Clinical considerations:

Oestrogen status.

• Oestrogen increases and decreases.

• Menopause and vaginal atrophy

• Premature ovarian failure/low oestrogens in the younger female

• Oestrogen dominance associated with heavy or prolonged bleeds

• Medication use

• Menses

• Frequency of bleed

• Heaviness/length of bleed • Lack of bleed • Prolonged bleeding can predispose the vagina to disbiosis. Menstrual discharge influences the pH to shift to a more alkaline environment.

• L. iners and G. vaginalis are shown to proliferate at menstruation. Both favouring an iron rich environment.

• The presence of BV was statistically associated with the history of a spontaneous abortion.

• There is a statistically significant relationship between BV and second trimester miscarriage.

• Lactobacillus crispatus is more prevalent in the vaginal flora of fertile women.

• L. crispatus is also associated with term births.

Premature rupture of membranes (PROM) found to be more common with low Lactobacillus and  the presence of Mycoplasma or Ureaplasma carriage.

• Lower Lactobacillus in the vagina and the presence of Mycoplasma or Urea plasma found to be more frequent in vagina of women experiencing preterm premature rupture of membrane.


• Bacterial vaginosis prevalence increased in women initiating copper intrauterine devices from 27 % at baseline, 35 % at 30 days, 40 % at 90 days, and 49 % at 180 days.

• Increased prevalence of BV from Mirena insertion.

• Proposed as a risk factor for recurrent vulvovaginal candidiasis (RVVC).

• Associated with the ability of Candida spp. to proliferate.

Clinical considerations:

• Clinical tip: UTI history should prompt questioning about vaginal health.

• Women with BV have higher rates of UTIs than those with a “healthy” Lactobacillus-dominated vaginal microbiota.

• A recent mouse study showed inoculation of the bladder with G. vaginalis triggered the cells lining of the bladder surface to undergo non-inflammatory cell death accompanied by exfoliation.

• In addition to the vaginal and faecal reservoirs, the bladder wall should also be considered as a reservoir for reinfection.

• Studies have shown that most recurrent UTIs are caused by the same bacterial strain as the initial infection . More specifically, the same bacterial strain that caused an initial UTI has been identified in the urine of women with recurrent infections up to 3 years later.

• Covert pathogenesis for bacteria is possible: situation whereby a microbe contributes to disease onset, progression, or severity even though it is not present at the time and place of disease itself.

Risk factors for vaginal bacteriosses:

Greater risk with some behaviours: • Unprotected sex • Anal sex to vaginal • Digital penetration • Oro-genital sex (microbial translocation) • Multiple or new sexual partners • Smoking • Genetic predisposition • Vaginal douches/hygiene • Lubricants pH/osmolality • History of sexually transmitted infection (STI) (esp. Chlamydia, GC, HIV) • Sex toys • Condom choice.

Sex and vaginal microbes:

 BV: abstaining from sex/consistent condom use reduced recurrence by 50 %.

• BV, VVC: clear that sexual transmission of the implicated organisms does play a role, especially in sex with uncircumcised partners.

 • “The epidemiology of BV suggests that it is acquired via sexual transmission, but it is unknown whether BV results from acquisition of G. vaginalis as the “founder” organism, leading to the complex changes in vaginal flora or whether BV is transmitted as a polymicrobial consortium.

Sharing microbiomes during sex?

Semen contains bacteria (both aerobic and anaerobic) the Seminal microbiome is more diverse than the vaginal one: 44 % of the strains identified in semen and 58 % of those in prostatic secretions were also found in the urethra.

 Biologically plausible: if BV is transmitted by males, the foreskin could facilitate survival of BV organisms and render an uncircumcised male a more efficient or a more prolonged transmitter of infection. Penile-vaginal sex did not alter the consistency of microbial communities but increased G. vaginalis clade diversity in young women with and without BV, suggesting sexual transmission of commensal and potentially pathogenic clades.

A female sexual partner conferred a 2-fold risk of BV infection.

Oral sex:

• Disruption of vaginal pH.

• Optimal pH of saliva = 7+.

• Optimal pH of the vagina = 3.6 - 4.5.

• Introduction of oral microbes including Candida species.

• Up to 108 microorganisms have been detected per millilitre of saliva, mostly derived from oral mucosal surfaces such as the tongue.

• Vaginal lubricants can disrupt microbiome homeostasis.

• pH of less than 4.5 and an osmolality that did not exceed 1,200 m0sm/kg.

• Clinical tip: ask about sexual interactions, contraception, lubricants, partners etc. Not asking may mean you overlook a modifiable factor.


• Women who were observed in the low-Lactobacillus CST-IV state were 25-fold more likely to be smokers than those dominated by L. crispatus • Cessation of smoking influenced BV status • “The anti-oestrogenic effect of smoking may predispose women to BV. Tabaco increases bacteriophage induction in Lactobacillus spp. and is found in the vaginal secretions of smokers.

Factors that have an impact on the vaginal PH:

Immunity, Sexual activity, Douching and personal care, Menses, Perineal hygiene, Smoking, Emotions, Pregnancy, Hormones, Age, Obesity, Genetics.

Clinical patterns of bacterial vaginoses:

• Often common after menstruation (G. vaginalis proliferation during menses) • Associated with low oestrogen states (in menses and in lifecycles) • In recurrent patterns: BV will self-resolve in parts of a menstrual cycle only to return again • Often reported to be triggered by sex (oral, digital and penetrative) • Look for cycles of self-douching, soaps and “fixes” for the smell • Screen hygiene, fabrics etc. • As there is no tissue based inflammation or excoriation, many people will live with a recurrent BV and not utilise treatment • BV can exist with vulvovaginal candidiasis (VVC) termed a mixed infection (acute and recurrent).


Probiotics: vaginally and orally. Balance hormonal influences. Regulate BGL. Optimise fertility outcomes. Immune support. Support nervous system. Quit smoking. Educate about hygiene. Biofilm busters. Modify sexual activity risks. Acute symptom relief: soothing, Prebiotics: vaginally and orally pH regulation with acidifiers. Support pharmaceutical efficacy.

• Restore Lactobacilli bacteria and eubiosis (in range) • Restore pH to between 3.6 - 4.5 • Disrupt biofilm to increase treatment efficacy and decrease recurrence • Support and improve the integrity of the mucous membranes • If appropriate: support pharmaceutical efficacy.


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