Anatomy and Normal Microbiota of the Urogenital Tract

The urinary system filters blood, excretes wastes, and maintains an appropriate electrolyte and water balance. The reproductive system is responsible for the production of gametes and participates in conception and, in females, development of offspring. Due to their proximity and overlap, these systems are often studied together and referred to as the urogenital system (or genitourinary system).

Anatomy of the Urinary Tract

The basic structures of the urinary tract are common in males and females. However, there are unique locations for these structures in females and males, and there is a significant amount of overlap between the urinary and genital structures in males. The figure below illustrates the urinary anatomy common to females and males.

The kidneys carry out the urinary system’s primary functions of filtering the blood and maintaining water and electrolyte balance. The kidneys are composed of millions of filtration units called nephrons. Each nephron is in intimate contact with blood through a specialized capillary bed called the glomerulus (plural glomeruli). Fluids, electrolytes, and molecules from the blood pass from the glomerulus into the nephron, creating the filtrate that becomes urine (shown below). Urine that collects in each kidney empties through a ureter and drains to the urinary bladder, which stores urine. Urine is released from the bladder to the urethra, which transports it to be excreted from the body through the urinary meatus, the opening of the urethra.

Extended description

The kidney’s outer region is outlined into triangular lobes; tubes beginning at the point of each lobe fuse into a single large tube, the ureter. A close-up of one lobe shows two nephrons feeding into that tube. Each nephron has a bulb at one end, the glomerulus, fed by an afferent arteriole and drained by an efferent arteriole, with a venule carrying blood away. The glomerulus becomes a tube, the proximal convoluted tubule, which becomes the loop of Henle, which becomes the distal convoluted tubule, which feeds into the collecting duct. From there, urine flows to the renal papilla and the ureter.

Anatomy of the Reproductive System

The male reproductive system (shown below) is located in close proximity to the urinary system, and the urethra is part of both systems. The testes are responsible for the production of sperm. The epididymis is a coiled tube that collects sperm from the testes and passes it on to the vas deferens. The epididymis is also the site of sperm maturation after they leave the testes. The seminal vesicles and prostate are accessory glands that produce fluid that supports sperm. During ejaculation, the vas deferens releases this mixture of fluid and sperm, called semen, into the urethra, which extends to the end of the penis.

The female reproductive system is located near the urinary system (shown below). The external genitalia (vulva) in females open to the vagina, a muscular passageway that connects to the cervix. The cervix is the lower part of the uterus (the organ where a fertilized egg will implant and develop). The cervix is a common site of infection, especially for viruses that may lead to cervical cancer. The uterus leads to the fallopian tubes and eventually to the ovaries. Ovaries are the site of ova (egg) production, as well as the site of estrogen and progesterone production that are involved in maturation and maintenance of reproductive organs, preparation of the uterus for pregnancy, and regulation of the menstrual cycle.

Extended description

Female panel: a tube labeled ureter leads to the urinary bladder, which leads to the urethra; the bladder sits just internal to the pubic bone. Above and behind the bladder is the oval, thick-walled uterus; above that, a fallopian tube connects to a small oval ovary. The uterus opens at the cervix into the vagina. Behind these structures are the rectum and anus; the labium minora and majora are the external folds of skin. Male panel: a tube labeled ureter leads to the urinary bladder, which sits just behind the pubic bone; the bladder leads to the urethra, which runs through the center of the penis. The vas deferens also feeds into the urethra. The testis has the epididymis on top, which becomes the vas deferens; the seminal vesicles connect to the vas deferens just before it passes through the prostate gland, a structure just below the bladder, and on into the urethra. The rectum and anus lie behind all of these structures.

Check Your Understanding

Normal Microbiota of the Urogenital System

The normal microbiota of different body sites provides an important nonspecific defense against infectious diseases (see Physical Defenses), and the urogenital tract is no exception. However, the kidneys are sterile. Although urine does contain some antibacterial components, bacteria will grow in urine left out at room temperature. Therefore, it is primarily the flushing action that keeps the ureters and bladder free of microbes.

Below the bladder, the normal microbiota of the male urogenital system is found primarily within the distal urethra and includes bacterial species that are commonly associated with the skin microbiota. In females, the normal microbiota is found within the distal one third of the urethra and the vagina. The normal microbiota of the vagina becomes established shortly after birth and is a complex and dynamic population of bacteria that fluctuates in response to environmental changes. Members of the vaginal microbiota play an important role in the nonspecific defense against vaginal infections and sexually transmitted infections by occupying cellular binding sites and competing for nutrients. In addition, the production of lactic acid by members of the microbiota provides an acidic environment within the vagina that also serves as a defense against infections. For the majority of females, the lactic-acid–producing bacteria in the vagina are dominated by a variety of species of Lactobacillus. For females who lack sufficient lactobacilli in their vagina, lactic acid production comes primarily from other species of bacteria such as Leptotrichia spp., Megasphaera spp., and Atopobium vaginae. Lactobacillus spp. use glycogen from vaginal epithelial cells for metabolism and production of lactic acid. This process is tightly regulated by the hormone estrogen. Increased levels of estrogen correlate with increased levels of vaginal glycogen, increased production of lactic acid, and a lower vaginal pH. Therefore, decreases in estrogen during the menstrual cycle and with menopause are associated with decreased levels of vaginal glycogen and lactic acid, and a higher pH. In addition to producing lactic acid, Lactobacillus spp. also contribute to the defenses against infectious disease through their production of hydrogen peroxide and bacteriocins (antibacterial peptides).

Check Your Understanding

General Signs and Symptoms of Urogenital Infections

Infections of the urinary tract most commonly cause inflammation of the bladder (cystitis) or of the urethra (urethritis). Urethritis can be associated with cystitis, but can also be caused by sexually transmitted infections. Symptoms of urethritis in males include burning sensation while urinating, discharge from the penis, and blood in the semen or the urine. In females, urethritis is associated with painful and frequent urination, vaginal discharge, fever, chills, and abdominal pain. The symptoms of cystitis are similar to those of urethritis. When urethritis is caused by a sexually transmitted pathogen, additional symptoms involving the genitalia can occur. These can include painful vesicles (blisters), warts, and ulcers. Ureteritis, a rare infection of the ureter, can also occur with cystitis. These infections can be acute or chronic.

Pyelonephritis and glomerulonephritis are infections of the kidney that are potentially serious. Pyelonephritis is an infection of one or both of the kidneys and may develop from a lower urinary tract infection; the upper urinary tract, including the ureters, is often affected. Signs and symptoms of pyelonephritis include fever, chills, nausea, vomiting, lower back pain, and frequent painful urination. Pyelonephritis usually only becomes chronic in individuals who have malformations in or damage to the kidneys.

Glomerulonephritis is an inflammation of the glomeruli of the nephrons. Symptoms include excessive protein and blood in urine, increased blood pressure, and fluid retention leading to edema of face, hands, and feet. Glomerulonephritis may be an acute infection or it can become chronic.

Infections occurring within the reproductive structures of males include epididymitis, orchitis, and prostatitis. Bacterial infections may cause inflammation of the epididymis, called epididymitis. This inflammation causes pain in the scrotum, testicles, and groin; swelling, redness, and warm skin in these areas may also be observed. Inflammation of the testicle, called orchitis, is usually caused by a bacterial infection spreading from the epididymis, but it can also be a complication of mumps, a viral disease. The symptoms are similar to those of epididymitis, and it is not uncommon for them both to occur together, in which case the condition is called epididymo-orchitis. Inflammation of the prostate gland, called prostatitis, can result from a bacterial infection. The signs and symptoms of prostatitis include fever, chills, and pain in the bladder, testicles, and penis. Patients may also experience burning during urination, difficulty emptying the bladder, and painful ejaculation.

Because of its proximity to the exterior, the vagina is a common site for infections. The general term for any inflammation of the vagina is vaginitis. Vaginitis often develops as a result of an overgrowth of bacteria or fungi that normally reside in the vaginal microbiota, although it can also result from infections by transient pathogens. Bacterial infections of the vagina are called bacterial vaginosis, whereas fungal infections (typically involving Candida spp.) are called yeast infections. Dynamic changes affecting the normal microbiota, acid production, and pH variations can be involved in the initiation of the microbial overgrowth and the development of vaginitis. Although some individuals may have no symptoms, vaginosis and vaginitis can be associated with discharge, odor, itching, and burning.

Pelvic inflammatory disease (PID) is an infection of the female reproductive organs including the uterus, cervix, fallopian tubes, and ovaries. The two most common pathogens are the sexually transmitted bacterial pathogens Neisseria gonorrhoeae and Chlamydia trachomatis. Inflammation of the fallopian tubes, called salpingitis, is the most serious form of PID. Symptoms of PID can vary between people and include pain in the lower abdomen, vaginal discharge, fever, chills, nausea, diarrhea, vomiting, and painful urination.

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General Causes and Modes of Transmission of Urogenital Infections

Hormonal changes, particularly shifts in estrogen due to pregnancy or menopause, can increase susceptibility to urogenital infections. As discussed earlier, estrogen plays an important role in regulating the availability of glycogen and subsequent production of lactic acid by Lactobacillus species. Low levels of estrogen are associated with an increased vaginal pH and an increased risk of bacterial vaginosis and yeast infections. Estrogen also plays a role in maintaining the elasticity, strength, and thickness of the vaginal wall, and keeps the vaginal wall lubricated, reducing dryness. Low levels of estrogen are associated with thinning of the vaginal wall. This thinning increases the risk of tears and abrasions, which compromise the protective barrier and increase susceptibility to pathogens.

Another common cause of urogenital infections in females is fecal contamination that occurs because of the close proximity of the anus and the urethra. Escherichia coli, an important member of the digestive tract microbiota, is the most common cause of urinary tract infections (urethritis and cystitis) in females; it generally causes infection when it is introduced to the urethra in fecal matter. Good hygiene can reduce the risk of urinary tract infections by this route. In males, urinary tract infections are more commonly associated with other conditions, such as an enlarged prostate, kidney stones, or placement of a urinary catheter. All of these conditions impair the normal emptying of the bladder, which serves to flush out microbes capable of causing infection.

Infections that are transmitted between individuals through sexual contact are called sexually transmitted infections (STIs) or sexually transmitted diseases (STDs). (The CDC prefers the term STD, but WHO prefers STI, which encompasses infections that result in disease as well as those that are subclinical or asymptomatic; World Health Organization, “Guidelines for the Management of Sexually Transmitted Infections,” 2003.) STIs often affect the external genitalia and skin, where microbes are easily transferred through physical contact. Lymph nodes in the genital region may also become swollen as a result of infection. However, many STIs have systemic effects as well, causing symptoms that range from mild (e.g., general malaise) to severe (e.g., liver damage or serious immunosuppression).

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Summary

• The urinary system is responsible for filtering the blood, excreting wastes, and helping to regulate electrolyte and water balance.
• The urinary system includes the kidneys, ureters, urinary bladder, and urethra; the bladder and urethra are the most common sites of infection.
• Common sites of infection in the male reproductive system include the urethra, as well as the testes, prostate and epididymis.
• The most common sites of infection in the female reproductive system are the vulva, vagina, cervix, and fallopian tubes.
• Infections of the urogenital tract can occur through colonization from the external environment, alterations in microbiota due to hormonal or other physiological and environmental changes, fecal contamination, and sexual transmission (STIs).

Key terms

• kidneys — organ that filters the blood, producing urine.
• glomerulus — capillary bed in the nephron of the kidney that filters blood to form urine.
• ureter — duct that transports urine from the kidneys to the urinary bladder.
• urinary bladder — an organ that stores urine until it is ready to be excreted.
• urethra — duct through which urine passes from the urinary bladder to leave the body through the urinary meatus.
• urinary meatus — the opening through which urine leaves the body.
• testes — (singular testis) pair of glands located in the scrotum of males that produce sperm and testosterone.
• epididymis — coiled tube that collects sperm from the testes and passes it on to the vas deferens.
• seminal vesicles — glands that contribute fluid to semen.
• prostate — gland that contributes fluid to semen.
• vas deferens — pair of ducts in the male reproductive system that conduct sperm from the testes and seminal fluid to the ejaculatory duct.
• penis — external genital organ in males through which urine and semen are discharged.
• vulva — the female external genitalia.
• vagina — female reproductive organ that extends from the vulva to the cervix.
• cervix — the part of the uterus that connects to the vagina.
• uterus — female reproductive organ in which a fertilized egg implants and develops.
• cystitis — inflammation of the bladder.
• urethritis — inflammation of the urethra.
• pyelonephritis — an infection of one or both kidneys.
• glomerulonephritis — a type of kidney infection involving the glomeruli of the nephrons.
• epididymitis — inflammation of the epididymis caused by a bacterial infection.
• orchitis — inflammation of one or both of the testes.
• prostatitis — inflammation of the prostate gland.
• vaginitis — inflammation of the vagina.
• vaginosis — an infection of the vagina caused by overgrowth of resident bacteria.
• yeast infection — fungal infection of the vagina typically caused by an overgrowth of resident Candida spp.
• pelvic inflammatory disease (PID) — infection of the female reproductive organs that may spread from the vagina to the cervix, uterus, fallopian tubes, and ovaries.
• salpingitis — inflammation of the fallopian tubes.

Practice

Compare the anatomy, function, and normal microbiota associated with the male and female urogenital systems

Explain how microorganisms, in general, overcome the defenses of the urogenital system to cause infection

Name, describe, and differentiate between general signs and symptoms associated with infections of the urogenital tract

This section is adapted from Microbiology, Section 23.1: Anatomy and Normal Microbiota of the Urogenital Tract by Nina Parker, Mark Schneegurt, Anh-Hue Thi Tu, Philip Lister, Brian M. Forster, and OpenStax, © OpenStax, licensed under CC BY-NC-SA 4.0. Access the original for free at openstax.org. Changes: all four source figures re-encoded as WebP and rendered as mediafigures after image and PDF inspection; kind="diagram" set on all four (each is a labeled anatomical line drawing), overriding the media manifest’s JPEG-based photo guess; the urogenital-system figure carries eager="true" as the page’s first figure; the urogenital-system figure’s source alt mislabels the pelvis “(5)” where the image’s own numbering reads “(6)” (renal artery is correctly “(5)”) — confirmed against the vendored image and corrected here with no inline note, on the same footing as a one-word source typo, and reported as a suspected source defect; the reproductive-anatomy figure’s source alt misspells “Behhind” for “Behind,” corrected here the same way; the Key Concepts and Summary misprints “commons” for “common” in its fourth bullet, corrected here with no inline note and reported as a suspected source defect; the Glossary appendix (m58950) has no entry for “prostate,” so its Key terms definition is written from this module’s own defining sentence rather than the appendix; the “Pyelonephritis” and “Pelvic inflammatory disease (PID)” Key terms bullets are lower-cased from the module’s sentence-initial capitalization, per house style for term headwords; the module’s one footnote (a WHO citation) is rendered as an inline parenthetical after the sentence it supports, with the bare access URL dropped; the two Multiple Choice and the one Fill in the Blank items are rendered as multiplechoice/textin exactly as keyed, in source wording and option order; the Short Answer “In the figure shown here, where would cystitis occur?” (unkeyed in source) is rendered as a mediafigure (its source alt kept, with grammar regularized) followed by a figure-keyed multiplechoice over the diagram’s own numbered structures, keyed “Structure 7,” because the body’s cystitis sentence together with the body figure’s own numbering fixes the whole answer; the Short Answer “Explain the difference between a sexually transmitted infection and a sexually transmitted disease” is one of the source’s rare keyed Short Answer items and is rendered as a multiplechoice keyed to its printed solution sentence, with distractors built from the module’s own STI/STD sentence stated wrongly; the Short Answer “When the microbial balance of the vagina is disrupted…” is rendered as its keyed textin (“vaginosis”); the unkeyed Critical Thinking question (antibiotics and vaginosis) is rendered as a selfcheck, since the module explains what generally triggers vaginal microbial overgrowth but does not itself discuss antibiotic use, and the model answer says so rather than inferring a mechanism the module does not print; of the module’s seven body Check Your Understanding bullets, all seven stay body self-checks; six need more than one module sentence assembled into an answer, and the seventh (“What structure in males is shared by the reproductive and the urinary systems?”) is answerable from a single sentence but is kept as a self-check rather than graded, because the source’s own keyed Multiple Choice (“What part of the male urogenital tract is shared by the urinary and reproductive systems?”) already grades the identical fact in Practice; four author-written items extend thin objective groups, disclosed here and in the ledger: a textin (“Escherichia coli”) built from the General Causes subsection’s own fecal-contamination sentence for the second objective, and a textin (“urethritis”), a multiplechoice (“Glomerulonephritis,” distractors the module’s own sibling kidney and urinary conditions), and a textin (“orchitis”) built from the Signs and Symptoms subsection’s own sentences for the third objective; no source exercise, table, or Check Your Understanding bullet is omitted; key terms are compiled from the module’s 28 <term> elements (no repeats) and the book’s Glossary appendix, giving 28 distinct bullets, 27 with a Glossary entry and one (“prostate”) sentence-derived as noted above; the Clinical Focus case (patient Nadia) opens this chapter with Part 1 on this page — the source’s closing “Jump to the next Clinical Focus box” link is replaced with “The case continues in Bacterial Infections of the Reproductive System,” an absolute site-root link to where Part 2 continues; the case’s closing questions stay inside the callout as unanswered bulleted prose, as printed.