Human microbiota are microorganisms (bacteria, viruses, fungi and archaea) found in a specific environment. They can be found in the stomach, intestines, skin, genitals and other parts of the body. [1] Various body parts have diverse microorganisms. Some microbes are specific to certain body parts and others are associated with many microbiomes. This article lists some of the species recognized as belonging to the human microbiome and focuses on the oral, vaginal, ovarian follicle, uterus and the male reproductive tract microbiota.
The "reference" 70 kg human body is estimated to have around 39 trillion bacteria with a mass of about 0.2 kg. [2] [3] [4] [5] These can be separated into about 10,000 microbial species, about 180 of the most studied is listed below here. However, these can broadly be put into three categories: [6]
Cocci are usually round or spherical in shape. They can form clusters and are non-motile. [7] Examples include Staphylococcus aureus, Streptococcus pyogenes, and Neisseria gonorrhea.
Bacilli usually have a rod or cylinder shape. Examples include Listeria, Salmonella typhimurium, Yersinia enterocolitica, and Escherichia coli.
Spirochetes are usually spiral or corkscrew shaped and move using axial filament. Examples include Treponema pallidum and Leptospira borgpetersenii. [8]
Column | Description |
---|---|
Binomial name | Name of the species, Ideally including the shape of the bacteria |
Location | Where it can be found in the body |
Pathological? | Can it harm humans or is it useful? the scale goes Not, Mostly not, Sometimes, Useful |
% of total Microbiome? | How many % does the bacteria in number of organisms make out of the entire human microbiome |
The vaginal microbiota is shaped by puberty, pregnancy and menopause. Vaginal microbiota including some Lactobacillus species protect the vagina from harmful pathogens. [10] They convert glucose to lactic acid and this acidic environment kills harmful pathogens. The vaginal microbiota in pregnancy varies markedly during the entire time of gestation. The species and diversity of the microorganisms may be related to the various levels of hormones during pregnancy. Vaginal flora can be transmitted to babies during birth. Vaginal dysbiosis can lead to vaginal infections like bacterial vaginosis which makes one relatively susceptible to sexually transmitted diseases. Good personal hygiene and probiotics promote a healthy vaginal microbiota. [11]
The healthy uterine microbiome has been identified and over 278 genera have been sequenced. Bacteria species like Fusobacterium are typically found in the uterus. [12] Although Lactobacillus may be beneficial in the vagina, “increased levels in the uterus through a breach in the cervical barrier” may be harmful to the uterus. [13]
The ovarian follicle microbiome has been studied using standard culturing techniques. It has been associated with the outcomes of assisted reproductive technologies and birth outcomes. Positive outcomes are related to the presence of Lactobacillus spp while the presence of Propionibacterium and Actinomyces were related to negative outcomes. The microbiome can vary from one ovary to the other. Studies are ongoing in the further identification of those bacteria present. [13]
The microbiome present in seminal fluid has been evaluated. Using traditional culturing techniques the microbiome differs between men who have acute prostatitis and those who have chronic prostatitis. Identification of the seminal fluid microbiome has become one of the diagnostic tools used in treating infertility in men that do not display symptoms of infection or disease. The taxa Pseudomonas , Lactobacillus , and Prevotella display a negative effect on the quality of sperm. The presence of Lactobacillus spp in semen samples is associated with a very high normal sperm count. [13]
The oral microbiota consists of all the microorganisms that exist in the mouth. It is the second largest of the human body and made of various bacteria, viruses, fungi and protozoa. [14] These organisms play an important role in oral and overall health. Anthony Van Leeuwenhoek was the first to view these organisms using a microscope he created. [14] The temperature and pH of saliva makes it conducive for bacteria to survive in the oral cavity. Bacteria in the oral cavity include Streptococcus mutans, Porphyromonas gingivalis, and Staphylococcus. [15] S. mutans is the main component of the oral microbiota. [15]
A healthy oral microbiome decreases oral infections and promotes a healthy gut microbiome. However, when disturbed, it can lead to gum inflammations and bad breath. [16] Dental plaque is formed when oral microorganisms form biofilms on the surfaces of teeth. Recommended practices to maintain a healthy oral microbiome include practicing good oral hygiene (brushing twice and flossing, replacing toothbrush often), eating healthy diet (food with little or no added sugars and ultra processed foods), drinking lots of water and taking probiotics.
Bacterial vaginosis (BV) is an infection of the vagina caused by excessive growth of bacteria. Common symptoms include increased vaginal discharge that often smells like fish. The discharge is usually white or gray in color. Burning with urination may occur. Itching is uncommon. Occasionally, there may be no symptoms. Having BV approximately doubles the risk of infection by a number of sexually transmitted infections, including HIV/AIDS. It also increases the risk of early delivery among pregnant women.
The endometrium is the inner epithelial layer, along with its mucous membrane, of the mammalian uterus. It has a basal layer and a functional layer: the basal layer contains stem cells which regenerate the functional layer. The functional layer thickens and then is shed during menstruation in humans and some other mammals, including other apes, Old World monkeys, some species of bat, the elephant shrew and the Cairo spiny mouse. In most other mammals, the endometrium is reabsorbed in the estrous cycle. During pregnancy, the glands and blood vessels in the endometrium further increase in size and number. Vascular spaces fuse and become interconnected, forming the placenta, which supplies oxygen and nutrition to the embryo and fetus. The speculated presence of an endometrial microbiota has been argued against.
Lactobacillus is a genus of gram-positive, aerotolerant anaerobes or microaerophilic, rod-shaped, non-spore-forming bacteria. Until 2020, the genus Lactobacillus comprised over 260 phylogenetically, ecologically, and metabolically diverse species; a taxonomic revision of the genus assigned lactobacilli to 25 genera.
The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the gastrointestinal tract, skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, and the biliary tract. Types of human microbiota include bacteria, archaea, fungi, protists, and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms; however, the term human metagenome has the same meaning.
Vaginitis, also known as vulvovaginitis, is inflammation of the vagina and vulva. Symptoms may include itching, burning, pain, discharge, and a bad smell. Certain types of vaginitis may result in complications during pregnancy.
Lactobacillus acidophilus is a rod-shaped, Gram-positive, homofermentative, anaerobic microbe first isolated from infant feces in the year 1900. The species is commonly found in humans, specifically the gastrointestinal tract and oral cavity as well as some speciality fermented foods such as fermented milk or yogurt, though it is not the most common species for this. The species most readily grows at low pH levels, and has an optimum growth temperature of 37 °C. Certain strains of L. acidophilus show strong probiotic effects, and are commercially used in dairy production. The genome of L. acidophilus has been sequenced.
Vaginal discharge is a mixture of liquid, cells, and bacteria that lubricate and protect the vagina. This mixture is constantly produced by the cells of the vagina and cervix, and it exits the body through the vaginal opening. The composition, amount, and quality of discharge varies between individuals and can vary throughout the menstrual cycle and throughout the stages of sexual and reproductive development. Normal vaginal discharge may have a thin, watery consistency or a thick, sticky consistency, and it may be clear or white in color. Normal vaginal discharge may be large in volume but typically does not have a strong odor, nor is it typically associated with itching or pain. While most discharge is considered physiologic or represents normal functioning of the body, some changes in discharge can reflect infection or other pathological processes. Infections that may cause changes in vaginal discharge include vaginal yeast infections, bacterial vaginosis, and sexually transmitted infections. The characteristics of abnormal vaginal discharge vary depending on the cause, but common features include a change in color, a foul odor, and associated symptoms such as itching, burning, pelvic pain, or pain during sexual intercourse.
Dysbiosis is characterized by a disruption to the microbiome resulting in an imbalance in the microbiota, changes in their functional composition and metabolic activities, or a shift in their local distribution. For example, a part of the human microbiota such as the skin flora, gut flora, or vaginal flora, can become deranged (unbalanced), when normally dominating species become underrepresented and species that normally are outcompeted or contained increase to fill the void. Similar to the human gut microbiome, diverse microbes colonize the plant rhizosphere, and dysbiosis in the rhizosphere, can negatively impact plant health. Dysbiosis is most commonly reported as a condition in the gastrointestinal tract or plant rhizosphere.
Vaginal flora, vaginal microbiota or vaginal microbiome are the microorganisms that colonize the vagina. They were discovered by the German gynecologist Albert Döderlein in 1892 and are part of the overall human flora. The amount and type of bacteria present have significant implications for an individual's overall health. The primary colonizing bacteria of a healthy individual are of the genus Lactobacillus, such as L. crispatus, and the lactic acid they produce is thought to protect against infection by pathogenic species.
Oral microbiology is the study of the microorganisms (microbiota) of the oral cavity and their interactions between oral microorganisms or with the host. The environment present in the human mouth is suited to the growth of characteristic microorganisms found there. It provides a source of water and nutrients, as well as a moderate temperature. Resident microbes of the mouth adhere to the teeth and gums to resist mechanical flushing from the mouth to stomach where acid-sensitive microbes are destroyed by hydrochloric acid.
A cervical mucus plug (operculum) is a plug that fills and seals the cervical canal during pregnancy. It is formed by a small amount of cervical mucus that condenses to form a cervical mucus plug during pregnancy.
Prevotella is a genus of Gram-negative bacteria.
The initial acquisition of microbiota is the formation of an organism's microbiota immediately before and after birth. The microbiota are all the microorganisms including bacteria, archaea and fungi that colonize the organism. The microbiome is another term for microbiota or can refer to the collected genomes.
The vaginal flora in pregnancy, or vaginal microbiota in pregnancy, is different from the vaginal flora before sexual maturity, during reproductive years, and after menopause. A description of the vaginal flora of pregnant women who are immunocompromised is not covered in this article. The composition of the vaginal flora significantly differs in pregnancy. Bacteria or viruses that are infectious most often have no symptoms.
The Human Microbiome Project (HMP), completed in 2012, laid the foundation for further investigation into the role the microbiome plays in overall health and disease. One area of particular interest is the role which delivery mode plays in the development of the infant/neonate microbiome and what potential implications this may have long term. It has been found that infants born via vaginal delivery have microbiomes closely mirroring that of the mother's vaginal microbiome, whereas those born via cesarean section tend to resemble that of the mother's skin. One notable study from 2010 illustrated an abundance of Lactobacillus and other typical vaginal genera in stool samples of infants born via vaginal delivery and an abundance of Staphylococcus and Corynebacterium, commonly found on the skin surfaces, in stool samples of infants born via cesarean section. From these discoveries came the concept of vaginal seeding, also known as microbirthing, which is a procedure whereby vaginal fluids are applied to a new-born child delivered by caesarean section. The idea of vaginal seeding was explored in 2015 after Maria Gloria Dominguez-Bello discovered that birth by caesarean section significantly altered the newborn child's microbiome compared to that of natural birth. The purpose of the technique is to recreate the natural transfer of bacteria that the baby gets during a vaginal birth. It involves placing swabs in the mother's vagina, and then wiping them onto the baby's face, mouth, eyes and skin. Due to the long-drawn nature of studying the impact of vaginal seeding, there are a limited number of studies available that support or refute its use. The evidence suggests that applying microbes from the mother's vaginal canal to the baby after cesarean section may aid in the partial restoration of the infant's natural gut microbiome with an increased likelihood of pathogenic infection to the child via vertical transmission.
The placental microbiome is the nonpathogenic, commensal bacteria claimed to be present in a healthy human placenta and is distinct from bacteria that cause infection and preterm birth in chorioamnionitis. Until recently, the healthy placenta was considered to be a sterile organ but now genera and species have been identified that reside in the basal layer.
The uterine microbiome refers to the community of commensal, nonpathogenic microorganisms—including bacteria, viruses, and yeasts/fungi—present in a healthy uterus, as well as in the amniotic fluid and endometrium. These microorganisms coexist in a specific environment within the uterus, playing a vital role in maintaining reproductive health. In the past, the uterus was believed to be a sterile environment, free of any microbial life. Recent advancements in microbiological research, particularly the improvement of 16S rRNA gene sequencing techniques, have challenged this long-held belief. These advanced techniques have made it possible to detect bacteria and other microorganisms present in very low numbers. Using this procedure that allows the detection of bacteria that cannot be cultured outside the body, studies of microbiota present in the uterus are expected to increase.
The salivary microbiome consists of the nonpathogenic, commensal bacteria present in the healthy human salivary glands. It differs from the oral microbiome which is located in the oral cavity. Oral microorganisms tend to adhere to teeth. The oral microbiome possesses its own characteristic microorganisms found there. Resident microbes of the mouth adhere to the teeth and gums. "[T]here may be important interactions between the saliva microbiome and other microbiomes in the human body, in particular, that of the intestinal tract."