List of human microbiota

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Human microbiota are microorganisms (bacteria, viruses, 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.

Contents

Categories of bacteria

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]

Spheres or ball-shaped (cocci bacteria)

They are ususally round or spherical in shape. They can form clusters and are non motile. [7] Examples include Staphylococcus aureus, Streptococcus pyogenes, and Neisseria gonorrhea

Staphylococcus aureus Staphylococcus aureus, 50,000x, USDA, ARS, EMU.jpg
Staphylococcus aureus

Rod-shaped bacteria (bacilli)

As the name implies, these usually have a rod or cylinder shape.Bacillus are generally rod shaped bacteria. Examples include listeria, Salmonella typhimurium, Yersinia enterocolitica, Escherichia coli

Yersinia enterocolitica colonies growing on XLD agar plates Yersinia enterocolitica 01.png
Yersinia enterocolitica colonies growing on XLD agar plates
Escherichia coli E. coli Bacteria (7316101966).jpg
Escherichia coli
Color-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells SalmonellaNIAID.jpg
Color-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells

Spirals or helixes (spirochetes)

These are usually spiral or corkscrew shaped and move using axial filament. Examples include Treponema pallidum and Leptospira borgpetersenii [8]

various forms of spirals Arrangement of spiral bacteria.JPG
various forms of spirals
Binomial nameLocationPathological?% of total Microbiome?
Acinetobacter calcoaceticus Whole-body distributed
Burkholderia cepacia Whole-body distributed
Peptostreptococcus sppWhole-body distributed
Pseudomonas pseudoalcaligenes Whole-body distributed
Eubacterium sppNatural cavities
Fusobacterium necrophorum Natural cavities
Microbacterium sppNatural cavities
Acinetobacter sppSkin
Bacillus sppSkin
Candida albicans Skin
Candida parapsilosis Skin
Corynebacterium parvum Skin
Corynebacterium sppSkin
Cutibacterium acnes Skin
Demodex folliculorum Skin
Enterobacter cloacae Skin
Epidermophyton floccosum Skin
Malassezia ovale Skin
Micrococcus luteus Skin
Micrococcus sppSkin
Mycobacterium sppSkin
Neisseria sppSkin
Peptostreptococcus sppSkin
Propionibacterium sppSkin
Pseudomonas aeruginosa SkinMostly
Sarcina sppSkin
Staphylococcus aureus Skin
Staphylococcus epidermidis SkinSometimes, mostly not
Staphylococcus haemolyticus Skin
Streptococcus viridans Skin
Trichophyton sppSkin
Staphylococcus aureus Hair follicles
Corynebacteriumspp External ear
Staphylococcus aureus External ear
Staphylococcus epidermidis External ear
Chlamydia trachomatis Mucous membranes
Hemophilus influenzae Mucous membranes
Staphylococcus aureus Mucous membranes
Staphylococcus epidermidis Mucous membranes
Chlamydophila pneumoniae Eye
Haemophilus aegyptius Eye
Haemophilus influenzae Eye
Moraxella sppEye
Neisseria sppEye
Staphylococcus aureus Eye
Staphylococcus epidermidis Eye
Streptococcus viridans Eye
Achromobacter sppLarge intestine, small intestine (Ileon)
Acidaminococcus fermentans Large intestine
Acinetobacter calcoaceticus Large intestine
Actinomyces sppMouth, small and large intestine
Actinomyces viscosus Mouth
Actinomyces naeslundii Mouth
Aeromonas sppLarge intestine, small intestine (Ileon)
Aggregatibacter actinomycetemcomitans Mouth
Anaerobiospirillum sppFeces
Alcaligenes faecalis Large intestine, small intestine (Ileon)
Arachnia propionica Mouth
Bacillus sppLarge intestine
Bacteroides sppMouth, GI tract
Bacteroides gingivalis Mouth
Bacteroides fragilis General distribution
Bacteroides intermedius Mouth
Bacteroides melaninogenicus Mouth, feces
Bacteroides pneumosintes Pharynx
Bacterionema matruchotii

(Corynebacterium matruchotii, new combination 1983 IJSB 33:438)

Gingiva
Bifidobacterium sppLarge intestine, feces
Buchnera aphidicola Mouth
Butyriviberio fibrosolvens Large intestine
Campylobacter sppLarge intestine
Campylobacter coli General distribution
Campylobacter sputorum Mouth
Campylobacter upsaliensis Mouth
Candida albicans Mouth
Capnocytophaga sppMouth
Clostridium sppLarge intestine, small intestine (Ileon)
Citrobacter freundii Sputum
Clostridium difficile Large intestine
Clostridium sordellii Stomach, small intestine, large intestine, rectus, anus channel
Corynebacterium sppMouth
Cutibacterium acnes General distribution
Eikenella corrodens General distribution, mouth
Enterobacter cloacae General distribution
Enterococcus sppMouth, GI tract
Enterococcus faecalis General distribution
Enterococcus faecium General distribution
Escherichia coli General distribution
Eubacterium sppMouth, GI tract
Faecalibacterium sppLarge intestine, small intestine (Ileon)
Flavobacterium sppLarge intestine, small intestine (Ileon)
Fusobacterium sppMouth, GI tract
Fusobacterium nucleatum Mouth
Gordonia sppSputum
Haemophilus parainfluenzae Mouth
Haemophilus paraphrophilus Mouth
Lactobacillus sppMouth, Saliva, GI tract (known probiotic)
Leptotrichia buccalis Mouth
Methanobrevibacter smithii Intestines
Morganella morganii Feces
Mycobacteria sppLarge intestine, small intestine (Ileon)
Mycoplasma sppLarge intestine, small intestine (Ileon)
Micrococcus sppMouth
Mycoplasma sppMouth
Mycobacterium chelonae Sputum
Neisseria sppMouth
Neisseria sicca Saliva, sputum
Peptococcus sppMouth, large intestine
Peptostreptococcus sppMouth, GI tract
Plesiomonas shigelloides General distribution
Porphyromonas gingivalis Mouth
Propionibacterium sppLarge intestine
Providencia sppFeces
Pseudomonas aeruginosa Large intestine, small intestine (Ileon)
Roseburia sppLarge intestine
Rothia dentocariosa Mouth
Ruminococcus sppCecum, large intestine
Ruminococcus bromii Large intestine
Sarcina sppLarge intestine
Staphylococcus aureus Mouth, large intestine, small intestine (Ileon)
Staphylococcus epidermidis Mouth
Streptococcus anginosus General distribution
Streptococcus mutans Teeth: dental plaque
Streptococcus oralis Teeth: dental plaque
Streptococcus pneumoniae Nasopharynx
Streptococcus sobrinus Teeth: dental plaque
Streptococcus viridans Mouth, large intestine, small intestine (Ileon)
Torulopsis glabrata Mouth
Treponema denticola Mouth
Treponema refringens Mouth
Veillonella sppMouth, large Intestine
Vibrio sppLarge intestine, small intestine (Ileon)
Vibrio sputorum Mouth
Wolinella succinogenes Mouth
Yersinia enterocolitica Large intestine
Acinetobacter sppNasopharynx
Burkholderia cepacia complex Lung
Campylobacter sputorum Nasopharynx
Candida albicans Pharynx
Cardiobacterium sppNose
Chlamydophila pneumoniae Lung
Citrobacter freundii Throat
Eikenella corrodens General distribution
Haemophilus sppNasopharynx
Haemophilus parainfluenzae Pharynx
Haemophilus paraphrophilus Pharynx
Kingella sppUpper respiratory tract
Kingella kingae Upper respiratory tract
Moraxella sppNasopharynx
Moraxella catarrhalis Nasopharynx
Mycoplasma orale Oropharynx
Mycoplasma pneumoniae Respiratory epithelium
Neisseria sppNasopharynx
Neisseria cinerea Nasopharynx
Neisseria elongata Pharynx
Neisseria gonorrhoeae Pharynx[ citation needed ]
Neisseria lactamica Nasopharynx
Neisseria meningitidis Nasopharynx
Neisseria mucosa Nasopharynx
Neisseria sicca Nasopharynx
Peptococcus sppUpper respiratory tract
Peptostreptococcus sppPharynx
Pseudomonas aeruginosa Lung
Selenomonas sputigena Nasopharynx
Staphylococcus aureus Nose
Streptobacillus sppThroat, nasopharynx
Streptococcus constellatus Oropharynx
Streptococcus intermedius Oropharynx
Streptococcus mitis General distribution
Streptococcus pyogenes Upper respiratory tract
Streptococcus viridans Pharynx
Acinetobacter sppAnterior urethra
Bacteroides sppExternal genitalia
Candida albicans Anterior urethra, external genitalia
Corynebacterium sppAnterior urethra, external genitalia
Enterobacteriaceae Anterior urethra, external genitalia
Streptococcus viridans Anterior urethra, external genitalia
Eikenella corrodens General distribution
Streptococcus anginosus General distribution
Staphylococcus aureus Perineum

Naming convention for the table

ColumnDescription
Binomial nameName of the species, Ideally including the shape of the bacteria
LocationWhere 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

Vagina

The vaginal microbiota is shaped by puberty, pregnancy and menopause. Vaginal microbiota including some Lactobacilli 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]

Uterus

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]

Ovarian follicle

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 Lactobacilli 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]

Male reproductive tract

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]

Mouth

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 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.

See also

Other lists of the human body's contents and building bricks

Related Research Articles

<span class="mw-page-title-main">Bacterial vaginosis</span> Excessive growth of bacteria in the vagina

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.

<span class="mw-page-title-main">Endometrium</span> Inner mucous membrane of the mammalian uterus

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.

<i>Lactobacillus</i> Genus of bacteria

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.

<span class="mw-page-title-main">Human microbiome</span> Microorganisms in or on human skin and biofluids

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.

<span class="mw-page-title-main">Vaginal discharge</span> Medical condition

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, with normally dominating species underrepresented and normally outcompeted or contained species increasing 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.

Levilactobacillus brevis is a gram-positive, rod shaped species of lactic acid bacteria which is heterofermentative, creating CO2, lactic acid and acetic acid or ethanol during fermentation. L. brevis is the type species of the genus Levilactobacillus (previously L. brevis group), which comprises 24 species. It can be found in many different environments, such as fermented foods, and as normal microbiota. L. brevis is found in food such as sauerkraut and pickles. It is also one of the most common causes of beer spoilage. Ingestion has been shown to improve human immune function, and it has been patented several times. Normal gut microbiota L. brevis is found in human intestines, vagina, and feces.

<span class="mw-page-title-main">Vaginal flora</span> Microorganisms present in the vagina

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.

<span class="mw-page-title-main">Oral microbiology</span>

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.

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.

Lactobacillus jensenii is a normal inhabitant of the lower reproductive tract in healthy women. L. jensenii makes up 23% of vaginal microflora that is naturally occurring. It is also found on the skins of grapes at the time of their harvest. L. jensenii is sometimes used in producing fermented foods.

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.

<span class="mw-page-title-main">Placental microbiome</span>

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.

<span class="mw-page-title-main">Uterine microbiome</span>

The uterine microbiome is the commensal, nonpathogenic, bacteria, viruses, yeasts/fungi present in a healthy uterus, amniotic fluid and endometrium and the specific environment which they inhabit. It has been only recently confirmed that the uterus and its tissues are not sterile. Due to improved 16S rRNA gene sequencing techniques, detection of bacteria that are present in low numbers is possible. 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.

<span class="mw-page-title-main">Human milk microbiome</span> Community of microorganisms in human milk

The human milk microbiota, also known as human milk probiotics (HMP), encompasses the microbiota–the community of microorganisms–present within the human mammary glands and breast milk. Contrary to the traditional belief that human breast milk is sterile, advancements in both microbial culture and culture-independent methods have confirmed that human milk harbors diverse communities of bacteria. These communities are distinct in composition from other microbial populations found within the human body which constitute the human microbiome.

<span class="mw-page-title-main">Lactobacillus vaccine</span> Vaccine using an inactivated strain of Lactobacillus

Lactobacillus vaccines are used in the therapy and prophylaxis of non-specific bacterial vaginitis and trichomoniasis. The vaccines consist of specific inactivated strains of Lactobacilli, called "aberrant" strains in the relevant literature dating from the 1980s. These strains were isolated from the vaginal secretions of patients with acute colpitis. The lactobacilli in question are polymorphic, often shortened or coccoid in shape and do not produce an acidic, anti-pathogenic vaginal environment. A colonization with aberrant lactobacilli has been associated with an increased susceptibility to vaginal infections and a high rate of relapse following antimicrobial treatment. Intramuscular administration of inactivated aberrant lactobacilli provokes a humoral immune response. The production of specific antibodies both in serum and in the vaginal secretion has been demonstrated. As a result of the immune stimulation, the abnormal lactobacilli are inhibited, the population of normal, rod-shaped lactobacilli can grow and exert its defense functions against pathogenic microorganisms.

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