This article lists some of the species recognized as belonging to the human microbiome.

Whole-body distributed

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Acinetobacter calcoaceticus ''Acinetobacter calcoaceticus'' is a bacterial species of the genus ''Acinetobacter''. It is a nonmotile, Gram-negative coccobacillus. It grows under aerobic conditions, is catalase positive and oxidase negative. ''A. calcoaceticus'' is a part ...

'' *'' Burkholderia cepacia'' *''

Pseudomonas pseudoalcaligenes ''Pseudomonas oleovorans'' is a Gram-negative, methylotrophic bacterium that is a source of rubredoxin (part of the hydroxylation-epoxidation system). It was first isolated in water-oil emulsions used as lubricants and cooling agents for cutting ...

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Peptostreptococcus ''Peptostreptococcus'' is a genus of anaerobic, Gram-positive, non-spore forming bacteria. The cells are small, spherical, and can occur in short chains, in pairs or individually. They typically move using cilia. ''Peptostreptococcus'' are slow-g ...

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Natural cavities

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Fusobacterium necrophorum ''Fusobacterium necrophorum'' is a species of bacteria responsible for Lemierre's syndrome and other medical problems. Biology ''F. necrophorum'' is a rod-shaped species of Gram-negative bacteria. It is an obligate anaerobe and is a common inh ...

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Eubacterium ''Eubacterium'' is a genus of Gram-positive bacteria in the family Eubacteriaceae. These bacteria are characterised by a rigid cell wall. They may either be motile or nonmotile. If motile, they have a flagellum A flagellum (; ) is a hair ...

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Microbacterium ''Microbacterium'' is a genus of bacteria in the family Microbacteriaceae. Microbacteria are common contaminants of laboratory reagents, which can lead to their being misrepresented in microbiome A microbiome () is the community of microo ...

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Skin

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Acinetobacter ''Acinetobacter'' is a genus of gram-negative bacteria belonging to the wider class of Gammaproteobacteria. ''Acinetobacter'' species are oxidase-negative, exhibit twitching motility, and occur in pairs under magnification. They are importan ...

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Bacillus ''Bacillus'' (Latin "stick") is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum '' Bacillota'', with 266 named species. The term is also used to describe the shape (rod) of other so-shaped bacteria; and the plural ''Bacill ...

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Candida albicans ''Candida albicans'' is an opportunistic pathogenic yeast that is a common member of the human gut flora. It can also survive outside the human body. It is detected in the gastrointestinal tract and mouth in 40–60% of healthy adults. It is usu ...

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Candida parapsilosis ''Candida parapsilosis'' is a fungal species of yeast that has become a significant cause of sepsis and of wound and tissue infections in immunocompromised people. Unlike ''Candida albicans'' and '' Candida tropicalis'', ''C. parapsilosis'' is no ...

'' *'' Corynebacterium spp'' *''

Corynebacterium parvum ''Cutibacterium acnes'' (formerly ''Propionibacterium acnes'') is the relatively slow-growing, typically aerotolerant anaerobic, gram-positive bacterium (rod) linked to the skin condition of acne; it can also cause chronic blepharitis and endopht ...

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Cutibacterium acnes ''Cutibacterium acnes'' (formerly ''Propionibacterium acnes'') is the relatively slow-growing, typically aerotolerant anaerobic, gram-positive bacterium (rod) linked to the skin condition of acne; it can also cause chronic blepharitis and endopht ...

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Demodex folliculorum ''Demodex folliculorum'' is a microscopic mite that can only survive on the skin of humans. Most people have ''D.folliculorum'' on their skin. Usually, the mites do not cause any harm, so are considered an example of commensalism rather than par ...

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Enterobacter cloacae ''Enterobacter cloacae'' is a clinically significant Gram-negative, facultatively-anaerobic, rod-shaped bacterium. Microbiology In microbiology labs, ''E. cloacae'' is frequently grown at 30 °C on nutrient agar or at 35 °C in tr ...

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Epidermophyton floccosum ''Epidermophyton floccosum'' is a filamentous fungus that causes skin and nail infections in humans. This anthropophilic dermatophyte can lead to diseases such as tinea pedis (athlete's foot), tinea cruris, tinea corporis and onychomycosis. Diag ...

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Micrococcus ''Micrococcus'' (mi’ krō kŏk’ Əs) is a genus of bacteria in the Micrococcaceae family. ''Micrococcus'' occurs in a wide range of environments, including water, dust, and soil. Micrococci have Gram-positive spherical cells ranging from abo ...

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Micrococcus luteus ''Micrococcus luteus'' is a Gram-positive, to Gram-variable, nonmotile, coccus, tetrad-arranging, pigmented, saprotrophic bacterium that belongs to the family Micrococcaceae. It is urease and catalase positive. An obligate aerobe, ''M. luteus' ...

'' *'' Mycobacterium spp'' *''

Neisseria ''Neisseria'' is a large genus of bacteria that colonize the mucosal surfaces of many animals. Of the 11 species that colonize humans, only two are pathogens, '' N. meningitidis'' and ''N. gonorrhoeae''. ''Neisseria'' species are Gram-negativ ...

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Propionibacterium ''Propionibacterium'' is a gram-positive, anaerobic, rod-shaped genus of bacteria named for their unique metabolism: They are able to synthesize propionic acid by using unusual transcarboxylase enzymes. Its members are primarily facultative pa ...

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Pseudomonas aeruginosa ''Pseudomonas aeruginosa'' is a common encapsulated, gram-negative, aerobic–facultatively anaerobic, rod-shaped bacterium that can cause disease in plants and animals, including humans. A species of considerable medical importance, ''P. aerug ...

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Sarcina The ''sarcina'' was the marching pack carried by Roman legionaries, the heavy infantry of the Roman legions. Most of a legionary's equipment other than his arms and armour would, in early times, have been consigned to a baggage train and b ...

spp'' *'' Staphylococcus aureus'' *'' Staphylococcus epidermidis'' *'' Staphylococcus haemolyticus'' *'' Streptococcus viridans'' *''

Trichophyton ''Trichophyton'' is a genus of fungi, which includes the parasitic varieties that cause tinea, including athlete's foot, ringworm, jock itch, and similar infections of the nail, beard, skin and scalp. Trichophyton fungi are molds characterize ...

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Hair follicles

*'' Staphylococcus aureus''

External ear

*'' Corynebacterium spp'' *'' Staphylococcus aureus'' *'' Staphylococcus epidermidis''

Mucous membranes

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Chlamydia trachomatis ''Chlamydia trachomatis'' (), commonly known as chlamydia, is a bacterium that causes chlamydia, which can manifest in various ways, including: trachoma, lymphogranuloma venereum, nongonococcal urethritis, cervicitis, salpingitis, pelvic infla ...

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Hemophilus influenzae ''Haemophilus influenzae'' (formerly called Pfeiffer's bacillus or ''Bacillus influenzae'') is a Gram-negative, non-motile, coccobacillary, facultatively anaerobic, capnophilic pathogenic bacterium of the family Pasteurellaceae. The bacter ...

'' *'' Staphylococcus aureus'' *'' Staphylococcus epidermidis''

Eye

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Chlamydophila pneumoniae ''Chlamydia pneumoniae'' is a species of ''Chlamydia'', an obligate intracellular bacterium that infects humans and is a major cause of pneumonia. It was known as the Taiwan acute respiratory agent (TWAR) from the names of the two original isola ...

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Haemophilus aegyptius ''Haemophilus influenzae'' biogroup ''aegyptius'' (''Hae'') is a causative agent of acute and often purulent conjunctivitis, more commonly known as pink eye. It was discovered independently by Koch and Weeks in the 1880s. During the mid-1980s ...

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Haemophilus influenzae ''Haemophilus influenzae'' (formerly called Pfeiffer's bacillus or ''Bacillus influenzae'') is a Gram-negative, non-motile, coccobacillary, facultatively anaerobic, capnophilic pathogenic bacterium of the family Pasteurellaceae. The bacter ...

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Moraxella ''Moraxella'' is a genus of gram-negative bacteria in the family Moraxellaceae. It is named after the Swiss ophthalmologist Victor Morax. The organisms are short rods, coccobacilli, or as in the case of ''Moraxella catarrhalis'', diplococci ...

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spp'' *'' Staphylococcus aureus'' *'' Staphylococcus epidermidis'' *'' Streptococcus viridans''

Gastrointestinal tract

Respiratory tract

Urogenital tract

Vagina

The

vaginal microbiota in pregnancy The vaginal flora in pregnancy, or vaginal microbiota in pregnancy, is different from the vaginal flora (the population of microorganisms that resides in the vagina) before sexual maturity, during reproductive years, and after menopause. A descrip ...

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.

Placenta

Uterus

The healthy uterine microbiome has been identified and over 278 genera have been sequenced.

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 The ''Lactobacillaceae'' are a family of lactic acid bacteria. It is the only family in the lactic acid bacteria which includes homofermentative and heterofermentative organisms; in the ''Lactobacillaceae,'' the pathway used for hexose fermentati ...

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Actinomyces ''Actinomyces'' is a genus of the Actinomycetia class of bacteria. They all are gram-positive. ''Actinomyces'' species are facultatively anaerobic and they grow best under anaerobic conditions. ''Actinomyces'' species may form endospores, an ...

'' 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.

Male reproductive tract

The microbiome present in

seminal fluid Semen, also known as seminal fluid, is an organic bodily fluid created to contain spermatozoa. It is secreted by the gonads (sexual glands) and other sexual organs of male or hermaphroditic animals and can fertilize the female ovum. Semen is ...

has been evaluated. Using traditional culturing techniques the microbiome differs between men who have acute

prostatitis Prostatitis is an umbrella term for a variety of medical conditions that incorporate bacterial and non-bacterial origin illnesses in the pelvic region. In contrast with the plain meaning of the word (which means "inflammation of the prostate"), the ...

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 ''Pseudomonas'' is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 described species. The members of the genus demonstrate a great deal of metabolic diversity and consequently are able t ...

Lactobacillus ''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 div ...

, and

Prevotella ''Prevotella'' is a genus of Gram-negative bacteria. ''Prevotella'' spp. are members of the oral, vaginal, and gut microbiota and are often recovered from anaerobic infections of the respiratory tract. These infections include aspiration pn ...

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.

References

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