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List of human microbiota

Adapted from Wikipedia · Discoverer experience

A magnified view of E. coli bacteria, showing their shape and structure under a microscope.

The human body is full of tiny living things called microorganisms, such as bacteria, viruses, fungi, and archaea. These tiny creatures live in different parts of our bodies, like our stomachs, intestines, skin, and even in places you might not expect! Each part of the body has its own special group of these microorganisms, and some of them can be found in many different places.

These tiny living things are very important because they help keep our bodies healthy. Some of them help us digest food, while others protect us from harmful germs. Even though we might not see them, they are always working to help us stay well.

This article talks about some of the known microorganisms that live in our bodies. It focuses especially on the ones found in our mouths, the area around the uterus, and other parts of the body that are important for health. Learning about these tiny helpers can help us understand how our bodies work and stay healthy.

Categories of bacteria

The human body has about 39 trillion bacteria, which are tiny living things. These bacteria can be grouped into three main shapes.

Staphylococcus aureus

One group, called cocci, are round like balls. Another group, called bacilli, are rod-shaped. The last group, called spirochetes, are spiral-shaped, like tiny corkscrews. Each shape has different examples of bacteria that live in our bodies.

Yersinia enterocolitica colonies growing on XLD agar plates

Eye

The eye is a special place in the body that also has its own tiny world of tiny living things. These tiny living things, called microorganisms, live on and help protect the eye. They are found in places like the surface of the eye and can be different types such as bacteria and fungi.

Mouth

Further information: Oral microbiology

The oral microbiota includes all the tiny living things found in our mouths. These include different types of bacteria, viruses, fungi, and other small organisms. They help keep our mouths and bodies healthy. A scientist named Anthony Van Leeuwenhoek was the first to see these tiny organisms using a microscope he made himself.

Keeping our mouths clean is important for staying healthy. Good habits like brushing our teeth twice a day, flossing, eating foods without too much sugar, drinking plenty of water, and using special healthy supplements can help keep these tiny organisms balanced and our mouths feeling fresh.

Binomial NamePhylumLocationPathogenicity
Abiotrophia sppMouth
Actinomyces sppActinomycetotaMouth
Actinomyces viscosusActinomycetotaMouth
Actinomyces naeslundiiActinomycetotaMouth
Aggregatibacter actinomycetemcomitansMouth
Arachnia propionicaMouth
Aspergillus sppAscomycota (fungi)MouthSometimes
Atopobium sppActinomycetotaMouth
Aureobasidium sppfungiMouth
Bacterionema matruchotii
(Corynebacterium matruchotii)
ActinomycetotaGingiva
Bacteroides sppBacteroidotaMouth
Bacteroides gingivalisBacteroidotaMouth
Bacteroides melaninogenicusBacteroidotaMouth
Bergeyella sppBacteroidotaMouth
Bifidobacterium sppActinomycetotaMouth
Buchnera aphidicolaMouth
Bulleidia sppFirmicutesMouth
Campylobacter sppCampylobacterotaMouth
Candida sppAscomycota (fungi)Mouth
Candida albicansAscomycota (fungi)MouthSometimes
Capnocytophaga sppBacteroidotaMouth
Cardiobacterium sppProteobacteriaMouth
Catonella sppFirmicutesHard palate
Citrobacter freundiiThroat
Cladosporium sppfungiMouth
Corynebacterium sppActinomycetotaMouthOnly C. diphtheriae
Cryptococcus sppfungiMouth
Desulfobacter sppMouth
Desulfovibrio sppMouth
Dialister sppFirmicutesMouth
Eikenella corrodensProteobacteriaMouthSometimes
Entamoeba gingivalisAmoebozoa (eukaryote)Mouth
Enterococcus sppFirmicutesMouthSometimes
Enterococcus faeciumFirmicutesMouth
Eubacterium sppFirmicutesMouth
Fusarium sppfungiMouth
Fusobacterium sppFusobacteriotaMouth
Fusobacterium necrophorumFusobacteriotaOropharynx
Fusobacterium nucleatumFusobacteriotaMouthSometimes
Gemella sppFirmicutesMouth
Gordonia sppSputum
Granulicatella sppFirmicutesMouth
Haemophilus sppProteobacteriaMouth
Kingella sppProteobacteriaMouth
Lactobacillus sppFirmicutesMouth, SalivaNo
Lautropia sppProteobacteriaMouth
Leptotrichia buccalisFusobacteriotaMouth
Methanobrevibacter oralisMethanobacteriota (archaea)Mouth
Methanosarcina mazeiiMethanobacteriota (archaea)Mouth
Micrococcus sppMouth
Mogibacterium sppFirmicutesMouth
Mycoplasma sppMouth
Mycoplasma oraleOropharynx
Mycobacterium chelonaeSputum
Candidatus Nanosynbacter lyticusCandidatus SaccaribacteriaMouth
Neisseria sppProteobacteriaMouthOnly N. gonorrheae and N. meningitidis
Oribacterium sppFirmicutesMouth
Parvimonas sppFirmicutesMouth
Peptococcus sppMouth
Peptostreptococcus sppFirmicutesMouth
Phocoenobacter sppProteobacteriaMouth
Porphyromonas gingivalisBacteroidotaMouthSometimes
Prevotella sppBacteroidotaMouthSometimes
Propionibacterium sppActinomycetotaMouth
Pseudoramibacter sppMouth
Rothia dentocariosaActinomycetotaMouthOccasionally
Selenomonas sppFirmicutesMouth
Simonsiella sppMouth
Staphylococcus aureusFirmicutesMouthSometimes
Staphylococcus epidermidisFirmicutesMouth
Streptococcus sppFirmicutesMouth
Streptococcus anginosusFirmicutesOropharynx
Streptococcus mitisFirmicutesMouth
Streptococcus mutansFirmicutesTeeth: dental plaque
Streptococcus oralisFirmicutesTeeth: dental plaque
Streptococcus sobrinusFirmicutesTeeth: dental plaque
Streptococcus constellatusFirmicutesOropharynx
Streptococcus intermediusFirmicutesOropharynx
Tannerella forsythiaBacteroidotaMouthSometimes
Torulopsis glabrataMouth
Treponema denticolaSpirochetotaMouth
Trichomonas tenaxeukaryoteMouth
Veillonella sppFirmicutesMouth
Vibrio sputorumMouth
Wolinella sppCampylobacterotaMouth

Respiratory System

The respiratory system includes parts like the nose, throat, and lungs. These areas also have tiny living things called microorganisms. These can be bacteria, viruses, fungi, and other very small organisms. They live on and inside our bodies, even in places we might not expect!

Binomial NamePhylumLocationPathogenicity
Acinetobacter sppNasopharynx
Citrobacter freundiiSputum
Burkholderia cepacia complexProteobacteriaLung
Campylobacter sputorumNasopharynx
Candida albicansAscomycota (fungi)Pharynx
Cardiobacterium sppNose
Chlamydophila pneumoniaeChlamydiotaLung
Fusobacterium sppFusobacteriotaLung
Haemophilus sppProteobacteriaNasopharynx, lung
Hemophilus influenzaeProteobacteriaMucous membranesSometimes
Haemophilus parainfluenzaeProteobacteriaPharynx
Haemophilus paraphrophilusProteobacteriaPharynx
Kingella sppProteobacteriaUpper respiratory tract
Kingella kingaeProteobacteriaUpper respiratory tract
Moraxella sppProteobacteriaNasopharynx
Moraxella catarrhalisProteobacteriaNasopharynx
Mycoplasma pneumoniaeRespiratory epithelium
Neisseria sppProteobacteriaNasopharynx
Neisseria cinereaProteobacteriaNasopharynx
Neisseria elongataProteobacteriaPharynx
Neisseria gonorrhoeaeProteobacteriaPharynxYes
Neisseria lactamicaProteobacteriaNasopharynx
Neisseria meningitidisProteobacteriaNasopharynxYes
Neisseria mucosaProteobacteriaNasopharynx
Neisseria siccaProteobacteriaNasopharynx
Peptococcus sppUpper respiratory tract
Peptostreptococcus sppFirmicutesPharynx
Pseudomonas sppProteobacteriaLung
Pseudomonas aeruginosaProteobacteriaLungYes
Selenomonas sputigenaFirmicutesNasopharynx
Staphylococcus aureusFirmicutesNoseSometimes
Streptobacillus sppThroat, nasopharynx
Streptococcus sppFirmicutesLung
Streptococcus pyogenesFirmicutesUpper respiratory tract
Streptococcus pneumoniaeFirmicutesNasopharynxSometimes

Gastrointestinal Tract

Main article: Gut microbiota

The gastrointestinal tract, also known as the stomach and intestines, is home to many tiny living things called microorganisms. These include different types of bacteria, viruses, fungi, and other tiny organisms that live together in our bodies. They help with digestion and keep our bodies healthy.

Binomial NamePhylumLocationPathogenicityFrequency/Abundance
Achromobacter sppIntestines
Acidaminococcus fermentansFirmicutesLarge intestine
Acinetobacter calcoaceticusLarge intestine
Actinomyces sppActinomycetotaSmall and large intestine
Adlercreutzia sppActinomycetotaLarge intestine
Aeromonas sppIntestines
Aflipia sppGI tract
Aggregatibacter sppGI tract
Akkermansia muciniphiliaVerrucomicrobiaLarge intestine
Alistripes sppGI tract
Alternaria sppAscomycota (fungi)GI tract
Anaerobiospirillum sppLarge intestine
Anaerostipes sppGI tract
Anaerotruncus sppFirmicutesLarge intestine
Alcaligenes faecalisIntestines
Asaccharobacter sppGI tract
Aspergillus sppAscomycota (fungi)GI tractSometimes58.3%
Aspergillus versicolorAscomycota (fungi)GI tract5%
AsteroleplasmaGI tract
Bacillus sppFirmicutesLarge intestine
Bacteroides sppBacteroidotaEsophagus, intestines
Bacteroides fragilisBacteroidotaLarge intestine
Bacteroides melaninogenicusBacteroidotaLarge intestine
Barnesiella sppBacteroidotaGI tract
Bifidobacterium sppActinomycetotaLarge intestineNo
Bifidobacterium longumActinomycetotaLarge intestine
Bilophilia wadsworthiaProteobacteriaLarge intestine
Blautia sppFirmicutesLarge intestine
Brachybacterium sppGI tract
Butyricimonas sppGI tract
Butyrivibrio crossotusLarge intestine
Campylobacter sppCampylobacterotaLarge intestine
Candida sppAscomycota (fungi)GI tract2.5 - 59.7%
Candida albicansAscomycota (fungi)GI tract5.8 - 80.8%
Catenibacterium sppGI tract
Christensenella minutaFirmicutesGI tract
Citrobacter sppProteobacteriaGI tract
Clostridium sppFirmicutesIntestines
Clostridium sordelliiFirmicutesStomach, small intestine, large intestine
Collinsella aerofaciensActinomycetotaLarge intestine
Coprobacter sppGI tract
Coprobacillus sppGI tract
Coprococcus comesFirmicutesLarge intestine
Cladosporium cladosporoidesAscomycota (fungi)GI tract
Cryptococcus sppBasidomycota (fungi)GI tract4.7%
Debaryomyces sppAscomycota (fungi)GI tract
Desulfovibrio sppProteobacteriaLarge intestine
DialisterFirmicutesLarge intestine
Dorea sppFirmicutesLarge intestine
Eggerthella sppActinomycetotaLarge intestine
Escherichia coliProteobacteriaGI tractSometimes
Enhydrobacter sppGI tract
Enterococcus sppFirmicutesStomach, intestinesSometimes
Enterobacter sppProteobacteriaLarge intestine
Enterobacter cloacaeProteobacteriaLarge intestine
Epulopiscium sppFirmicutesLarge intestine
Eubacterium sppFirmicutesColon
Exophiala sppAscomycota (fungi)GI tract
Faecalibacterium sppFirmicutesLarge intestine
Faecalibacterium prausnitziiFirmicutesLarge intestineNo
Ferrimonas sppProteobacteriaIntestines
Flavobacterium sppIntestines
Fusobacterium sppFusobacteriotaLarge intestine
Galactomyces sppAscomycota (fungi)GI tract0.8 - 46%
Gemella sppFirmicutesEsophagus, intestines
Geotrichium silvicolaAscomycota (fungi)GI tract9.7%
Helicobacter pyloriCampylobacterotaStomachYes
Hemophilus sppProteobacteriaIntestines
Holdemania sppGI tract
Holdemanella sppGI tract
Howardella sppGI tract
Hungatella sppGI tract
Intestinibacter bartlettiiGI tract
Lachnobacterium sppFirmicutesLarge intestine
Lachnospira sppFirmicutesIntestines
Joetgalicoccus sppGI tract
Klesbiella sppProteobacteriaIntestines
Kocuria sppGI tract
Lactobacillus sppFirmicutesStomach, intestines
Lactococcus lactisFirmicutesIntestines
Leuconostoc sppGI tract
Malessezia sppBasidomycota (fungi)GI tract88.3%
MegaspheraFirmicutesEsophagus
Mesorhizobium sppGI tract
Methanobrevibacter smithiiMethanobacteriota (archaea)IntestinesNo
Methylobacterium sppGI tract
Microbacterium sppGI tract
Morganella morganiiIntestines
Mycobacteria sppActinomycetotaIntestines
Mycoplasma sppIntestines
Ochrobactrum sppGI tract
Oscillospira sppFirmicutesLarge intestine
Oxalobacter sppGI tract
Parabacteroides sppBacteroidotaLarge intestine
ParaprevotellaBacteroidotaLarge intestine
Parasutterella sppGI tract
Pediococcus sppFirmicutesIntestines
Pelomonas sppGI tract
Peptococcus sppLarge intestine
Peptostreptococcus sppFirmicutesColon
Penicillium sppAscomycota (fungi)GI tract7 - 65.3%
Penicillium brevicompactumAscomycota (fungi)GI tract
PhascolarctobacteriumGI tract
Pichia sppAscomycota (fungi)GI tract
Planomicrobium sppGI tract
Prevotella sppBacteroidotaEsophagus, stomach, intestines
Propionibacterium sppActinomycetotaLarge intestine
Providencia sppLarge intestine
Pseudochrobactrum sppGI tract
Pseudomonas sppProteobacteriaEsophagus
Pseudomonas aeruginosaProteobacteriaIntestinesSometimes
Porphyromonas sppLarge intestine
Pyramidobacter sppGI tract
Rheinheimera sppGI tract
Rhodoturula sppBasidiomycota (fungi)GI tract7 - 15.3%
Rhomboutsia sppGI tract
Roseburia sppFirmicutesLarge intestine
Rothia sppActinomycetotaEsophagus
Ruminococcus sppFirmicutesLarge intestine
Ruminococcus gnavusFirmicutesLarge intestine
Rummeliibacillus sppFirmicutesIntestines
Saccharomyces sppAscomycota (fungi)GI tract1.1 - 100%
Saccharomyces cerevisiaeAscomycota (fungi)GI tract
Sarcina sppLarge intestine
Sellimonas sppGI tract
Senegalimassilia sppGI tract
Serratia sppGI tract
Slackia sppGI tract
Sphingobacterium spiritivorumGI tract
Sphingomonas sppGI tract
Streptococcus sppFirmicutesEsophagus, stomach, intestines
Streptococcus anginosusFirmicutesGI tract
Subdoligranulum sppGI tract
Succinatomonas sppGI tract
Succinovibrio sppGI tract
Sutterella sppProteobacteriaLarge intestine
Taonella sppGI tract
Trabulsiella sppProteobacteriaIntestines
Trichosporon sppBasidiomycota (fungi)GI tract30.6%
Tsukamurella sppGI tract
Turicibacter sppFirmicutesIntestines
Veillonella sppFirmicutesEsophagus, intestines
Vibrio sppIntestines
Weissella sppGI tract
Yersinia enterocoliticaLarge intestine

Skin

Main article: Skin microbiome

The skin is covered with tiny living things, like tiny plants and tiny animals, that live together in a community called the skin microbiome. These microorganisms help keep our skin healthy and protect us from harmful germs.

Binomial NamePhylumLocationPathogenicity
Acinetobacter sppSkin
Bacillus sppFirmicutesSkin
Candida albicansAscomycota (fungi)Skin
Candida parapsilosisAscomycota (fungi)Skin
Corynebacterium sppActinomycetotaSkin
Corynebacterium parvumActinomycetotaSkin
Cutibacterium acnesActinomycetotaSkin
Demodex folliculorumSkin
Enterobacter cloacaeSkin
Epidermophyton floccosumSkin
Malassezia ovaleSkin
Micrococcus luteusSkin
Micrococcus sppSkin
Mycobacterium sppActinomycetotaSkin
Neisseria sppProteobacteriaSkin
Peptostreptococcus sppFirmicutesSkin
Propionibacterium sppActinomycetotaSkin
Pseudomonas aeruginosaProteobacteriaSkinMostly
Sarcina sppSkin
Staphylococcus aureusFirmicutesSkinSometimes
Staphylococcus epidermidisFirmicutesSkinSometimes, mostly not
Staphylococcus haemolyticusFirmicutesSkin
Streptococcus viridansFirmicutesSkin
Trichophyton sppSkin

Female Reproductive Tract

Main article: Vaginal flora

The vaginal microbiota changes with puberty, pregnancy, and menopause. Helpful bacteria, like some Lactobacillus species, keep the vagina safe by turning sugar into lactic acid, which creates an acidic environment that stops harmful germs. During pregnancy, the vaginal microbiota changes a lot due to hormone levels. These helpful bacteria can pass to babies during birth.

The uterus also has its own set of microorganisms, with over 278 types identified. While Lactobacillus is good for the vagina, too much of it in the uterus can be harmful. Research on the ovarian follicle microbiome is ongoing, looking at how bacteria might affect fertility treatments and birth outcomes. Some bacteria, like Lactobacillus, are linked to positive results, while others, like Propionibacterium and Actinomyces, are linked to challenges.

Binomial NamePhylumLocationPathogenicity
Acinetobacter sppAnterior urethra
Bacteroides sppBacteroidotaExternal genitalia
Candida albicansAscomycota (fungi)Anterior urethra, external genitaliaSometimes
EnterobacteriaceaeAnterior urethra, external genitalia
Gardnerella vaginalisVagina
Lactobacillus spp.FirmicutesVagina
Mycoplasma hominisVagina
Prevotella spp.BacteroidotaVagina
Streptococcus viridansFirmicutesAnterior urethra, external genitalia

Male reproductive tract

The tiny living things found in seminal fluid have been studied. Scientists use special tools to look at the differences in these living things between men with certain prostate conditions. These tiny living things can help doctors understand and treat problems with fertility in men who don’t show signs of illness. Some types of these living things, like Pseudomonas, Lactobacillus, and Prevotella, can affect sperm quality. When Lactobacillus is found in semen, it often means the sperm count is very healthy.

Binomial NamePhylumLocationPathogenicity
Acinetobacter sppAnterior urethra
Bacteroides sppBacteroidotaExternal genitalia
Candida albicansAscomycota (fungi)Anterior urethra, external genitaliaSometimes
EnterobacteriaceaeAnterior urethra, external genitalia
Streptococcus viridansFirmicutesAnterior urethra, external genitalia

Images

A colorful microscope picture showing tiny germs called Salmonella interacting with human cells.
A beautiful butterfly resting on a flower, showing the intricate patterns on its wings.
Illustration showing the spiral shape of common bacteria.

Related articles

This article is a child-friendly adaptation of the Wikipedia article on List of human microbiota, available under CC BY-SA 4.0.

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