List of human microbiota
Adapted from Wikipedia · Discoverer experience
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.
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.
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 Name | Phylum | Location | Pathogenicity |
|---|---|---|---|
| Abiotrophia spp | Mouth | ||
| Actinomyces spp | Actinomycetota | Mouth | |
| Actinomyces viscosus | Actinomycetota | Mouth | |
| Actinomyces naeslundii | Actinomycetota | Mouth | |
| Aggregatibacter actinomycetemcomitans | Mouth | ||
| Arachnia propionica | Mouth | ||
| Aspergillus spp | Ascomycota (fungi) | Mouth | Sometimes |
| Atopobium spp | Actinomycetota | Mouth | |
| Aureobasidium spp | fungi | Mouth | |
| Bacterionema matruchotii (Corynebacterium matruchotii) | Actinomycetota | Gingiva | |
| Bacteroides spp | Bacteroidota | Mouth | |
| Bacteroides gingivalis | Bacteroidota | Mouth | |
| Bacteroides melaninogenicus | Bacteroidota | Mouth | |
| Bergeyella spp | Bacteroidota | Mouth | |
| Bifidobacterium spp | Actinomycetota | Mouth | |
| Buchnera aphidicola | Mouth | ||
| Bulleidia spp | Firmicutes | Mouth | |
| Campylobacter spp | Campylobacterota | Mouth | |
| Candida spp | Ascomycota (fungi) | Mouth | |
| Candida albicans | Ascomycota (fungi) | Mouth | Sometimes |
| Capnocytophaga spp | Bacteroidota | Mouth | |
| Cardiobacterium spp | Proteobacteria | Mouth | |
| Catonella spp | Firmicutes | Hard palate | |
| Citrobacter freundii | Throat | ||
| Cladosporium spp | fungi | Mouth | |
| Corynebacterium spp | Actinomycetota | Mouth | Only C. diphtheriae |
| Cryptococcus spp | fungi | Mouth | |
| Desulfobacter spp | Mouth | ||
| Desulfovibrio spp | Mouth | ||
| Dialister spp | Firmicutes | Mouth | |
| Eikenella corrodens | Proteobacteria | Mouth | Sometimes |
| Entamoeba gingivalis | Amoebozoa (eukaryote) | Mouth | |
| Enterococcus spp | Firmicutes | Mouth | Sometimes |
| Enterococcus faecium | Firmicutes | Mouth | |
| Eubacterium spp | Firmicutes | Mouth | |
| Fusarium spp | fungi | Mouth | |
| Fusobacterium spp | Fusobacteriota | Mouth | |
| Fusobacterium necrophorum | Fusobacteriota | Oropharynx | |
| Fusobacterium nucleatum | Fusobacteriota | Mouth | Sometimes |
| Gemella spp | Firmicutes | Mouth | |
| Gordonia spp | Sputum | ||
| Granulicatella spp | Firmicutes | Mouth | |
| Haemophilus spp | Proteobacteria | Mouth | |
| Kingella spp | Proteobacteria | Mouth | |
| Lactobacillus spp | Firmicutes | Mouth, Saliva | No |
| Lautropia spp | Proteobacteria | Mouth | |
| Leptotrichia buccalis | Fusobacteriota | Mouth | |
| Methanobrevibacter oralis | Methanobacteriota (archaea) | Mouth | |
| Methanosarcina mazeii | Methanobacteriota (archaea) | Mouth | |
| Micrococcus spp | Mouth | ||
| Mogibacterium spp | Firmicutes | Mouth | |
| Mycoplasma spp | Mouth | ||
| Mycoplasma orale | Oropharynx | ||
| Mycobacterium chelonae | Sputum | ||
| Candidatus Nanosynbacter lyticus | Candidatus Saccaribacteria | Mouth | |
| Neisseria spp | Proteobacteria | Mouth | Only N. gonorrheae and N. meningitidis |
| Oribacterium spp | Firmicutes | Mouth | |
| Parvimonas spp | Firmicutes | Mouth | |
| Peptococcus spp | Mouth | ||
| Peptostreptococcus spp | Firmicutes | Mouth | |
| Phocoenobacter spp | Proteobacteria | Mouth | |
| Porphyromonas gingivalis | Bacteroidota | Mouth | Sometimes |
| Prevotella spp | Bacteroidota | Mouth | Sometimes |
| Propionibacterium spp | Actinomycetota | Mouth | |
| Pseudoramibacter spp | Mouth | ||
| Rothia dentocariosa | Actinomycetota | Mouth | Occasionally |
| Selenomonas spp | Firmicutes | Mouth | |
| Simonsiella spp | Mouth | ||
| Staphylococcus aureus | Firmicutes | Mouth | Sometimes |
| Staphylococcus epidermidis | Firmicutes | Mouth | |
| Streptococcus spp | Firmicutes | Mouth | |
| Streptococcus anginosus | Firmicutes | Oropharynx | |
| Streptococcus mitis | Firmicutes | Mouth | |
| Streptococcus mutans | Firmicutes | Teeth: dental plaque | |
| Streptococcus oralis | Firmicutes | Teeth: dental plaque | |
| Streptococcus sobrinus | Firmicutes | Teeth: dental plaque | |
| Streptococcus constellatus | Firmicutes | Oropharynx | |
| Streptococcus intermedius | Firmicutes | Oropharynx | |
| Tannerella forsythia | Bacteroidota | Mouth | Sometimes |
| Torulopsis glabrata | Mouth | ||
| Treponema denticola | Spirochetota | Mouth | |
| Trichomonas tenax | eukaryote | Mouth | |
| Veillonella spp | Firmicutes | Mouth | |
| Vibrio sputorum | Mouth | ||
| Wolinella spp | Campylobacterota | Mouth |
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 Name | Phylum | Location | Pathogenicity |
|---|---|---|---|
| Acinetobacter spp | Nasopharynx | ||
| Citrobacter freundii | Sputum | ||
| Burkholderia cepacia complex | Proteobacteria | Lung | |
| Campylobacter sputorum | Nasopharynx | ||
| Candida albicans | Ascomycota (fungi) | Pharynx | |
| Cardiobacterium spp | Nose | ||
| Chlamydophila pneumoniae | Chlamydiota | Lung | |
| Fusobacterium spp | Fusobacteriota | Lung | |
| Haemophilus spp | Proteobacteria | Nasopharynx, lung | |
| Hemophilus influenzae | Proteobacteria | Mucous membranes | Sometimes |
| Haemophilus parainfluenzae | Proteobacteria | Pharynx | |
| Haemophilus paraphrophilus | Proteobacteria | Pharynx | |
| Kingella spp | Proteobacteria | Upper respiratory tract | |
| Kingella kingae | Proteobacteria | Upper respiratory tract | |
| Moraxella spp | Proteobacteria | Nasopharynx | |
| Moraxella catarrhalis | Proteobacteria | Nasopharynx | |
| Mycoplasma pneumoniae | Respiratory epithelium | ||
| Neisseria spp | Proteobacteria | Nasopharynx | |
| Neisseria cinerea | Proteobacteria | Nasopharynx | |
| Neisseria elongata | Proteobacteria | Pharynx | |
| Neisseria gonorrhoeae | Proteobacteria | Pharynx | Yes |
| Neisseria lactamica | Proteobacteria | Nasopharynx | |
| Neisseria meningitidis | Proteobacteria | Nasopharynx | Yes |
| Neisseria mucosa | Proteobacteria | Nasopharynx | |
| Neisseria sicca | Proteobacteria | Nasopharynx | |
| Peptococcus spp | Upper respiratory tract | ||
| Peptostreptococcus spp | Firmicutes | Pharynx | |
| Pseudomonas spp | Proteobacteria | Lung | |
| Pseudomonas aeruginosa | Proteobacteria | Lung | Yes |
| Selenomonas sputigena | Firmicutes | Nasopharynx | |
| Staphylococcus aureus | Firmicutes | Nose | Sometimes |
| Streptobacillus spp | Throat, nasopharynx | ||
| Streptococcus spp | Firmicutes | Lung | |
| Streptococcus pyogenes | Firmicutes | Upper respiratory tract | |
| Streptococcus pneumoniae | Firmicutes | Nasopharynx | Sometimes |
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 Name | Phylum | Location | Pathogenicity | Frequency/Abundance |
|---|---|---|---|---|
| Achromobacter spp | Intestines | |||
| Acidaminococcus fermentans | Firmicutes | Large intestine | ||
| Acinetobacter calcoaceticus | Large intestine | |||
| Actinomyces spp | Actinomycetota | Small and large intestine | ||
| Adlercreutzia spp | Actinomycetota | Large intestine | ||
| Aeromonas spp | Intestines | |||
| Aflipia spp | GI tract | |||
| Aggregatibacter spp | GI tract | |||
| Akkermansia muciniphilia | Verrucomicrobia | Large intestine | ||
| Alistripes spp | GI tract | |||
| Alternaria spp | Ascomycota (fungi) | GI tract | ||
| Anaerobiospirillum spp | Large intestine | |||
| Anaerostipes spp | GI tract | |||
| Anaerotruncus spp | Firmicutes | Large intestine | ||
| Alcaligenes faecalis | Intestines | |||
| Asaccharobacter spp | GI tract | |||
| Aspergillus spp | Ascomycota (fungi) | GI tract | Sometimes | 58.3% |
| Aspergillus versicolor | Ascomycota (fungi) | GI tract | 5% | |
| Asteroleplasma | GI tract | |||
| Bacillus spp | Firmicutes | Large intestine | ||
| Bacteroides spp | Bacteroidota | Esophagus, intestines | ||
| Bacteroides fragilis | Bacteroidota | Large intestine | ||
| Bacteroides melaninogenicus | Bacteroidota | Large intestine | ||
| Barnesiella spp | Bacteroidota | GI tract | ||
| Bifidobacterium spp | Actinomycetota | Large intestine | No | |
| Bifidobacterium longum | Actinomycetota | Large intestine | ||
| Bilophilia wadsworthia | Proteobacteria | Large intestine | ||
| Blautia spp | Firmicutes | Large intestine | ||
| Brachybacterium spp | GI tract | |||
| Butyricimonas spp | GI tract | |||
| Butyrivibrio crossotus | Large intestine | |||
| Campylobacter spp | Campylobacterota | Large intestine | ||
| Candida spp | Ascomycota (fungi) | GI tract | 2.5 - 59.7% | |
| Candida albicans | Ascomycota (fungi) | GI tract | 5.8 - 80.8% | |
| Catenibacterium spp | GI tract | |||
| Christensenella minuta | Firmicutes | GI tract | ||
| Citrobacter spp | Proteobacteria | GI tract | ||
| Clostridium spp | Firmicutes | Intestines | ||
| Clostridium sordellii | Firmicutes | Stomach, small intestine, large intestine | ||
| Collinsella aerofaciens | Actinomycetota | Large intestine | ||
| Coprobacter spp | GI tract | |||
| Coprobacillus spp | GI tract | |||
| Coprococcus comes | Firmicutes | Large intestine | ||
| Cladosporium cladosporoides | Ascomycota (fungi) | GI tract | ||
| Cryptococcus spp | Basidomycota (fungi) | GI tract | 4.7% | |
| Debaryomyces spp | Ascomycota (fungi) | GI tract | ||
| Desulfovibrio spp | Proteobacteria | Large intestine | ||
| Dialister | Firmicutes | Large intestine | ||
| Dorea spp | Firmicutes | Large intestine | ||
| Eggerthella spp | Actinomycetota | Large intestine | ||
| Escherichia coli | Proteobacteria | GI tract | Sometimes | |
| Enhydrobacter spp | GI tract | |||
| Enterococcus spp | Firmicutes | Stomach, intestines | Sometimes | |
| Enterobacter spp | Proteobacteria | Large intestine | ||
| Enterobacter cloacae | Proteobacteria | Large intestine | ||
| Epulopiscium spp | Firmicutes | Large intestine | ||
| Eubacterium spp | Firmicutes | Colon | ||
| Exophiala spp | Ascomycota (fungi) | GI tract | ||
| Faecalibacterium spp | Firmicutes | Large intestine | ||
| Faecalibacterium prausnitzii | Firmicutes | Large intestine | No | |
| Ferrimonas spp | Proteobacteria | Intestines | ||
| Flavobacterium spp | Intestines | |||
| Fusobacterium spp | Fusobacteriota | Large intestine | ||
| Galactomyces spp | Ascomycota (fungi) | GI tract | 0.8 - 46% | |
| Gemella spp | Firmicutes | Esophagus, intestines | ||
| Geotrichium silvicola | Ascomycota (fungi) | GI tract | 9.7% | |
| Helicobacter pylori | Campylobacterota | Stomach | Yes | |
| Hemophilus spp | Proteobacteria | Intestines | ||
| Holdemania spp | GI tract | |||
| Holdemanella spp | GI tract | |||
| Howardella spp | GI tract | |||
| Hungatella spp | GI tract | |||
| Intestinibacter bartlettii | GI tract | |||
| Lachnobacterium spp | Firmicutes | Large intestine | ||
| Lachnospira spp | Firmicutes | Intestines | ||
| Joetgalicoccus spp | GI tract | |||
| Klesbiella spp | Proteobacteria | Intestines | ||
| Kocuria spp | GI tract | |||
| Lactobacillus spp | Firmicutes | Stomach, intestines | ||
| Lactococcus lactis | Firmicutes | Intestines | ||
| Leuconostoc spp | GI tract | |||
| Malessezia spp | Basidomycota (fungi) | GI tract | 88.3% | |
| Megasphera | Firmicutes | Esophagus | ||
| Mesorhizobium spp | GI tract | |||
| Methanobrevibacter smithii | Methanobacteriota (archaea) | Intestines | No | |
| Methylobacterium spp | GI tract | |||
| Microbacterium spp | GI tract | |||
| Morganella morganii | Intestines | |||
| Mycobacteria spp | Actinomycetota | Intestines | ||
| Mycoplasma spp | Intestines | |||
| Ochrobactrum spp | GI tract | |||
| Oscillospira spp | Firmicutes | Large intestine | ||
| Oxalobacter spp | GI tract | |||
| Parabacteroides spp | Bacteroidota | Large intestine | ||
| Paraprevotella | Bacteroidota | Large intestine | ||
| Parasutterella spp | GI tract | |||
| Pediococcus spp | Firmicutes | Intestines | ||
| Pelomonas spp | GI tract | |||
| Peptococcus spp | Large intestine | |||
| Peptostreptococcus spp | Firmicutes | Colon | ||
| Penicillium spp | Ascomycota (fungi) | GI tract | 7 - 65.3% | |
| Penicillium brevicompactum | Ascomycota (fungi) | GI tract | ||
| Phascolarctobacterium | GI tract | |||
| Pichia spp | Ascomycota (fungi) | GI tract | ||
| Planomicrobium spp | GI tract | |||
| Prevotella spp | Bacteroidota | Esophagus, stomach, intestines | ||
| Propionibacterium spp | Actinomycetota | Large intestine | ||
| Providencia spp | Large intestine | |||
| Pseudochrobactrum spp | GI tract | |||
| Pseudomonas spp | Proteobacteria | Esophagus | ||
| Pseudomonas aeruginosa | Proteobacteria | Intestines | Sometimes | |
| Porphyromonas spp | Large intestine | |||
| Pyramidobacter spp | GI tract | |||
| Rheinheimera spp | GI tract | |||
| Rhodoturula spp | Basidiomycota (fungi) | GI tract | 7 - 15.3% | |
| Rhomboutsia spp | GI tract | |||
| Roseburia spp | Firmicutes | Large intestine | ||
| Rothia spp | Actinomycetota | Esophagus | ||
| Ruminococcus spp | Firmicutes | Large intestine | ||
| Ruminococcus gnavus | Firmicutes | Large intestine | ||
| Rummeliibacillus spp | Firmicutes | Intestines | ||
| Saccharomyces spp | Ascomycota (fungi) | GI tract | 1.1 - 100% | |
| Saccharomyces cerevisiae | Ascomycota (fungi) | GI tract | ||
| Sarcina spp | Large intestine | |||
| Sellimonas spp | GI tract | |||
| Senegalimassilia spp | GI tract | |||
| Serratia spp | GI tract | |||
| Slackia spp | GI tract | |||
| Sphingobacterium spiritivorum | GI tract | |||
| Sphingomonas spp | GI tract | |||
| Streptococcus spp | Firmicutes | Esophagus, stomach, intestines | ||
| Streptococcus anginosus | Firmicutes | GI tract | ||
| Subdoligranulum spp | GI tract | |||
| Succinatomonas spp | GI tract | |||
| Succinovibrio spp | GI tract | |||
| Sutterella spp | Proteobacteria | Large intestine | ||
| Taonella spp | GI tract | |||
| Trabulsiella spp | Proteobacteria | Intestines | ||
| Trichosporon spp | Basidiomycota (fungi) | GI tract | 30.6% | |
| Tsukamurella spp | GI tract | |||
| Turicibacter spp | Firmicutes | Intestines | ||
| Veillonella spp | Firmicutes | Esophagus, intestines | ||
| Vibrio spp | Intestines | |||
| Weissella spp | GI tract | |||
| Yersinia enterocolitica | Large 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 Name | Phylum | Location | Pathogenicity |
|---|---|---|---|
| Acinetobacter spp | Skin | ||
| Bacillus spp | Firmicutes | Skin | |
| Candida albicans | Ascomycota (fungi) | Skin | |
| Candida parapsilosis | Ascomycota (fungi) | Skin | |
| Corynebacterium spp | Actinomycetota | Skin | |
| Corynebacterium parvum | Actinomycetota | Skin | |
| Cutibacterium acnes | Actinomycetota | Skin | |
| Demodex folliculorum | Skin | ||
| Enterobacter cloacae | Skin | ||
| Epidermophyton floccosum | Skin | ||
| Malassezia ovale | Skin | ||
| Micrococcus luteus | Skin | ||
| Micrococcus spp | Skin | ||
| Mycobacterium spp | Actinomycetota | Skin | |
| Neisseria spp | Proteobacteria | Skin | |
| Peptostreptococcus spp | Firmicutes | Skin | |
| Propionibacterium spp | Actinomycetota | Skin | |
| Pseudomonas aeruginosa | Proteobacteria | Skin | Mostly |
| Sarcina spp | Skin | ||
| Staphylococcus aureus | Firmicutes | Skin | Sometimes |
| Staphylococcus epidermidis | Firmicutes | Skin | Sometimes, mostly not |
| Staphylococcus haemolyticus | Firmicutes | Skin | |
| Streptococcus viridans | Firmicutes | Skin | |
| Trichophyton spp | Skin | ||
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 Name | Phylum | Location | Pathogenicity |
|---|---|---|---|
| Acinetobacter spp | Anterior urethra | ||
| Bacteroides spp | Bacteroidota | External genitalia | |
| Candida albicans | Ascomycota (fungi) | Anterior urethra, external genitalia | Sometimes |
| Enterobacteriaceae | Anterior urethra, external genitalia | ||
| Gardnerella vaginalis | Vagina | ||
| Lactobacillus spp. | Firmicutes | Vagina | |
| Mycoplasma hominis | Vagina | ||
| Prevotella spp. | Bacteroidota | Vagina | |
| Streptococcus viridans | Firmicutes | Anterior 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 Name | Phylum | Location | Pathogenicity |
|---|---|---|---|
| Acinetobacter spp | Anterior urethra | ||
| Bacteroides spp | Bacteroidota | External genitalia | |
| Candida albicans | Ascomycota (fungi) | Anterior urethra, external genitalia | Sometimes |
| Enterobacteriaceae | Anterior urethra, external genitalia | ||
| Streptococcus viridans | Firmicutes | Anterior urethra, external genitalia |
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