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. 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.
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. 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:
Spheres or ball-shaped (cocci bacteria) Cocci are usually round or spherical in shape. They can form clusters and are non-motile. Examples include Staphylococcus aureus, Streptococcus pyogenes, and Neisseria gonorrhea.
Rod-shaped bacteria (bacilli)
Bacilli usually have a rod or cylinder shape. Examples include Listeria, Salmonella typhimurium, Yersinia enterocolitica, and Escherichia coli.
Spirals or helixes (spirochetes) Spirochetes are usually spiral or corkscrew shaped and move using axial filament. Examples include Treponema pallidum and Leptospira borgpetersenii.
Eye +Binomial NamePhylumLocationPathogenicityFrequency/AbundanceChlamydia pneumoniaeChlamydiotaEyeYesChlamydia trachomatisChlamydiotaEyeYesHaemophilus aegyptiusProteobacteriaEyeHaemophilus influenzaeProteobacteriaEyeSometimesMoraxella sppProteobacteriaEyeSometimesNeisseria sppProteobacteriaEyeOnly N. gonorrheae and N. meningitidisStaphylococcus aureusFirmicutesEyeSometimesStaphylococcus epidermidisFirmicutesEyeStreptococcus viridansFirmicutesEye
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. 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. 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. S. mutans is the main component of the oral microbiota.
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. 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. +Binomial NamePhylumLocationPathogenicityFrequency/AbundanceAbiotrophia sppMouthActinomyces sppActinomycetotaMouthActinomyces viscosusActinomycetotaMouthActinomyces naeslundiiActinomycetotaMouthAggregatibacter actinomycetemcomitansMouthArachnia propionicaMouthAspergillus sppAscomycota (fungi)MouthSometimesAtopobium sppActinomycetotaMouthAureobasidium sppfungiMouthBacterionema matruchotii (Corynebacterium matruchotii)ActinomycetotaGingivaBacteroides sppBacteroidotaMouthBacteroides gingivalisBacteroidotaMouthBacteroides melaninogenicusBacteroidotaMouthBergeyella sppBacteroidotaMouthBifidobacterium sppActinomycetotaMouthBuchnera aphidicolaMouthBulleidia sppFirmicutesMouthCampylobacter sppCampylobacterotaMouthCandida sppAscomycota (fungi)MouthCandida albicansAscomycota (fungi)MouthSometimesCapnocytophaga sppBacteroidotaMouthCardiobacterium sppProteobacteriaMouthCatonella sppFirmicutesHard palateCitrobacter freundiiThroatCladosporium sppfungiMouthCorynebacterium sppActinomycetotaMouthOnly C. diphtheriaeCryptococcus sppfungiMouthDesulfobacter sppMouthDesulfovibrio sppMouthDialister sppFirmicutesMouthEikenella corrodensProteobacteriaMouthSometimesEntamoeba gingivalisAmoebozoa (eukaryote)MouthEnterococcus sppFirmicutesMouthSometimesEnterococcus faeciumFirmicutesMouthEubacterium sppFirmicutesMouthFusarium sppfungiMouthFusobacterium sppFusobacteriotaMouthFusobacterium necrophorumFusobacteriotaOropharynxFusobacterium nucleatumFusobacteriotaMouthSometimesGemella sppFirmicutesMouthGordonia sppSputumGranulicatella sppFirmicutesMouthHaemophilus sppProteobacteriaMouthKingella sppProteobacteriaMouthLactobacillus sppFirmicutesMouth, SalivaNoLautropia sppProteobacteriaMouthLeptotrichia buccalisFusobacteriotaMouthMethanobrevibacter oralisMethanobacteriota (archaea)MouthMethanosarcina mazeiiMethanobacteriota (archaea)MouthMicrococcus sppMouthMogibacterium sppFirmicutesMouthMycoplasma sppMouthMycoplasma oraleOropharynxMycobacterium chelonaeSputumCandidatus Nanosynbacter lyticusCandidatus SaccaribacteriaMouthNeisseria sppProteobacteriaMouthOnly N. gonorrheae and N. meningitidisOribacterium sppFirmicutesMouthParvimonas sppFirmicutesMouthPeptococcus sppMouthPeptostreptococcus sppFirmicutesMouthPhocoenobacter sppProteobacteriaMouthPorphyromonas gingivalisBacteroidotaMouthSometimesPrevotella sppBacteroidotaMouthSometimesPropionibacterium sppActinomycetotaMouthPseudoramibacter sppMouthRothia dentocariosaActinomycetotaMouthOccasionallySelenomonas sppFirmicutesMouthSimonsiella sppMouthStaphylococcus aureusFirmicutesMouthSometimesStaphylococcus epidermidisFirmicutesMouthStreptococcus sppFirmicutesMouthStreptococcus anginosusFirmicutesOropharynxStreptococcus mitisFirmicutesMouthStreptococcus mutansFirmicutesTeeth: dental plaqueStreptococcus oralisFirmicutesTeeth: dental plaqueStreptococcus sobrinusFirmicutesTeeth: dental plaqueStreptococcus constellatusFirmicutesOropharynxStreptococcus intermediusFirmicutesOropharynxTannerella forsythiaBacteroidotaMouthSometimesTorulopsis glabrataMouthTreponema denticolaSpirochetotaMouthTrichomonas tenaxeukaryoteMouthVeillonella sppFirmicutesMouthVibrio sputorumMouthWolinella sppCampylobacterotaMouth
Respiratory System +Binomial NamePhylumLocationPathogenicityFrequency/AbundanceAcinetobacter sppNasopharynxCitrobacter freundiiSputumBurkholderia cepacia complexProteobacteriaLungCampylobacter sputorumNasopharynxCandida albicansAscomycota (fungi)PharynxCardiobacterium sppNoseChlamydophila pneumoniaeChlamydiotaLungFusobacterium sppFusobacteriotaLungHaemophilus sppProteobacteriaNasopharynx, lungHemophilus influenzaeProteobacteriaMucous membranesSometimesHaemophilus parainfluenzaeProteobacteriaPharynxHaemophilus paraphrophilusProteobacteriaPharynxKingella sppProteobacteriaUpper respiratory tractKingella kingaeProteobacteriaUpper respiratory tractMoraxella sppProteobacteriaNasopharynxMoraxella catarrhalisProteobacteriaNasopharynxMycoplasma pneumoniaeRespiratory epitheliumNeisseria sppProteobacteriaNasopharynxNeisseria cinereaProteobacteriaNasopharynxNeisseria elongataProteobacteriaPharynxNeisseria gonorrhoeaeProteobacteriaPharynxYesNeisseria lactamicaProteobacteriaNasopharynxNeisseria meningitidisProteobacteriaNasopharynxYesNeisseria mucosaProteobacteriaNasopharynxNeisseria siccaProteobacteriaNasopharynxPeptococcus sppUpper respiratory tractPeptostreptococcus sppFirmicutesPharynxPseudomonas sppProteobacteriaLungPseudomonas aeruginosaProteobacteriaLungYesSelenomonas sputigenaFirmicutesNasopharynxStaphylococcus aureusFirmicutesNoseSometimesStreptobacillus sppThroat, nasopharynxStreptococcus sppFirmicutesLungStreptococcus pyogenesFirmicutesUpper respiratory tractStreptococcus pneumoniaeFirmicutesNasopharynxSometimes
Gastrointestinal Tract