List of human microbiota

Bacteroides spp. anaerobically cultured in blood agar medium

Yersinia enterocolitica colonies growing on XLD agar plates

This article lists some of the species recognized as human flora in humans.

Whole-body distributed

• Acinetobacter calcoaceticus
• Burkholderia cepacia
• Pseudomonas pseudoalcaligenes
• Peptostreptococcus spp

Natural cavities

• Fusobacterium necrophorum
• Eubacterium spp
• Microbacterium spp

Skin

Staphylococcus aureus

• Acinetobacter spp
• Bacillus spp
• Candida albicans
• Corynebacterium spp
• Corynebacterium parvum
• Demodex folliculorum
• Enterobacter cloacae
• Epidermophyton floccosum
• Micrococcus spp
• Micrococcus luteus
• Mycobacterium spp
• Neisseria spp
• Peptostreptococcus spp
• Malassezia ovale
• Propionibacterium spp
• Propionibacterium acnes
• Pseudomonas aeruginosa
• Sarcina spp
• Staphylococcus aureus
• Staphylococcus epidermidis
• Staphylococcus haemolyticus
• Streptococcus viridans
• Trichophyton spp

Hair follicles

• Staphylococcus aureus

External ear

• Corynebacterium spp
• Staphylococcus aureus
• Staphylococcus epidermidis

Mucous membranes

• Chlamydia trachomatis
• Hemophilus influenzae
• Staphylococcus aureus
• Staphylococcus epidermidis

Eye

Conjunctiva

• Chlamydia trachomatis
• Chlamydophila pneumoniae
• Haemophilus aegyptius
• Haemophilus influenzae
• Moraxella spp
• Neisseria spp
• Staphylococcus aureus
• Staphylococcus epidermidis
• Streptococcus viridians

Gastro-intestinal tract

Escherichia coli

Binomial name	Location
Achromobacter spp	Large intestine, small intestine (Ileon)
Acidaminococcus fermentans	Large intestine
Acinetobacter calcoaceticus	Large intestine
Actinomyces spp	Mouth, small and large intestine
Actinomyces viscosus	Mouth
Actinomyces naeslundii	Mouth
Aeromonas spp	Large intestine, small intestine (Ileon)
Aggregatibacter actinomycetemcomitans	Mouth
Anaerobiospirillum spp	Feces
Alcaligenes faecalis	Large intestine, small intestine (Ileon)
Arachnia propionica	Mouth
Bacillus spp	Large intestine
Bacteroides spp	Mouth, 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 spp	Large intestine, feces
Buchnera aphidicola	Mouth
Butyriviberio fibrosolvens	Large intestine
Campylobacter spp	Large intestine
Campylobacter coli	General distribution
Campylobacter sputorum	Mouth
Campylobacter upsaliensis	Mouth
Candida albicans	Mouth
Capnocytophaga spp	Mouth
Clostridium spp	Large intestine, small intestine (Ileon)
Citrobacter freundii	Sputum
Clostridium difficile	Large intestine
Clostridium sordellii	Stomach, small intestine, large intestine, rectus, anus channel
Corynebacterium spp	Mouth
Eikenella corrodens	General distribution, mouth
Enterobacter cloacae	General distribution
Enterococcus spp	Mouth, GI tract
Enterococcus faecalis	General distribution
Enterococcus faecium	General distribution
Escherichia coli	General distribution
Eubacterium spp	Mouth, GI tract
Flavobacterium spp	Large intestine, small intestine (Ileon)
Fusobacterium spp	Mouth, GI tract
Fusobacterium nucleatum	Mouth
Gordonia Bacterium spp	Sputum
Haemophilus parainfluenzae	Mouth
Haemophilus paraphrophilus	Mouth
Lactobacillus spp	Mouth, Saliva, GI tract (known probiotic)
Leptotrichia buccalis	Mouth
Methanobrevibacter smithii	Intestines
Morganella morganii	Feces
Mycobacteria spp	Large intestine, small intestine (Ileon)
Mycoplasma spp	Large intestine, small intestine (Ileon)
Micrococcus spp	Mouth
Mycoplasma spp	Mouth
Mycobacterium chelonae	Sputum
Neisseria spp	Mouth
Neisseria sicca	Saliva, sputum
Peptococcus spp	Mouth, large intestine
Peptostreptococcus spp	Mouth, GI tract
Plesiomonas shigelloides	General distribution
Porphyromonas gingivalis	Mouth
Propionibacterium spp	Large intestine
Propionibacterium acnes	General distribution
Providencia spp	Feces
Pseudomonas aeruginosa	Large intestine, small intestine (Ileon)
Ruminococcus bromii	Large intestine
Rothia dentocariosa	Mouth
Ruminococcus spp	Cecum, large intestine
Sarcina spp	Large 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 spp	Mouth, large Intestine
Vibrio spp	Large intestine, Small intestine (Ileon)
Vibrio sputorum	Mouth
Wolinella succinogenes	Mouth
Yersinia enterocolitica	Large intestine

Respiratory tract

Color-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells

Binomial name	Location
Acinetobacter spp	Nasopharynx
Burkholderia cepacia complex	Lung
Campylobacter sputorum	Nasopharynx
Candida albicans	Pharynx
Cardiobacterium spp	Nose
Chlamydophila pneumoniae	Lung
Citrobacter freundii	Throat
Eikenella corrodens	General distribution
Haemophilus spp	Nasopharynx
Haemophilus parainfluenzae	Pharynx
Haemophilus paraphrophilus	Pharynx
Kingella spp	Upper respiratory Tract
Kingella kingae	Upper respiratory Tract
Moraxella spp	Nasopharynx
Moraxella catarrhalis	Nasopharynx
Mycoplasma orale	Oropharynx
Mycoplasma pneumoniae	Respiratory epithelium
Neisseria spp	Nasopharynx
Neisseria cinerea	Nasopharynx
Neisseria elongata	Pharynx
Neisseria gonorrhoeae	Pharynx
Neisseria lactamica	Nasopharynx
Neisseria meningitidis	Nasopharynx
Neisseria mucosa	Nasopharynx
Neisseria sicca	Nasopharynx
Peptococcus spp	Upper respiratory tract
Peptostreptococcus spp	Pharynx
Pseudomonas aeruginosa	Lung
Selenomonas sputigena	Nasopharynx
Staphylococcus aureus	Nose
Streptobacillus spp	Throat, nasopharynx
Streptococcus constellatus	Oropharynx
Streptococcus intermedius	Oropharynx
Streptococcus mitis	General distribution
Streptococcus pyogenes	Upper respiratory tract
Streptococcus viridans	Pharynx

Urogenital tract

Binomial name	Location
Acinetobacter spp	Anterior urethra, vagina
Bacteroides spp	External genitalia
Bifidobacterium spp	Vagina
Candida albicans	Anterior urethra, external genitalia, vagina
Chlamydia trachomatis	Urethra, vagina, fallopian tubes, prostate gland
Clostridium spp	Vagina
Corynebacterium spp	Anterior urethra, external genitalia, vagina
Enterobacteriaceae	Anterior urethra, external genitalia, vagina
Neisseria gonorrhoeae	Urethra, vagina, prostate gland
Streptococcus viridans	Anterior urethra, external genitalia, vagina
Eikenella corrodens	General distribution
Streptococcus anginosus	General distribution
Staphylococcus aureus	Perineum
Gardnerella vaginalis	Female reproductive system
Mycoplasma hominis	Cervix, vagina
Mobiluncus curtisii	Vagina
Mobiluncus mulieris	Vagina

External links

• National Library of Medicine. Medical Subject Heading