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 belonging to the human microbiome.

Whole-body distributed

Natural cavities

Skin

Staphylococcus aureus


Hair follicles

External ear

Mucous membranes

Eye

Gastrointestinal tract

Escherichia coli
Binomial nameLocation
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
Cutibacterium acnes General distribution
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
Faecalibacterium spp Large intestine, small intestine (Ileon)
Flavobacterium spp Large intestine, small intestine (Ileon)
Fusobacterium spp Mouth, GI tract
Fusobacterium nucleatum Mouth
Gordonia 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
Providencia spp Feces
Pseudomonas aeruginosa Large intestine, small intestine (Ileon)
Roseburia spp Large intestine
Rothia dentocariosa Mouth
Ruminococcus spp Cecum, large intestine
Ruminococcus bromii 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 nameLocation
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 nameLocation
Acinetobacter spp Anterior urethra
Bacteroides spp External genitalia
Candida albicans Anterior urethra, external genitalia,
Corynebacterium spp Anterior urethra, external genitalia,
Enterobacteriaceae Anterior urethra, external genitalia,
Streptococcus viridans Anterior urethra, external genitalia,
Eikenella corrodens General distribution
Streptococcus anginosus General distribution
Staphylococcus aureus Perineum

Vagina

The vaginal microbiota in pregnancy 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.[1]

Placenta

Uterus

The healthy uterine microbiome has been identified and over 278 genera have been sequenced.[2]

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 spp while the presence of Propionibacterium and Actinomyces were related to negative outcomes. Also, the microbiome can vary from one ovary to the other. Studies are ongoing in the further identification of those bacteria present.[2]

Male reproductive tract

The microbiome present in seminal fluid has been evaluated. Using traditional culturing techniques the microbiome differs between men who have acute prostatitis 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, Lactobacillus, and Prevotella 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.[2]

References

  1. ↑ Fox, Chelsea; Eichelberger, Kacey (2015). "Maternal microbiome and pregnancy outcomes". Fertility and Sterility. 104 (6): 1358–1363. doi:10.1016/j.fertnstert.2015.09.037. ISSN 0015-0282. PMID 26493119; Access provided by the University of Pittsburgh{{cite journal}}: CS1 maint: postscript (link)
  2. 1 2 3 Franasiak, Jason M.; Scott, Richard T. (2015). "Reproductive tract microbiome in assisted reproductive technologies". Fertility and Sterility. 104 (6): 1364–1371. doi:10.1016/j.fertnstert.2015.10.012. ISSN 0015-0282. PMID 26597628; Access provided by the University of Pittsburgh{{cite journal}}: CS1 maint: postscript (link)
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