List of human microbiota

Source: Wikipedia, the free encyclopedia.
(Redirected from 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. The "reference" 70 kg human body is estimated to have around 39 trillion bacterias with their total mass of about 0.2 kg. [1][2][3][4] These can be separated into about 10,000 microbial species. about 180 of the most studied is listed below here. However all of these can broadly be put into 3 categories:[5]

  • Spheres or ball-shaped (cocci bacteria).
  • Rod-shaped bacteria (bacilli).
  • Spirals or helixes (spirochetes).

Whole-body distributed

Staphylococcus aureus
Escherichia coli
Color-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells
Binomial name Location Pathological? % of total Microbiome?
Acinetobacter calcoaceticus Whole-body distributed
Burkholderia cepacia Whole-body distributed
Peptostreptococcus spp Whole-body distributed
Pseudomonas pseudoalcaligenes Whole-body distributed
Eubacterium spp Natural cavities
Fusobacterium necrophorum Natural cavities
Microbacterium spp Natural cavities
Acinetobacter spp Skin
Bacillus spp Skin
Candida albicans Skin
Candida parapsilosis Skin
Corynebacterium parvum Skin
Corynebacterium spp Skin
Cutibacterium acnes Skin
Demodex folliculorum Skin
Enterobacter cloacae Skin
Epidermophyton floccosum Skin
Malassezia ovale Skin
Micrococcus luteus Skin
Micrococcus spp Skin
Mycobacterium spp Skin
Neisseria spp Skin
Peptostreptococcus spp Skin
Propionibacterium spp Skin
Pseudomonas aeruginosa Skin Mostly
Sarcina spp Skin
Staphylococcus aureus Skin
Staphylococcus epidermidis Skin Sometimes, mostly not
Staphylococcus haemolyticus Skin
Streptococcus viridans Skin
Trichophyton spp Skin
Staphylococcus aureus Hair follicles
Corynebacterium spp External ear
Staphylococcus aureus External ear
Staphylococcus epidermidis External ear
Chlamydia trachomatis Mucous membranes
Hemophilus influenzae Mucous membranes
Staphylococcus aureus Mucous membranes
Staphylococcus epidermidis Mucous membranes
Chlamydophila pneumoniae Eye
Haemophilus aegyptius Eye
Haemophilus influenzae Eye
Moraxella spp Eye
Neisseria spp Eye
Staphylococcus aureus Eye
Staphylococcus epidermidis Eye
Streptococcus viridans Eye
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
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[citation needed]
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
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

Naming convention for the table

Column Description
Binomial name Name of the species, Ideally including the shape of the bacteria
Location Where it can be found in the body
Pathological? Can it harm humans or is it usefull? the scale goes Not, Mostly not, Sometimes, Usefull
% of total Microbiome? How many % does the bacteria in number of organisms make out of the entire human microbiome

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.[6]

Uterus

The healthy uterine microbiome has been identified and over 278 genera have been sequenced.[7]

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. The microbiome can vary from one ovary to the other. Studies are ongoing in the further identification of those bacteria present.[7]

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.[7]

See also

Other lists of the Human body's contents and building bricks

References

  1. ^ "Revised Estimates for the Number of Human and Bacteria Cells in the Body". PLOS Biology. 2016-08-19. doi:10.1371/journal.pbio.1002533. PMC 4991899.
  2. ^ Abbott, Alison (2016-01-08). "Scientists bust myth that our bodies have more bacteria than human cells". Nature. doi:10.1038/nature.2016.19136. ISSN 1476-4687.
  3. ^ "Do our bodies contain far more bacteria than human cells? - Eppendorf Handling Solutions". handling-solutions.eppendorf.com. 2022-01-10. Retrieved 2023-07-16.
  4. ^ "NIH Human Microbiome Project defines normal bacterial makeup of the body". National Institutes of Health (NIH). 2015-08-31. Retrieved 2023-07-16.
  5. ^ "Bacteria: Definition, Types, Benefits, Risks & Examples". Cleveland Clinic. Retrieved 2023-07-16.
  6. ^ 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)
  7. ^ a b c 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)