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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 [ edit ]
Staphylococcus aureus
Escherichia coli
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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 [ edit ]
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
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]
The healthy uterine microbiome has been identified and over 278 genera have been sequenced.[7]
Ovarian follicle [ edit ]
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 [ edit ]
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 [ edit ]
Other lists of the Human body's contents and building bricks [ edit ]
References [ edit ]