Human microbiota are microorganisms (bacteria, viruses, and archaea) found in a specific environment. They can be found in the stomach, intestines, skin, genitals and other parts of the body.[1] 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.
The "reference" 70 kg human body is estimated to have around 39 trillion bacteria with a mass of about 0.2 kg.[2] [3] [4] [5] 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:[6]
They are usually round or spherical in shape. They can form clusters and are non motile.[7] Examples include Staphylococcus aureus, Streptococcus pyogenes, and Neisseria gonorrhea
As the name implies, these usually have a rod or cylinder shape.Bacillus are generally rod shaped bacteria. Examples include listeria, Salmonella typhimurium, Yersinia enterocolitica, Escherichia coli
These are usually spiral or corkscrew shaped and move using axial filament. Examples include Treponema pallidum and Leptospira borgpetersenii
| 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 | |||
| 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 |
| 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 useful? the scale goes Not, Mostly not, Sometimes, Useful | |
| % of total Microbiome? | How many % does the bacteria in number of organisms make out of the entire human microbiome |
The vaginal microbiota is shaped by puberty, pregnancy and menopause. Vaginal microbiota including some Lactobacilli species protect the vagina from harmful pathogens.[8] They convert glucose to lactic acid and this acidic environment kills harmful pathogens. 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. Vaginal flora can be transmitted to babies during birth. Vaginal dysbiosis can lead to vaginal infections like bacterial vaginosis which makes one relatively susceptible to sexually transmitted diseases. Good personal hygiene and probiotics promote a healthy vaginal microbiota.[9]
The healthy uterine microbiome has been identified and over 278 genera have been sequenced. Bacteria species like Fusobacterium are typically found in the uterus.[10] Although Lactobacillus may be beneficial in the vagina, “increased levels in the uterus through a breach in the cervical barrier” may be harmful to the uterus.[11]
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.[11]
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.[11]
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.[12] 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.[13] 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 can lead to gum inflammations and bad breath.[14] 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.