List of human microbiota

Last updated

Bacteroides spp. anaerobically cultured in blood agar medium Bacteroides biacutis 01.jpg
Bacteroides spp. anaerobically cultured in blood agar medium
Yersinia enterocolitica colonies growing on XLD agar plates Yersinia enterocolitica 01.png
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]

Contents

Whole-body distributed

Staphylococcus aureus Staphylococcus aureus, 50,000x, USDA, ARS, EMU.jpg
Staphylococcus aureus
Escherichia coli E. coli Bacteria (7316101966).jpg
Escherichia coli
Color-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells SalmonellaNIAID.jpg
Color-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells
Binomial nameLocationPathological?% of total Microbiome?
Acinetobacter calcoaceticus Whole-body distributed
Burkholderia cepacia Whole-body distributed
Peptostreptococcus sppWhole-body distributed
Pseudomonas pseudoalcaligenes Whole-body distributed
Eubacterium sppNatural cavities
Fusobacterium necrophorum Natural cavities
Microbacterium sppNatural cavities
Acinetobacter sppSkin
Bacillus sppSkin
Candida albicans Skin
Candida parapsilosis Skin
Corynebacterium parvum Skin
Corynebacterium sppSkin
Cutibacterium acnes Skin
Demodex folliculorum Skin
Enterobacter cloacae Skin
Epidermophyton floccosum Skin
Malassezia ovale Skin
Micrococcus luteus Skin
Micrococcus sppSkin
Mycobacterium sppSkin
Neisseria sppSkin
Peptostreptococcus sppSkin
Propionibacterium sppSkin
Pseudomonas aeruginosa SkinMostly
Sarcina sppSkin
Staphylococcus aureus Skin
Staphylococcus epidermidis SkinSometimes, mostly not
Staphylococcus haemolyticus Skin
Streptococcus viridans Skin
Trichophyton sppSkin
Staphylococcus aureus Hair follicles
Corynebacteriumspp 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 sppEye
Neisseria sppEye
Staphylococcus aureus Eye
Staphylococcus epidermidis Eye
Streptococcus viridans Eye
Achromobacter sppLarge intestine, small intestine (Ileon)
Acidaminococcus fermentans Large intestine
Acinetobacter calcoaceticus Large intestine
Actinomyces sppMouth, small and large intestine
Actinomyces viscosus Mouth
Actinomyces naeslundii Mouth
Aeromonas sppLarge intestine, small intestine (Ileon)
Aggregatibacter actinomycetemcomitans Mouth
Anaerobiospirillum sppFeces
Alcaligenes faecalis Large intestine, small intestine (Ileon)
Arachnia propionica Mouth
Bacillus sppLarge intestine
Bacteroides sppMouth, 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 sppLarge intestine, feces
Buchnera aphidicola Mouth
Butyriviberio fibrosolvens Large intestine
Campylobacter sppLarge intestine
Campylobacter coli General distribution
Campylobacter sputorum Mouth
Campylobacter upsaliensis Mouth
Candida albicans Mouth
Capnocytophaga sppMouth
Clostridium sppLarge intestine, small intestine (Ileon)
Citrobacter freundii Sputum
Clostridium difficile Large intestine
Clostridium sordellii Stomach, small intestine, large intestine, rectus, anus channel
Corynebacterium sppMouth
Cutibacterium acnes General distribution
Eikenella corrodens General distribution, mouth
Enterobacter cloacae General distribution
Enterococcus sppMouth, GI tract
Enterococcus faecalis General distribution
Enterococcus faecium General distribution
Escherichia coli General distribution
Eubacterium sppMouth, GI tract
Faecalibacterium sppLarge intestine, small intestine (Ileon)
Flavobacterium sppLarge intestine, small intestine (Ileon)
Fusobacterium sppMouth, GI tract
Fusobacterium nucleatum Mouth
Gordonia sppSputum
Haemophilus parainfluenzae Mouth
Haemophilus paraphrophilus Mouth
Lactobacillus sppMouth, Saliva, GI tract (known probiotic)
Leptotrichia buccalis Mouth
Methanobrevibacter smithii Intestines
Morganella morganii Feces
Mycobacteria sppLarge intestine, small intestine (Ileon)
Mycoplasma sppLarge intestine, small intestine (Ileon)
Micrococcus sppMouth
Mycoplasma sppMouth
Mycobacterium chelonae Sputum
Neisseria sppMouth
Neisseria sicca Saliva, sputum
Peptococcus sppMouth, large intestine
Peptostreptococcus sppMouth, GI tract
Plesiomonas shigelloides General distribution
Porphyromonas gingivalis Mouth
Propionibacterium sppLarge intestine
Providencia sppFeces
Pseudomonas aeruginosa Large intestine, small intestine (Ileon)
Roseburia sppLarge intestine
Rothia dentocariosa Mouth
Ruminococcus sppCecum, large intestine
Ruminococcus bromii Large intestine
Sarcina sppLarge 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 sppMouth, large Intestine
Vibrio sppLarge intestine, small intestine (Ileon)
Vibrio sputorum Mouth
Wolinella succinogenes Mouth
Yersinia enterocolitica Large intestine
Acinetobacter sppNasopharynx
Burkholderia cepacia complex Lung
Campylobacter sputorum Nasopharynx
Candida albicans Pharynx
Cardiobacterium sppNose
Chlamydophila pneumoniae Lung
Citrobacter freundii Throat
Eikenella corrodens General distribution
Haemophilus sppNasopharynx
Haemophilus parainfluenzae Pharynx
Haemophilus paraphrophilus Pharynx
Kingella sppUpper respiratory tract
Kingella kingae Upper respiratory tract
Moraxella sppNasopharynx
Moraxella catarrhalis Nasopharynx
Mycoplasma orale Oropharynx
Mycoplasma pneumoniae Respiratory epithelium
Neisseria sppNasopharynx
Neisseria cinerea Nasopharynx
Neisseria elongata Pharynx
Neisseria gonorrhoeae Pharynx[ citation needed ]
Neisseria lactamica Nasopharynx
Neisseria meningitidis Nasopharynx
Neisseria mucosa Nasopharynx
Neisseria sicca Nasopharynx
Peptococcus sppUpper respiratory tract
Peptostreptococcus sppPharynx
Pseudomonas aeruginosa Lung
Selenomonas sputigena Nasopharynx
Staphylococcus aureus Nose
Streptobacillus sppThroat, nasopharynx
Streptococcus constellatus Oropharynx
Streptococcus intermedius Oropharynx
Streptococcus mitis General distribution
Streptococcus pyogenes Upper respiratory tract
Streptococcus viridans Pharynx
Acinetobacter sppAnterior urethra
Bacteroides sppExternal genitalia
Candida albicans Anterior urethra, external genitalia
Corynebacterium sppAnterior 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

ColumnDescription
Binomial nameName of the species, Ideally including the shape of the bacteria
LocationWhere 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

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

Related Research Articles

<span class="mw-page-title-main">Endometrium</span> Inner mucous membrane of the mammalian uterus

The endometrium is the inner epithelial layer, along with its mucous membrane, of the mammalian uterus. It has a basal layer and a functional layer: the basal layer contains stem cells which regenerate the functional layer. The functional layer thickens and then is shed during menstruation in humans and some other mammals, including other apes, Old World monkeys, some species of bat, the elephant shrew and the Cairo spiny mouse. In most other mammals, the endometrium is reabsorbed in the estrous cycle. During pregnancy, the glands and blood vessels in the endometrium further increase in size and number. Vascular spaces fuse and become interconnected, forming the placenta, which supplies oxygen and nutrition to the embryo and fetus. The speculated presence of an endometrial microbiota has been argued against.

Reproductive technology encompasses all current and anticipated uses of technology in human and animal reproduction, including assisted reproductive technology (ART), contraception and others. It is also termed Assisted Reproductive Technology, where it entails an array of appliances and procedures that enable the realization of safe, improved and healthier reproduction. While this is not true of all people, for an array of married couples, the ability to have children is vital. But through the technology, infertile couples have been provided with options that would allow them to conceive children.

<span class="mw-page-title-main">Intracytoplasmic sperm injection</span> In vitro fertilization procedure

Intracytoplasmic sperm injection is an in vitro fertilization (IVF) procedure in which a single sperm cell is injected directly into the cytoplasm of an egg. This technique is used in order to prepare the gametes for the obtention of embryos that may be transferred to a maternal uterus. With this method, the acrosome reaction is skipped.

Infertility is the inability of an animal or plant to reproduce by natural means. It is usually not the natural state of a healthy adult, except notably among certain eusocial species. It is the normal state of a human child or other young offspring, because they have not undergone puberty, which is the body's start of reproductive capacity.

<span class="mw-page-title-main">Human microbiome</span> Microorganisms in or on human skin and biofluids

The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the gastrointestinal tract, skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, and the biliary tract. Types of human microbiota include bacteria, archaea, fungi, protists, and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms; however, the term human metagenome has the same meaning.

<span class="mw-page-title-main">Epididymis</span> Tube that connects a testicle to a vas deferens

The epididymis is an elongated tubular structure attached to the posterior side of each one of the two male reproductive glands, the testicles. It is a single, narrow, tightly coiled tube in adult humans, 6 to 7 centimetres in length; uncoiled the tube would be approximately 6 m long. It connects the testicle to the vas deferens in the male reproductive system. The epididymis serves as an interconnection between the multiple efferent ducts at the rear of a testicle (proximally), and the vas deferens (distally). Its primary function is the storage, maturation and transport of sperm cells.

Fertility medications, also known as fertility drugs, are medications which enhance reproductive fertility. For women, fertility medication is used to stimulate follicle development of the ovary. There are very few fertility medication options available for men.

<span class="mw-page-title-main">Semen analysis</span> Scientific analysis of semen

A semen analysis, also called seminogram or spermiogram, evaluates certain characteristics of a male's semen and the sperm contained therein. It is done to help evaluate male fertility, whether for those seeking pregnancy or verifying the success of vasectomy. Depending on the measurement method, just a few characteristics may be evaluated or many characteristics may be evaluated. Collection techniques and precise measurement method may influence results.

<span class="mw-page-title-main">Vaginal flora</span> Microorganisms present in the vagina

Vaginal flora, vaginal microbiota or vaginal microbiome are the microorganisms that colonize the vagina. They were discovered by the German gynecologist Albert Döderlein in 1892 and are part of the overall human flora. The amount and type of bacteria present have significant implications for an individual's overall health. The primary colonizing bacteria of a healthy individual are of the genus Lactobacillus, such as L. crispatus, and the lactic acid they produce is thought to protect against infection by pathogenic species.

A cervical mucus plug (operculum) is a plug that fills and seals the cervical canal during pregnancy. It is formed by a small amount of cervical mucus that condenses to form a cervical mucus plug during pregnancy.

Pregnancy rate is the success rate for getting pregnant. It is the percentage of all attempts that leads to pregnancy, with attempts generally referring to menstrual cycles where insemination or any artificial equivalent is used, which may be simple artificial insemination (AI) or AI with additional in vitro fertilization (IVF).

Prevotella is a genus of Gram-negative bacteria.

Ureaplasma parvum is a species of Ureaplasma, a genus of bacteria belonging to the family Mycoplasmataceae.

The vaginal flora in pregnancy, or vaginal microbiota in pregnancy, is different from the vaginal flora before sexual maturity, during reproductive years, and after menopause. A description of the vaginal flora of pregnant women who are immunocompromised is not covered in this article. The composition of the vaginal flora significantly differs in pregnancy. Bacteria or viruses that are infectious most often have no symptoms.

<span class="mw-page-title-main">Placental microbiome</span>

The placental microbiome is the nonpathogenic, commensal bacteria claimed to be present in a healthy human placenta and is distinct from bacteria that cause infection and preterm birth in chorioamnionitis. Until recently, the healthy placenta was considered to be a sterile organ but now genera and species have been identified that reside in the basal layer.

<span class="mw-page-title-main">Uterine microbiome</span>

The uterine microbiome is the commensal, nonpathogenic, bacteria, viruses, yeasts/fungi present in a healthy uterus, amniotic fluid and endometrium and the specific environment which they inhabit. It has been only recently confirmed that the uterus and its tissues are not sterile. Due to improved 16S rRNA gene sequencing techniques, detection of bacteria that are present in low numbers is possible. Using this procedure that allows the detection of bacteria that cannot be cultured outside the body, studies of microbiota present in the uterus are expected to increase.

Antisperm antibodies (ASA) are antibodies produced against sperm antigens.

Morphokinetics (‘morpho’’ form/shape and ‘kinetics’ movement) refers to time specific morphological changes during embryo development providing dynamic information on a fertilized egg. The detailed information eases morphological selection of embryos with high implantation potential to be used in In-Vitro Fertilisation treatment.

<span class="mw-page-title-main">Sperm Chromatin Structure Assay</span>

Sperm Chromatin Structure Assay (SCSA) is a diagnostic approach that detects sperm abnormality with a large extent of DNA fragmentation. First described by Evenson in 1980, the assay is a flow cytometric test that detects the vulnerability of sperm DNA to acid-induced denaturation DNA in situ. SCSA measures sperm DNA fragmentation attributed to intrinsic and extrinsic factors and reports the degree of fragmentation in terms of DNA Fragmentation Index (DFI). The use of SCSA expands from evaluation of male infertility and subfertility, toxicology studies and evaluation of quality of laboratory semen samples. Notably, SCSA outcompetes other convention sperm DNA fragmentation (sDF) assays such as TUNEL and COMET in terms of efficiency, objectivity, and repeatability.

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. 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)