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Microbiota: What is it and where is it found in the body?

Microbiota: What is it and where is it found in the body?

Published: 17 May, 2024 | 8'

Our body is associated with a very large and diverse population of microorganisms that live on body surfaces and in the cavities that connect our body with the outside world.

While the intestinal microbiota is the most widely known and has been the subject of numerous studies, it is important to know that there are other bacterial communities in our body and that all of them are relevant to our well-being and health.

In this article, we explore what the microbiota is and how many types exist, along with biologist and nutrition doctor Rita Cava.

What is the microbiota?

The term microbiota is defined as a community of microorganisms that stably inhabit a specific location in our body. It is mainly made up of bacteria, and it is estimated that a healthy person can host between 10 and 100 million microorganisms, most of which are in the intestine.

These microbial communities interact with each other and with the surface they are on. "There is a complex interrelation that can be mutualistic or symbiotic (beneficial to themselves and the host) or commensal (beneficial to themselves but not to the host) or opportunistic (harmful to the host's health)," explains biologist and nutrition doctor Rita Cava.

What is the purpose of the microbiota?

"The microbiota is considered to be able to identify a person more accurately than fingerprints. In fact, when the microorganisms that make up the microbiota are in balance or homeostasis (eubiosis), the health of the human body is favored, and when there is an imbalance (disbiosis), the probability of developing gastrointestinal or immunological diseases increases significantly," adds the specialist.

Overall, they fulfill three basic functions: supplying essential nutrients (i.e., amino acids, vitamins), developing the immune system, and protecting against pathogens (antimicrobial antagonism).

What is the human microbiota composed of?

This microbial community includes bacteria, fungi, and viruses. It is estimated that the composition of the microbiota associated with humans is made up of at least 40,000 bacterial strains from 1,800 genera, and the estimated mass of the microbiota (1-2 kg in an adult body) is comparable to the weight of the adult human brain (approximately 1.5 kg).

"This microbiota is primarily acquired during birth (being in line with the maternal microbiota), and then it is modified during growth and exposure to other external factors," explains the expert.

Types of microbiotas according to the colonized surface


The microbiota, depending on the colonized surface or where it resides, is characterized by specific microbial communities with specialized structures and functions.

This is why we can find characteristic microorganisms mainly (in order) in the digestive tract, oral cavity, vagina, and skin. In addition, there are other microbiotas in places like the respiratory tract or mammary gland.

Let's look at some of them.

The intestinal microbiota and its impact on health

The gastrointestinal tract harbors the most abundant and diverse number of microorganisms, containing at least 1014 bacteria, with approximately 200 species.

They are mainly represented by the groups Firmicutes (Clostridium spp., Ruminococcus spp., Peptidococcus spp., etc.) and Bacteroidetes (Bacteroides spp.), accounting for more than 70-75% of the total. The next most common groups are Actinobacteria (Bifidobacterium spp.), Proteobacteria, and Verrucomicrobia. The most studied bacteria in the gastrointestinal tract are Lactobacillus spp. (Firmicutes) and Escherichia spp. (Pseudomonadota), although they are present in smaller numbers.

The intestinal microbiota colonizes throughout the entire gastrointestinal tract:

  • Esophagus: there is no permanent colonization in the esophagus as it is a conduit where ingested food carries possible microorganisms.
  • Stomach: lactobacilli are present mainly in low concentrations in the stomach, mainly because they can withstand the acidic environment, although it has not been established whether they exert any mutualistic activity.
  • Small intestine: there is minimal colonization in the upper part of this section (duodenum) due to the action of bile. In the lower sections (jejunum and ileum), the presence of bacteria, mainly lactobacilli, increases.
  • Large intestine: this is the section of the digestive tract with the highest bacterial density (50% of fecal mass is bacteria), although yeasts (fungi) can also be present. It is estimated that each individual harbors more than 500-1500 species that coexist, creating an extraordinarily balanced and stable environment, therefore resistant to changes from the outside.

Functions of the intestinal microbiota

The metabolic processes of this microbiota are carried out through fermentation and in an oxygen-free environment (anaerobic).

"A large number of substances are produced from the metabolism of this intestinal microbiota, which not only provide energy for their own sustenance but are also used by our body in energy processes, as well as in processes related to the regeneration of the intestinal barrier, intestinal cells, organ function, and modulation of the immune system," explains Rita Cava.

The oral microbiota: gateway to the body

The microorganisms in the oral cavity do not form a stable community; instead, they vary considerably and are mainly represented by at least 700 species of bacteria, fungi, and others. The most representative bacterial groups are Actinobacteria (Actinobaculum spp., Atopobium spp., Cryptobacterium spp.), Bacteroidetes (Bergeyella spp., Prevotella spp., Tannerella spp.), Firmicutes (Abiotrophia spp., Anaerococcus spp., Mogibacterium spp.), Proteobacteria (Lautropia spp., Suttonella spp.), and Synergistetes (Jonquetella spp., Pyramidobacter spp.).

The oral microbiota plays an important protective function against the colonization of extrinsic bacteria that could affect our health. As Dr. Cava explains: "the oral microbiota varies according to its location and displacement within the mouth, and it also varies as we grow older."

  • Location: they can be found in the saliva (which is the main agent for dispersing microorganisms both inside the mouth and to the digestive tract), tongue, teeth, palate, and the mucosa that covers the entire inside of the oral cavity.
  • Displacement: microorganisms "prefer" certain places within the mouth. For example, Streptococcus mutans is found in saliva, dental plaque, and the tongue, and its displacement in these sites is related to mutualistic benefits.
  • Age: the oral microbiota varies with dental changes from childhood to aging, as well as with dental treatments.
  • Replacement: the oral microbiota not only changes over the years but also from day to day, especially the one found on teeth. "For example, on day 1 of a week, there may be streptococci, while on day 7, there may be gram-negative bacilli, spirochetes, etc.," adds Cava.

The vaginal microbiota: balance and women's health

The normal vaginal microbiota is predominantly composed of lactobacilli along with other, less common organisms (including Staphylococcus epidermidis, Corynebacterium spp., Ureaplasma spp., Streptococcus/Enterococcus spp., Gardnerella vaginalis, Candida spp.).

The vaginal mucosa of women of reproductive age contains more than ten different species of Lactobacillus, with L. crispatus, L. gasseri, L. jensenii, and L. iners being the most predominant.

The presence of vaginal lactobacilli is directly related to hormonal levels. The metabolic activity of lactobacilli in the vagina leads to a normal pH of 3.8-4.4. Furthermore, lactobacilli produce antimicrobial substances (such as bacteriocins) and hydrogen peroxide (H2O2), which inhibit the adhesion of pathogens.

"Both hormones and age influence vaginal microbiota," says Dr Cava. Thus, we see that in childhood, there is a small amount of vaginal microbiota, which develops with growth and hormonal presence (estrogens and progesterone).

During menopause, due to the reduction of estrogen levels, the vaginal microbiota undergoes significant changes, especially in lactobacilli, with intestinal bacteria and those from the skin prevailing. These changes can lead to an increased risk of gynecological infections.

Skin microbiota

As we mentioned before, the skin ranks fourth among the parts of the human body colonized by microbiota.

The skin organ is densely colonized by a diverse and highly active microbiota, which performs protective functions due to the development of the so-called acid mantle of the skin (or cutaneous barrier).

In a healthy adult's skin, there can be approximately 108-1010 microorganisms distributed in different cutaneous areas. For example, in the armpits, we find a high concentration of up to 106/cm2, or in the fingertips, there can be a concentration of 102/cm2.

The most abundant group is bacteria, represented by Actinobacteria (Corynebacterium spp., Propionibacterium spp.), Firmicutes (Staphylococcus spp., Streptococcus spp.), and Proteobacteria (Acinetobacter spp., Methylobacterium spp.). The most abundant species among fungi are yeast (Malassezia spp.). Little is known about the role of virus species that can be transmitted mainly through our hands on the skin.

"The activity of skin microbiota stimulates the cutaneous immune system, preventing the establishment of pathogenic strains on its surface or their penetration into our body," says the specialist.

Respiratory tract microbiota


Another place that houses its own microbiota is the respiratory tract. The respiratory passages of an adult have a surface area of approximately 70 m2, which is 40 times larger than the surface area of the skin. This entire surface area is colonized by bacterial communities that vary in each section of the respiratory tract.

"The highest bacterial densities are observed in the upper part of the respiratory tract (which includes the nose, pharynx, and larynx)," says the specialist. The most commonly found bacteria, from the upper to the lower respiratory tract, include Staphylococcus spp., Propionibacterium spp., Moraxella spp., Streptococcus spp., Haemophilus spp., Prevotella spp., Veillonella spp., among others. Adenoviruses and fungi (Aspergillus spp. or Candida spp.) may also be present.

Functions of respiratory microbiota

The upper respiratory tract microbiota is the first line of defense against possible colonization by pathogenic strains, thus preventing respiratory infections. This is referred to as "colonization resistance."

Furthermore, "the respiratory microbiota may also be involved in maintaining respiratory function and immunity," says the specialist.

Mammary gland microbiota

Another representative microbiota is found in the mammary glands.

The mammary glands are mucosal structures with a complex system of ducts. During the end of pregnancy and throughout the lactation period, this becomes an ideal environment for bacterial growth due to the availability of nutrients and the optimal temperature for many microorganisms.

In addition, the mammary structure is exposed to the exterior through the nipple, which contains a microbiota with cutaneous characteristics.

Bacterial flora of breast milk

Breast milk contains between 105 to 107 bacteria, and the most common genera are Staphylococcus spp., Streptococcus spp., Lactococcus spp., Propionibacterium spp., Lactobacillus spp., and Bifidobacterium spp.

This microbial flora is considered "maternal probiotics," and breast milk also contains prebiotics that selectively stimulate bacterial growth and colonize the neonatal gut.

"The benefits of breastfeeding are essential for the intestinal maturation of the child and confer immunomodulatory effects, as well as positive effects on intellectual development," concludes specialist Rita Cava.

Other microbiotas in our body

Although we have reviewed the most prominent microorganism communities in this article, it is important to note that "microorganisms are present in all mucosal surfaces, so there is bacterial colonization or colonization by other species, for example, in the eyes, ears or the urinary tract, which also have characteristic microbial populations," says Cava.

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Content created by the specialists from MARNYS Scientific Information department in collaboration with Dr. Rita Cava. This article is informative and does not replace consultation with a specialist.

Rita CavaAbout the specialist

Dr. Rita Cava Roda, Biologist and PhD in Nutrition and Food Technology. University professor with over 20 years of experience in research and teaching, as well as a nutritionist and dietitian.