MICROBIOTA: COMPOSITION, FUNCTIONS AND WHERE IT IS FOUND - BIOLOGY - 2025

The normal microbiota of human beings is the set of microorganisms that inhabit the body in a standard way, without causing any disease. Today the term bacterial flora is considered inappropriate.

Taxonomically, the microbiota is composed of very diverse organisms, from bacteria, archaea and eukaryotes to viruses. Microbial communities vary significantly in different areas of the body. In other words, the composition of microbes in the mouth does not correspond to that found in the intestine.

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When we think of bacteria - and microorganisms in general - we tend to evoke pejorative feelings about the presence of these entities in our body. Although it is true that various bacteria cause serious diseases, generalizing this conception is not correct.

The microorganisms in our bodies are indispensable and establish mutualistic and commensal relationships with our organism. Our microbiota significantly impacts our physiology - both directly and indirectly -, contributes to a number of metabolic functions, protects us against pathogens, educates the immune system, among other functions.

Different factors affect the composition of the human microbiota. Among the most prominent are the diet - both in childhood and adulthood -, the mode of birth, use of antibiotics, certain medical conditions, the genotype of the host, among others.

Currently, there is a series of novel molecular methods that allow characterizing the microbiota using advanced and rapid sequencing techniques. The most widely used is the gene that codes for 16S ribosomal RNA and is compared with a database.

What is the microbiota?

The microbiota is defined as the assembly of microorganisms present in a defined environment. In this case, the microorganisms associated with the human body. The term was proposed by Lederberg and McCray, who emphasized the consequences and benefits of these biological entities for human health.

There is a very similar term: the microbiome. In the literature, microbiome and microbiota are often interchangeable concepts. However, if we want to be precise, the microbiome is the catalog of microbes, together with their genes.

An associated term is bacterial "flora", microflora or intestinal flora. Both were used for several decades and were particularly relevant in the medical and scientific literature.

However, this term dating from 1900 is inappropriate, since flora is a term derived from the Latin flower, associated with the plants that inhabit a particular region. And since reference is not being made to the set of microplants that inhabit the human body, the term must be abandoned and replaced by microbiota, or microbiome as the case may be.

Composition of the normal microbiota

Number

The microbiota consists of multiple microorganisms that inhabit the body of each person. In numerical terms there are between 10 and 100 trillion (exceeding the number of host cells) of these symbiotic organisms, which are located mainly in the gastrointestinal tract.

Factors that affect the composition of the microbiota

The microbiota begins to form from the birth of the baby, where its body represents a new environment for microbial colonization. This colonization is dependent on the mode of birth - that is, natural delivery or cesarean section (the latter significantly affects the microbiota).

As the infant grows and develops, the diversity of the microbiota increases linearly, depending on the first colonizers. This will change depending on a wide range of factors, such as breast milk feeding, consumption of certain foods, development of diseases, among others.

Current research indicates that diet is the most important factor that helps determine the type of microbiota that will exist in each individual.

Taxonomy

Taxonomically these microorganisms belong to the three domains of life: eukaryotes, bacteria and archaea.

The identity of these organisms is widely variable between individuals, the individual's body regions and the geographical area where they live. In the next section we will describe in more detail the taxonomic identity of the typical microbiota of each body region.

So are we really human?

Now, knowing the enormous diversity of organisms that inhabit our body, we must ask ourselves who we are and if we can really consider ourselves an individual.

A more adequate view is to consider ourselves a superorganism or holobiont, since we consist of 90% microbial cells and 99% genes from microbes.

Where is it located?

Our body is a rich assemblage of microorganisms, where each structure provides a potential niche for their development. These mutualistic relationships are usually site specific, where a certain set of microorganisms forms colonies in specific regions of the body. The most important regions are:

Gut microbiota

Within the niches provided by the human body, there is no doubt that the best studied - in terms of its microbiota - is the gastrointestinal tract.

Thousands of species are found in the intestine of an adult individual, dominated by the phyla Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria and Verrucomicrobia.

This colonization varies throughout the digestive tract. Lactobacillaceae, Erysiopelotrichaceae and Enterobacteriaceae predominate in the small intestine, rich in the genera Bacteroides spp., Clostridium spp., Bifidobacterium spp.

In the colon the most common inhabitants are Bacteroideceae, Prevotellaceae, Rikenellaceae, Lachnospiraceae and Ruminococcaceae.

This difference in the family of bacteria throughout the intestine reflects the physiological differences that exist throughout the intestine.

In the small intestine, bacterial growth is limited by oxygen concentration, the presence of antimicrobial peptides, and pH values, while in the colon the bacterial load is higher.

In addition, there is a bacterial restriction in the small intestine to avoid competition for nutrient absorption between the microorganisms and the host.

In the feces, the main ones detected belong to the bacterium domain, although there are also representatives of archaea (order Methanobacteriales) and eukaryotes (order Saccharomycetales.)

Oral microbiota

The oral cavity and contiguous extensions represent suitable housing regions for certain types of microorganisms, including the tooth surface, the surface of the tongue, and other keratinized and non-keratinized structures.

A fundamental component of the oral cavity is saliva. In one milliliter of this fluid we can find up to 100 million bacterial cells. Of these, around 300 species have been identified, while another 360 have not been assigned a specific taxonomic identity.

The phylum that dominates the oral cavity is Firmicutes, followed by Proteobacteria, Bacteroides, Actinobacteria, Spirochaetes and Fusobacteria.

Regarding the diversity of archaea, the genus Methanobrevibacter has been isolated on multiple occasions from the oral cavity.

Studies reveal that the presence of archaea is related to the development of periodontal diseases. Thus, the role of these organisms in establishing commensal relationships with guests is not yet clear.

The dominant fungus in the oral cavity belongs to the genus Candida. Like archaea species, they have been related to the development of multiple diseases. Other common genera in the cavity are: Cladosporium, Aureobasidium, Saccharomycetales, Aspergillus and Fusarium.

Finally, the most common viruses in the mouth are herpesviruses. It is estimated that 90% of the population owns them.

Urogenital microbiota

Female urogenital tract

The microbes that inhabit the interior of the vagina are in a fine and balanced association of the mutualistic type, protecting their host and exchanging nutrients, in exchange for an anoxic environment appropriate for their growth.

In women of reproductive age, the vagina contains significant amounts of lactic acid and other antimicrobial substances, which limit the growth of the microbiota. This environment is maintained thanks to the presence of lactic acid producing bacteria, particularly Lactobacillus spp.

In fact, bacteria belonging to this genus have been considered since 1892 as indispensable inhabitants for vaginal health.

In addition to Lactobacillus, the vagina is characterized by the presence of microorganisms of the genera: Staphylococcus, Ureaplasma, Corynebacterium, Streptococcus, Peptostreptococcus, Gardnerella, Bacteroides, Mycoplasma, Enterococcus, Escherichia, Veillonella, Bifidobandida, and the fungus.

As women get older and hormonal levels fluctuate, the microbiota is modified.

Male urogenital tract

Compared to the female urogenital tract, the male microbiota has been little studied and is not known in as much detail.

Some of the genera that have been reported in the penis include Staphylococus epidermidis, Corynebacterium spp., Lactobacillus spp., Among others.

Microbiota of the lungs

The lungs have been organs of great interest for the study of their microbiota. However, there are very limited studies on the subject - coupled with the difficulty in taking samples. Although previously they were considered sterile areas, today this vision has been modified.

The presence of the Streptococcus genera has been found, and in some samples Haemophilus, Rothia, Prevotella, Veillonella and Fusobacterium.

Microbiota of the skin

The largest organ of human beings is the skin, which is covered with a great diversity of microorganisms and is colonized by them from the moment of birth.

About 200 bacterial genera have been identified that are considered residents of the skin. Most of these species belong to three phyla, namely: Actinobacteria, Firmicutes and Proteobacteria.

The composition of the skin's microbiota is closely linked to the skin type, habits and genetics of the host, making it extremely variable.

Most microbes feed on skin secretions, so they form very close relationships.

Features

Digestion and vitamin production

The microbiota fulfills a series of functions in the human body, highlighting its role in improving digestion.

Bacteria that live at the end of the colon are related to the cleavage of polysaccharides that cannot be efficiently metabolized in the small intestine, which increases nutrient absorption.

It has also been shown that different bacteria are capable of producing essential vitamins that will be absorbed by the host. An example of this is one of the organisms best known to scientists: E. coli.

Competition and protection against pathogens

Competition is defined as an antagonistic interaction that involves two or more species competing for a common resource.

The spectrum of harmless microorganisms that we harbor in our body is in constant competition with pathogens and in most cases they manage to displace them - thanks to what in ecology is known as the principle of competitive exclusion.

They are believed to establish the first line of defense against infection by these potential pathogens.

How is the microbiota studied?

The study of the microbiota dates back to the times of Antonie van Leewenhoek, at the beginning of 1680. This researcher studied in a comparative way the different microorganisms that inhabited the oral area and in the feces, noting significant differences in both areas.

The differences went beyond the body region, since this researcher also included comparisons between healthy and sick individuals in his experimental design. In this way, he managed to show the importance of microorganisms in human health.

Historically, the study of the microbiota involved the investment of time and energy in the generation of multiple crops.

At present, this methodology has been replaced by a molecular approach that allows the analysis of genetic sequences of microorganisms (generally the molecular marker used is the gene for 16S and 18S ribosomal RNA.)

By analyzing these sequences, the taxon (eukaryotes, bacteria or archaea) can be assigned to different taxonomic levels, until we reach the species.

The term metagenomics was originally used for the characterization of total DNA, and today it is used more precisely to refer to the study of genetic markers, such as the 16S ribosomal DNA gene.

What happens when imbalances occur in the microbiota?

Although there is no clear and precise outline of all the organisms that inhabit the human body, it is known that the change in their abundance and composition affects health, from digestion disorders to the development of anxious behaviors.

Currently, treatments focused on the reestablishment of the healthy microbiota are managed in patients suffering from some disorders.

References

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