The microbiome is the set of genomes (genetic material) included in the microbiota, which is the set of microorganisms that co-inhabit the same niche. This community of microorganisms is composed of bacteria, fungi, archaea and viruses.

Almost any niche has a microbiota associated and the study of its microbiome can be achieved through the use of metagenomics. In other words, we can study entire communities of microorganisms by sequencing their genomes or part of them.


It is estimated that there are more microbial cells than human cells in our body, and that the microbiome is about 100 times larger than the human genome.

Microbial communities inhabit almost all surfaces of the body, including the skin, mucous membranes, and the intestinal tract.

  • The microbiota is not static, it changes throughout life. These changes depend on genetic, environmental and cultural factors.
  • In a healthy state, interactions between the microbiota and the host are beneficial and influence both metabolism and the immune response.
  • Sudden changes in the microbiota, or dysbiosis, are observed in the presence of diseases such as: diabetes, irritable bowel syndrome, Chron’s disease, autoimmune diseases, cancer, COPD, caries, etc.

Therefore, knowing the composition of the microbiota and its variation is essential for the development of preventive, diagnostic and therapeutic measures.

Environment and lifestyle

Living in a rural environment helps promote                a richer microbiota, while avoiding a                  sedentary lifestyle.

Stages of life

Our microbiota timidly varies its composition                over the years, in more advanced stages the              general richness decreases while a certain             group of bacteria associated with fragility             increases.


The formation of the intestinal microbiota          begins at birth. Fecal and vaginal              microorganisms transmitted by mothers          (vaginal delivery), or from the environment                     (cesarea) initiate colonization of the                   microbiota.


A diet high in fiber and low in sugars, fats                   and meat as in Eastern countries can                         promote a richer microbiota.


The soil is host to a complex microbiota. It is estimated that 1 g of soil can contain thousands of species of microorganisms and more than 40 million cells.

The health and growth of agricultural crops are linked to the soil microbiota. Microorganisms play a fundamental role in the metabolism and acquisition of nutrients (nitrogen, phosphorus, potassium, etc.) by plants. Therefore the diversity and composition of the soil microbiota are indicators of quality.

Like humans, plants also have an associated microbiome which, together with the soil microbiome, regulates their health and growth.

Knowledge of the microbiota associated with crops allows better decision-making for agricultural management in pursuit of sustainable production.


Like humans, animals host complex microbial communities. The balance of this symbiotic relationship is important for the animal health and nutrition.

The presence of dysbiosis in the animal microbiota is related to the appearance of infectious and reproductive pathologies.

The use of prebiotic and probiotic additives in animal production is on the rise and its purpose is to modulate the host’s microbiota to promote its health and nutrition.

The knowledge of the microbiota constitutes, then, a fundamental tool in production, allowing to improve nutrition, pathogen control, etc.


A comprehensive study of the microbiota of any niche is based on the possibility of knowing its genomic composition, that is, its microbiome.

Current sequencing technologies allow knowing the microbiome without the need for isolation or culture. The set of tools that allow the sequencing of the microbiome is called metagenomics.

There are different metagenomic approaches, among which shotgun metagenomics and barcoding metagenomics stand out.

  • Shotgun metagenomics is based on the sequencing of all the DNA present in an environmental sample. It tries to capture all the genomes of the microbiome and is the gold standard method to study the functional profiles of the microbiome.
  • Barcoding metagenomics is based on the use of marker genes to study the diversity and composition of the microbiota. The most used marker genes are 16S rRNA for prokaryotes and 18S rRNA for eukaryotes.

Metatranscriptomics, metaproteomics and metabolomics represent complements for the understanding of the microbiome, since they allow capturing information on the expression of genes, proteins and metabolites in a given scenario.