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.
Therefore, knowing the composition of the microbiota and its variation is essential for the development of preventive, diagnostic and therapeutic measures.
Living in a rural environment helps promote a richer microbiota, while avoiding a sedentary lifestyle.
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.
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.