Gut, skin, mouth, soil or food: each one hosts an invisible community of microorganisms, most of which cannot be cultured. Sequencing its DNA and RNA reveals who makes it up, which genes it carries and what it is doing, and how it changes with disease, diet or treatment.
Hundreds of species of bacteria, fungi and viruses live together in a single sample. Most will not grow on a lab plate, but all of them leave their trace in the sample's DNA and RNA.
Metagenomics reads that trace without culturing. The result is not just a list of species: it is the composition of the community, its functional capacity and its activity, compared between groups or over time.
The level is chosen according to the question, the sample type and the budget, or several are combined in the same study.
A marker gene shared by bacteria (16S), eukaryotes (18S) or fungi (ITS) is sequenced. It is the most cost-effective way to compare the composition of many samples.
All the DNA in the sample is sequenced. It reaches species and strain level, reconstructs genomes and reveals functions, resistance and virulence.
The community's RNA is sequenced to find out which genes are active, not just which ones exist. It is the layer closest to real function.
Depending on the technique, the analysis can reach these levels:
Which microorganisms are present and in what proportion, down to species and, with shotgun, to strain.
Richness and balance of the community, and how similar samples are to each other.
Which species or functions change between conditions or treatments.
Reconstruction of community members' genomes directly from the sample.
Antibiotic resistance genes, which organisms carry them and how they can spread.
Toxins, adhesins and other factors that make a microorganism pathogenic.
Metabolic pathways and capabilities of the community, including the production of compounds of interest.
With metatranscriptomics, which genes and pathways are working at that moment.
Telling strains of the same species apart, useful to track a specific pathogen or probiotic.
How resistance genes move between bacteria in the community.
Longitudinal studies: how the community evolves before, during and after an intervention.
Published microbiome studies, reanalyzed to compare with or extend your own results.
The reconstructed genomes of a community are also a source of new compounds. Many bacteria carry in their DNA the instructions to make antibiotics and other active molecules that have never been studied.
The microbiome is behind questions in health, nutrition, cosmetics and the environment:
Each sample is reviewed and host DNA is removed before analysis.
Abundance of each microorganism per sample, ready for your own analyses.
When the design allows: reconstructed genomes, resistance, virulence and pathways.
What the results mean and what the next steps are.
The analysis is validated against a certified 20-strain reference community: it detected 100% of the species, with a detection limit characterized at around 0.025%. That is how real species are told apart from noise. See the validation.
Starting from the question, the sample type and the number of samples, the most suitable technique is chosen and a proposal is prepared.