On May 20-21, Skoltech hosted an intensive on “Metagenome Analysis in the Oral Cavity”. The participants worked with sequencing data of DNA preparations isolated from samples of human buccal epithelium - the epithelium of the oral cavity.
There are many different microbes living inside the human body and on its surface. By some estimates, the number of microbial cells in the human body is comparable to the number of cells that make up the body. We live in symbiosis with microbes: we influence their lives and they influence ours. The interactions between the human body and its microbiome are difficult to study, although in some cases it is possible to identify the influence of the microbiome on human health and trace the mechanistic underpinnings of this influence.
In addition to microbes, viruses that infect these microbes can also be found in the human body. Viruses are known to be a major factor regulating bacterial populations, so one would expect that the human virome (the totality of viruses) should also be related to health status. In addition, some viruses, by infecting cells, can give them new properties, for example, the ability to secrete toxins. The impact of the virome on human health is less well researched, and we currently know only a small fraction of the variety of viruses living in the human body.
At the previous intensives we used data from natural sources - rivers, seas, soils and found out what kind of bacteria and viruses live in them; we studied bacteriophage strains obtained in the laboratory. This time for the first time together with the students we investigated metagenomic data of samples isolated from the human body.
The human oral cavity is home to many bacteria, so it is not surprising that the epithelial preparations contained a lot of bacterial DNA in addition to human DNA. The bacterial DNA was sequenced along with the human DNA; the BioTechCampus staff who processed the data eliminated the reads corresponding to human genomes and passed the remaining reads to us.
Bacterial mobile genetic elements - bacteriophages and plasmids - can be found in almost any natural bacterial population. Bacteria, in turn, have defense systems that they use to suppress the multiplication of mobile genetic elements.
At our event, we tried to analyze several metagenomic assemblies derived from bacterial reads. We first predicted sequences corresponding to plasmids and viral genomes, and then tried to detect CRISPR-Cas systems in the metagenomic sequences.
Interestingly, many samples contained predicted plasmids and viruses whose nucleotide sequences either do not match at all with known plasmids and viruses from the database, or the similarity is very remote. It is possible that these sequences correspond to the genomes of previously unstudied bacteriophages.
CRISPR-Cas systems were also found in the metagenomic sequences, with loci of type II systems encoding Cas9 proteins, which, in particular, include proteins used in genome editing technologies. This is also a very interesting observation - type II systems are quite rare and are not found in all bacteria, and these proteins can potentially be used as new genome editors.