This approach is conventionally based on the total gDNA extraction present in a given sample, thus making not possible to differentiate, living and therefore active bacteria, from dead and non-functional bacteria to have release their DNA, in the given sample.
Illumina “short read” sequencing limits the sequencing of amplicons of 550 bp maximum, therefore short fragments, which will allow the amplification even of degraded gDNA of dead bacteria.
It thus comes to the limit of this method of sequencing 16S rRNA from gDNA, for the distinction of living and active bacteria from dead and non-functional bacteria.
In collaboration with the “ Staphylococcal pathogenesis” team of the International Center for Infectiology Research of Lyon (INSERM U1111 – CNRS UMR5308 – ENS Lyon – Lyon 1 University), more particularly with Dr Jean-Philippe RASIGADE and Anaïs BARRAY, we have developed a method allowing sequencing and identification only of live and active bacteria in a given sample.
If you are interested in this approach, please do not hesitate to contact us.