Shotgun metagenomics is used to characterize the complete bacterial phylogeny and taxonomy of complex, microbiome samples. Another commonly used method is amplicon sequencing targeted at the highly conserved 16S rRNA gene marker. Compared to shotgun metagenomics, 16S rRNA sequencing results are biased due to reliance on PCR amplification and captures microbial profiles at a particular moment in time rather than an absolute of the actual quantity of a particular bacteria present in the sample. With the decrease in sequencing cost and novel rRNA removal technologies, researchers can now easily interrogate microbiome samples beyond the 16S rRNA genes.
While metagenomics (DNA) has been more common, metatranscriptomics (RNA) is growing in importance because it better represents metabolically active organisms, provides vital information on active gene pathways, and can be used to understand the effect on gene expression of changing environmental conditions or treatments.
Microbiome sample types are diverse and come from a variety of sources including soil, water sources, saliva, gut, and everywhere a microbial community can be found. Microbiome samples often consist of a mixture of eukaryotic and bacterial cells. For instance, stool samples are generally comprised of mostly bacterial species and very little human cells, but saliva samples are the opposite. Depending on the sample type and the research goal, the mixture of eukaryotic and bacterial cells present in a sample can be a challenge. For metatranscriptomics, low-expressing genes are sometimes barely detectable due to the overabundance of host information and abundant ribosomal RNA in the sample. For metagenomics, host contamination obscures interesting microbial community detection.
With CRISPRclean, you can now identify more microbial species and characterize the bacterial phylogeny and taxonomy of complex, microbiome samples.