How the 16s rRNA based taxonomic analysis can be used to decipher the functional potential of microbial species either in isolated conditions or in case of community genomics. As the 16srRNA gene is a very short sequence of a microbe DNA, highlighting the taxonomic conservation among the bacterial species. Moreover, they are untranslatable sequences of rRNA. So on which basis they are used to predict the microbial pathways and functional genes in the microbial species identified using them?
Dear Nitish
16rdna sequence generally used to identify the microbial species. These are sequences from which transcription and translation start. ORF contain lot of genes or bases depicts the particular proteins played major role in microbial pathways. Single 16s sequence not decide the future of microbial pathways it is depends on other proteins...
A paper that you might look at is Langille et al., 2017. 'Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences'
https://www.nature.com/articles/nbt.2676
This describes the software PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states). It uses Human Microbiome data to make predictions about metabolic capacity from 16S based on sequenced genomes.
This is true indeed that the 16SrRNA genes are only valid for species identification only. The functional potential prediction form these genes are quite conceptual and strongly depends upon the percentage identity of 16S rRNA genes to the respective species. If the identity of these genes is low so, in that case, the predictions of functional genes with the reference genomes are illusive. So truly speaking, it is not only difficult but illogical also to predict the fuctional genes by analysing the 16S rRNA genes.
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