For intestinal microbiota analysis which culture independent method (Sanger and Pyrosequencing) can analyse bacterial identification at the level of species.
First of all, this question lacks some information about the kind of analysis you want to perform. Du you want to do metagenomics or metamircobiomic? WGS or targeted approaches (marker genes)?
Because primarily the phylogenetic resolution depends not on the sequencing platform but on the material you're basing your conclusions on. For instance the 16S rRNA gene is a nice marker gene, but it lacks resolution. Of course, sequencing the full 16S rRNA gene with Sanger yields better resolution compared to shorter pyrosequencing reads but you still wont be able to reliable differentiate between several species, no matter whether full length or fragments are used. Per se, provided the appropriate study design, library, specimen and so on any platform is capable to generate sequencing reads which allows for species level identification.
So what is the nature of the main hypothesis you're trying to answer? If you want by all means be able to identify species and differentiate at species level or do you want to do community diversity analysis, for which resolution down to species level is not absolutely necessary?
After clarifying these question you can make decisions about what approach and which platform suits best.
Dear Sebastian
Thanks for the answer.
My project is to establish gut microbiota profile in a group of patients. at the same time I will do culture dependent method to compare the results.
I need to profile them at the level of species to find prominent bacterial species. So, I need to use the best technology that give me more species identification.
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