Metagenome (Microbiome) composition and functional profiling

Question

[dpc]

Hi there!!! I have several number of metagenomic 16S rRNA gene sequence. Firstly, I want to know the composition (i.e. all the species and strains out there in the metagenome) of the metagenome. Secondly, I will do the functional profiling.

1. Can i use MOTHUR software for the first purpose?
2. What should I do for the second one?

THANK YOU...

Answer 1

[Asaf]

1. Yes, you can use Mothur to do that. You can also use DADA2 which has some advantages over Mothur.
2. You can use PiCrust. If it's mouse microbiome make sure you read this new publication: https://www.cell.com/cell-reports/fulltext/S2211-1247(20)30197-2

[dpc]

Thanks Sir for your response. I have installed and trial run MOTHUR. I am a newbie in bioinformatics and a little confused. So it would be a great help if you please in short tell me the steps to run MOTHUR for profiling the species composition and their abundances.

Regards

[Asaf]

Actually they have a great manual: https://mothur.org/wiki/mothur_manual/

[dpc]

Thanks Sir. I wanted a protocol. And I have got one.