Hi Junaid,

There is no one test to compare your sample, I guess you have to be spectifc about what you want to check?  an where did you do your basic analysis (quality filtering, chimera, creating OTUs etc).  If you are using QIIME or similar tools, you can run one or more of the following tests

Please note that each one will test different things and each one has a lot of options to chose from. If you are new to this field, let me know and maybe I can take you step by step

Good luck 

Ahmed

It's best to go in with a specific hypothesis.

From there you can do a stats test but remember with any stats you need to be objective in relation to your hypothesis.

Because microbiome datasets are largely related to what's already known regardless of stats it might sound difficult to maintain objectivity so the question goes again back to the quality of your hypothesis.

If you know R, I would start with the numerous tutorial from the Vegan package from Jari Oksanen (I joined the pdfs but they are available online as well), it's a really great package for community analysis. Even if you don't know R, I think his tutorials are possible to follow but it might be harder of course (in that case I would suggest using RStuio). The Vegan package is more for global analysis, e.g. you want to know if globally the community of your controls differs from the community of your cases, but if you want to look at particular species that drives the differences, try the indicspecies package.