Hi everyone!

I have taxonomic abundance count data obtained from shotgun metagenome analysis. My data is not normally distributed and  zero-inflated. Each of the samples in my dataset has unequal library size. 
In this case, how can I normalize my dataset to do all downstream analysis? 
Let's say, ones I normalize the data, can I use it for all downstream analysis? what i mean is, does each different analysis need a different normalization method?

I am open to any tips/ suggestions and information.

Thank you all!
You should probably be handling your data as compositional. See for example: [Microbiome Datasets Are Compositional: And This Is Not Optional.][1]  
The reference on the topic is the book Statistical analysis of compositional data by John Aitchison (and the [original article][2]) and a more recent view can be found in [Aitchison’s Compositional Data Analysis 40 Years On: A Reappraisal][3]


  [1]: https://www.frontiersin.org/articles/10.3389/fmicb.2017.02224/full
  [2]: https://www.jstor.org/stable/2345821
  [3]: https://arxiv.org/pdf/2201.05197.pdf