I am analysing my data from wetland soil. I would like to draw some indicators species not only for bacteria but also for archaea. I am excelling in metagenomics field.
Thanks in advance for your kind reply,
Donald,
A literature review will help you identify the expected key species. Comparing your data with sequence at Genbank will confirm or challenge the current literature. A number automated pipelines are available at NCBI.
Hi Donald, it would be better if you can provide more information on what you are looking for. For example, if you want to find which bacteria or archaea taxa differ significantly between your treatments you can use the R package DESeq2 which also works with one of the most used tools for analyzing microbial community data "phyloseq". Another option could be to use LEfSe (Linear discriminant analysis Effect Size), but again all depends on what you are looking for.
In the case that you are looking for taxa commonly found in wetland soil, I recommend to search the literature for studies conducted on that type of soil and compare your results with them.
Kindly check https://onlinelibrary.wiley.com/doi/10.1111/ejss.12977
Also check https://link.springer.com/article/10.1007/s00374-017-1248-3
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