Dear Colleagues,
Is it possible/feasible to assign Gram-positive and Gram-negative bacteria in a sample purely based on 16S or metagenomic sequences without gram staining?
Thank you very much.
Regards,
Nathanael
Yes it is very much possible.
Now for more details, please read articles or blogs or discussions. There are literally thousands of them on the internet.
It is a very basic topic and can easily be understood with investment of little time.
Yes. It is possible. All you need is the appropriate database and software for analysis depending on the type of 16S (Illumina or PacBio)
Yes, it is possible, first, you have to generate the OTU table by various stand-alone (QIIME2, Mothur, PhyloSeq) or web-based server (MG-RAST, CosmosID) after that the generated OTU abundance table uploaded on MetaGenAssist (http://www.metagenassist.ca/METAGENassist/faces/Home.jsp) Web-based pipeline and follow the instructions. It will assign all the sequences on the basis of Gram Stating phenotype.
I hope this information will help you.
Hi, Samrendra. I have tried MetaGenAssist (http://www.metagenassist.ca/METAGENassist/faces/Home.jsp) Web-based pipeline as you mentioned. However, I did not find any database about gram stating phenotype on this website, except for statistic analysis, like PCA, random-forest, heatmap, and so on. Could you please tell us more detailed methods or databases? Samrendra Singh Thakur
Thanks a lot. Looking forward to your reply.
Hello, Jue Zhao you may go to Statistics > chart and select the Analyze by phenotype in this part when you scroll it you will find many various phenotype categories such as Gram staining, Metabolism, Oxygen requirement, Energy Source, and many more. Please try this and let me know, whether it's working or not?
Jue Zhao yes it's a better idea to download the abundance table and do what you want in your analysis.
Consider checking the mo_gramstain() function from AMR R package: https://msberends.github.io/AMR/reference/mo_property.html
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