Are stool samples true representative of Gut microbiome for NGS studies?

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Offline @PKPoonia

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Almost all microbiome studies use stool samples as a representative of gut microbiome to study abundance, diversity and composition of microbita using Next Generation Sequencing (NGS). There are some recent studies showing the difference in composition of actual gut microbe and microbes from stool samples. It is also true that getting gut sample is practically tough by method like biopsy. What are the ways to minimize this limitation?