I am new to the field of microbiome community analysis. How common is it to validate sequencing data, say from lung tissue, with a gram stain? Essentially, I want to visually highlight the difference in the abundance of gram-negative bacteria in the lungs between treatment groups.
Hi there,
In my opinion, visually highlighting the difference in the abundance of gram-negative bacteria in the lungs between treatment groups is a qualitative strategy instead of quantitative. That is unless you'll be using another method to estimate the number of bacteria. And also, I think the differences in abundance should be quite significant to be able to tell apart which group has higher or lower abundance.
Then again, there's the question of abundance in terms of what? Bacterial diversity, abundance of specific bacteria and such. So I would say running NGS would be better for this case.
Thank you for your input. We do plan on running 16s rRNA seq from bronchial alveolar lavage but I want to visualize the difference in the treatment groups and in the airways. This test would complement our sequencing data but I am not sure how common a technique gram staining lung tissue is.
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