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2.9 years ago
isa.baer
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20
Hello Everyone,
I am new to microbiome analysis. I have cultured bacteria with different culturing methods from the same fecal sample. Now I have got results for the bacterial compositions from these cultures and from the original sample as relative abundances. I would like to calculate how similar the cultured bacterial compositions are to each other and also how similar each of the cultured bacterial compositions is to the original sample. Does someone know a method to do this or is there a bioinformatics pipeline or package for R that could help me solve this question?
Thank you!
isa.baer Are you sure that you performed bacterial culture? Microbiome experiments typically take on the following format: (1) Collect some samples; (2) Extract the DNA; (3) PCR amplify a specific hypervariable region OR enzymatically/mechanically shear the DNA; (4) and then sequence the amplified or fragmented DNA.
In any case, you can visually compare community structures between experimental groups using one of a number of ordination methods implemented in the
phyloseqR package. You can statistically compare community structures between experimental groups using a PERMANOVA, implemented in theveganR package. Good luck ;)!Thank you very much for your fast reply.
And yes, I am sure I cultured the bacteria. ;) I used a culturomic approach with different pre-treatements & media, and cultured in an anaerobic workstation. I picked single colonies, but I also scraped the plates in the end to get the whole composition of bacteria that grew. From the scrapings and from the original sample I extracted the DNA and proceeded as you explained.
I managed to do the visual comparison via plotting and with PCA , but would like to do further analysis to describe changes in obtained compositions. But for sure I will now try to do PERMANOVA.
Oh, nice, sounds like a cool study design! Sorry about that, I haven't seen too many of these! Thanks for the explanation ;)! I would be super curious to learn how similar/dissimilar the cultures are compared to the entire sample as you mentioned!