microbiota analysis of insect species

[cherman2 (Chloe Herman)]

Hi @Linda_Abenaim,
Welcome to the forum!

Many of your questions are preference-based, meaning that it mostly is about your preference and how you go about analyzing your data. I am more than happy to share how I would go about this analysis but I do want to just give a big disclaimer. This is just how I would go about this analysis and that does mean that it is the most right way. Its just a way to go about it

@Linda_Abenaim

I would like to compare the bacterial communities of the three insect species. Do you think I should first analyse the differences in the bacteria of the three insect species raised on a control diet and then on a treated diet? Would you then recommend that I analyse the differences in each species between the control and treated diets?

Do you think that there will be a difference composition in insect species?

I would probably filter down to just the control samples and compare your 3 different insect microbiomes.

Similarly you could test if there is a difference in the 3 insects microbiome on treated by filtering down to treated samples and comparing the 3 insects microbiome.

Here is a tutorial for filtering data: Filtering data — QIIME 2 2023.9.2 documentation

I would probably investigate all the insects together and test if the composition is different between diet. Then I would filtered down to just the insects and test diet again!

I am prone to looking at more comparisons than less.
I hope this clarified things! Please let me know if you are still confused and I am more than happy to clarify.

@Linda_Abenaim

Sorry for the question, it may seem trivial but I often get confused. Unfortunately, this is the first time I've tried bioinformatics.

This isn't trivial and we are here to help!

@Linda_Abenaim

Regarding the taxonomic analysis, do you recommend training the classifier? I tried to do the analysis without training greengenes2 for my V3-V4 region, but unfortunately some features are not identified beyond the domain and a lot of data is lost.
Do you think that training the classifier will improve the situation?

I believe that you will have to train your own classifier because q2 only has V4 classifiers. This would explain your issue with taxonomic classification.

Here is the tutorial for that Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

I hope all this helps! Feel free to post again if your run into any errors!