Collecting samples for metagenome yourself, building portfolio on GitHub

[A. Ekergård]

I am writing this after discussing DIY biology, or more precisely bioinformatics, with an LLM. It suggested that I should make a proof of concept for GitHub, start by sequencing 16S rRNA from two different samples, analyse and present the results on said platform. Building a portfolio that way. (I would like to point out that my ideas for samples are my own not the AIs.)

Here are my thoughts on this:

Value and credibility: Even if it were possible to implement, and sceptical I could do it myself, I usually have hybris, what would the value be to others? No one would be able to verify if I handled the tests correctly. I could even lie about the results.

Cost and logistics: Sending samples to companies that do this type of sequencing can be expensive. I live in Europe so for customs, and other reasons, it could be nice to use a European company. (Not that I do not think the Chinese or the Americans can do science.)

That's why I'm turning to you. Has anyone done something similar? What are your experiences and which companies can you recommend? Are there any specific challenges or tips you would like to share?

Thanks in advance for your answers and opinions!

PS. I kind of wrote this for Reddit but where you need "karma" to be read?

[Dakota Hamill]

Check out DNA Barcoding – International Barcode of Life https://share.google/zzdycN3eoOyPDlnI2

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[Dakota Hamill]

Phone sent it too fast, my bad.

Ibol.org or since you're familiar with it, you can DNA barcode most anything.  Your question of what's the point is a good one.  

Mushroom identification is a fun one.  

Besides taxonomy people see if anything they sequence is a potentially new species or strain of bacteria, and if their genome is worth exploring.   If it's a new strain, it's genome might harbour brand new secondary metabolite clusters for say, drug discovery.  The NCBI database is confusing(to me), but I've heard things like anything with a 16s of less than 98% matching could be entirely new.  

IDT does 16s for like $15 a sample, there has to be a cheap place to get PCR, clean up, and sequencing done for cheap even in Europe.  

You can even send in a petri dish with colonies and they'll pick right from the plate.  

I've heard some people use it in conjunction with iNaturalist to kind of announce finding new species in different places.  

[A. Ekergård]

Thank you very much! Find new species and drugs and not in my original plan. Ok the last wouldn't happen, how likely one is to find a new species I don't know anything about. I was more interested in the microbial community and difference between two environments.

Then the practical to do should be collecting samples. On agar plates one would merely found cultivatable microorganisms, right? Otherwise, as said before, I'm likely to screw that up, not good at practical things.