Re: [DIYbio] Re: Where to get project ideas for beginners

Great response Reggie.  You should do a post about how you make vinegar and at what scale, of course without giving away any proprietary recipe information!

Always neat to see how a real microbe can turn something into a product we use daily in our lives.

On Mon, Jan 1, 2018 at 12:05 AM, Reginald Smith <reg...@gmail.com> wrote:

Hi, my suggestion would be undertaking a few small projects that involve several steps that are critical to DIY Bio. I can speak from my experience as I own a small vinegar manufacturing company and often analyze my acetic acid bacteria to compare fermentation efficiencies, peak acidity, etc.

Start with a fermented food from the grocery store like (raw and unpasteurized) apple cider vinegar, probiotic yogurt with life culture, kefir, or sauerkraut. First step is learning to culture bacteria properly. You can buy media but it is more instructive to learn how to make it so order so petri dishes off Amazon (100 x 15 mm would be good). Openwetware has a  lot of growth media ingredient lists. For example, if you use raw vinegar you can use the media for Acetobacter Xylinum. I actually have a remix of this recipe adding ethanol and acetic acid (from store bought vinegar) and can post it if you would like. All the ingredients can be found online easily and if  you can't find yeast extract, Marmite works fine. If you are doing yogurt etc. a lactic acid bacteria media is preferable.

From here you would learn how to properly autoclave/sterilize the petri dishes, mix the media with agar in hot water and pour it into the petri dishes to solidify. Culture your bacteria, learn about serial dilution to try to get pure colonies on a new culture, and then the real fun starts.

At this point you can just send the petri dish to a lab to do 16S rRNA sequencing (I recommend Genewiz in NJ for this, about $20 a sample). When you get the sequence back, you can align it in NCBI Blast or download MEGA7 and download a bunch of bacterial 16S rRNA sequences to align and match. From here you can learn about basic bioinformatics like DNA distance metrics, alignment, and making phylogenetic trees to explore the approximate relationship of what you cultured.

If you want to do it the harder, but more educational way, you can learn how to extract chromosome DNA (don't confuse this with plasma DNA) from bacteria using centrifugation and boiling water to get raw DNA. Then you can make a homemade PCR (or buy mini PCR for $650) along with DNA bases, buffer, Taq DNA polymerase, and PCR water along with 16S rRNA primer you can buy from Odin to get a bunch of DNA you can send for Sanger sequencing at a lab for cheap.

Just remember 16S rRNA is a very conserved sequence (and has multiple regions) and evolves so slowly that it is better at distinguishing more distantly related bacteria (see the DIY Bio thread on Odin contamination) than distinguishing between species under the same genus.

Sorry this seems long winded and maybe not quite relevant but I am just trying to give you a simple project that teaches you basic culturing, bioinformatics and phylogeny, DNA extraction, PCR, and sequencing basics. From there you can go wherever you want. Have fun!

Reggie Smith

Supreme Vinegar LLC

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diy...@googlegroups.com. To unsubscribe from this group, send email to diybio+un...@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+un...@googlegroups.com.
To post to this group, send email to diy...@googlegroups.com.
Visit this group at https://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/21a8f8d4-25ce-484b-9550-891822aedbe6%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.