16S Community Analysis - DIY or Outsource?

General
1

Trying to find the most cost effective way to determine what’s growing in our electroPioreactors. Please correct me if I’m wrong, but 16S community analysis appears to be the way to go.

So far the best price I have found in the UK is £106+VAT per sample for:

  • DNA extraction
  • Library preparation
  • Sequencing
  • Data analysis and provision of raw sequencing data files

OR, these are the best value prices I have found to do this in-house:

Item Product Price (GBP)
Centrifuge[1] SciSpin Micro Centrifuge £536
PCR Machine[2] miniPCR Thermal Cycler $820
DNA Extraction Kits[3] Qiagen DNeasy Blood & Tissue Kit (50 preps) £218
Library Prep[4] Oxford Nanopore 16S Barcoding Kit (24 samples) £810
Sequencer Oxford Nanopore MinION Starter Pack £1,799
Data Analysis Qiime2/DADA2 £0
Total ~£4,010

That kit should provide enough for 24x 16S community analysis at £167/sample. Thereafter the consumables for 24 more samples would be 2x Flow Cells + 1x Library Prep + ½x DNA Extraction Kit = £2175 = £91/sample. So the breakeven with contracting it out (unless we can find a cheaper lab) would be 122 samples, assuming I haven’t missed anything critical and we don’t need to pay for training.

What do you think? Can you find anything that’s better value for money? Should we start off with commercial analysis or try to find funding for our own kit?

  1. I have been struggling to find a safe opensource centrifuge, but just stumbled upon OpenCell when looking for open DNA extraction kits. ↩︎

  2. There are Open Source Thermocyclers like OpenPCR (was $499 until discontinued) or PocketPCR (€99 but limited throughput). ↩︎

  3. I’m not sure what reagents are required if we go for OpenCell ↩︎

  4. I beieve we could save on library prep by ~50% if using open protocols and buying reagents in bulk, but I’m nervous that I’d screw this up and waste the sequencing. ↩︎

2

If we screw things up, electrophoresis capability could be really useful:

Item Product Price (GBP)
Gel Electrophoresis Kit[1] Cleaver Scientific multiSUB Mini 10 System £262.00
Agarose Powder Electrophoresis Agarose, A0169-10G £41.50
Buffer Thermo Scientific™ TAE Buffer (Tris-acetate-EDTA) (50X), 1L £80.50
DNA Stain[2] SYBR Safe DNA Gel Stain, 400 µL £65.65
Transilluminator[3] Cleaver Scientific SAFEVIEW-MINI2 £397.00
Total £846.65

  1. many open source options exist, I’d probably go with an easy Printables option or, while overkill for 16S, OpenPFGE looks tempting ↩︎

  2. we could use cheaper and/or non proprietary DNA stains ↩︎

  3. Many open source options exist like FluoPi and these on instructables and Hackster ↩︎

3

If you’re looking for a centrifuge, a PCR machine, gel electrophoresis and transilluminator, I think a Bento Lab as a four-in-one may be cheaper. They’re commonly used with Oxford Nanopores, see e.g. Rapid Water Testing with Portable Technology | Bento Lab (16s rRNA analysis)

For data analysis, I’d suggest using the Galaxy Project, where you can run the analysis for free on their servers - it’s pretty amazing: Hands-on: 16S Microbial analysis with Nanopore data / 16S Microbial analysis with Nanopore data / Microbiome

4

Yea, GPT 4o seemed to have it in for the Bento Lab. It rulled it out based on centrifuge speed, but said the 7000g OpenCell would suffice. I’ve now seen it’s not comparing the Bento Lab Pro, however when it does, the savings aren’t as big as you’d imagine:

Cost Comparison Table

Component Original Custom Setup Bento Lab Pro Setup Maximally Open Source Setup
Centrifuge SciSpin Micro Centrifuge £536 Included in Bento Lab Pro £1,995 OpenCell Centrifuge £50 insufficient 3000g for DNA pelleting Same as Original Kit £536
PCR Machine miniPCR Thermal Cycler $820 Included in Bento Lab Pro openPCR ~£500
DNA Extraction Kit Qiagen DNeasy Blood & Tissue Kit (50 preps) £218 Same as Original Kit £218 OpenCell DNA Extraction ~£50 + reagents ~£80
Library Prep Oxford Nanopore 16S Kit (24) £810 Same as Original Kit £810 ~~£500
Sequencer Oxford Nanopore MinION Starter Pack £1,799 Same as Original Kit £1,799 Same as Original Kit £1,799
Electrophoresis System Cleaver Gel Box £262 Included in Bento Lab Pro DIY Open-Source Gel Box £50
Agarose Powder Electrophoresis Agarose £41.50 Included in Bento Lab Pro Electrophoresis Agarose £41.50
TAE Buffer TAE Buffer £80.50 Included in Bento Lab Pro DIY TAE Buffer Recipe ~£10
Transilluminator Blue Light Transilluminator £397 Included in Bento Lab Pro DIY Blue Light Transilluminator £50
Total Cost ~£4,790 (~£4,010 excluding electrophoresis) £4,822 ~£3,600

4o now says “The Bento Lab Pro is compact but costs nearly as much as the Original Custom Setup without the same performance.” - I think what it misses[1] is the community/support elements of Bento Lab. What kills it though is if we decide that we should go as Open Source as possible, or that we can probably get the job done without electrophoresis.

Galaxy Project looks amazing - yes whatever we do we should be able to run or rerun the bioinformatics there.

  1. as well as the $/£ exchange rate which makes the custom setup even cheaper ↩︎

5

Chai.bio, maker of the OpenPCR, have gone closed source. If we do want to go the full open source route, this would be another option: PocketPCR – The thermocycler for the rest of us