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I have a lot of experience with isolating individual colonies / species / organisms from the environment and then sequencing them for identification, but the process is slow and cumbersome.

My goal is to build an organism library so actually having the individual isolates is desired. The metagenomic approaches are great for screening a pool of organisms for something I'm looking for, but I still have to separate it out if I want to keep it.

I currently create soil dilutions, plate them, isolate colonies early on to create axenic cultures and then DNA barcode the microbes. This process is time-consuming and often biased towards faster growing microbes.

Are there any high-throughput methods of isolating and identifying microbes (mainly fungi and bacilli) from a mixed-substrate like soil?

A literature search on this subject doesn't reveal many options that are currently accessible. I'm seeing some research on microfluidic devices that may help, but I'm not aware of any microfluidic platforms that are available to consumers.

Aside from this technique and microfluidic techniques (not currently available to my knowledge), are there any other techniques to consider to improve throughput?

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    $\begingroup$ Can you please provide more detail and focus your question a bit more narrowly as this kind of open ended question isn't a good fit for this site. (e.g. Do you really need to isolate and why?) ——— If I search for "soil genomics" the top two hits are articles from Nature Reviews Microbiology titled "Soil genomics" and "The metagenomics of soil". Have you read these and looked for more recent reviews and articles that reference them? Does this not allow you to find answers? $\endgroup$
    – tyersome
    Feb 26 at 1:58
  • $\begingroup$ The question is very specific: what high-throughput methods are available for isolating and identifying microbes like fungi and bacteria? I don't know how to make it more specific than that. I stated what I want to do which is separate (isolate) the microbes and identify them (their species). I would like to know what high-throughput methods are available. The reason why has nothing to do with the question. $\endgroup$
    – doremi
    Feb 26 at 18:27
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    $\begingroup$ Have you looked into metagenome-assembled genomes? E.g. don't bother with isolation, just process everything together and rely on data analysis to pull the different genomes apart. This can be done with or without extra lab steps that add additional info (I once worked at a company that did this as a service: phasegenomics.com/products/proximeta, so conflict of interest there). This is pretty routine at this point. You can also do it on standard shotgun metagenomes (e.g. nature.com/articles/s41587-020-00777-4), it's just slightly messier. $\endgroup$ Feb 27 at 19:01
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    $\begingroup$ Do you now see why I suggested you tell us why you want to do this? SE sites get many questions that fall into a trap known as the X-Y problem, which means it is almost always a good idea to include "why" information in your questions. It is also best to include such information in the text rather than responding in comments — this is because comments are ephemeral and often overlooked. Finally edits should be incorporated directly into the text and not labeled — changes are tracked by the site anyways. $\endgroup$
    – tyersome
    Feb 28 at 20:49
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    $\begingroup$ If your goal is just to get a lot of unique isolates, picking colonies from agar plates is pretty much a necessary evil. Colony picker robots can automate that part of the process. One potentially faster alternative to DNA barcoding is whole cell MALDI-TOF-MS, which can dereplicate isolates and potentially ID some of them with medium-ish throughput. I can pick and screen about 1000 colonies in a day without automation. Most of the ID libraries are geared for pathogen ID, so you'd probably end up sequencing still. But you can add your own spectra as your collection grows. $\endgroup$
    – MikeyC
    Mar 1 at 19:46

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Hard to know what you would consider "high-throughput", but it might be worth checking out the work by Kim Lewis at Northeastern University — see for example his 2020 Perspective in Cell1.

One of the tools his group uses is what they call the ichip, which allows them to grow "uncultivable" microbes2. This is done by placing the device in soil after sealing in 384 separate samples.

References:

  1. Lewis, K. (2020). The science of antibiotic discovery. Cell, 181(1), 29-45.

  2. Nichols, D., Cahoon, N., Trakhtenberg, E. M., Pham, L., Mehta, A., Belanger, A., ... & Epstein, S. (2010). Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species. Applied and environmental microbiology, 76(8), 2445-2450.

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