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?