I want to start this thread to discuss some possible ways to simultaneously quantify multiple (20+) microorganisms (phylogenetically unrelated). qPCR or ddPCR basically can only target one or a few (as multiplex is challenging). Microarrays can detect a lot, but seems only produce qualitative results with limited sensitivity. I am more than happy to hear different ideas and learn. Thanks in advance.
Just go straight into high throughput sequencing.
You can also use FISH, but it can be a real pain to count so many bugs and having appropriate probes for all the taxa you want to evaluate.
NSG still cannot be used as a regular monitoring tools considering it takes days to get the sequences and a huge burden on data analysis.
Well, there was no mention of "monitoring" in the original question. Still, the MinION has a sample prep time of 90 min* and running of 6h aprox. Data analysis can be done in real time as sequences are being generated.
Off course, MinION is not a commercial machine right now, and it is a single-cell machine. But the possibility of using HTS for this is not that far.
*Nanopore is working in a 15 min prep protocol.
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