Here are some best practices for isolating and characterizing rare or uncultivable microbes from complex environments:

Use a Variety of Cultivation Approaches

• Employ multiple cultivation media and conditions to select for a broader range of microbes. This includes using low-nutrient media like R2A, anaerobic conditions, and a range of temperatures.
• Employ enrichment cultures by providing specific substrates or conditions to enrich for target microbes.
• Use miniaturized cultivation systems like microfluidic devices to isolate and cultivate rare microbes.

Optimize Sample Collection and Processing

• Collect samples aseptically and process them rapidly to preserve microbial diversity.
• Use gentle extraction methods to avoid cell lysis and preserve fragile microbes.
• Employ techniques like density gradient centrifugation to separate microbes from soil particles and debris.

Employ Culture-Independent Methods

• Use metagenomics and single-cell genomics to obtain genomic information on uncultivated microbes.
• Combine metagenomics with microfluidics to link phylogeny and function for uncultivated microbes.
• Use stable isotope probing to link identity and function for uncultivated microbes.

Characterize Isolates Comprehensively

• Sequence the 16S rRNA gene or other phylogenetic markers to taxonomically identify isolates.
• Perform phenotypic characterization like carbon source utilization assays to determine functional traits.
• Perform genome sequencing of isolates to obtain their complete genetic blueprint.
• Deposit isolates in culture collections to make them available for further research.

There is no best method.

1) they are not cultivable

2) complex environments will have their own flora that will obscure the putative 1st time isolate

3) you'll have no idea what the novel growth will appear to be