Which samples can be used?
At least two samples are needed where the target organisms are in different abundances. In the paper we applied two different extraction methods to the same sludge sample, which resulted in different abundances of the target orgamisms, due to species specific extraction properties. However, we have also succesfully used timeseries and spatial related data. Any combination of samples can be used as long as the target organisms are present in both samples.
The approach only concerns the binning, finishing and validation part of assembling genomes from metagenomes. If there are many strains of the same species they will not be assembled in the de novo assembly. Hence, the approach can help you to get the most out of what you could assemble. It can not help you to recover complete genomes in samples with massive strain diversity of the target species as they will not assemble in the first place.