I understand that differential coverage binning relies on a bunch of metagenomic samples taken continually over a period of time from a single location. For example, sampling the fecal microbiome for 7 days from one individual. The differential coverage binning algorithm would group contigs with a similar abundance across the samples into a single Bin.
However, what if I have samples that are not from the same location, and I only sample them at a single time point, would the differential coverage binning method still work? For example, sampling the fecal microbiome from 5 individuals at the same time. Would the binning algorithm still be able to bin contigs from these 5 metagenomes?
The reason I am asking this is that I came across a similar situation. So I have 6 soil metagenomes taken from a patch of soil from a single time point. I first assembled them individually (NOT co-assembly), next I mapped the reads from every sample back onto every assembly. For example, I mapped samples 1 reads onto samples 1 assembly, sample 2 reads onto sample 1 assembly, sample 3 reads onto sample1 assembly ….. samples 6 onto samples 1 assembly. Then I repeat this process for all samples. (Eventually ended up with 36 mapping files). I used the 6 mapping files from each sample as input for 3 binning algorithms CONCOCT, metabat2, and maxbin2, and combined the final set of bins using MetaWRAP.
As you can see, these samples are not from a times series, but rather samples taken within close proximity at a single time point, so my question is that is this a valid approach to obtain bins, are the bins obtained this way usable for downstream analyses? I know some of these binners also use nucleotide frequencies, but would that be sufficient? Sorry for the lengthy question, just wanted to give as many details as possible.