Hi,
I have 3 metagenomes, all of which are from enrichment cultures. My aim is to assemble the genomes of bacterial strains I have not been able to isolate which may degrade my compound of interest. I thought it would be best to merge the samples beforehand and this would improve the coverage of the MAGs but after reading some other posts I'm not so sure. Would it be best to concatenate samples? If so, is it ok that I have done this prior to the trimming stage, i.e I have concatenated all the r1.fq.gz and all the r2.fq.gz files and now plan to trim these files?
Thanks,
Jess 
Hi Jess and welcome at Biostars. 

To make it short: Yes your approach very likely will work. I do similar merging operations when I get WGS metagenome data from, for example, a time series experiment. 

To outweigh the posts you mentioned, maybe take a look at [metabat][1] or [concoct][2], two software packages that can be used to isolate genomes from you metagenome. Though both essentially start binning using k-mer frequencies, they also assume bam file input of reads aligned to a common reference. That common reference is an assembly of pooled reads from all your experiments.


  [1]: https://bitbucket.org/berkeleylab/metabat/overview
  [2]: https://concoct.readthedocs.io/en/latest/