The predominant use of dsDNA as the genomic material of bacterial viruses (phages) is supported by many studies. Brevundimonas goettingensis was characterized and employed as a viral host system for isolation- and metagenomic-based phage investigation to validate this observation. The host strain was utilized for phage enrichment with water samples from the primary treatment step of a local sewage plant (Göttingen, Germany). We specifically targeted phages containing dsDNA, ssDNA, dsRNA, or ssRNA as genetic material. In total, five Brevundimonas-associated dsDNA phages ranging from 62 to 265 kb were isolated. All of them utilized dsDNA as genomic material, isolates with a different genome type were not obtained. Metagenomic data, however, were retrieved from dsDNA- and ssRNA-based viruses. By combining genome data from the obtained isolates with the dsDNA metagenomic data, we demonstrated that even stringent isolation covers, at best, only 70% of potential phages infecting a host present in a sample. However, a CRISPR-Cas9 system with an artificial CRISPR array was established and used to discriminate abundant and well-known B. goettingensis phages from a host-based metagenome enrichment. Here, we were able to isolate further five dsDNA phages and showed that the isolation of more phages resulted in a coverage of 96% of potential metagenome-based detected phages infecting a host. In conclusion, we showed that dsDNA phages are the easiest to obtain. We highlighted the need to expand our experimental procedures to obtain isolates with a different genome type by using the CRISPR-Cas9 system.