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Application of antibiotics for the selective isolation of previously uncultured species from activated sludge | Microbiology Spectrum
Biological wastewater treatment relies on diverse microbial communities to degrade pollutants and drive nutrient transformations. Understanding the physiology and metabolism of these microorganisms is essential for improving the efficiency and cost-effectiveness of treatment processes. Much of our current knowledge is derived from 16S rRNA gene amplicon sequencing and metagenomic analyses. However, validating these sequencing- and genome-based insights requires bacterial species as pure cultures, and only a limited number of taxa common in wastewater treatment plants are currently available in culture. Here, we present an isolation strategy that uses antibiotics as a selective pressure to reduce microbial complexity and alleviate competitive exclusion during cultivation, while full-length 16S rRNA gene amplicon sequencing is used to monitor enrichment and guide targeted isolation, thereby facilitating the recovery of process-relevant activated sludge bacteria, including potentially uncultured taxa. These isolates can serve as model organisms for experimental validation of genome-based predictions.
![[13] Ragnar Groot Koerkamp. Personal communication, 2026.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:olhpu3lwhpafue3jjmhat4mj/bafkreigzywxbl7xvbfcqpg3lxzuxy2jtyrnoabooxd63oefcthfb42ffqa)
