Comparison of high-throughput sequencing methods for bacterial microbiota profiling in catfish aquaculture

Bacterial community profiling in aquaculture can be useful for monitoring environmental conditions that may lead to disease outbreaks, understanding the impact of dietary treatments on fish health, and identifying microbes that have potential as probiotics. Microbiota characterization is commonly performed with high-throughput sequencing using short-read platforms (i.e., Illumina) targeting variable regions of the bacterial 16S ribosomal RNA (rRNA) gene. Long-read platforms (i.e., Oxford Nanopore Technologies [ONT]) enable sequencing of full-length 16S rRNA genes. While short-read platforms are highly accurate, long-read platforms sacrifice sequence quality in exchange for longer read lengths.