Gut microbiome of cold-tolerant and sensitive Piaractus mesopotamicus

We investigate the impact of low-temperature thermal stress on the gut microbiome of pacu, Piaractus mesopotamicus, an important aquaculture species indigenous to South America's warm waters. We used the long-read nanopore MinION sequencer to characterize sixteen gut microbiome samples from pacu individuals previously classified as either cold-water tolerant or sensitive. We also included a mock sample (ZymoBIOMICS Microbial Community Standard II, Log Distribution). To this aim, we developed a highly multiplexed nanopore sequencing protocol for the 16S rRNA gene based on a closed family of 36mer barcodes whose specific composition allowed the minimization of crosstalk events among samples (DOI https://doi.org/10.1038/s41598-022-11656-0). Nanopore reads were demultiplexed accordingly and filtered with the NanoFilt tool from the NanoPack package (DOI: 10.1093/bioinformatics/bty149) to retain reads between 1350-1650 nt and quality above 10.