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Fig. 1 | Environmental Microbiome

Fig. 1

From: Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems

Fig. 1

Study design and experimental steps. A Three types of samples were taken. Tank biofilm was collected by rubbing a foam swab against the sidewall of a tank. Tank and biofilter water was collected by filtering 120 ml of water through a 0.22 um cellulose filter. B Samples were taken at two farms, A and B. In farm A, all three sample types were collected. In farm B, sampling focused on tank biofilm. C Three DNA extraction methods were compared. The Purelink Microbiome Kit outperformed other DNA extraction methods in quality, quantity, and consistent yield. D Two amplicon approaches (short and long reads) and an amplification-free shotgun approach were used. E Short amplicons were sequenced on an Illumina MiSeq with a v3 2 × 300PE kit. Long amplicons were sequenced with the PacBio Shoreline StrainID kit, producing an average read length of 2500 bp. Shotgun sequencing was performed with a 2 × 150PE Illumina kit. F Illumina MiSeq sequencing data were processed with the DADA2 pipeline, and ASVs were blasted against the SILVA v138 database for taxonomic assignment. PacBio long-read data was processed with the SBAnalyzer program and taxonomically assigned using Athena. Shotgun metagenomics sequencing data were processed with an in-house pipeline that uses the Kraken-Bracken method

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