Abstract:

The microbiome associated with organisms plays a vital role in disease susceptibility via competitive exclusion of opportunistic pathogens. Unbalanced bacterial communities (dysbiosis) can decrease the ability of the microbiome to exclude pathogens, leading to increased susceptibility to infection. This study used 16S rRNA sequencing in order to characterize the adherent gut microbiome of red snapper (Lutjanus campechanus) during exposure to chemically enhanced water accommodated fraction of oil (CEWAF) to determine the impacts of exposure on microbiome structure as well as identify if dysbiosis plays a role in disease.

Suggested Citation:

Andrea Tarnecki. 2019. Metagenomics characterization of red snapper microbiome following CEWAF and pathogen exposure. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-8804-yj09

Purpose:

To characterize the metagenomics of the red snapper microbiome following CEWAF and pathogen exposure.

Data Parameters and Units:

The excel file contains details of experimental condition and treatment, CEWAF preparation, description of fish (total length, body weight), Vibrio anguillarum loads, and OTU (operational taxonomic unit) results organized under different worksheets. Significant differences between bacterial operational taxonomic units (OTUs) between CEWAF exposed and control fish were determined by linear effect size (P < 0.05). Main parameters: MML; Collected Date (DD-Mon-YY); Fish ID; Species (Red Snapper); Exposure System; Exposure Treatment; Matrix; Body Weight (g); Total Length (cm); CEWAF Preparation; CFUs; Inoculation Time; Loading Concentration (CFU/ml); OTU (operational taxonomic unit) results - Phylum, Class, Order, Family, Genus; Sequencing Accession Numbers - Sample ID, Bioproject, Biosample. Naming convention: Sample IDs are named as "CII-15-0000", where three letter laboratory project code(CII=CIMAGE-II)-two digit year(2015=15)-four digit integral assigned by laboratory beginning at 0000 for each new year(0000 through 9999). Note: MML= Mote Marine Laboratory; MDL= Minimum Detectable Limit; CEWAF = chemically enhanced water accommodated fraction of oil; CFU/ml is the measure of viable bacterial cells.

Methods:

External mucus samples were collected using sterile swabs and stored at -80°C until further analysis. DNA was extracted from swabs using the DNeasy PowerSoil Kit (Qiagen). Samples were subjected to 16S rRNA sequencing using the primers 515F/806R, 2x250 bp reads, on an Illumina MiSeq. Data were processed using the Mothur MiSeq SOP. The CEWAF preparation method is included in the data file.

Instruments:

Illumina MiSeq System.

Error Analysis:

Sequences were screened to remove sequences greater than 275 bp, sequences with ambiguous base calls, and sequences with homopolymer lengths greater than 8 bp. Chimeras were identified and removed. Identities associated with primer mismatches were removed, including Archaea, Eukaryota, mitochondria, chloroplast, and unknown identities. OTUs were identified at 97% sequence similarity.

Individual Files: