High-throughput amplicon sequencing datasets of coastal sediments from three locations of the Gulf of Mexico, USA

George B H Green; Angelo DePaola; Jason G Linville; Casey D Morrow; Asim K Bej

doi:10.1016/j.dib.2023.108895

High-throughput amplicon sequencing datasets of coastal sediments from three locations of the Gulf of Mexico, USA

Data Brief. 2023 Jan 11:47:108895. doi: 10.1016/j.dib.2023.108895. eCollection 2023 Apr.

Authors

George B H Green¹, Angelo DePaola², Jason G Linville³, Casey D Morrow⁴, Asim K Bej³

Affiliations

¹ Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, United States.
² DePe Oysters, LLC, Coden, AL 36523, United States.
³ Department of Criminal Justice, The University of Alabama at Birmingham, Birmingham, AL 35294, United States.
⁴ Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, United States.

Abstract

We present high-throughput amplicon sequence (HTS) datasets of the purified microbial metacommunity DNA of coastal surface sediments from Portersville Bay (PVB) (n = 3), Bayou La Batre (BLB) (n = 3), and Mobile Bay (MOB) (n = 3) of the U.S. Gulf of Mexico (U.S. Gulf Coast). The PVB samples were collected from the oyster aquaculture Shellevator™ system; the BLB samples were from locations on the shoreline adjacent to wild oysters attached to rocks and likely polluted from sewage and possibly chemical contamination from boats, shipyards, and seafood processing facilities; and MOB samples were adjacent to aquaculture oysters in bottom cages. The amplicons of the V4 hypervariable segment of the 16S rRNA gene from each sample were sequenced on an Illumina MiSeq to generate these HTS datasets. The raw sequences were quality-checked, demultiplexed into FASTQ files, denoised using DADA2, and subsampled. Then, the FASTA formatted sequences were assigned the taxonomic ids to amplicon sequence variants (ASVs) against the silva-138-99-nb-classifier using the Quantitative Insights Into Microbial Ecology (QIIME2 v2022.2). The applicability of the HTS datasets was confirmed by microbial taxa analysis at the phylum level using the "qiime taxa collapse" command. All HTS datasets are available through the BioSample Submission Portal under the BioProject ID PRJNA876773 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA876773).

Keywords: 16S rRNA gene; Illumina; Metagenome; Oysters; QIIME2; Sediment; U.S. Gulf Coast.

Abstract

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