DOI: 10.7280/d13t1w
title: Coastal urbanization influences human pathogens and microdebris contamination in seafood

description: Seafood is one of the leading imported products implicated in foodborne
 outbreaks worldwide. Coastal marine environments are being increasingly
 subjected to reduced water quality from urbanization and leading to
 contamination of important fishery species. Given the importance of
 seafood exchanged as a global protein source, it is imperative to maintain
 seafood safety worldwide. To illustrate the potential health risks
 associated with urbanization in a coastal environment, we use
 next-generation high-throughput amplicon sequencing of the 16S ribosomal
 RNA gene combined with infrared spectroscopy to characterize and quantify
 a vast range of potential human bacterial pathogens and microdebris
 contaminants in seawater, sediment and an important oyster fishery along
 the Mergui Archipelago in Myanmar. Through the quantification of
 &gt;1.25 million high-quality bacterial operational taxonomic unit
 (OTU) reads, we detected 5,459 potential human bacterial pathogens
 belonging to 87 species that are commonly associated with gut microbiota
 and an indication of terrestrial runoff of human and agricultural waste.
 Oyster tissues contained 51% of all sequenced bacterial pathogens that are
 considered to be both detrimental and of emerging concern to human health.
 Using infrared spectroscopy, we examined a total of 1,225 individual
 microdebris particles, from which we detected 78 different types of
 contaminant materials. The predominant microdebris contaminants recovered
 from oyster tissues included polymers (48%), followed by non-native
 minerals (20%), oils (14%) and milk supplement powders (14%). Emerging
 technologies provide novel insights into the impacts of coastal
 development on food security and risks to human and environmental health.
description: <b>Script
 S.1.</b> Myanmar_Oysters.Rproj: R project file to create the
 workspace and file paths used for the r script file: Coastal urbanization
 influences human pathogens and microdebris contamination.r   <b>Script S.2.</b>
 Coastal urbanization influences human pathogens and microdebris
 contamination.r: Code script implemented in r that contains code for
 analyses, figures, and supplemental information corresponding to Littman
 et al. Coastal urbanization influences human pathogens and microdebris
 contamination in seafood.    <b>Data D.1.</b>
 HumanPath_OysterDat.csv: Extracted human pathogen OTU reads for oyster
 gill tissue samples. Each row is a sample with sample descriptors and
 pathogenic species as columns.   <b>Data D.2.</b>
 HumanPath_SedimentDat.csv: Extracted human pathogen OTU reads for sediment
 samples. Each row is a sample with sample descriptors and pathogenic
 species as columns.   <b>Data D.3.</b>
 HumanPath_SeawaterDat.csv: Extracted human pathogen OTU reads for seawater
 samples. Each row is a sample with sample descriptors and pathogenic
 species as columns.   <b>Data D.4.</b>
 Oysters_Particles.csv: Microdebris identified from oyster samples. Each
 row is an individual particle and columns information on the identity of
 the debris material and sample metadata.   <b>Data D.5.</b>
 Sediment_Particles.csv: Microdebris identified from sediment samples. Each
 row represents an individual particle and columns information on the
 identity of the debris material and sample metadata.   <b>Data D.6.</b>
 Seawater_Particles.csv: Microdebris identified from seawater samples. Each
 row is an individual particle and columns contain information on the
 identity of the debris material and sample metadata.   <b>Data D.7.</b>
 Oyster_sample_info.csv: Metadata of the oyster tissue samples including
 the size, weight, and parasite abundance for samples used for human
 pathogen analysis and microdebris contamination.