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Coastal urbanization influences human pathogens and microdebris contamination in seafood

Citation

Littman, Raechel et al. (2020), Coastal urbanization influences human pathogens and microdebris contamination in seafood, Dryad, Dataset, https://doi.org/10.7280/D13T1W

Abstract

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 >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.

Usage Notes

Script S.1. 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

 

Script S.2. 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. 

 

Data D.1. 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.

 

Data D.2. HumanPath_SedimentDat.csv: Extracted human pathogen OTU reads for sediment samples. Each row is a sample with sample descriptors and pathogenic species as columns.

 

Data D.3. HumanPath_SeawaterDat.csv: Extracted human pathogen OTU reads for seawater samples. Each row is a sample with sample descriptors and pathogenic species as columns.

 

Data D.4. 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.

 

Data D.5. 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.

 

Data D.6. 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.

 

Data D.7. 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.

Funding

Environmental Defense Fund, Award: Innovation for Impact