Metagenomic Next-Generation Sequencing Reveals Miamiensis Avidus (Ciliophora: Scuticociliatida) in the 2017 Epizootic of Leopard Sharks (Triakis Semifasciata) in San Francisco Bay, California, Usa

Abstract

Metagenomic next-generation sequencing reveals Miamiensis avidus (Ciliophora: Scuticociliatida) in the 2017 epizootic of leopard sharks (Triakis semifasciata) in San Francisco Bay, California

Genome Sequence of a Divergent Avian Metapneumovirus from a Monk Parakeet ( Myiopsitta monachus )

“…A representative host database was built using all genome assemblies and mitochondrial genomes under taxonomy identifier (TaxID) 9224 (Psittacidae, parrots) available in the National Center for Biotechnology Information (NCBI) database as of 7 December 2018. Host subtraction and quality control were performed as described previously (3). The remaining 1,670,686 unique nonhost read pairs (4.8% of raw) were processed using the IDseq pathogen detection pipeline v3.2 (reference, NCBI nucleotide and nonredundant protein (nt/nr) databases, as of 1 December 2018) (4), which identified metapneumovirus reads in the sample.…”

IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring

“…Its sample-type–agnostic implementation enables its application for a broad range of research questions related to understanding the distribution of microbes in a sample. The IDseq pipeline has been a key component in recent studies investigating undiagnosed causes of infection and surveying the landscape of circulating pathogens, in both humans and animals [ 64 , 65 ].…”

Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations

“…There have been only a few investigations of chondrichthyan microbiomes [99,[111][112][113][114][115][116], but these few studies have vastly increased our understanding of chondrichthyan ecology and interactions with the environment. Two of these studies were conducted using whole shot-gun metagenomics to describe microbial taxa and function on the skin of thresher sharks, Alopias vulpinus [99,116], while the rest used 16S rRNA amplicon sequencing to describe microbial diversity [111][112][113].…”

“…There have been only a few investigations of chondrichthyan microbiomes [99,[111][112][113][114][115][116], but these few studies have vastly increased our understanding of chondrichthyan ecology and interactions with the environment. Two of these studies were conducted using whole shot-gun metagenomics to describe microbial taxa and function on the skin of thresher sharks, Alopias vulpinus [99,116], while the rest used 16S rRNA amplicon sequencing to describe microbial diversity [111][112][113]. The skin microbiome was the focus of two chondrichthyan microbiome studies [99,112], first because shark skins being covered in dermal denticles have unusual characteristics and provide an interesting environment for microbiome studies, and second because skin microbiome samples can be collected non-invasively.…”

“…Genomic techniques can be used to forensically identify the cause of death of wild organisms. In 2017, hundreds of leopard sharks washed up on beaches in California and whole shotgun metagenomics was used to identify the potential pathogens [116]. Moribund and healthy sharks were collected and subcutaneous fluid surrounding the endolymphatic ducts, inner ear perilymph, and cerebrospinal fluid were collected, and DNA extracted for targeted and whole shotgun metagenomics.…”