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Wet collections accession: a workflow based on a large stonefly (Insecta, Plecoptera) donation.

ABSTRACT: AbstractThis study details a workflow used to accession a large stonefly (Plecoptera) collection resulting from several donations. The eastern North American material of Kenneth W. Stewart (deceased, University of North Texas), the entire collection of Stanley W. Szczytko (deceased, University of Wisconsin, Stevens Point), and a small portion of the Barry C. Poulton collection (active, United States Geological Survey, Columbia, Missouri) were donated to the Illinois Natural History Survey in 2013. These 5,767 vials of specimens were processed to help preserve the specimen legacy of these world renowned Plecoptera researchers. The workflow used an industrialized approach to organize the specimens taxonomically, image the specimens and labels, and place the specimens into new storage. Utilizing the images as a verbatim data source, we transcribed labels in iterative steps that yielded more information with each pass. The data were normalized, locations georeferenced, all specimen data formatted to meet Darwin Core Archive format for occurrence data, and a data set created using Pensoft's Integrated Publishing Toolkit. This is the first time that any of the specimen data has been made available electronically. We also provide two important electronic supplements that include the Bill P. Stark (active, Mississippi College) Oklahoma field notebook for 1971 and 1972 detailing locations for many coded stonefly specimens in the Stewart collection, and the coded locations of B. C. Poulton's Arkansas and Missouri study. Again, we have linked coded labels in vials to normalized and georefenced site data. We confirmed 243 stonefly species were contained within the collections, and the potential for many more species exists among the specimens identified to family and genus level. Twenty-one new state, province, and other significant stonefly records are reported herein with all identifications verified by the senior author, often through consultation with other stonefly taxonomists. Researchers are encouraged to utilize the specimen data, form collaborations with the authors, and borrow specimens for research.

SUBMITTER: DeWalt RE

PROVIDER: S-EPMC6294822 | biostudies-other | 2018

REPOSITORIES: biostudies-other

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Project description:The advent of high-throughput sequencing techniques has recently provided an astonishing insight into the composition and function of the human microbiome. Next-generation sequencing (NGS) has become the gold standard for advanced microbiome analysis; however, 3rd generation real-time sequencing, such as Oxford Nanopore Technologies (ONT), enables rapid sequencing from several kilobases to >2 Mb with high resolution. Despite the wide availability and the enormous potential for clinical and translational applications, ONT is poorly standardized in terms of sampling and storage conditions, DNA extraction, library creation, and bioinformatic classification. Here, we present a comprehensive analysis pipeline with sampling, storage, DNA extraction, library preparation, and bioinformatic evaluation for complex microbiomes sequenced with ONT. Our findings from buccal and rectal swabs and DNA extraction experiments indicate that methods that were approved for NGS microbiome analysis cannot be simply adapted to ONT. We recommend using swabs and DNA extractions protocols with extended washing steps. Both 16S rRNA and metagenomic sequencing achieved reliable and reproducible results. Our benchmarking experiments reveal thresholds for analysis parameters that achieved excellent precision, recall, and area under the precision recall values and is superior to existing classifiers (Kraken2, Kaiju, and MetaMaps). Hence, our workflow provides an experimental and bioinformatic pipeline to perform a highly accurate analysis of complex microbial structures from buccal and rectal swabs. IMPORTANCE Advanced microbiome analysis relies on sequencing of short DNA fragments from microorganisms like bacteria, fungi, and viruses. More recently, long fragment DNA sequencing of 3rd generation sequencing has gained increasing importance and can be rapidly conducted within a few hours due to its potential real-time sequencing. However, the analysis and correct identification of the microbiome relies on a multitude of factors, such as the method of sampling, DNA extraction, sequencing, and bioinformatic analysis. Scientists have used different protocols in the past that do not allow us to compare results across different studies and research fields. Here, we provide a comprehensive workflow from DNA extraction, sequencing, and bioinformatic workflow that allows rapid and accurate analysis of human buccal and rectal swabs with reproducible protocols. This workflow can be readily applied by many scientists from various research fields that aim to use long-fragment microbiome sequencing.

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Wet collections accession: a workflow based on a large stonefly (Insecta, Plecoptera) donation.

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