Museum metabarcoding: A novel method revealing gut helminth communities of small mammals across space and time

Authors: GREIMAN, STEPHEN - Georgia Southern University; COOK, JOSEPH - University Of New Mexico; TKACH, VASYL - University Of North Dakota; Hoberg, Eric; MENNING, DAMIAN - Us Geological Survey (USGS); HOPE, ANDREW - Kansas State University; SONSTHAGEN, SARAH - Us Geological Survey (USGS); TALBOT, SANDRA - Us Geological Survey (USGS)

Submitted to: International Journal for Parasitology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2018
Publication Date: 10/11/2018
Citation: Greiman, S., Cook, J., Tkach, V., Hoberg, E.P., Menning, D., Hope, A., Sonsthagen, S., Talbot, S. 2018. Museum metabarcoding: A novel method revealing gut helminth communities of small mammals across space and time. International Journal for Parasitology. 48(13):1061-1070. https://doi.org/10.1016/j.ijpara.2018.08.001.
DOI: https://doi.org/10.1016/j.ijpara.2018.08.001

Interpretive Summary: Natural history collections spanning multiple decades have the potential to provide critical historical baselines to measure and understand changing biodiversity. New technologies, such as next generation sequencing to reveal genetic diversity, have considerably increased the use of museum specimens to address significant questions regarding environmental change and shifts in species interactions. In our pilot and model study we explored parasites among shrews (Eulipotyphla: Soricidae). These small mammals occupy diverse habitats, host an abundant parasite fauna (97 helminth species in North America alone), and are widespread across the globe. We applied a new technique to identify the helminth parasites and microbiomes (bacteria) of these small insectivorous mammals. We included museum specimens prepared in varying ways to explore the efficacy of using metagenomics analyses to explore helminth and intestinal bacterial symbiont community changes across temporal and spatial scales. We successfully sequenced the parasite communities (using 12S mtDNA, 16S mtDNA, 28S rDNA as target genes) and bacterial microbiota (16S rDNA) of 23 whole gastrointestinal tracts (GI) of spirit-preserved whole shrews. Internal organs were obtained from the specimen archives of the Museum of Southwestern Biology and from recent field collections. Specimens varied both in time since fixation (ranging from 16 years to 4 months old) and preservation method (70% ethanol stored at room temperature, 95% ethanol at room temperature, and flash frozen in liquid nitrogen and stored at -80°C). We developed an efficient and robust methodological pipeline preparing these specimens for metagenomic sequencing and subsequent analysis. This newly developed metagenomic technique serves as a powerful model allowing critical examination of the distributions and interactions among multiple groups of organisms through time. Broad applications are apparent for assessing parasite distribution and diversity for parasitologists, and disease ecologists in a variety of federal agencies including the USDA, and across a broad sector of the biological community.

Technical Abstract: Natural history collections spanning multiple decades have the potential to provide critical historical baselines to measure and understand changing biodiversity. New technologies, such as next generation sequencing, have considerably increased the use of museum specimens to address significant questions regarding environmental change and shifts in species interactions. Because shrews (Eulipotyphla: Soricidae) occupy diverse habitats, host a speciose and abundant parasite fauna (97 helminth species in North America alone), and are widespread across the globe, we applied a new technique to identify the helminth parasites and microbiomes (bacteria) of these small insectivorous mammals. Critically, we included museum specimens prepared in varying ways to explore the efficacy of using metagenomics analyses to explore helminth and intestinal bacterial symbiont community changes across temporal and spatial scales. We successfully sequenced the parasite communities (using 12S mtDNA, 16S mtDNA, 28S rDNA as target genes) and bacterial microbiota (16S rDNA) of 23 whole gastrointestinal tracts (GI) of spirit-preserved whole shrews. Guts were obtained from the Museum of Southwestern Biology and from recent field collections and varied both in time since fixation (ranging from 16 years to 4 months old) and preservation method (70% ethanol stored at room temperature, 95% ethanol at room temperature, and flash frozen in liquid nitrogen and stored at -80°C). We outline the methodological pipeline preparing these specimens for metagenomic sequencing and subsequent analysis. This newly developed metagenomic technique serves as a powerful model allowing critical examination of the distributions and interactions among multiple groups of organisms through time.