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

Abstract

Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing have considerably increased the potential of museum specimens to address significant questions regarding the impact of environmental changes on host and parasite/pathogen dynamics. We developed a new technique to identify intestinal helminth parasites and applied it to shrews (Eulipotyphla: Soricidae) because they are ubiquitous, occupy diverse habitats, and host a diverse and abundant parasite fauna. Notably, we included museum specimens preserved in various ways to explore the efficacy of using metabarcoding analyses that may enable identification of helminth symbiont communities from historical archives. We successfully sequenced the parasite communities (using 12S mtDNA, 16S mtDNA, 28S rDNA) of 23 whole gastrointestinal tracts. All gastrointestinal tracts were obtained from the Museum of Southwestern Biology, USA, and from recent field collections, varying both in time since fixation (ranging from 4 months to 16 years) and preservation method (70% or 95% ethanol stored at room temperature, or flash frozen in liquid nitrogen and stored at À80°C). Our proof of concept demonstrates the feasibility of applying next generation DNA sequencing techniques to authoritatively identify the parasite/pathogen communities within whole gastrointestinal tracts from museum specimens of varying age and fixation, and the value of future preservation of host-associated whole gastrointestinal tracts in public research archives. This powerful approach facilitates future comparative examinations of the distributions and interactions among multiple associated groups of organisms through time and space.

Sustained impact of holistic specimens for mammalogy and parasitology in South America: Sydney Anderson’s legacy

“…The traditional voucher (skin and skeleton-- Hafner et al 1984, or fluid preserved specimen) was supplemented by an array of ultrafrozen tissues, chromosome cell suspensions, fecal samples, and endo and ectoparasites. Now termed the "Holistic Specimen" (Cook et al 2016;Galbreath et al 2019), but also known as the "Extended Specimen" (Webster 2017), these specimens provide a breadth of materials to address not only traditional systematic and taxonomic questions, but now facilitate and integrate questions in environmental change (e. g., climate change, habitat conversion, pollutants and toxicants, biodiversity loss, introduction of exotics), and other novel and evolving contemporary research areas (e. g., pathogen emergence and discovery, genomics, microbiomes, isotopic and molecular ecology, metagenomics, transcriptomics, and proteomics; Cook et al 2017;Dunnum et al 2017;Greiman et al 2018;Schindel and Cook 2018).…”

The Global Museum: natural history collections and the future of evolutionary science and public education

“…Specimen-based field work should aim to preserve extensive sets of natural history material at a particular time and place that would represent multiple individuals of each species, multiple species per collecting locale, and multiple diverse aspects of individual specimens. For example, collection of mammals and their associated ectoparasites and digestive tracts has led to detailed understanding of co-evolution of hosts and parasites (Cook et al, 2017) and can fuel future studies of the role of the microbiome in such processes (Roggenbuck-Wedemayer et al, 2014;Greiman et al, 2018). Such holistic collection events can better capture the complex interactions of biotic communities and, if repeated, over time could provide key insights into changing conditions.…”

On the role of (and threat to) natural history museums in mammal conservation: an African small mammal perspective

“…Other examples involving the use of museum specimens in documenting the impacts of disease with a conservation angle include tracing the evolutionary dynamics of retroviruses in koalas (Ávila-Arcos et al 2013) and the documentation of the occurrence of white-nose syndrome in a bat specimen collected from France in the early 20 th century (Campana et al 2017). As novel technologies continue to develop, museum specimens will continue to provide a unique opportunity for studying pathogens in wild mammals, as was recently demonstrated in a study that used DNA metabarcoding to characterise small mammal helminth communities across space and time (Greiman et al 2018).…”