Historical DNA Metabarcoding of the Prey and Microbiome of Trematomid Fishes Using Museum Samples

Abstract

Antarctic specimens collected during various research expeditions are preserved in natural history collections around the world potentially offering a cornucopia of morphological and molecular data. Historical samples of marine species are, however, often preserved in formaldehyde which may render them useless for genetic analysis. We sampled stomachs and hindguts from 225 Trematomus specimens from the Natural History Museum London. These samples were initially collected between 20 and 100 years ago and fixed in either formaldehyde or ethanol. A 313 bp fragment of the cytochrome c oxidase subunit I (COI) was amplified and sequenced for prey item identification in the stomach and a 450 bp region of the 16S rRNA gene to investigate microbiome composition in the gut system. Both data sets were characterized by large dropout rates during extensive quality controls. Eventually, no unambiguous results regarding stomach content (COI) were retained, possibly due to degraded DNA, inefficient primers and contamination. In contrast, reliable microbiome composition data (16S rRNA) was obtained from 26 samples. These data showed a correlation in change of microbiome composition with fish size as well as year of the catch, indicating a microbiome shift throughout ontogeny and between samples from different decades. A comparison with contemporary samples indicated that the intestinal microbiome of Trematomus may have drastically changed within the last century. Further extensive studies are needed to confirm these patterns with higher sample numbers. Molecular analyses of museum stored fish can provide novel micro evolutionary insights that may benefit current efforts to prioritize conservation units in the Southern Ocean.

Decade‐scale stability and change in a marine bivalve microbiome

“…More importantly, very few studies have investigated whether host tissue preserved in ethanol, the most common preservative used for museum collections, could be used to investigate long‐term variations in microbiomes of non‐human hosts. The most extensive study on this topic, conducted using trematomid fish tissue collected between 1901 and 2006, showed that only ~10% of samples selected could be successfully used for microbiome analyses (Heindler et al, 2018). However, the authors suggest that many of those samples were probably first stored in formalin before transferring to ethanol (a common practice for museum samples in the past), which may explain the low yield, as formalin is known to cause multiple structural changes in DNA (Heindler et al, 2018).…”

“…The most extensive study on this topic, conducted using trematomid fish tissue collected between 1901 and 2006, showed that only ~10% of samples selected could be successfully used for microbiome analyses (Heindler et al, 2018). However, the authors suggest that many of those samples were probably first stored in formalin before transferring to ethanol (a common practice for museum samples in the past), which may explain the low yield, as formalin is known to cause multiple structural changes in DNA (Heindler et al, 2018). Overall, while there is some indication that samples preserved using a variety of methods may be useful for analysing long‐term trends in host microbiomes, such analyses need to consider the potential for preservational biases.…”

Microbiomes From Biorepositories? 16S rRNA Bacterial Amplicon Sequencing of Archived and Contemporary Intestinal Samples of Wild Mammals (Eulipotyphla: Soricidae)

“…The advent of genomic sequencing technologies, for example, demonstrated that many historical samples can be valuable to large scale phylogenomic and phylogeographic works (Holmes et al, 2016). Even given the large increase in museum specimen use for genomic sequencing, limited work has focused on characterizing the microbial communities associated with these archived host specimens (Heindler et al, 2018).…”

“…To date, a single study has examined gastrointestinal microbiomes of museum archives (Heindler et al, 2018) using DNA metabarcoding to identify the prey and microbiomes of trematomid fishes. They found limited overlap in microbiome composition between contemporary and museum samples of three Trematomus species archived in either formaldehyde or ethanol; however, they hypothesized that differences could reflect actual biological shifts in the gut microbiome of these fishes.…”

“…They found limited overlap in microbiome composition between contemporary and museum samples of three Trematomus species archived in either formaldehyde or ethanol; however, they hypothesized that differences could reflect actual biological shifts in the gut microbiome of these fishes. Heindler et al (2018) emphasized that further extensive studies are needed to confirm that shift in microbial composition over time. Herein, we expand on assessing the use of natural history collections for gastrointestinal tract (GIs) microbiome characterization to small mammals in the genus Sorex (shrews).…”