Gut Microbiome of Century-Old Snail Specimens Stable Across Time in Preservation

Abstract

Background Oreohelix strigosa (Rocky Mountainsnail) is a land snail found in the talus slopes of the Rocky Mountains. The University of Colorado’s Museum of Natural History has densely sampled Oreohelix for the past century; many are preserved in ethanol and available for molecular research. While microbiome compositions in other systems are not affected by short-term field season preservation, the effects of decades-long preservation have yet to be assessed. Results We used 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing to examine Oreohelix strigosa gut microbiomes from museum specimens across a 98-year range, as well as within short term preservation treatments collected in 2018. Treatment groups included samples extracted fresh, without preservation; samples starved prior to extraction; and samples preserved for 1 month, 6 months, and 9 months. General microbiome composition was similar across all years. Sample groups belonging to specific years, or specific short-term treatments, showed unique associations with select bacterial taxa. Collection year was not a significant predictor of microbial richness, though unpreserved short-term treatments showed significantly higher richness than preserved treatments. While year was a significant factor in microbiome composition, it did not explain much of the variation across samples. Other factors like location collected and drought index were also significant drivers of community composition and explained as much or more of the variability. Conclusions This study is the first to examine animal host associated microbiome change across a period of nearly one century. Generally, geographic location was a greater factor in shaping gut microbiome composition, rather than year collected. Consistent patterns across this temporal range indicate that historic specimens can answer many ecological questions surrounding the host associated microbiome.

Rocky Mountainsnail gut microbiome varies significantly across its native geographic range

“…The taxonomic compositions of snail gut microbiomes across the native range were generally consistent with previous findings looking only at snails from Colorado (Chalifour & Li 2021b;Chalifour, Elder, & Li, 2022; Fig. 3A).…”

“…Out of the top five ASVs found in snail guts, the top four were all bacteria from family Enterobacteriaceae, and the fifth was a member of family Sphingobacteriaceae (from genus Pedobacter ). Results from previous work examining O. strigosa across life stage, time in preservation, and location similarly show the core microbiome primarily consists of members of Enterobacteriaceae and Sphingobacteriaceae (Chalifour & Li 2021b;Chalifour et al, 2022), which are hypothesized to aid in the degradation and fermentation of cellulose, hemicellulose, and lignin, all typical in this snail's inferred diet (Dar et al, 2017). Our finding further supports that these core microbial strains likely form obligate symbiotic relationships with O. strigose , as they are consistently found across a wide geographic range.…”

“…Previous work has shown that members of Enterobacteriaceae, which were in significantly lower abundances in soil and vegetation samples compared to gut samples, are present in both adult and fetal, unborn O. strigosa gut microbiomes, indicating these may be some of the taxa that snails receive vertically rather than horizontally (Chalifour & Li, 2021b). Importantly, many of the previously identified core microbiome taxa Chalifour, Elder, &Li, 2022) were found only in high abundances in snail gut samples, and not in the soil or vegetation samples. Since the core bacteria may be directly passed down from parent to offspring, this could augment the effects of geography on snail gut microbiome compositions, as snail populations separated by great distances don't typically interact.…”

Microbiome and floral associations of a wild bee using biodiversity survey collections

“…Studies of the microbiome have predominantly utilised bees caught on the wing and immediately flash frozen (Liberti et al, 2022;Nguyen & Rehan, 2022a;Tarpy et al, 2015;Thamm et al, 2023), but this can be expensive in time and materials spent collecting and freezing whereas passive methods can capture a wider snapshot of the bee community with fewer hours of labour. Non-destructive DNA extraction has allowed for the use of pinned specimens to characterise microbiota, and microbial detection has been shown to withstand lengthy periods spent in storage (Chalifour et al, 2022;Madison et al, 2023;Martoni et al, 2021;Santos et al, 2018). While studies of the microbiome often focus on the gut, whole-body specimens and the cuticular microbiome have also been shown to harbour distinct microbes (Reiß et al, 2023;Thamm et al, 2023).…”

“…While studies of the microbiome often focus on the gut, whole-body specimens and the cuticular microbiome have also been shown to harbour distinct microbes (Reiß et al, 2023;Thamm et al, 2023). In using these alternative methods, microbial characterisations are increasingly performable on a wider variety of collections, including pinned museum specimens (Chalifour et al, 2022;Hammer et al, 2015;Madison et al, 2023;Martoni et al, 2021).…”