The Impact of Whole-Animal Fluid Preservation on the Observed Gut Microbiome of Vertebrates: Implications for the Use of Museum Specimens in Microbiome Research.

Abstract

The vertebrate gut houses diverse microbial communities that provide insights into their host's ecological and evolutionary histories. Nevertheless, microbiome research has not been distributed equally across host taxonomy, geography and timescales. The millions of fluid-preserved specimens stored in natural history museums worldwide represent a potentially untapped resource for microbiome information. However, it is unknown how fluid preservation and long-term storage change the composition and diversity of the original microbial community across a variety of host taxa. Here, we present the largest study to date aimed at addressing this question. Specifically, we identified an optimal method for extracting DNA from preserved samples using commercially available kits. Next, for 11 host species representing four vertebrate classes, we compared the gut microbiomes between animals dissected freshly and those collected simultaneously but subsequently fixed in formalin and stored in 70% ethanol for 1 year, similar to museum conditions. In a secondary analysis in amphibians, we compared our collected samples with those from decades-old historical museum specimens. We found that while fluid preservation altered the community composition and reduced the diversity of the recovered microbiome inventories, host species identity predominated in shaping the gut microbiome, and differences across species and geographic localities were retained after preservation. Historical specimens had microbiomes that were the most different from fresh specimens, suggesting that over time, changes in the microbiome of populations have occurred, or preservation effects have compounded. Considering these findings, we discuss the potential for use of fluid-preserved museum specimens in future microbiome studies.