Anslan, S., H. Li, S. Künzel & M. Vences

Microbiomes from feces vs. gut in tadpoles: distinct community compositions between substrates and preservation methods. pp. 96-104 plus Supplementary Figures, Supplementary Table S1, Supplementary Table S2, Supplementary Table S3, Supplementary Table S4

Abstract. Sample type and preservation methods are likely to influence the results of microbiome analyses. Here, we sampled tadpoles of Nanorana parkeri non-invasively for feces, and subsequently for hindgut through dissection. Gut and fecal samples were stored in ethanol, and additionally, part of the gut samples were frozen, but temporarily thawed during transport as it often happens under difficult field conditions. Our results showed that both substrate (gut vs. feces) as well as preservation method can influence the analysis of intestinal microbiomes. Frozen gut samples strongly differed from ethanol-stored samples, and most of the frozen samples were dominated (in relative abundance) by a set of Proteobacteria OTUs that were completely absent from the ethanol-stored samples. This blooming of contaminant bacteria occurred after less than 12 h of thawing, thus caution should be taken when constancy of cold temperatures cannot be maintained in the field for sample preservation purposes. Among ethanol-stored samples, whereas the recovered bacterial richness and phylogenetic diversity did not differ, the community structure varied significantly. Thus, for meaningful gut microbiome meta-analyses it is important to acknowledge the effect of the sampling substrate for the microbial community composition.

Key words. Amphibia, Anura, Nanorana parkeri, gut microbiota, fecal samples, metabarcoding, 16S rRNA gene.