Interpretation of gut microbiota data in the 'eye of the beholder': A commentary and re-evaluation of data from 'Impacts of radiation exposure on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone'

Abstract

Evidence that exposure to environmental pollutants can alter the gut microbiota composition of wildlife includes studies of rodents exposed to radionuclides. Antwis et al. (2021) used amplicon sequencing to characterise the gut microbiota of four species of rodent (Myodes glareolus, Apodemus agrarius, A. flavicollis and A. sylvaticus) inhabiting the Chernobyl Exclusion Zone (CEZ) to examine possible changes in gut bacteria (microbiota) and gut fungi (mycobiota) associated with exposure to radionuclides and whether the sample type (from caecum or faeces) affected the analysis. The conclusions derived from the analyses of gut mycobiota are based on data that represent a mixture of ingested fungi (e.g. edible macrofungi, polypores, lichens and ectomycorrhizae) and gut mycobiota (e.g. microfungi and yeasts), which mask the patterns of inter- and intraspecific variation in the authentic gut mycobiota. Implying that 'faecal samples are not an accurate indicator of gut composition' creates an unnecessary controversy about faecal sampling because the comparison of samples from the caecum and faeces confounds many other possible drivers (including different animals from different locations, sampled in different years) of variation in gut microbiota. It is relevant also that Antwis et al.'s (2021) data lack statistical power to detect an effect of exposure to radionuclides on the gut microbiota because (1) all of their samples of Apodemus mice had experienced a medium or high total absorbed dose rate and (2) they did not collect samples of bank voles (M. glareolus) from replicate contaminated and uncontaminated locations. Discussion of Antwis et al.'s (2021) analysis, especially the claims presented in the Abstract, is important to prevent controversy about the outcome of research on the biological impacts of wildlife inhabiting the CEZ.

Keywords: amplicon sequencing; diet; microbiota; mycobiota; radiation effects.

FIGURE 1

Distribution of samples of rodent gut microbiota from within the Chernobyl Exclusion Zone (CEZ) collected by Antwis et al. (2021) and Lavrinienko, Mappes, et al. (2018), Lavrinienko et al. (2020) (note that Lavrinienko, Mappes, et al.  also collected microbiota samples from two locations outside the CEZ [~80 km south, near Kyiv]) and these data are not shown in this figure. Dashed line represents the border around the CEZ in Ukraine (area ~2,050 km²). Shapes indicate trapping locations used in Lavrinienko, Mappes, et al. (, circles), in Lavrinienko et al. (, triangles) and in Antwis et al. (, squares). The figure was created using the ggmap (https://github.com/dkahle/ggmap) package in R

FIGURE 2

Proportions of fungal classes identified in the gut and faecal samples from four species of rodent, separated by their possible resident (mycobiota) or non‐resident (ingested) status in the host’s gastrointestinal tract

FIGURE 3

Effect of filtering fungal sequence variants (SVs) by their traits on alpha diversity (observed number of SVs) of the assemblage of gut fungi present in caecum and faeces in four species of rodent. (a) All SV data, (b) the likely resident gut fungi (mycobiota) and (c) the possible fungal SVs that were ingested as part of the host’s diet (non‐resident fungi). Red, bank vole (Myodes glareolus, MG); light blue, striped field mouse (Apodemus agrarius, AA); blue, wood mouse (A. sylvaticus, AS); purple, yellow‐necked mouse (A. flavicollis, AF)

FIGURE 4

Effect of filtering fungal sequence variants (SVs) by their traits on the apparent pattern of interspecific differences in fungal assemblage present in rodent caecum and faecal samples. (a) All SV data, (b) the likely resident gut fungi (mycobiota) and (c) the possible fungal SVs that were ingested as part of the host’s diet (non‐resident fungi). Red, bank vole (Myodes glareolus, MG); light blue, striped field mouse (Apodemus agrarius, AA); blue, wood mouse (A. sylvaticus, AS); purple, yellow‐necked mouse (A. flavicollis, AF). Ordination is a principal coordinate analysis (PCoA) based on Bray–Curtis dissimilarities