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.

Some observations on meaningful and objective inference in radioecological field studies

“…In summary, we agree with Watts et al (2022) that faecal samples may be indispensable for longitudinal studies, or where destructive sampling is otherwise not logistically or ethically possible.…”

“…To demonstrate their point, Watts et al (2022) identified candidate resident and non‐resident taxa using Microfungi Collections Consortium (http://www.microfungi.org/table1) and FUNGUILD v.1.2 (Nguyen et al, 2016). They then filtered possible non‐resident fungi from the fungal dataset published by Antwis et al (2021).…”

“…This will be compounded by a lack of precision with taxonomic assignments inherent in current metabarcoding methods (Abarenkov et al, 2018; Hleap et al, 2021; Lücking et al, 2020). Watts et al (2022) and Lavrinienko, Scholier, et al (2021) found that their filtering made some changes in relation to associations with radiation. Watts et al (2022) noted changes in data dispersion and Lavrinienko, Scholier, et al (2021), using permutational multivariate analysis of variance (PERMANOVA), found a change in R 2 for radiation from 0.007 in an unfiltered analysis to 0.006 for resident taxa and 0.007 for non‐resident taxa.…”

“…Antwis et al (2021) observed differing associations between microbiome composition and radiation dose rate in gut samples compared to in faecal samples. Watts et al (2022) discount this observation stating that the gut and faeces samples were unmatched (and thus subject to confounding variation). In fact, we explicitly acknowledged that our faeces and gut samples were not matched and this is reflected in the quote that Watts et al provide in their criticism (i.e.…”

“…wildfires) on this area ’. Watts et al (2022) appear to challenge this opinion. The Red Forest is a virtually unique area within the Chornobyl Exclusion Zone.…”