This blog post is provided by Ilze Brila and tells the #StoryBehindthePaper for the paper “Idiosyncratic effects of coinfection on the association between systemic pathogens and the gut microbiota of a wild rodent, the bank vole (Myodes glareolus”, which was recently published in Journal of Animal Ecology. In their paper they explore how coinfection of pathogens impact the microbiota of bank voles.

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Gut microbiota is the collection of microorganisms (such as bacteria and microfungi) inhabiting the gastrointestinal tract of an animal. The gut microbiota provides many important functions and services to its host and is, therefore, a crucial part of animal physiology and health. It is thus unsurprising, that the number of studies examining factors affecting gut microbiota has skyrocketed in recent years to demonstrate how the gut microbiota can be affected by diverse features of the host and its environment, including infection by pathogens. 

Wild animals can be infected by a variety of pathogens, both macroscopic such as helminths, and microscopic, such as protozoans or bacteria. The possibility of interactions between gastrointestinal pathogens and the gut microbiota might seem obvious, as both the parasite and the microbiota inhabit the same environment. But one unresolved question is whether infection by systemic pathogens (those found in blood or multiple tissues) is associated with changes in the gut microbiota of wild animals. Importantly, coinfections (infections by multiple pathogens simultaneously) are the norm in nature, and it is, therefore, essential to understand whether coinfections would affect the pattern of the pathogen-microbiota interactions.

To answer these questions, we determined whether bank voles (Myodes glareolus) were infected by four systemic pathogens: Puumala orthohantavirus, apicomplexan protozoan Babesia microti, and the bacteria Anaplasma phagocytophilum and Borrelia burgdorferi sensu lato. We investigated the gut microbiota – systemic pathogen relationships by asking (1) whether the effects of systemic pathogens depend on the pathogen’s identity and/or whether they affected by coinfections and (2) whether the effects of coinfection (compared to a single infection) on gut microbiota are similar for all pathogens. In short, the respective answers to our questions are “yes”, and “no”. Let me dive into the details. 

Out of the 67 voles that were infected with any of the four pathogens, 36 were coinfected, with a high number of different coinfections – we detected 9 types of coinfections out of the 11 possible combinations of coinfection. Clearly, coinfection is commonplace in nature. This diversity of different coinfections, unfortunately, prevented us from examining the effects of specific coinfections. However, one of the strengths of our work is the ability to compare associations between each pathogen and the gut microbiota when the coinfection status of the animal is overlooked versus the case when coinfection is considered. Do the associations found between pathogens and the gut microbiota stand true after controlling for effects of coinfection? 

While each pathogen indeed had a unique association with the gut microbiota of bank voles, we found that only Anaplasma phagocytophilum had the same association with gut microbiota ß-diversity (between-sample diversity) regardless of whether the coinfection status is overlooked or considered. For the other three pathogens, overlooking coinfection status led to misleading conclusions on the pathogen-microbiota associations in a pathogen-specific way. 

How did the effects of a pathogen differ in a single-infection vs coinfection scenario? To answer this question, we used a framework outlined by Schmid et al. to compare the effects of coinfection with those of a single pathogen infection for each pathogen. In brief, we focussed on identifying whether the effects of a coinfection when compared to those of a single infection are best described as a) synergistic, whereby the effects of a pathogen are exacerbated by coinfection, b) neutral, when there is no significant difference between single infection versus coinfection scenarios, and c) antagonistic, where coinfection apparently counteracts the effects of a single pathogen infection. We uncovered evidence for all three possible effects of coinfection, with antagonistic effects occurring more often. The type of effect of coinfection was, again, dependent on the pathogen identity. Moreover, the impacts of coinfection also depended on the type of metric used to characterise variation in the gut microbiota community, potentially indicating infection-specific impacts on the rare or abundant gut bacteria. 

So, what are the take-home messages from our article? We show that overlooking coinfections can affect the pattern of pathogen-microbiota associations. We, therefore, encourage future studies to examine a wider diversity of pathogens relevant to study species in the specific region to better account for this apparent effect of coinfection. This, of course, will not be easy, given the potentially large number of pathogens that may (co)infect an animal, and the difficulties of pathogen screening in wildlife. Yet we believe that acknowledging infection heterogeneity (the number of concurrent infections and infection length or sequence) present in wild animal populations will provide interesting insights and lead to a better understanding of the complex interactions between hosts, their pathogens, and the gut microbiota. This in turn could provide a better understanding of how these multi-directional relationships may affect host health and disease dynamics in wild animals. 

A few final notes for those who have made it to (or scrolled down to) the end of this blog post. I am grateful for the constructive comments of all reviewers and the editor during the review process. However, I am especially grateful for one reviewer, whose detailed, constructive, and encouraging comments considerably improved the manuscript and were greatly appreciated by an early career researcher such as myself. Thank you. Another note I want to add is that all of our sequencing data, as well as metadata and code, are publicly available in NCBI SRA and Figshare. So, if reading our paper makes you want to dig a little bit deeper – please do! None of this work would have been possible without the community of researchers who make their analysis and code freely available. If you can repay this help by sharing your code, I encourage you to do so. 

Read the paper

Read the paper here: Brila, I., Lavrinienko, A., Tukalenko, E., Kallio, E. R., Mappes, T., & Watts, P. C. (2022). Idiosyncratic effects of coinfection on the association between systemic pathogens and the gut microbiota of a wild rodent, the bank vole Myodes glareolus. Journal of Animal Ecology, 00, 1– 12. https://doi.org/10.1111/1365-2656.13869