The gut of vertebrates is a host for hundreds or thousands of different species of microorganisms named the gut microbiome. This latter may differ greatly in natural environments between individuals, populations and species (1). The vertebrate gut microbiome plays key roles in host fitness through functions including nutrient acquisition, immunity and defense against infectious agents. While bank voles are small mammals potentially reservoirs of a large number of infectious agents, questions about the links between their gut microbiome and the presence of pathogens are scarcely addressed. 

In this study, Bouilloud et al. (2) used complementary analyses of community and microbial ecology to (i) assess the variability of gut bacteriome diversity and composition in wild populations of the bank vole Myodes glareolus collected in four different sites in Eastern France and (ii) evaluate the three-way interactions between the gut bacteriota, the gastro-intestinal helminths and pathogenic bacteria detected in the spleen. Authors identified important variations of the gut bacteriota composition and diversity among bank voles mainly explained by sampling localities. They found positive correlations between the specific richness of both the gut bacteria and the helminth community, as well as between the composition of these two communities, even when accounting for the influence of geographical distance. The helminths Aonchotheca murissylvatici, Heligmosomum mixtum and the bacteria Bartonella sp were the main taxa associated with the whole gut bacteria composition. Besides, changes in relative abundance of particular gut bacterial taxa were specifically associated with other helminths (Mastophorus muris, Catenotaenia henttoneni, Paranoplocephala omphalodes and Trichuris arvicolae) or pathogenic bacteria. Infections with Neoehrlichia mikurensis, Orientia sp, Rickettsia sp and P. omphalodes were especially associated with lower relative abundance of members of the family Erysipelotrichaceae (Firmicutes), while coinfections with higher number of bacterial infections were associated with lower relative abundance of members of the Bacteroidales family (Bacteroidetes). 

As pointed out by both reviewers, this study represents a significant advance in the field. I would like to commend the authors for this enormous work. The amount of data, analyses and results is considerable which has sometimes complicated the understanding of the story at the beginning of the evaluation process. Thanks to constructive scientific interactions with both reviewers through the two rounds of evaluation, the authors have efficiently addressed the reviewer's concerns and improved the manuscript, making this great story easier to read. The innovative results of this study emphasize the complex interlinkages between gut bacteriome and infections in wild animal populations and I strongly recommend this article for publication In Peer Community Infections. 

References

(1) Vujkovic-Cvijin I, Sklar J, Jiang L, Natarajan L, Knight R, Belkaid Y (2020) Host variables confound gut microbiota studies of human disease. Nature, 587, 448–454. https://doi.org/10.1038/s41586-020-2881-9

(2) Bouilloud M, Galan M, Dubois A, Diagne C, Marianneau P, Roche B, Charbonnel N (2023) Three-way relationships between gut microbiota, helminth assemblages and bacterial infections in wild rodent populations. biorxiv, 2022.05.23.493084, ver. 2 peer-reviewed and recommended by Peer Community in Infections. https://doi.org/10.1101/2022.05.23.493084

Most infectious diseases of humans are zoonoses, and many of these come from particularly species diverse reservoir taxa, such as bats, birds, and rodents (1). Because of our changing landscape, there is increased exposure of humans to wildlife diseases reservoirs, yet we have little basic information about prevalence, hotspots, and transmission factors of most zoonotic pathogens. Viruses are particularly worrisome as a public health risk due to their fast mutation rates and well-known cross-species transmission abilities. There is a global push to better survey wildlife for viruses (2), but these studies are difficult, and the problem is vast. Astroviruses (AstVs) comprise a diverse family of ssRNA viruses known from mammals and birds. Astroviruses can cause gastroenteritis in humans and are more common in elderly and young children, but the relationship of human to non-human Astroviridae as well as transmission routes are unclear.  AstVs have been detected at high prevalence in bats in multiple studies (3,4), but it is unclear what factors, such as co-infecting viruses and bat reproductive phenology, influence viral shedding and prevalence.
In this recommended study, Vimbiso et al. (5) study the prevalence and diversity of astroviruses in different insectivorous and frugivorous chiropteran species roosting in trees, caves and building basements across Zimbabwe, a region never investigated for astroviruses. Using both pooled population samples and individual samples from 11 different sites, the authors screened for astrovirus prevalence via RT-PCR and identified bat taxa using mitochondrial gene sequencing. An overall prevalence of 10-14% infection was recorded. No clear association of increased astrovirus and coronavirus coinfection was detected, and although astrovirus infection varied over the season, it did not do so in consistent ways across the two primary sampling sites, Magweto and Chirundu. A phylogeny generated by sequencing all of the astrovirus positive samples showed evidence that most of the viral lineages are transmitting within species but across Zibabwae such that most phylogenetic lineages grouped viruses from the same host species together. However, there was ample evidence for interspecies transmission between bats. Finally, a small percentage of the total astrovirus diversity from Zibabwae clustered with sequences from humans. The timing and direction of the transmission between humans and bats need further investigation.
 
This study provides important baseline data about viral diversity and does an excellent job of capturing the spatial, temporal, host species, and sequence level dynamics of the astroviruses. There are clear limitations on how this study can be interpreted due to different sampling regimes and, in particular, the fact that each of the two primary sites was only explored for temporal variation over a single calendar year. That said, the grand diversity of astroviruses demonstrated in insectivorous bats in Zibabwae shows that we are only seeing the very tip of the iceberg with respect to viral diversity with zoonotic potential. As suggested by the reviewers, more studies like this are needed to understand the basic ecology of viruses and to aid in predicting epidemics.

References

1. Mollentze N, Streicker DG. Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts. Proceedings of the National Academy of Sciences. 2020 Apr 28;117(17):9423-30. https://doi.org/10.1073/pnas.1919176117
2. Carroll D, Daszak P, Wolfe ND, Gao GF, Morel CM, Morzaria S, et al. The Global Virome Project. Science. 2018 Feb 23;359(6378):872-4. https://doi.org/10.1126/science.aap7463
3. Lee SY, Son KD, Yong-Sik K, Wang SJ, Kim YK, Jheong WH, et al. Genetic diversity and phylogenetic analysis of newly discovered bat astroviruses in Korea. Arch Virol. 2018;163(11):3065-72. https://doi.org/10.1007/s00705-018-3992-6
4. Seltmann A, Corman VM, Rasche A, Drosten C, Czirják GÁ, Bernard H, et al. Seasonal Fluctuations of Astrovirus, But Not Coronavirus Shedding in Bats Inhabiting Human-Modified Tropical Forests. EcoHealth. 2017 Jun 1;14(2):272-84. https://doi.org/10.1007/s10393-017-1245-x
5. Vimbiso C, Hélène DN, Malika A, Getrude M, Valérie P, Ngoni C, et al. Longitudinal Survey of Astrovirus infection in different bat species in Zimbabwe: Evidence of high genetic Astrovirus diversity. bioRxiv, 2023.04.14.536987, ver. 6 peer-reviewed and recommended by Peer Community In Infections. https://doi.org/10.1101/2023.04.14.536987