Synchronized shift of oral, faecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction

Dietrich, Muriel; Kearney, Teresa; Seamark, Ernest C. J.; Paweska, Janusz T.; Markotter, Wanda

We did not find any association between HV shedding in saliva and associated bacterial microbiota for both bat species (both PERMANOVAs: p > 0.05). By contrast, we found a significant association between AdV presence and faecal microbiota composition in M. natalensis (PERMANOVA: p = 0.001), but this coincided with the effect of sampling session, as bats were found shedding AdVs only in November. Therefore, it is difficult to conclude if there was an interaction between AdV shedding in faeces and the faecal microbiota composition. Finally, as noted with the urinary microbiota diversity, we also found a strong correlation between Leptospira shedding (measured by RT-PCR) and urinary microbiota composition in M. natalensis (PERMANOVA: p = 0.001). LEfSe analysis confirmed that Leptospira RT-PCR positive samples were enriched in Leptospira but also in Illumatobacter, while 31 other phylotypes, including Clostridium sensu stricto and unclassified Bacillales, were predominantly associated with negative samples. Altogether, our results suggested no interaction between DNA virus shedding dynamics and shift of bacterial microbiota in bats. To our knowledge, interactions between virus dynamics and microbiota have never been demonstrated in wild animals, but recent field studies have reported an association between microbiota composition and other types of parasites, such as in frogs naturally infected by the chytrid fungus [54] , rodents parasitized by multiple helminths [55] or even bats for which invasion by the fungus Pseudogymnoascus destructans leads to a shift in the skin microbiota [56] . Moreover, experimental studies performed in mice, using RNA viruses, have shown interactions with the microbiota, through diverse effects such as pathogen inhibition, co-aggregation and regulation of the immune system and metabolism [2] . Our lack of interaction for herpes-and adenoviruses may be due to the fact that other aspects of the microbiome (other than bacteria) could interact with viral infection. These viruses are also both DNA viruses capable of latency and reactivation at the individual level, and thus may be more involved in long-lasting changes of the microbiota and the modulation of immune functions [57] . Further investigations, targeting virus pool dynamics in bats and specifically RNA viruses, will assist in determining how transient and chronic infections may interact with the dynamics of microbiota composition.