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

To analyse microbiota composition, non-metric multidimensional scaling ordinations were conducted on Bray-Curtis dissimilarities, calculated from rarefied sequence counts, after square root transformation and Wisconsin standardization. For each infectious agent, separate permutational MANOVA (PERMANOVA) tests with 999 permutations were performed to test the microbiota structure between sampling months, sexes, reproductive conditions and infection status. We then used linear discriminant analysis effect size (LEfSe; Galaxy v. 1.0) to identify phylotypes that differed significantly in relative abundance between the identified factors. We set the α value for the Kruskal-Wallis test at 0.05 and the threshold on the logarithmic LDA score at 2.0. In September 2015, we trapped exclusively non-scrotal males in the M. natalensis colony, while in the R. aegyptiacus colony, there were both non-scrotal and scrotal males, along with non-pregnant females (figure 1). In November 2015, most (90%) of the females sampled in the M. natalensis colony were parturient (i.e. had given birth very recently; pregnant females were released without sampling) and the males were again all non-scrotal. For R. aegyptiacus, the sampling performed in October 2015 comprised a majority (64%) of pregnant females, but also non-pregnant females, and both scrotal and non-scrotal males. In January 2016, large amounts of juveniles were present in both colonies, with mainly postlactating females for M. natalensis and lactating females for R. aegyptiacus. Finally, in April 2016, most of the bats caught in the R. aegyptiacus colony (83%) were flying juveniles.