Characterization of the bacterial microbiome of non-hematophagous bats and associated ectoparasites from Brazil

Abstract

Introduction: Bats, along with their ectoparasites, harbor a wide diversity of symbiotic and potential pathogenic bacteria. Despite the enormous diversity of bats (181 species), few studies aimed to investigate the bacterial microbiome of Brazilian chiropterans and associated ectoparasites. This study aimed to characterize the bacterial microbiome of non-hematophagous bats and associated Streblidae flies and Macronyssidae and Spinturnicidae mites in the state of Mato Grosso do Sul, midwestern Brazil.

Methods: Oral and rectal swabs were collected from 30 bats (Artibeus lituratus [n = 13], Artibeus planirostris [n = 9], Eptesicus furinalis [n = 5], Carollia perspicillata [n = 2], and Platyrrhinus lineatus [n = 1]). In addition, a total of 58 mites (15 Macronyssidae and 43 Spinturnicidae) and 48 Streblidae bat flies were collected from the captured bats. After DNA extraction and purification, each sample's bacterial composition was analyzed with metagenomic sequencing.

Results: The microbiome composition of both oral and rectal bat swab samples showed that Gammaproteobacteria was the most abundant bacterial class. Spiroplasma, Wolbachia and Bartonella represented the most abundant genera in Streblidae flies. While Wolbachia (Alphaproteobacteria) was the most abundant genus found in Spinturnicidae, Arsenophonus (Gammaproteobacteria) was found in high abundance in Macronyssidae mites. In addition to characterizing the microbiome of each sample at the class and genus taxonomic levels, we identified medically significant bacteria able to infect both animals and humans in oral (Streptococcus and Anaplasma) and rectal swabs (Enterobacter, Klebsiella, Escherichia, Enterococcus, Streptococcus), Macronyssidae (Anaplasma, Bartonella, Ehrlichia) and Spinturnicidae (Anaplasma, Bartonella) mites as well as Streblidae flies (Spiroplasma, Bartonella).

Discussion and conclusion: Besides expanding the knowledge on the bacterial microbiome of non-hematophagous bats and Streblidae flies from Brazil, the present work showed, for the first time, the bacterial community of bat-associated Macronyssidae and Spinturnicidae mites.

Keywords: Chiroptera; Macronyssidae; Spinturnicidae; Streblidae; bat flies; microbiome composition; mites.

Figure 1

Map of the collection locations (“CEA Florestinha” and “Polonês”) for biological samples and ectoparasites from non-hematophagous bats in the city of Campo Grande, Mato Grosso do Sul state, Brazil.

Figure 2

(A) Percentage of all taxa at the class level found in the different oral swab samples from bats. (B) Percentage of all taxa at the genus level found in the different oral swab samples from bats.

Figure 3

(A) Percentage of all taxa at the class level found in the different fecal swab samples from bats. (B) Percentage of all taxa at the genus level found in the different fecal swab samples from bats.

Figure 4

(A) Occurrence map of each taxon per sample at the class level found in the fecal and oral swab samples from bats. (B) Occurrence map of taxa at the genus level found in the fecal and oral swab samples from bats.

Figure 5

(A) Percentage of all taxa at the class level found in Spinturnicidae mites collected from bats. (B) Percentage of all taxa at the genus level found in Spinturnicidae mites collected from bats.

Figure 6

(A) Occurrence map of each taxon per sample at the class level found in the Spinturnicidae mite samples. (B) Occurrence map of taxa at the genus level found in the Spinturnicidae mite samples.

Figure 7

(A) Percentage of all taxa at the class level found in Macronyssidae mites collected from bats. (B) Percentage of all taxa at the genus level found in Macronyssidae mites collected from bats.

Figure 8

(A) Occurrence map of each taxon per sample at the class level found in the Macronyssidae mite samples. (B) Occurrence map of taxa at the genus level found in the Macronyssidae mite samples.

Figure 9

(A) Percentage of all taxa at the class level found in Streblidae flies collected from bats. (B) Percentage of all taxa at the genus level found in Streblidae flies collected from bats.

Figure 10

(A) Occurrence map of each taxon per sample at the class level found in the Streblidae fly samples. (B) Occurrence map of taxa at the genus level found in the Streblidae fly samples.