Small subunit ribosomal metabarcoding reveals extraordinary trypanosomatid diversity in Brazilian bats

(Uploaded by Plazi for the Bat Literature Project) Background Bats are a highly successful, globally dispersed order of mammals that occupy a wide array of ecological niches. They are also intensely parasitized and implicated in multiple viral, bacterial and parasitic zoonoses. Trypanosomes are thought to be especially abundant and diverse in bats. In this study, we used 18S ribosomal RNA metabarcoding to probe bat trypanosome diversity in unprecedented detail. Editor: Carlos A. Buscaglia, Instituto de Investigaciones Biotecnolo´gicas, ARGENTINA Received: April 13, 2017 Accepted: July 10, 2017 Published: July 20, 2017 Copyright: © 2017 Dario et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All sequences have been deposited in the NCBI Sequence Read Archive (SRA) under accession numbers SRR5451077SRR5451120. Methodology/Principal Findings Total DNA was extracted from the blood of 90 bat individuals (17 species) captured along Atlantic Forest fragments of Esp´ırito Santo state, southeast Brazil. 18S ribosomal RNA was amplified by standard and/or nested PCR, then deep sequenced to recover and identify Operational Taxonomic Units (OTUs) for phylogenetic analysis. Blood samples from 34 bat individuals (13 species) tested positive for infection by 18S rRNA amplification. Amplicon sequences clustered to 14 OTUs, of which five were identified as Trypanosoma cruzi I, T. cruzi III/V, Trypanosoma cruzi marinkellei, Trypanosoma rangeli, and Trypanosoma dionisii, and seven were identified as novel genotypes monophyletic to basal T. cruzi clade types of the New World. Another OTU was identified as a trypanosome like those found in reptiles. Surprisingly, the remaining OTU was identified as Bodo saltans–closest non-parasitic relative of the trypanosomatid order. While three blood samples featured just one OTU (T. dionisii), all others resolved as mixed infections of up to eight OTUs. Funding: This study was funded by the Oswaldo Cruz Foundation (Fiocruz), the National Council for Scientific and Technological Development (CNPq) and the Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ). A doctoral grant was provided by CNPq and a SWP grant was provided by FAPERJ to MAD. Conclusions/Significance This study demonstrates the utility of next-generation barcoding methods to screen parasite diversity in mammalian reservoir hosts. We exposed high rates of local bat parasitism by multiple trypanosome species, some known to cause fatal human disease, others non-pathogenic, novel or yet little understood. Our results highlight bats as a long-standing nexus