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Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework

AuthorsCampo, Javier del ; Heger, Thierry; Rodríguez-Martínez, Raquel ; Worden, A.Z.; Richards, Thomas A.; Massana, Ramon ; Keeling, Patrick
Environmental sequencing
Reference database
Issue DateOct-2019
PublisherFrontiers Media
CitationFrontiers in Microbiology 10: 2373 (2019)
AbstractApicomplexans are a group of microbial eukaryotes that contain some of the most well-studied parasites, including the causing agents of toxoplasmosis and malaria, and emergent diseases like cryptosporidiosis or babesiosis. Decades of research have illuminated the pathogenic mechanisms, molecular biology, and genomics of model apicomplexans, but we know little about their diversity and distribution in natural environments. In this study we analyze the distribution of apicomplexans across a range of both host-associated and free-living environments. Using publicly available small subunit (SSU) rRNA gene databases, high-throughput environmental sequencing (HTES) surveys, and our own generated HTES data, we developed an apicomplexan reference database, which includes the largest apicomplexan SSU rRNA tree available to date and encompasses comprehensive sampling of this group and their closest relatives. This tree allowed us to identify and correct incongruences in the molecular identification of apicomplexan sequences. Analyzing the diversity and distribution of apicomplexans in HTES studies with this curated reference database also showed a widespread, and quantitatively important, presence of apicomplexans across a variety of free-living environments. These data allow us to describe a remarkable molecular diversity of this group compared with our current knowledge, especially when compared with that identified from described apicomplexan species. This is most striking in marine environments, where potentially the most diverse apicomplexans apparently exist, but have not yet been formally recognized. The new database will be useful for microbial ecology and epidemiological studies, and provide valuable reference for medical and veterinary diagnosis especially in cases of emerging, zoonotic, and cryptic infections
Description15 pages, 5 figures, supplementary material https://doi.org/10.3389/fmicb.2019.02373.-- The datasets generated for this study can be found in NCBI Sequence Read Archive, PRJNA521526 and PRJNA396681. The reference database generated in this study and provided in Supplementary Table S1 has also been deposited in PR2 (Guillou et al., 2013) and it is available at https://github.com/pr2database/pr2database. PR2 will also host future updates of this reference database
Publisher version (URL)https://doi.org/10.3389/fmicb.2019.02373
Identifiersdoi: 10.3389/fmicb.2019.02373
e-issn: 1664-302X
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