Data_Sheet_5_Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework.ZIP

Apicomplexans 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.

顶复门生物（Apicomplexans）是一类微生物真核生物，其中包含诸多研究最为深入的寄生虫类群，例如弓形虫病、疟疾的致病病原体，以及隐孢子虫病、巴贝斯虫病等新发传染病的病原。数十年来的研究已阐明模式顶复门生物的致病机制、分子生物学特性与基因组学特征，但学界对这类生物在自然环境中的多样性与分布情况却知之甚少。本研究针对顶复门生物在宿主关联环境与自由生活环境中的分布展开分析，依托公开可用的小亚基（SSU）rRNA基因数据库、高通量环境测序（HTES）调研数据，以及本研究自主生成的HTES数据，构建了顶复门生物参考数据库。该数据库包含目前公开可用的最大规模顶复门SSU rRNA系统发育树，全面涵盖该类群及其近缘类群的采样信息。借助该系统发育树，我们可识别并修正顶复门生物序列分子鉴定中存在的不一致性问题。利用这一经过人工整理的参考数据库，对HTES研究中的顶复门生物多样性与分布情况进行分析后发现，顶复门生物广泛存在于各类自由生活环境中，且在群落丰度中占据重要比例。相较于当前已有认知，尤其是相较于已定名顶复门物种所揭示的多样性，本研究数据展现了该类群极为可观的分子多样性。这一点在海洋环境中尤为突出：海洋中极有可能存在多样性最为丰富的顶复门类群，但目前尚未被正式定名。这一全新参考数据库将在微生物生态学与流行病学研究中发挥重要作用，同时可为医学与兽医诊断提供极具价值的参考依据，尤其针对新发、人畜共患及隐匿性感染病例。