Data_Sheet_8_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，其中包含了一批研究最为深入的寄生虫，例如弓形虫病与疟疾的致病原，以及隐孢子虫病、巴贝西虫病等新发传染病的病原体。数十年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，但我们对该类群在自然环境中的多样性与分布情况却知之甚少。 本研究分析了顶复门生物在宿主关联环境与自由生活环境中的分布格局。研究依托公开可用的小亚基（SSU）核糖体RNA（rRNA）基因数据库、高通量环境测序（HTES）调查数据集，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。该数据库涵盖了目前已发布的规模最大的顶复门SSU rRNA系统发育树，并对该类群及其近缘类群完成了全面采样。该系统发育树可帮助我们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。 依托该经人工整理筛选的参考数据库对HTES研究中的顶复门生物多样性与分布进行分析后发现，顶复门生物在各类自由生活环境中广泛存在，且其丰度具有重要的生态学意义。 相较于当前已有的认知，尤其是相较于已正式描述的顶复门生物物种所对应的相关数据，本研究的数据揭示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：海洋中可能存在多样性最高的顶复门生物类群，但尚未被正式定名。 该全新数据库将为微生物生态学与流行病学研究提供重要支撑，并可为医学及兽医诊断提供极具价值的参考依据，尤其适用于新发、人畜共患及隐匿性感染的诊疗场景。