Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far. To tackle this issue, we compared blocking and excluding primers to analyze microeukaryotic communities associated with Crassostrea gigas oysters. High-throughput sequencing of 18S rRNA genes variable loops revealed that excluding primers performed better by not amplifying oyster DNA, whereas the blocking primer did not totally prevent host contaminations. However, blocking and excluding primers showed similar pattern of alpha and beta diversities when protist communities were sequenced using metabarcoding. Alveolata, Stramenopiles and Archaeplastida were the main protist phyla associated with oysters. In particular, Codonellopsis, Cyclotella, Gymnodinium, Polarella, Trichodina, and Woloszynskia were the dominant genera. The potential pathogen Alexandrium was also found in high abundances within some samples. Our study revealed the main protist taxa within oysters as well as the occurrence of potential oyster pathogens. These new primer sets are promising tools to better understand oyster homeostasis and disease development, such as the Pacific Oyster Mortality Syndrome (POMS) targeting juveniles.

中文翻译：

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使用封闭和排除引物，揭示与太平洋牡蛎Crassostrea gigas相关的原生生物多样性。

大型微生物的微生物组可能直接或间接影响宿主的发育和体内平衡。许多研究集中在这些组合中的原核生物的多样性和分布上，但是到目前为止，真核微生物区室仍未得到充分的研究。为了解决这个问题，我们比较了封闭和排除引物来分析与Crassostrea gigas牡蛎有关的微真核生物群落。18S rRNA基因可变环的高通量测序表明，不扩增牡蛎DNA，排除引物的性能更好，而封闭引物不能完全防止宿主污染。但是，使用元条形码对原生生物群落进行测序时，封闭和排除引物显示出相似的alpha和β多样性模式。肺泡 鞘翅目和古菌是与牡蛎有关的主要原生生物门。特别是，党参，小环藻，裸子植物，极地菌，毛癣菌属和沃洛辛斯基属是主要的属。在某些样品中还发现了潜在的病原体亚历山大藻。我们的研究揭示了牡蛎中主要的原生生物类群以及潜在的牡蛎病原体的发生。这些新的引物组是有望更好地了解牡蛎稳态和疾病发展的有前途的工具，例如针对少年的太平洋牡蛎死亡率综合症（POMS）。我们的研究揭示了牡蛎中主要的原生生物类群以及潜在的牡蛎病原体的发生。这些新的引物组是有望更好地了解牡蛎稳态和疾病发展的有前途的工具，例如针对少年的太平洋牡蛎死亡率综合症（POMS）。我们的研究揭示了牡蛎中主要的原生生物类群以及潜在的牡蛎病原体的发生。这些新的引物组是有望更好地了解牡蛎稳态和疾病发展的有前途的工具，例如针对少年的太平洋牡蛎死亡率综合症（POMS）。