A targeted approach to enrich host-associated bacteria for metagenomic sequencing

Multicellular eukaryotic organisms are hosts to complex communities of bacteria that reside on or inside their tissues. Often the eukaryotic members in complex communities contribute to high proportions of metagenomic sequencing reads, making it challenging to achieve sufficient sequencing depth to evaluate bacterial ecology. Stony corals are one such complex community; however, separation of bacterial from eukaryotic (primarily coral and algal symbiont) cells has so far not been successful. Using a combination of hybridization chain reaction fluorescence in situ hybridization and fluorescence activated cell sorting (HCR-FISH + FACS), we sorted two populations of bacteria from five genotypes of the coral Acropora loripes, targeting 1) Endozoicomonas spp, and 2) all other bacteria. These are the raw reads for this data set.

多细胞真核生物是栖息于其组织表面或组织内部的复杂细菌群落的宿主。通常，复杂群落中的真核生物组分在宏基因组测序读段中占比极高，这使得获取足够测序深度以解析细菌生态学特征颇具挑战。石珊瑚便是这类复杂群落之一；然而，目前尚未能成功将细菌细胞与真核细胞（主要为珊瑚及藻类共生体）分离开来。本研究采用杂交链反应荧光原位杂交（hybridization chain reaction fluorescence in situ hybridization, HCR-FISH）与荧光激活细胞分选（fluorescence activated cell sorting, FACS）联用的方法，从5种基因型的洛氏鹿角珊瑚（Acropora loripes）中分选得到两类细菌群体，分别靶向1）内生杆菌属（Endozoicomonas）物种，以及2）其余所有细菌。以下即为该数据集的原始测序读段。