Laboratory cultures of heterotrophic protists are often xenic, meaning that the culture contains more than one microbial organism. In this study, we analyzed genome-assembly data from cultures of four marine protist flagellates—the marine malawimonad Imasa heleensis, the undescribed mantamonad strain SRT-306, the discobid Ophirina amphinema, and the cryptist Palpitomonas bilix—specifically to search for genomes of cocultured bacteria. As no external bacteria have been added to the protist stock cultures, it is probable that the cocultured bacteria came from the original water samples from which the protists were isolated. At least some of these bacteria are consumed as a food source by the protists, all of which are obligate heterotrophs. From four separate metagenomic de novo assemblies for these mixed cultures, we identified 28 scaffolds, which BUSCO analyses suggest represent complete or near-complete bacterial genomes. These scaffolds range in length from 3,139,436 to 6,090,282 bp and encode 2873 to 5666 genes. Only eight of the 28 scaffolds corresponded to entries in the NCBI genome database, meaning that 20 of these scaffolds represent genomes from putatively novel bacterial species. Our findings highlight that data like these, which are often discarded or overlooked, can be a source of novel genomes and/or species.

中文翻译：

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潜伏在原生生物细胞培养物中的细菌多样性

异养原生生物的实验室培养物通常是异养的，这意味着培养物包含不止一种微生物。在这项研究中，我们分析了来自四种海洋原生鞭毛虫培养物的基因组组装数据——海洋马拉维单胞菌 Imasa heleensis、未描述的 mantamonad 菌株 SRT-306、discobid Ophirina amphinema 和神秘的 Palpitomonas bilix——专门用于寻找共培养的基因组细菌。由于未将外部细菌添加到原生生物原种培养物中，因此共培养的细菌很可能来自分离原生生物的原始水样。至少其中一些细菌被原生生物作为食物来源消耗，所有这些细菌都是专性异养生物。从这些混合培养物的四个单独的宏基因组从头组装中，我们确定了 28 个支架，BUSCO 分析表明它们代表完整或接近完整的细菌基因组。这些支架的长度从 3,139,436 到 6,090,282 bp 不等，编码 2873 到 5666 个基因。28 个支架中只有 8 个对应于 NCBI 基因组数据库中的条目，这意味着这些支架中的 20 个代表来自假定的新型细菌物种的基因组。我们的研究结果强调，像这些经常被丢弃或忽视的数据可以成为新基因组和/或物种的来源。