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基准测试组装免费的纳米孔读取映射器通过牛津纳米孔测序技术对复杂的千足虫肠道微生物群进行分类

Orlando J Geli-Cruz¹, Carlos J Santos-Flores¹, Matias J Cafaro¹

¹Universidad de Puerto Rico, Recinto Universitario de Mayagüez, Call Box 9000 Mayagüez, PR 00681-9000.

Journal of biological methods

|November 8, 2023

概括

克拉肯2核酸模式最好地分类复杂的千足虫肠道微生物群. 这种超基因组选方法有效地识别了多种类型,超过了分析千足动物肠道DNA序列的其他工具.

科学领域:

微生物学微生物学
生物信息学是一种生物信息学.
生态生态学生态生态学

背景情况:

千足动物对于热带生态系统的营养循环至关重要,通过叶子垃圾分解.
了解千足动物肠道微生物群对于生态研究至关重要.
超基因组脱皮是一种分析复杂微生物群落的强大技术.

研究的目的:

为了对不同生物信息学工具进行基因组皮测试,对千足动物肠道微生物群进行基因组皮测试.
确定从千足动物肠道DNA中分类长读序列数据的最有效方法.
评估波多黎各千足动物肠道社区中的微生物多样性.

主要方法:

在波多黎各收集的千足动物的肠道DNA使用牛津纳米孔技术 (ONT) 的MinION进行了测序.
使用五种分类工具分析了长时间的ONT读数:MEGAN-LR,Kraken2 (蛋白质模式),Kraken2 (核酸模式),GraphMap和Minimap2.
绩效的评估是基于类和类级别的阅读分类率以及类型稀有化曲线.

主要成果:

克拉肯2核酸模式表现出卓越的性能,在族群和类级别分类75%的读数.
其他方法未能分类足够数量的读数,表明需要更深的测序深度.
千足的肠道微生物群非常多样化,在各种方法中确定了20-50个类.

结论:

克拉肯2核酸模式是复杂的千足动物微生物组的元基因组脱皮最合适的工具.
这一发现有助于有效地描述未经研究的关节动物中的微生物群落.
准确的微生物组分析对于了解千足动物的生态作用至关重要.

关键词:

提取DNA 提取DNA的方法我们的肠道微生物群.转基因组学是指转基因组学.梅里亚波达 (Myriapoda) 是一个纳米孔测序的测序

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