通过空间元转录基因组测序,同时对宿主表达和微生物丰度进行分析.
1Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
Genome research
|June 13, 2023
概括
我们创建了一个空间转录基因组 (SMT) 管道来分析微生物和宿主基因表达在组织中. 这种方法揭示了空间宿主-微生物相互作用,推进了空间生物学和微生物组研究.
科学领域:
- 微生物组研究的研究.
- 空间生物学 空间生物学
- 文字转录学 (Transcriptomics) 是一个学科.
背景情况:
- 空间转录基因 (ST) 数据通常集中在宿主基因表达上.
- 了解微生物在宿主组织中的空间分布对于研究宿主-微生物相互作用至关重要.
- 目前的方法缺乏同时分析宿主和微生物空间信息的能力.
研究的目的:
- 开发和验证用于从ST数据中提取和分析微生物序列的计算管道.
- 为了使宿主基因表达和微生物丰富性在空间环境中同时分析.
- 研究组织内的各种空间尺度上的宿主微生物相互作用.
主要方法:
- 开发了空间元转录组 (SMT) 分析管道,从ST数据中提取微生物序列并赋予分类标签.
- 与宿主表达矩阵一起生成了一个空间微生物丰富度矩阵.
- 将SMT管道应用于人类和小鼠肠道部分,并通过替代分析验证结果.
主要成果:
- 成功生成空间微生物丰富度矩阵,使宿主表达和微生物分布的同时分析成为可能.
- 使用独立的实验方法验证了空间微生物丰度数据的准确性.
- 确定了对不同空间尺度的宿主微生物相互作用的新生物学见解.
- 优化了实验条件,以增强微生物捕获,同时保持宿主表达质量.
结论:
- 空间元转录组 (SMT) 管道是分析微生物和宿主空间数据的可行方法.
- SMT分析为在现场调查宿主-微生物相互作用开辟了新的途径.
- 这项工作为进一步优化和应用空间微生物组分析在生物研究中的基础.
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