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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
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相关实验视频

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CAIM:用于识别微生物群的基于覆盖范围的分析.

Daniel A Acheampong1,2, Piroon Jenjaroenpun1,3, Thidathip Wongsurawat1,3

  • 1Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, United States.

Briefings in bioinformatics
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概括

我们开发了CAIM,这是一个新的生物信息学工具,用于在元基因组样本中准确的微生物分类学概况. CAIM使用基因组覆盖来准确识别,并且在分类物种和估计丰度方面优于其他方法.

关键词:
生物信息学是一种生物信息学.我们的肠道微生物组.甲基基因组 (metagenome) 是一个基因组.超基因组覆盖范围的覆盖范围分类学识别的标识.

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科学领域:

  • 微生物生态学 微生物生态学
  • 生物信息学是一种生物信息学.
  • 基因组学就是基因组学.

背景情况:

  • 准确的分类学概况对于理解微生物生态学至关重要.
  • 步枪元基因组学和测序技术的进步使得物种级微生物分析成为可能.

研究的目的:

  • 开发一种新的生物信息学工具,即基于覆盖的微生物群识别分析 (CAIM),用于精确的分类学分类和量化.
  • 改进现有的分析长读和短读元基因组数据的方法.

主要方法:

  • 开发了基于对齐的工具CAIM,该工具利用制技术和基因组覆盖面用于物种识别.
  • 实施了基于核酸计数的丰度估计方法.
  • 评估CAIM在模拟和合成数据集上的性能,并与其他领先的工具进行比较.

主要成果:

  • 在识别微生物种群和估计不同数据集的相对丰度方面,CAIM表现一致.
  • 在纳米孔和Illumina测序平台之间观察到分类学概况的高度相似性.
  • 使用CAIM的基因组覆盖切断值的模型在与相对丰度切断值相比,在将癌症患者与对照组区分开来方面表现出优异的预测性能.

结论:

  • 凯姆提供准确的分类学概况和丰富度估计的元基因组样本.
  • 该工具有效地处理长读和短读数据,并在不同的测序平台上显示高一致性.
  • 在复杂的数据集中,CAIM的基因组覆盖方法提供了一种可靠的方法来识别与疾病相关的微生物标记物.