在哺乳动物肠道中通过宿主衍生的读取正常化对绝对细菌生物质的元基因学估计
Gechlang Tang1,2, Alex V Carr1, Crystal Perez1,3,4
1Institute for Systems Biology, Seattle, WA 98109, USA.
bioRxiv : the preprint server for biology
|January 20, 2025
概括
估计肠道中的细菌生物量至关重要. 一种新方法使用从元基因组读取细菌与宿主 (B:H) 的读取比率,提供一种简单,经济高效的方法来跟踪变化,如在抗生素治疗期间.
科学领域:
- 微生物组研究的研究.
- 宿主-微生物相互作用
- 转基因组学是指转基因组学.
背景情况:
- 精确量化人类肠道中的细菌生物质对于理解微生物组动态至关重要.
- 现有的流式细胞计,qPCR和spike-in等方法往往是劳动密集型,昂贵的,容易出现技术偏差.
- 挑战包括可变的水含量,DNA提取效率和PCR抑制剂.
研究的目的:
- 引入一种简单,具有成本效益的方法,以使用元基因组数据来估计便中的绝对细菌生物量.
- 为了验证细菌与宿主 (B:H) 的读数比作为细菌生物质的代理值.
- 为了证明B:H比在跟踪抗生素治疗反应中的有用性.
主要方法:
- 通过计算细菌与宿主 (B:H) 读取比率,直接估计来自元基因组的细菌生物量.
- 将B:H比率与传统的生物质量量计方法进行比较.
- 在抗生素治疗和恢复期间,分析人类和小鼠样本中的B:H比率.
主要成果:
- B:H比率可以作为便样本中的细菌生物质的可靠代理.
- 在小鼠和人类中,抗生素治疗导致细菌生物量显著减少 (分别为403倍和45倍).
- 健康个体的宿主和细菌DNA分数显示出稳定的纵向平均值,具有有限的个体间变异 (<8-9倍).
结论:
- B:H读数比为绝对细菌生物质估计提供了一个方便和可访问的替代方案.
- 这种方法避免了需要额外的测量或复杂的实验设计.
- 它可以从现有的元基因组数据集进行回顾性生物量估计,从而促进微生物组研究.
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