Cruz-Flores Roberto, López-Carvallo Jesús Antonio, Cáceres-Martínez Jorge, Dhar Arun K
Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, 22860 Ensenada, Baja California, Mexico.
Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, 22860 Ensenada, Baja California, Mexico.
J Microbiol Methods. 2022 May;196:106476. doi: 10.1016/j.mimet.2022.106476. Epub 2022 Apr 28.
Formalin-fixed paraffin-embedded (FFPE) tissues stored in thousands of human and animal pathology laboratories around the globe represent mines of stored genetic information. In recent years, the use of FFPE tissues as a viable source of DNA for diverse genetic studies has attracted attention for interrogating microbiomes from this sample type. These studies have proven that 16S rRNA amplicon sequencing-based microbiome studies are possible from FFPE samples but present some particular challenges. In this review, we summarize all aspects of microbiome studies from FFPE tissues including the challenges associated with working highly degraded DNA, best practices for reducing environmental contamination, and we propose solutions to address these issues. Finally, we discuss how the combination of FFPE microbiome studies and Laser Capture Microdissection and/or Laser Microdissection could enable to determine the spatial heterogeneity underlying complex bacterial communities.
保存在全球数千个人类和动物病理学实验室中的福尔马林固定石蜡包埋（FFPE）组织是储存遗传信息的宝库。近年来，将FFPE组织用作多种基因研究的可行DNA来源，已引起人们对从这种样本类型中研究微生物组的关注。这些研究证明，基于16S rRNA扩增子测序的微生物组研究可以从FFPE样本中进行，但存在一些特殊挑战。在本综述中，我们总结了FFPE组织微生物组研究的各个方面，包括处理高度降解DNA的相关挑战、减少环境污染的最佳做法，并提出了解决这些问题的方案。最后，我们讨论了FFPE微生物组研究与激光捕获显微切割和/或激光显微切割相结合如何能够确定复杂细菌群落背后的空间异质性。
