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Related Concept Videos

Fixation and Sectioning01:03

Fixation and Sectioning

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Two basic types of preparation are used to visualize specimens with a light microscope: wet mounts and fixed specimens.
The simplest type of preparation is the wet mount, in which the specimen is placed in a drop of liquid on the slide. A liquid specimen can be directly deposited on the slide using a dropper. Solid specimens, such as skin scraping, can be placed on the slide before adding a drop of liquid to prepare the wet mount. Sometimes the liquid is simply water, but stains are often added...
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Related Experiment Video

Updated: Sep 25, 2025

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
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Microbiome analysis from formalin-fixed paraffin-embedded tissues: Current challenges and future perspectives.

Roberto Cruz-Flores1, Jesús Antonio López-Carvallo1, Jorge Cáceres-Martínez1

  • 1Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, 22860 Ensenada, Baja California, Mexico.

Journal of Microbiological Methods
|May 1, 2022
PubMed
Summary

Microbiome studies using formalin-fixed paraffin-embedded (FFPE) tissues are feasible, despite challenges with degraded DNA. This review outlines best practices for FFPE microbiome analysis and contamination reduction.

Keywords:
FFPEMicrobiomeformalin-fixed paraffin-embedded

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Area of Science:

  • Microbiology
  • Genetics
  • Pathology

Background:

  • Formalin-fixed paraffin-embedded (FFPE) tissues are abundant global resources for genetic information.
  • FFPE tissues are increasingly utilized for DNA extraction in genetic studies, including microbiome analysis.
  • Investigating microbiomes from FFPE samples presents unique challenges due to DNA degradation.

Purpose of the Study:

  • To review the feasibility and challenges of microbiome studies using FFPE tissues.
  • To summarize best practices for minimizing contamination in FFPE microbiome analyses.
  • To propose solutions for overcoming technical hurdles in FFPE microbiome research.

Main Methods:

  • Review of existing literature on microbiome studies from FFPE samples.
  • Discussion of DNA extraction and amplification techniques for degraded FFPE DNA.
  • Exploration of contamination control strategies relevant to FFPE tissues.

Main Results:

  • 16S rRNA amplicon sequencing is a viable method for microbiome profiling from FFPE samples.
  • Significant challenges exist due to highly degraded DNA in FFPE tissues.
  • Environmental contamination is a critical factor to manage in FFPE microbiome studies.

Conclusions:

  • Microbiome analysis from FFPE tissues is achievable with careful methodology.
  • Implementing best practices is crucial for reliable FFPE microbiome data.
  • Combining FFPE microbiome studies with Laser Capture Microdissection can reveal spatial bacterial community heterogeneity.