Microbiome analysis from formalin-fixed paraffin-embedded tissues: Current challenges and future perspectives

Roberto Cruz-Flores, Jesús Antonio López-Carvallo, Jorge Cáceres-Martínez, Arun K. Dhar

Research output: Contribution to journalReview articlepeer-review

8 Scopus citations


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.

Original languageEnglish (US)
Article number106476
JournalJournal of Microbiological Methods
StatePublished - May 2022


  • FFPE
  • formalin-fixed paraffin-embedded
  • Microbiome

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology
  • Microbiology (medical)


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