ArticleInternational journal of molecular sciences2020
Evaluation of the Use of Formalin-Fixed and Paraffin-Embedded Archive Gastric Tissues for Microbiota Characterization Using Next-Generation Sequencing.
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it, 28 citations in OpenAlex.
- Esophageal microbiota composition and outcome of esophageal cancer treatment: a systematic review.Diseases of the esophagus : official journal of the International Society for Diseases of the Esophagus · 2022Pooled it
- Potential of Clinical Care-Collected Gut Biopsies for Advancing Personalised Medicine in Inflammatory Bowel Disease.United European gastroenterology journal · 2026Review
- Article
- Optimized protocol for profiling mucosa-associated microbiota from formalin-fixed paraffin-embedded gut tissues from treatment-naïve pediatric patients with Crohn's disease.Frontiers in cellular and infection microbiology · 2026Article
- The microbiome of pseudomyxoma peritonei: a scoping review.Pleura and peritoneum · 2025Review
- Immune profiling of gastric adenocarcinomas in EU and LATAM countries identifies global differences in immune subgroups and microbiome influence.British journal of cancer · 2025Article
- Storage, Retention, and Use of Leftover Pathology Specimens: The Underestimated Treasures.Cureus · 2024Review
- Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data.Nature biotechnology · 2023Article
- Colorectal Cancer Archaeome: A Metagenomic Exploration, Tunisia.Current issues in molecular biology · 2023Article
- Potential values of formalin-fixed paraffin-embedded tissues for intratumoral microbiome analysis in breast cancer.Heliyon · 2023Article
- Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M.Genome biology · 2022Article
- Crohn's disease recurrence updates: first surgeryFrontiers in immunology · 2022Article
- Article
- Performance of 16S Metagenomic Profiling in Formalin-Fixed Paraffin-Embedded versus Fresh-Frozen Colorectal Cancer Tissues.Cancers · 2021Article
- Technical challenges regarding the use of formalin-fixed paraffin embedded (FFPE) tissue specimens for the detection of bacterial alterations in colorectal cancer.BMC microbiology · 2021Article
- Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer.Genome medicine · 2021Article
- Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients.Scientific reports · 2021Article
- Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels.Microbial genomics · 2020Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Large numbers of well-characterized clinical samples are fundamental to establish relevant associations between the microbiota and disease. Formalin-fixed and paraffin-embedded (FFPE) tissues are routinely used and are widely available clinical materials. Since current approaches to study the microbiota are based on next-generation sequencing (NGS) targeting the bacterial 16S rRNA gene, our aim was to evaluate the feasibility of FFPE gastric tissues for NGS-based microbiota characterization. Analysis of sequencing data revealed the presence of bacteria in the paraffin control. After the subtraction of the operational taxonomic units (OTUs) present in the paraffin control to the FFPE tissue sample dataset, we evaluated the microbiota profiles between paired FFPE and frozen gastric tissues, and between different times of archiving. Compared with frozen gastric tissues, we detected a lower number of OTUs in the microbiota of paired FFPE tissues, regardless of the time of archiving. No major differences in microbial diversity were identified, but taxonomic variation in the relative abundance of phyla and orders was observed between the two preservation methods. This variation was also evident in each case and throughout the times of FFPE archiving. The use of FFPE tissues for NGS-based microbiota characterization should be considered carefully, as biases can be introduced by the embedding process and the time of tissue archiving.
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Registered trials
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