ArticleBMC microbiology2021
Technical challenges regarding the use of formalin-fixed paraffin embedded (FFPE) tissue specimens for the detection of bacterial alterations in colorectal cancer.
Article in BMC microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it, 23 citations in OpenAlex.
- Gut microbiota-associated predictors as biomarkers of neoadjuvant treatment response in rectal cancer-a systematic review.British journal of cancer · 2026Pooled it
- Association of FUT2 rs601338 Genotype with Colonic Mucosal Microbiome Composition, Post-Transplant Bacteremia, and All-Cause Mortality After Liver Transplantation for Primary Sclerosing Cholangitis: A Retrospective Cohort Study.Journal of clinical medicine · 2026Article
- Potential of Clinical Care-Collected Gut Biopsies for Advancing Personalised Medicine in Inflammatory Bowel Disease.United European gastroenterology journal · 2026Review
- Setting higher standards for reports of microbial species in human cancers.Nature cancer · 2026Review
- Metabolic modeling and functional genomics reveal taxa and host gene interactions in colorectal cancer.bioRxiv : the preprint server for biology · 2026Article
- PCR profiling of tumor-associated microorganisms in tissue of primary epithelial malignant tumors of colorectal origin: associations with key clinicopathological characteristics.Frontiers in cellular and infection microbiology · 2026Article
- Tumour tissue-associated microbiome differences between colonic adenoma and carcinoma revealed by 5R 16S rRNA sequencing of formalin-fixed paraffin-embedded tissues: a case-control study.Frontiers in microbiology · 2026Article
- 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
- A broad-range polymerase chain reaction on a formalin-fixed, paraffin-embedded tissue is a powerful diagnostic tool, but requires cautious interpretation: a case report.Frontiers in medicine · 2026Article
- Capturing breast cancers' copy-number landscape in routine pathology: Exploiting low-resolution, genome-wide sequencing to identify HRD and beyond.British journal of cancer · 2025Article
- Relationships between the Microbiome and Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer.Cancer research and treatment · 2025Article
- What every neuropathologist needs to know: Update on neuro infectious disease workups and consultation resources.Journal of neuropathology and experimental neurology · 2025Review
- Low Bacterial Biomass in Human Pancreatic Cancer and Adjacent Normal Tissue.International journal of molecular sciences · 2024Article
- Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data.Nature biotechnology · 2023Article
- Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring.Cancer cell · 2023Article
- Colorectal Cancer Archaeome: A Metagenomic Exploration, Tunisia.Current issues in molecular biology · 2023Article
- Breast cancer: the first comparative evaluation of oncobiome composition between males and females.Biology of sex differences · 2023Article
- Potential values of formalin-fixed paraffin-embedded tissues for intratumoral microbiome analysis in breast cancer.Heliyon · 2023Article
- Article
- Immunohistochemical Differentiation between Western and East Asian Types of CagA-PositiveCanadian journal of gastroenterology & hepatology · 2022Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFormalin-fixed paraffin embedded (FFPE) tissues may provide an exciting resource to study microbial associations in human disease, but the use of these low biomass specimens remains challenging. We aimed to reduce unintentional bacterial interference in molecular analysis of FFPE tissues and investigated the feasibility of conducting quantitative polymerase chain reaction (qPCR) and 16S rRNA amplicon sequencing using 14 colorectal cancer, 14 normal adjacent and 13 healthy control tissues.
resultsBacterial contaminants from the laboratory environment and the co-extraction of human DNA can affect bacterial analysis. The application of undiluted template improves bacterial DNA amplification, allowing the detection of specific bacterial markers (Escherichia coli and Faecalibacterium prausnitzii) by qPCR. Nested and non-nested PCR-based 16S rRNA amplicon sequencing approaches were employed, showing that bacterial communities of tissues and paired paraffin controls cluster separately at genus level on weighted Unifrac in both non-nested (R2 = 0.045; Pr(> F) = 0.053) and nested (R2 = 0.299; Pr(> F) = 0.001) PCR datasets. Nevertheless, considerable overlap of bacterial genera within tissues was seen with paraffin, DNA extraction negatives (non-nested PCR) or PCR negatives (nested PCR). Following mathematical decontamination, no differences in α- and β diversity were found between tumor, normal adjacent and control tissues.
conclusionsBacterial marker analysis by qPCR seems feasible using non-normalized template, but 16S rRNA amplicon sequencing remains challenging. Critical evaluation of laboratory procedures and incorporation of positive and negative controls for bacterial analysis of FFPE tissues are essential for quality control and to account for bacterial contaminants.
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