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

Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients

(2021) Gabriela Debesa-Tur et al.   Scientific Reports

Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer

(2021) Kellyanne Duncan et al.   Gut Microbes

Technical challenges regarding the use of formalin-fixed paraffin embedded (FFPE) tissue specimens for the detection of bacterial alterations in colorectal cancer

(2021) Suk Yee Lam et al.   BMC MICROBIOLOGY

Formalin-fixed paraffin-embedded tissues for microbiome analysis in rainbow trout (Oncorhynchus mykiss)

(2021) Roberto Cruz-Flores et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Evaluation of the Use of Formalin-Fixed and Paraffin-Embedded Archive Gastric Tissues for Microbiota Characterization Using Next-Generation Sequencing

(2020) Ines Pinto-Ribeiro et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice

(2020) Sidney P. Walker et al.   Frontiers in Oncology

Disentangling the mechanisms shaping the surface ocean microbiota

(2020) Ramiro Logares et al.   Microbiome

Genome reconstruction of white spot syndrome virus (WSSV) from archival Davidson’s-fixed paraffin embedded shrimp (Penaeus vannamei) tissue

(2020) Roberto Cruz-Flores et al.   Scientific Reports

Endoscopic ultrasound (EUS)-guided fine needle biopsy (FNB) formalin fixed paraffin-embedded (FFPE) pancreatic tissue samples are a potential resource for microbiota analysis

(2020) Andrea C Masi et al.   GUT

Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis

(2020) Sidney P. Walker et al.   Scientific Reports

Protoblock - A biological standard for formalin fixed samples

(2020) Yensi Flores Bueso et al.   Microbiome

Complete genome reconstruction and genetic analysis of Taura syndrome virus of shrimp from archival Davidson's-fixed paraffin embedded tissue

(2020) Roberto Cruz-Flores et al.   VIROLOGY

Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue

(2019) Christopher J. Stewart et al.   BMC MICROBIOLOGY

The presence of bacteria varies between colorectal adenocarcinomas, precursor lesions and non-malignant tissue

(2019) Caspar Bundgaard-Nielsen et al.   BMC CANCER

Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments

(2019) Lisa Karstens et al.   mSystems

A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome

(2019) Alessandra Riva et al.   Nature Communications

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

Recognizing the reagent microbiome

(2018) Marcus C. de Goffau et al.   Nature Microbiology

PARP1 Is Up-Regulated in Non-small Cell Lung Cancer Tissues in the Presence of the Cyanobacterial Toxin Microcystin

(2018) Patrick L. Apopa et al.   Frontiers in Microbiology

Laser microdissection: A promising tool for exploring microorganisms and their interactions with hosts

(2017) Oleg V. Podgorny et al.   JOURNAL OF MICROBIOLOGICAL METHODS

The Gastrointestinal Microbiome: A Review

(2017) P.C. Barko et al.   JOURNAL OF VETERINARY INTERNAL MEDICINE

16S rRNA Next Generation Sequencing Analysis Shows Bacteria in Alzheimer’s Post-Mortem Brain

(2017) David C. Emery et al.   Frontiers in Aging Neuroscience

Assessment of the quality of DNA from various formalin-fixed paraffin-embedded (FFPE) tissues and the use of this DNA for next-generation sequencing (NGS) with no artifactual mutation

(2017) Naoki Einaga et al.   PLoS One

Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque

(2015) Koji Yasuda et al.   Cell Host & Microbe

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

Virus characterization and discovery in formalin-fixed paraffin-embedded tissues

(2015) Rogier Bodewes et al.   JOURNAL OF VIROLOGICAL METHODS

Measuring the Formaldehyde Protein–DNA Cross-Link Reversal Rate

(2014) Julia Kennedy-Darling et al.   ANALYTICAL CHEMISTRY

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota

(2014) Lindsey Albenberg et al.   GASTROENTEROLOGY

Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea

(2013) Anne E. Dekas et al.   ENVIRONMENTAL MICROBIOLOGY

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing

(2013) D. Berry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses

(2012) Natalie Ludyga et al.   VIRCHOWS ARCHIV

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

The Antibacterial Lectin RegIII  Promotes the Spatial Segregation of Microbiota and Host in the Intestine

(2011) S. Vaishnava et al.   SCIENCE

Spatial organization of intestinal microbiota in the mouse ascending colon

(2010) Gerardo M Nava et al.   ISME Journal

Structural Characterization of Formaldehyde-Induced Cross-Links Between Amino Acids and Deoxynucleosides and Their Oligomers

(2010) Kun Lu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evaluation of the preservation of shrimp samples with Davidson’s AFA fixative for infectious myonecrosis virus (IMNV) in situ hybridization

(2008) Thales P.D. Andrade et al.   AQUACULTURE