Species- and strain-level assessment using rrn long-amplicons suggests donor’s influence on gut microbial transference via fecal transplants in metabolic syndrome subjects

Is oxford nanopore sequencing ready for analyzing complex microbiomes?

(2021) L J Kerkhof   FEMS MICROBIOLOGY ECOLOGY

Sex, Food, and the Gut Microbiota: Disparate Response to Caloric Restriction Diet with Fiber Supplementation in Women and Men

(2021) Alfonso Benítez‐Páez et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Nanopore sequencing and its application to the study of microbial communities

(2021) Laura Ciuffreda et al.   Computational and Structural Biotechnology Journal

Responses to faecal microbiota transplantation in female and male patients with irritable bowel syndrome

(2021) Magdy El-Salhy et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity

(2021) Brooke C. Wilson et al.   Microbiome

MinION technology for microbiome sequencing applications for the conservation of cultural heritage

(2021) Jelena Pavlovic et al.   MICROBIOLOGICAL RESEARCH

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects

(2021) Sandeep Verma et al.   PLoS One

Dynamic Colonization of Microbes and Their Functions after Fecal Microbiota Transplantation for Inflammatory Bowel Disease

(2021) Nathaniel D. Chu et al.   mBio

Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes

(2021) Varun Aggarwala et al.   Nature Microbiology

Fecal microbiota transplantation to maintain remission in Crohn’s disease: a pilot randomized controlled study

(2020) Harry Sokol et al.   Microbiome

Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system

(2020) R. A. Dowden et al.   Scientific Reports

Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial

(2020) Elaine W. Yu et al.   PLOS MEDICINE

Species-level evaluation of the human respiratory microbiome

(2020) Olufunmilola Ibironke et al.   GigaScience

Effects of Diet-Modulated Autologous Fecal Microbiota Transplantation on Weight Regain

(2020) Ehud Rinott et al.   GASTROENTEROLOGY

Infusion of donor feces affects the gut–brain axis in humans with metabolic syndrome

(2020) Annick V. Hartstra et al.   Molecular Metabolism

Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

(2019) Henrik Krehenwinkel et al.   GigaScience

A Comparison of Three Different Bioinformatics Analyses of the 16S–23S rRNA Encoding Region for Bacterial Identification

(2019) Nilay Peker et al.   Frontiers in Microbiology

An identification protocol for ESBL-producing Gram-negative bacteria bloodstream infections using a MinION nanopore sequencer

(2019) Jun Sakai et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Unlinked rRNA genes are widespread among bacteria and archaea

(2019) Tess E. Brewer et al.   ISME Journal

Elucidation of the bacterial communities associated with the harmful microalgae Alexandrium tamarense and Cochlodinium polykrikoides using nanopore sequencing

(2018) HyeonSeok Shin et al.   Scientific Reports

Correcting for batch effects in case-control microbiome studies

(2018) Sean M. Gibbons et al.   PLoS Computational Biology

Specific Bacteria and Metabolites Associated with Response to Fecal Microbiota Transplantation in Patients with Ulcerative Colitis

(2018) Sudarshan Paramsothy et al.   GASTROENTEROLOGY

Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection

(2017) Stephan J. Ott et al.   GASTROENTEROLOGY

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer

(2017) Alfonso Benítez-Páez et al.   GigaScience

Profiling bacterial communities by MinION sequencing of ribosomal operons

(2017) Lee J. Kerkhof et al.   Microbiome

Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing

(2016) Jongoh Shin et al.   Scientific Reports

Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer

(2016) Alfonso Benítez-Páez et al.   GigaScience

Fecal Microbiota Transplantation for the Treatment of Clostridium difficile Infection

(2014) Giovanni Cammarota et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS