High-resolution ISR amplicon sequencing reveals personalized oral microbiome

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling

(2018) Garold Fuks et al.   Microbiome

Stability of the human faecal microbiome in a cohort of adult men

(2018) Raaj S. Mehta et al.   Nature Microbiology

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin

(2017) Kaisa Koskinen et al.   mBio

Host-genotype dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria

(2017) Emilie Macke et al.   Nature Communications

Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species

(2017) Artur J. Sabat et al.   Scientific Reports

The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization

(2017) Damien J. Cabral et al.   Scientific Reports

The lung microbiome in patients with pneumocystosis

(2017) J. Kehrmann et al.   BMC Pulmonary Medicine

Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity

(2017) Michael W. Hall et al.   npj Biofilms and Microbiomes

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis

(2016) Bo Yang et al.   BMC BIOINFORMATICS

Temporal Stability of the Human Skin Microbiome

(2016) Julia Oh et al.   CELL

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Database Resources of the National Center for Biotechnology Information

(2016)   NUCLEIC ACIDS RESEARCH

Individuality, Stability, and Variability of the Plaque Microbiome

(2016) Daniel R. Utter et al.   Frontiers in Microbiology

β-Amyloid and α-Synuclein Cooperate To Block SNARE-Dependent Vesicle Fusion

(2015) Bong-Kyu Choi et al.   BIOCHEMISTRY

High-Resolution Analyses of Overlap in the Microbiota Between Mothers and Their Children

(2015) Melissa Schanche et al.   CURRENT MICROBIOLOGY

Reproductive tract microbiome in assisted reproductive technologies

(2015) Jason M. Franasiak et al.   FERTILITY AND STERILITY

Identifying personal microbiomes using metagenomic codes

(2015) Eric A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer

(2014) Paul M. Ruegger et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Identification of Lactobacillus strains of goose origin using MALDI-TOF mass spectrometry and 16S–23S rDNA intergenic spacer PCR analysis

(2014) Marta Dec et al.   RESEARCH IN MICROBIOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The altered landscape of the human skin microbiome in patients with primary immunodeficiencies

(2013) J. Oh et al.   GENOME RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Unipro UGENE: a unified bioinformatics toolkit

(2012) Konstantin Okonechnikov et al.   BIOINFORMATICS

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood

(2012) S. S. Stahringer et al.   GENOME RESEARCH

Pathogenic Potential of Bacillus cereus Strains as Revealed by Phenotypic Analysis

(2012) Rita Kamar et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Genotyping ofMycobacterium tuberculosis: application in epidemiologic studies

(2011) Midori Kato-Maeda et al.   Future Microbiology

Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing

(2011) Ann L Griffen et al.   ISME Journal

CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome

(2011) Ann L. Griffen et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The Human Oral Microbiome

(2010) F. E. Dewhirst et al.   JOURNAL OF BACTERIOLOGY

Bacterial 16S Sequence Analysis of Severe Caries in Young Permanent Teeth

(2010) E. L. Gross et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Porphyromonas gingivalis Strain Diversity

(2009) C. O. Igboin et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE