Microbiome sequencing: challenges and opportunities for molecular medicine

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans

(2016) Ron Sender et al.   CELL

Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition

(2016) Mark R. Charbonneau et al.   CELL

The mouse gut microbiome revisited: From complex diversity to model ecosystems

(2016) Thomas Clavel et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Graphene nanodevices for DNA sequencing

(2016) Stephanie J. Heerema et al.   Nature Nanotechnology

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

(2015) Saeed Shoaie et al.   Cell Metabolism

Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence

(2015) Monika Schaubeck et al.   GUT

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

Analyses of Intestinal Microbiota: Culture versus Sequencing: Figure 1

(2015) Andreas Hiergeist et al.   ILAR JOURNAL

Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses

(2015) Leah Cuthbertson et al.   Journal of Cystic Fibrosis

The human gut mycobiome: pitfalls and potentials--a mycologists perspective

(2015) M. J. Suhr et al.   MYCOLOGIA

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes

(2015) Samuel C. Forster et al.   NUCLEIC ACIDS RESEARCH

Whole genome sequencing in clinical and public health microbiology

(2015) J.C. Kwong et al.   PATHOLOGY

Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain development

(2015) Manu S. Goyal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Dynamic Changes in the Subgingival Microbiome and Their Potential for Diagnosis and Prognosis of Periodontitis

(2015) Baochen Shi et al.   mBio

Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities

(2015) Andreas Henschel et al.   PLoS Computational Biology

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

(2015) Alan W. Walker et al.   Microbiome

The vocabulary of microbiome research: a proposal

(2015) Julian R. Marchesi et al.   Microbiome

Metagenomic Analysis of the Stool Microbiome in Patients Receiving Allogeneic Stem Cell Transplantation: Loss of Diversity Is Associated with Use of Systemic Antibiotics and More Pronounced in Gastrointestinal Graft-versus-Host Disease

(2014) Ernst Holler et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation

(2014) Y. Taur et al.   BLOOD

Processing faecal samples: a step forward for standards in microbial community analysis

(2014) Alba Santiago et al.   BMC MICROBIOLOGY

Comparison of methods for fecal microbiome biospecimen collection

(2014) Christine Dominianni et al.   BMC MICROBIOLOGY

Evaluation of the impact of refrigeration on next generation sequencing-based assessment of the canine and feline fecal microbiota

(2014) J Scott Weese et al.   BMC Veterinary Research

Fecal microbiota transplant after hematopoietic SCT: report of a successful case

(2014) C G de Castro et al.   BONE MARROW TRANSPLANTATION

The Human Gut Microbiome as a Screening Tool for Colorectal Cancer

(2014) J. P. Zackular et al.   Cancer Prevention Research

The Virome in Mammalian Physiology and Disease

(2014) Herbert W. Virgin   CELL

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

(2014) S. N. Naccache et al.   GENOME RESEARCH

Time between Collection and Storage Significantly Influences Bacterial Sequence Composition in Sputum Samples from Cystic Fibrosis Respiratory Infections

(2014) L. Cuthbertson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Potential of fecal microbiota for early-stage detection of colorectal cancer

(2014) G. Zeller et al.   Molecular Systems Biology

Fecal microbiota transplantation: effectiveness, complexities and lingering concerns

(2014) E G Pamer   Mucosal Immunology

Standardised animal models of host microbial mutualism

(2014) A J Macpherson et al.   Mucosal Immunology

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

(2013) Ilias Lagkouvardos et al.   ISME Journal

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Molecular Studies Neglect Apparently Gram-Negative Populations in the Human Gut Microbiota

(2013) P. Hugon et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rifaximin for Preventing Acute Graft-Versus-Host Disease

(2013) Muna Qayed et al.   JOURNAL OF PEDIATRIC HEMATOLOGY ONCOLOGY

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Dietary intervention impact on gut microbial gene richness

(2013) Aurélie Cotillard et al.   NATURE

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Modern clinical microbiology: new challenges and solutions

(2013) Pierre-Edouard Fournier et al.   NATURE REVIEWS MICROBIOLOGY

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

(2013) Els van Nood et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor

(2013) M. I. Smith et al.   SCIENCE

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

The Intestinal Microbiota Modulates the Anticancer Immune Effects of Cyclophosphamide

(2013) S. Viaud et al.   SCIENCE

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

(2013) Sandra Reuter et al.   JAMA Internal Medicine

Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut

(2013) Elaine O Petrof et al.   Microbiome

Storage conditions of intestinal microbiota matter in metagenomic analysis

(2012) Silvia Cardona et al.   BMC MICROBIOLOGY

Microbial culturomics: paradigm shift in the human gut microbiome study

(2012) J.-C. Lagier et al.   CLINICAL MICROBIOLOGY AND INFECTION

Transfer of Intestinal Microbiota From Lean Donors Increases Insulin Sensitivity in Individuals With Metabolic Syndrome

(2012) Anne Vrieze et al.   GASTROENTEROLOGY

Evaluation of the GenBank, EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates That Were Unidentifiable or Misidentified by Conventional Methods

(2012) K. S. Park et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Characterization of the Fecal Microbiota Using High-Throughput Sequencing Reveals a Stable Microbial Community during Storage

(2012) Ian M. Carroll et al.   PLoS One

Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

(2012) Claudio U. Köser et al.   PLoS Pathogens

"Who owns your poop?": insights regarding the intersection of human microbiome research and the ELSI aspects of biobanking and related studies

(2011) Alice K Hawkins et al.   BMC Medical Genomics

Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study

(2011) Laura García-Álvarez et al.   LANCET INFECTIOUS DISEASES

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

(2011) N. P. McNulty et al.   Science Translational Medicine

Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method

(2010) Jin-Ya Wu et al.   BMC MICROBIOLOGY

High temporal and inter-individual variation detected in the human ileal microbiota

(2010) Carien C. G. M. Booijink et al.   ENVIRONMENTAL MICROBIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Forensic identification using skin bacterial communities

(2010) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Towards the human intestinal microbiota phylogenetic core

(2009) Julien Tap et al.   ENVIRONMENTAL MICROBIOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Use of broad range16S rDNA PCR in clinical microbiology

(2008) Sushama Sontakke et al.   JOURNAL OF MICROBIOLOGICAL METHODS