Optimizing methods and dodging pitfalls in microbiome research

Comparison of Collection Methods for Fecal Samples in Microbiome Studies

(2016) Emily Vogtmann et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Intricacies of assessing the human microbiome in epidemiologic studies

(2016) Courtney K. Robinson et al.   ANNALS OF EPIDEMIOLOGY

Compositional data analysis of the microbiome: fundamentals, tools, and challenges

(2016) Matthew C.B. Tsilimigras et al.   ANNALS OF EPIDEMIOLOGY

Effects of Specimen Collection Methodologies and Storage Conditions on the Short-Term Stability of Oral Microbiome Taxonomy

(2016) Ting Luo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR

(2016) Vladimir Lazarevic et al.   BMC MICROBIOLOGY

Confounding Effects of Metformin on the Human Gut Microbiome in Type 2 Diabetes

(2016) Adil Mardinoglu et al.   Cell Metabolism

Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD

(2016) João Sabino et al.   GUT

Prescription drugs obscure microbiome analyses

(2016) S. Devkota   SCIENCE

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

(2016) Angela Glassing et al.   Gut Pathogens

Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data

(2016) Ran Blekhman et al.   Scientific Reports

Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease

(2016) Kelly A. Shaw et al.   Genome Medicine

Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures

(2016) Xinchen Wang et al.   eLife

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

(2016) Patrick D. Schloss et al.   PeerJ

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants

(2016) Cian J. Hill et al.   Microbiome

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

(2016) Abigail P. Lauder et al.   Microbiome

Gut Microbiota Linked to Sexual Preference and HIV Infection

(2016) Marc Noguera-Julian et al.   EBioMedicine

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

(2016) Se Jin Song et al.   mSystems

Effects of Varied Housing Density on a Hybrid Mouse Strain Followed for 20 Months

(2016) Beverly Paigen et al.   PLoS One

Fast disease progression in simian HIV-infected female macaque is accompanied by a robust local inflammatory innate immune and microbial response

(2015) Wuze Ren et al.   AIDS

The preterm placental microbiome varies in association with excess maternal gestational weight gain

(2015) Kathleen M. Antony et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

(2015) Brendan J. Kelly et al.   BIOINFORMATICS

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

(2015) James D. Lewis et al.   Cell Host & Microbe

The influence of diet on the gut microbiota and its consequences for health

(2015) Joël Doré et al.   CURRENT OPINION IN BIOTECHNOLOGY

Influence of high-fat diet on gut microbiota

(2015) E. Angela Murphy et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Diet in the Pathogenesis and Treatment of Inflammatory Bowel Diseases

(2015) Dale Lee et al.   GASTROENTEROLOGY

Proton pump inhibitors affect the gut microbiome

(2015) Floris Imhann et al.   GUT

Alterations of the Subgingival Microbiota in Pediatric Crohnʼs Disease Studied Longitudinally in Discovery and Validation Cohorts

(2015) Judith Kelsen et al.   INFLAMMATORY BOWEL DISEASES

Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease

(2015) Christel Chehoud et al.   INFLAMMATORY BOWEL DISEASES

Deciphering the human microbiome using next-generation sequencing data and bioinformatics approaches

(2015) Yihwan Kim et al.   METHODS

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

(2015) Kristoffer Forslund et al.   NATURE

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock

(2015) Xue Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Placental Microbiome Varies in Association with Low Birth Weight in Full-Term Neonates

(2015) Jia Zheng et al.   Nutrients

Sample storage conditions significantly influence faecal microbiome profiles

(2015) Jocelyn M Choo et al.   Scientific Reports

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

(2015) Brett Wagner Mackenzie et al.   Frontiers in Microbiology

Primer and platform effects on 16S rRNA tag sequencing

(2015) Julien Tremblay et al.   Frontiers in Microbiology

Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data

(2015) Jake Jervis-Bardy et al.   Microbiome

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

The microbiome of the human lower airways: a next generation sequencing perspective

(2015) Velma T. E. Aho et al.   World Allergy Organization Journal

Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome

(2015) Shirley Bikel et al.   Computational and Structural Biotechnology Journal

Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing

(2015) Changin Oh et al.   PLoS One

Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes

(2015) Shira R. Abeles et al.   PLoS One

Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles

(2014) Katherine Kennedy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Comparison of methods for fecal microbiome biospecimen collection

(2014) Christine Dominianni et al.   BMC MICROBIOLOGY

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

Time in Motion: The Molecular Clock Meets the Microbiome

(2014) Xue Liang et al.   CELL

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production

(2014) Gary D Wu et al.   GUT

Interplay Between the Temporal Dynamics of the Vaginal Microbiota and Human Papillomavirus Detection

(2014) R. M. Brotman et al.   JOURNAL OF INFECTIOUS DISEASES

Microbiome of the placenta in pre-eclampsia supports the role of bacteria in the multifactorial cause of pre-eclampsia

(2014) Ranmalee Amarasekara et al.   JOURNAL OF OBSTETRICS AND GYNAECOLOGY RESEARCH

Minireview: Gut Microbiota: The Neglected Endocrine Organ

(2014) Gerard Clarke et al.   MOLECULAR ENDOCRINOLOGY

Gut microbiota, the immune system and diet influence the neonatal gut–brain axis

(2014) Michael P. Sherman et al.   PEDIATRIC RESEARCH

Optimized Cryopreservation of Mixed Microbial Communities for Conserved Functionality and Diversity

(2014) Frederiek-Maarten Kerckhof et al.   PLoS One

Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes

(2014) Martin Laurence et al.   PLoS One

The Placenta Harbors a Unique Microbiome

(2014) K. Aagaard et al.   Science Translational Medicine

Fecal Microbiota Transplantation for Clostridium difficile Infection: Systematic Review and Meta-Analysis

(2013) Zain Kassam et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Influence of diet on gut microbiota, inflammation and type 2 diabetes mellitus. First experience with macrobiotic Ma-Pi 2 diet

(2013) Francesco Fallucca et al.   DIABETES-METABOLISM RESEARCH AND REVIEWS

Differential recovery of bacterial and archaeal 16S rRNA genes from ruminal digesta in response to glycerol as cryoprotectant

(2013) Nest McKain et al.   JOURNAL OF MICROBIOLOGICAL METHODS

High throughput sequencing methods and analysis for microbiome research

(2013) Julia M. Di Bella et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

The microbiome explored: recent insights and future challenges

(2013) Martin Blaser et al.   NATURE REVIEWS MICROBIOLOGY

Sequence-Based Discovery of Bradyrhizobium enterica in Cord Colitis Syndrome

(2013) Ami S. Bhatt et al.   NEW ENGLAND JOURNAL OF MEDICINE

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

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

Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs

(2013) Orna Mizrahi-Man et al.   PLoS One

Fungi of the Murine Gut: Episodic Variation and Proliferation during Antibiotic Treatment

(2013) Serena Dollive et al.   PLoS One

Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity

(2013) J. G. M. Markle et al.   SCIENCE

Cohabiting family members share microbiota with one another and with their dogs

(2013) Se Jin Song et al.   eLife

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

(2013) Falk Hildebrand et al.   GENOME BIOLOGY

Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis

(2013) Jacques Ravel et al.   Microbiome

Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life

(2012) J. A. Foster et al.   BRIEFINGS IN BIOINFORMATICS

Influence of a high-fat diet on gut microbiota, intestinal permeability and metabolic endotoxaemia

(2012) Ana Paula Boroni Moreira et al.   BRITISH JOURNAL OF NUTRITION

Long-term monitoring of the human intestinal microbiota composition

(2012) Mirjana Rajilić-Stojanović et al.   ENVIRONMENTAL MICROBIOLOGY

Host genetic and environmental effects on mouse intestinal microbiota

(2012) James H Campbell et al.   ISME Journal

A framework for human microbiome research

(2012)   NATURE

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

The influence of diet on the gut microbiota

(2012) Karen P. Scott et al.   PHARMACOLOGICAL RESEARCH

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

(2012) Sanqing Yuan et al.   PLoS One

Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

(2012) Patricio S. La Rosa et al.   PLoS One

Gender-dependent consequences of chronic olanzapine in the rat: effects on body weight, inflammatory, metabolic and microbiota parameters

(2012) Kieran J. Davey et al.   PSYCHOPHARMACOLOGY

Temporal Dynamics of the Human Vaginal Microbiota

(2012) P. Gajer et al.   Science Translational Medicine

The human gut microbiome: current knowledge, challenges, and future directions

(2012) Maneesh Dave et al.   Translational Research

Evolution of the gut microbiota and the influence of diet

(2012) M. Rothe et al.   Beneficial Microbes

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract

(2011) Emily S. Charlson et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

A method to sequence and quantify DNA integration for monitoring outcome in gene therapy

(2011) Troy Brady et al.   NUCLEIC ACIDS RESEARCH

Intestinal Microbiota in Healthy Adults: Temporal Analysis Reveals Individual and Common Core and Relation to Intestinal Symptoms

(2011) Jonna Jalanka-Tuovinen et al.   PLoS One

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples

(2010) Christian L. Lauber et al.   FEMS MICROBIOLOGY LETTERS

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

Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome

(2010) Hedvig E. Jakobsson et al.   PLoS One

Composition, variability, and temporal stability of the intestinal microbiota of the elderly

(2010) M. J. Claesson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Vaginal microbiome of reproductive-age women

(2010) J. Ravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Succession of microbial consortia in the developing infant gut microbiome

(2010) J. E. Koenig 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

Statistical assessment of DNA extraction reagent lot variability in real-time quantitative PCR

(2009) R.N. Bushon et al.   LETTERS IN APPLIED MICROBIOLOGY

Individual housing of mice — Impact on behaviour and stress responses

(2009) Saskia S. Arndt et al.   PHYSIOLOGY & BEHAVIOR

Gut microbiota and lipopolysaccharide content of the diet influence development of regulatory T cells: studies in germ-free mice

(2008) Tomas Hrncir et al.   BMC IMMUNOLOGY

The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis

(2008) Philip McKenna et al.   PLoS Pathogens

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY