Novel Strategies for Applied Metagenomics

The most widespread problems in the function-based microbial metagenomics

(2015) Agnieszka Felczykowska et al.   ACTA BIOCHIMICA POLONICA

The relationship between faecal-associated and mucosal-associated microbiota in irritable bowel syndrome patients and healthy subjects

(2015) I. Rangel et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

The functional impact of the intestinal microbiome on mucosal immunity and systemic autoimmunity

(2015) Randy S. Longman et al.   CURRENT OPINION IN RHEUMATOLOGY

Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers

(2015) A Lavelle et al.   GUT

Gut Fungal Microbiota

(2015) Mathias L. Richard 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

The fungal microbiota of de-novo paediatric inflammatory bowel disease

(2015) I. Mukhopadhya et al.   MICROBES AND INFECTION

Optimal sampling of the intestinal microbiota for research

(2015) R. Balfour Sartor   Nature Reviews Gastroenterology & Hepatology

BioMiCo: a supervised Bayesian model for inference of microbial community structure

(2015) Mahdi Shafiei et al.   Microbiome

From next-generation sequencing to systematic modeling of the gut microbiome

(2015) Boyang Ji et al.   Frontiers in Genetics

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

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

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

Diets that differ in their FODMAP content alter the colonic luminal microenvironment

(2014) Emma P Halmos et al.   GUT

Effects of bowel cleansing on the intestinal microbiota

(2014) Jonna Jalanka et al.   GUT

Anatomical localization of commensal bacteria in immune cell homeostasis and disease

(2014) Thomas C. Fung et al.   IMMUNOLOGICAL REVIEWS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads

(2014) Rogan Carr et al.   PLoS One

Characterization of virus-like particles associated with the human faecal and caecal microbiota

(2014) Lesley Hoyles et al.   RESEARCH IN MICROBIOLOGY

BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities

(2014) Mahdi Shafiei et al.   PLoS Computational Biology

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information

(2013) Kishori M Konwar et al.   BMC BIOINFORMATICS

The microbiome and regulation of mucosal immunity

(2013) Andrew J. McDermott et al.   IMMUNOLOGY

Semisynthetic Diet Ameliorates Crohn’s Disease–Like Ileitis in TNFΔARE/WT Mice Through Antigen-Independent Mechanisms of Gluten

(2013) Stefan J. Wagner et al.   INFLAMMATORY BOWEL DISEASES

Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota

(2013) Zhigang Zhang et al.   ISME Journal

The gut microbiome: the role of a virtual organ in the endocrinology of the host

(2013) James M Evans et al.   JOURNAL OF ENDOCRINOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

Long-Term Temporal Analysis of the Human Fecal Microbiota Revealed a Stable Core of Dominant Bacterial Species

(2013) Inés Martínez et al.   PLoS One

Microbiota of De-Novo Pediatric IBD: Increased Faecalibacterium Prausnitzii and Reduced Bacterial Diversity in Crohn's But Not in Ulcerative Colitis

(2012) Richard Hansen et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Colonic mucosal microbiome differs from stool microbiome in cirrhosis and hepatic encephalopathy and is linked to cognition and inflammation

(2012) Jasmohan S. Bajaj et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

The microbiome as a human organ

(2012) F. Baquero et al.   CLINICAL MICROBIOLOGY AND INFECTION

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

The gut microbiota in IBD

(2012) Chaysavanh Manichanh et al.   Nature Reviews Gastroenterology & Hepatology

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Intestinal luminal nitrogen metabolism: Role of the gut microbiota and consequences for the host

(2012) Anne-Marie Davila et al.   PHARMACOLOGICAL RESEARCH

Standard Colonic Lavage Alters the Natural State of Mucosal-Associated Microbiota in the Human Colon

(2012) Laura Harrell et al.   PLoS One

Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer

(2012) Weiguang Chen et al.   PLoS One

Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence Colitis

(2012) I. D. Iliev et al.   SCIENCE

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

(2012) Maneesh Dave et al.   Translational Research

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Chapter 12: Human Microbiome Analysis

(2012) Xochitl C. Morgan et al.   PLoS Computational Biology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

(2011) Patrick D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

Lateral gene transfer

(2011) Olga Zhaxybayeva et al.   CURRENT BIOLOGY

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Gut microbiome, obesity, and metabolic dysfunction

(2011) Herbert Tilg et al.   JOURNAL OF CLINICAL INVESTIGATION

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

IMG/M: the integrated metagenome data management and comparative analysis system

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

Bacterial biogeography of the human digestive tract

(2011) Jennifer C. Stearns et al.   Scientific Reports

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

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

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

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

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen 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

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies

(2009) Yong Wang et al.   PLoS One

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Fungi and inflammatory bowel diseases: Alterations of composition and diversity

(2008) Stephan J. Ott et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY