Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life

(2018) Moran Yassour et al.   Cell Host & Microbe

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

(2018) Pamela Ferretti et al.   Cell Host & Microbe

Selective maternal seeding and environment shape the human gut microbiome

(2018) Katri Korpela et al.   GENOME RESEARCH

Elevated Fecal pH Indicates a Profound Change in the Breastfed Infant Gut Microbiome Due to Reduction of Bifidobacterium over the Past Century

(2018) Bethany M. Henrick et al.   mSphere

Clostridial Strain-Specific Characteristics Associated with Necrotizing Enterocolitis

(2018) Sophia Schönherr-Hellec et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prospects for primary prevention of type 1 diabetes by restoring a disappearing microbe

(2018) Richard Insel et al.   PEDIATRIC DIABETES

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Prokaryote genome fluidity is dependent on effective population size

(2017) Nadia Andrea Andreani et al.   ISME Journal

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery

(2017) Derrick M Chu et al.   NATURE MEDICINE

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children

(2017) Guoyan Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants

(2017) Steven A. Frese et al.   mSphere

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling

(2017) Francesco Asnicar et al.   mSystems

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

(2016) Tommi Vatanen et al.   CELL

Emerging evidence of the role of gut microbiota in the development of allergic diseases

(2016) Kotryna Simonyte Sjödin et al.   Current Opinion in Allergy and Clinical Immunology

Association between intestinal permeability and faecal microbiota composition in Italian children with beta cell autoimmunity at risk for type 1 diabetes

(2016) Claudio Maffeis et al.   DIABETES-METABOLISM RESEARCH AND REVIEWS

Extensive Mobilome-Driven Genome Diversification in Mouse Gut-AssociatedBacteroides vulgatusmpk

(2016) Anna Lange et al.   Genome Biology and Evolution

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Environmental risk factors for type 1 diabetes

(2016) Marian Rewers et al.   LANCET

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

(2016) Hilary P. Browne et al.   NATURE

The microbiota in adaptive immune homeostasis and disease

(2016) Kenya Honda et al.   NATURE

The microbiome and innate immunity

(2016) Christoph A. Thaiss et al.   NATURE

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

The role of the intestinal microbiota in type 1 diabetes mellitus

(2016) Mikael Knip et al.   Nature Reviews Endocrinology

Gut microbiota-host interactions and juvenile idiopathic arthritis

(2016) Miika Arvonen et al.   Pediatric Rheumatology

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

(2016) Moran Yassour et al.   Science Translational Medicine

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants

(2016) Doyle V. Ward et al.   Cell Reports

Association of Early Exposure of Probiotics and Islet Autoimmunity in the TEDDY Study

(2016) Ulla Uusitalo et al.   JAMA Pediatrics

Genomic diversity of EPEC associated with clinical presentations of differing severity

(2016) Tracy H. Hazen et al.   Nature Microbiology

A novel gene cluster allows preferential utilization of fucosylated milk oligosaccharides in Bifidobacterium longum subsp. longum SC596

(2016) Daniel Garrido et al.   Scientific Reports

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

(2015) Aleksandar D. Kostic et al.   Cell Host & Microbe

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

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Early infancy microbial and metabolic alterations affect risk of childhood asthma

(2015) Marie-Claire Arrieta et al.   Science Translational Medicine

Can probiotic yogurt prevent diarrhoea in children on antibiotics? A double-blind, randomised, placebo-controlled study

(2015) M. J. Fox et al.   BMJ Open

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

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

Persistent gut microbiota immaturity in malnourished Bangladeshi children

(2014) Sathish Subramanian et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

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

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

MetaRef: a pan-genomic database for comparative and community microbial genomics

(2013) Katherine Huang et al.   NUCLEIC ACIDS RESEARCH

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

(2013) Connor T. Skennerton et al.   NUCLEIC ACIDS RESEARCH

Emergence of Epidemic Multidrug-Resistant Enterococcus faecium from Animal and Commensal Strains

(2013) F. Lebreton et al.   mBio

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

(2013) Jose U Scher et al.   eLife

The biodiversity hypothesis and allergic disease: world allergy organization position statement

(2013) Tari Haahtela et al.   World Allergy Organization Journal

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Bifidobacterial utilization of human milk oligosaccharides

(2011) David A. Sela   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

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

(2011) Daniel McDonald et al.   ISME Journal

Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa

(2011) Peter A. Bron et al.   NATURE REVIEWS MICROBIOLOGY

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides

(2010) David A. Sela et al.   TRENDS IN MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

(2008) D. A. Sela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA