Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite

The Role of Lung and Gut Microbiota in the Pathology of Asthma

(2020) Weronika Barcik et al.   IMMUNITY

Gut microbiota-derived metabolites as key actors in inflammatory bowel disease

(2020) Aonghus Lavelle et al.   Nature Reviews Gastroenterology & Hepatology

Immune-Microbiota Interplay and Colonization Resistance in Infection

(2020) Avner Leshem et al.   MOLECULAR CELL

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Structural variation in the gut microbiome associates with host health

(2019) David Zeevi et al.   NATURE

The Integrative Human Microbiome Project

(2019)   NATURE

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Bacterial Metabolism and Antibiotic Efficacy

(2019) Jonathan M. Stokes et al.   Cell Metabolism

Mapping human microbiome drug metabolism by gut bacteria and their genes

(2019) Michael Zimmermann et al.   NATURE

Therapeutic Opportunities in Inflammatory Bowel Disease: Mechanistic Dissection of Host-Microbiome Relationships

(2019) Damian R. Plichta et al.   CELL

Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans

(2019) Thomas Hagan et al.   CELL

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

(2019) Hila Sberro et al.   CELL

Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans

(2019) Michael L. Patnode et al.   CELL

Diet–microbiota interactions and personalized nutrition

(2019) Aleksandra A. Kolodziejczyk et al.   NATURE REVIEWS MICROBIOLOGY

Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics

(2019) Ryan M. Ziels et al.   mSystems

Modularity as a universal emergent property of biological traits

(2019) Mary Jane West‐Eberhard   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Microbiota and the social brain

(2019) Eoin Sherwin et al.   SCIENCE

Multiscale Evolutionary Dynamics of Host-Associated Microbiomes

(2018) Aura Ferreiro et al.   CELL

The Human Gut Microbiome: From Association to Modulation

(2018) Thomas S.B. Schmidt et al.   CELL

The microbiome in cancer immunotherapy: Diagnostic tools and therapeutic strategies

(2018) Laurence Zitvogel et al.   SCIENCE

A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection

(2018) Amanda Jacobson et al.   Cell Host & Microbe

Branching Out: Alterations in Bacterial Physiology and Virulence Due to Branched-Chain Amino Acid Deprivation

(2018) Julienne C. Kaiser et al.   mBio

Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification

(2018) Matthew T. Sorbara et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Species-level functional profiling of metagenomes and metatranscriptomes

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

Homeostatic Immunity and the Microbiota

(2017) Yasmine Belkaid et al.   IMMUNITY

Prioritization of polysaccharide utilization and control of regulator activation inBacteroides thetaiotaomicron

(2017) Nathan D. Schwalm et al.   MOLECULAR MICROBIOLOGY

The evolution of the host microbiome as an ecosystem on a leash

(2017) Kevin R. Foster et al.   NATURE

Chemical transformation of xenobiotics by the human gut microbiota

(2017) Nitzan Koppel et al.   SCIENCE

An insider's perspective: Bacteroides as a window into the microbiome

(2017) Aaron G. Wexler et al.   Nature Microbiology

Counterselection employing mutated pheS for markerless genetic deletion in Bacteroides species

(2016) Yasuhiro Kino et al.   ANAEROBE

Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

(2016) Michael J. Coyne et al.   BMC GENOMICS

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

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

A microbial perspective of human developmental biology

(2016) Mark R. Charbonneau et al.   NATURE

Diet–microbiota interactions as moderators of human metabolism

(2016) Justin L. Sonnenburg et al.   NATURE

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

Engineered Production of Short Chain Fatty Acid in Escherichia coli Using Fatty Acid Synthesis Pathway

(2016) Kamran Jawed et al.   PLoS One

Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens

(2016) Eric G. Pamer   SCIENCE

Three CoA Transferases Involved in the Production of Short Chain Fatty Acids in Porphyromonas gingivalis

(2016) Mitsunari Sato et al.   Frontiers in Microbiology

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron , to Sense and Respond to Stimuli in the Murine Gut Microbiota

(2016) Mark Mimee et al.   Cell Systems

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

(2015) Sharon Greenblum et al.   CELL

High-Resolution Metabolomics with Acyl-CoA Profiling Reveals Widespread Remodeling in Response to Diet

(2015) Xiaojing Liu et al.   MOLECULAR & CELLULAR PROTEOMICS

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

(2015) M. Wu et al.   SCIENCE

Small molecules from the human microbiota

(2015) M. S. Donia et al.   SCIENCE

TRANSIT - A Software Tool for Himar1 TnSeq Analysis

(2015) Michael A. DeJesus et al.   PLoS Computational Biology

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts

(2013) Seth Rakoff-Nahoum et al.   CURRENT BIOLOGY

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

How glycan metabolism shapes the human gut microbiota

(2012) Nicole M. Koropatkin et al.   NATURE REVIEWS MICROBIOLOGY

Bacteroides in the Infant Gut Consume Milk Oligosaccharides via Mucus-Utilization Pathways

(2011) Angela Marcobal et al.   Cell Host & Microbe

Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

(2011) Michael A. Fischbach et al.   Cell Host & Microbe

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations

(2010) Erica D. Sonnenburg et al.   CELL

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Rapid acid treatment of Escherichia coli: transcriptomic response and recovery

(2008) Geetha Kannan et al.   BMC MICROBIOLOGY

A microbial symbiosis factor prevents intestinal inflammatory disease

(2008) Sarkis K. Mazmanian et al.   NATURE

Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices

(2008) Nicole M. Koropatkin et al.   STRUCTURE