Modeling Metabolic Interactions in a Consortium of the Infant Gut Microbiome

Human milk oligosaccharides and infant gut bifidobacteria: Molecular strategies for their utilization

(2017) Pamela Thomson et al.   FOOD MICROBIOLOGY

Prebiotics Mediate Microbial Interactions in a Consortium of the Infant Gut Microbiome

(2017) Daniel Medina et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence

(2017) Yunus E. Tuncil et al.   mBio

Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation

(2017) Sebastián N. Mendoza et al.   Frontiers in Microbiology

Strain competition restricts colonization of an enteric pathogen and prevents colitis

(2016) Aaron L Hecht et al.   EMBO REPORTS

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

Bifidobacterial inulin-type fructan degradation capacity determines cross-feeding interactions between bifidobacteria and Faecalibacterium prausnitzii

(2016) Frédéric Moens et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

The microbiome in early life: implications for health outcomes

(2016) Sabrina Tamburini et al.   NATURE MEDICINE

Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations

(2016) Tatiana Shashkova et al.   PLoS One

Chemical communication in the gut: Effects of microbiota-generated metabolites on gastrointestinal bacterial pathogens

(2015) Stefanie L. Vogt et al.   ANAEROBE

Generation and structural validation of a library of diverse xyloglucan-derived oligosaccharides, including an update on xyloglucan nomenclature

(2015) Sami T. Tuomivaara et al.   CARBOHYDRATE RESEARCH

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

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

The gut microbiota and host health: a new clinical frontier

(2015) Julian R Marchesi et al.   GUT

Glycan complexity dictates microbial resource allocation in the large intestine

(2015) Artur Rogowski et al.   Nature Communications

The Role of Microbial Amino Acid Metabolism in Host Metabolism

(2015) Evelien Neis et al.   Nutrients

Metabolic engineering of the mixed-acid fermentation pathway of Escherichia coli for anaerobic production of glutamate and itaconate

(2015) Kiira S. Vuoristo et al.   AMB Express

Mucin glycan foraging in the human gut microbiome

(2015) Louise E. Tailford et al.   Frontiers in Genetics

Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks

(2015) Hugo Roume et al.   npj Biofilms and Microbiomes

Metabolism of Sialic Acid by Bifidobacterium breve UCC2003

(2014) Muireann Egan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

fastGapFill: efficient gap filling in metabolic networks

(2014) Ines Thiele et al.   BIOINFORMATICS

Cross-feeding by Bifidobacterium breve UCC2003 during co-cultivation with Bifidobacterium bifidum PRL2010 in a mucin-based medium

(2014) Muireann Egan et al.   BMC MICROBIOLOGY

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences

(2014) Laura M. Cox et al.   CELL

Modelling the emergent dynamics and major metabolites of the human colonic microbiota

(2014) Helen Kettle et al.   ENVIRONMENTAL MICROBIOLOGY

Cesarean Section and Chronic Immune Disorders

(2014) A. Sevelsted et al.   PEDIATRICS

Multifunctional Nutrient-Binding Proteins Adapt Human Symbiotic Bacteria for Glycan Competition in the Gut by Separately Promoting Enhanced Sensing and Catalysis

(2014) E. A. Cameron et al.   mBio

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks

(2013) Dmitry A Ravcheev et al.   BMC GENOMICS

A systems biology approach to studying the role of microbes in human health

(2012) Ines Thiele et al.   CURRENT OPINION IN BIOTECHNOLOGY

Utilization of galactooligosaccharides by Bifidobacterium longum subsp. infantis isolates

(2012) Daniel Garrido et al.   FOOD MICROBIOLOGY

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Improved calibration of a solid substrate fermentation model

(2011) Claudio A. Gelmi et al.   ELECTRONIC JOURNAL OF BIOTECHNOLOGY

Bifidobacteria can protect from enteropathogenic infection through production of acetate

(2011) Shinji Fukuda et al.   NATURE

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prebiotic effects: metabolic and health benefits

(2010) Marcel Roberfroid et al.   BRITISH JOURNAL OF NUTRITION

Web of ecological interactions in an experimental gut microbiota

(2010) Pål Trosvik et al.   ENVIRONMENTAL MICROBIOLOGY

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

(2010) Alan W Walker et al.   ISME Journal

Convergent temporal dynamics of the human infant gut microbiota

(2009) Pål Trosvik et al.   ISME Journal

Development of Chemically Defined Media Supporting High-Cell-Density Growth of Lactococci, Enterococci, and Streptococci

(2008) G. Zhang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast stable direct fitting and smoothness selection for generalized additive models

(2008) Simon N. Wood   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY