Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R

Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria

(2022) Nicholas A. Pudlo et al.   mSystems

Acetate reprograms gut microbiota during alcohol consumption

(2022) Cameron Martino et al.   Nature Communications

Selective Utilization of the Human Milk Oligosaccharides 2′-Fucosyllactose, 3-Fucosyllactose, and Difucosyllactose by Various Probiotic and Pathogenic Bacteria

(2021) Krista Salli et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

The Mean of Milk: A Review of Human Milk Oligosaccharide Concentrations throughout Lactation

(2021) Buket Soyyılmaz et al.   Nutrients

Engineering Bacteroides thetaiotaomicron to produce non-native butyrate based on a genome-scale metabolic model-guided design

(2021) Kangsan Kim et al.   METABOLIC ENGINEERING

Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data

(2021) Anurag Passi et al.   Metabolites

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

Human Milk Oligosaccharides: Health Benefits, Potential Applications in Infant Formulas, and Pharmacology

(2020) Michał Wiciński et al.   Nutrients

The association between breastmilk oligosaccharides and faecal microbiota in healthy breastfed infants at two, six, and twelve weeks of age

(2020) Klaudyna Borewicz et al.   Scientific Reports

A soluble fiber diet increases Bacteroides fragilis group and IgA production in the gut

(2020) Akihito Nakajima et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

An Overview on Fecal Branched Short-Chain Fatty Acids Along Human Life and as Related With Body Mass Index: Associated Dietary and Anthropometric Factors

(2020) David Rios-Covian et al.   Frontiers in Microbiology

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

Temporal development of the infant gut microbiome

(2019) Rebecca E. Moore et al.   Open Biology

How accurate is automated gap filling of metabolic models?

(2018) Peter D. Karp et al.   BMC Systems Biology

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

(2018) Yara Seif et al.   Nature Communications

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

(2018) Hao Wang et al.   PLoS Computational Biology

Microbial nitrogen limitation in the mammalian large intestine

(2018) Aspen T. Reese et al.   Nature Microbiology

Amino acid composition of rumen bacteria and protozoa in cattle

(2017) M. Sok et al.   JOURNAL OF DAIRY SCIENCE

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Shaping the Metabolism of Intestinal Bacteroides Population through Diet to Improve Human Health

(2017) David Rios-Covian et al.   Frontiers in Microbiology

Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition

(2016) Mark R. Charbonneau et al.   CELL

Interactions between the microbiota and pathogenic bacteria in the gut

(2016) Andreas J. Bäumler et al.   NATURE

Short-chain fatty acids in control of body weight and insulin sensitivity

(2015) Emanuel E. Canfora et al.   Nature Reviews Endocrinology

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Identification of genes required for the survival of B. fragilis using massive parallel sequencing of a saturated transposon mutant library

(2014) Yaligara Veeranagouda et al.   BMC GENOMICS

Efficient utilization of complex N-linked glycans is a selective advantage for Bacteroides fragilis in extraintestinal infections

(2014) Y. Cao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

(2013) Katharine M. Ng et al.   NATURE

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

Consumption of Human Milk Oligosaccharides by Gut-Related Microbes

(2010) Angela Marcobal et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Presence of Quorum-sensing Systems Associated with Multidrug Resistance and Biofilm Formation in Bacteroides fragilis

(2008) Lilian Pumbwe et al.   MICROBIAL ECOLOGY