High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure

Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome

(2022) German A. Ashniev et al.   Microorganisms

Extracellular Metabolism Sets the Table for Microbial Cross-Feeding

(2021) Ryan K. Fritts et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Blue poo: impact of gut transit time on the gut microbiome using a novel marker

(2021) Francesco Asnicar et al.   GUT

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis

(2021) Almut Heinken et al.   npj Systems Biology and Applications

Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods

(2021) Mariana Noto Guillen et al.   Cell Systems

Emerging connections between gut microbiome bioenergetics and chronic metabolic diseases

(2021) Brendan A. Daisley et al.   Cell Reports

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

U1 snRNP regulates cancer cell migration and invasion in vitro

(2020) Jung-Min Oh et al.   Nature Communications

B vitamin acquisition by gut commensal bacteria

(2020) Emily E. Putnam et al.   PLoS Pathogens

Sharing vitamins: Cobamides unveil microbial interactions

(2020) Olga M. Sokolovskaya et al.   SCIENCE

Vitamin Biosynthesis by Human Gut Butyrate-Producing Bacteria and Cross-Feeding in Synthetic Microbial Communities

(2020) Eva C. Soto-Martin et al.   mBio

Core Gut Bacteria Analysis of Healthy Mice

(2019) Jingjing Wang et al.   Frontiers in Microbiology

Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients with Inflammatory Bowel Diseases

(2019) Konrad Aden et al.   GASTROENTEROLOGY

B-Vitamin Sharing Promotes Stability of Gut Microbial Communities

(2019) Vandana Sharma et al.   Frontiers in Microbiology

The social network of microorganisms — how auxotrophies shape complex communities

(2018) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

Challenges in modeling the human gut microbiome

(2018) Parizad Babaei et al.   NATURE BIOTECHNOLOGY

Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain

(2017) C Menni et al.   INTERNATIONAL JOURNAL OF OBESITY

Microbial Metabolic Networks at the Mucus Layer Lead to Diet-Independent Butyrate and Vitamin B 12 Production by Intestinal Symbionts

(2017) Clara Belzer et al.   mBio

Quinones are growth factors for the human gut microbiota

(2017) Kathrin Fenn et al.   Microbiome

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

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Dysfunctional gut microbiota and relative co-abundance network in infantile eczema

(2016) Heping Wang et al.   Gut Pathogens

Species–function relationships shape ecological properties of the human gut microbiome

(2016) Sara Vieira-Silva et al.   Nature Microbiology

Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella

(2015) Petia Kovatcheva-Datchary et al.   Cell Metabolism

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes

(2015) Stefanía Magnúsdóttir et al.   Frontiers in Genetics

Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children

(2015) Chenhong Zhang et al.   EBioMedicine

Human Gut Microbes Use Multiple Transporters to Distinguish Vitamin B12 Analogs and Compete in the Gut

(2014) Patrick H. Degnan et al.   Cell Host & Microbe

Vitamin B 12 as a Modulator of Gut Microbial Ecology

(2014) Patrick H. Degnan et al.   Cell Metabolism

LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA

(2014) Glen D'Souza et al.   EVOLUTION

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

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

The Health Advantage of a Vegan Diet: Exploring the Gut Microbiota Connection

(2014) Marian Glick-Bauer et al.   Nutrients

Microbial Enterotypes, Inferred by the Prevotella-to-Bacteroides Ratio, Remained Stable during a 6-Month Randomized Controlled Diet Intervention with the New Nordic Diet

(2013) Henrik M. Roager et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Human Gut Microbiome and Risk for Colorectal Cancer

(2013) Jiyoung Ahn et al.   JNCI-Journal of the National Cancer Institute

Bacteria as vitamin suppliers to their host: a gut microbiota perspective

(2012) Jean Guy LeBlanc et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2012) J. J. Morris et al.   mBio

Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome

(2011) Ian M. Carroll et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

Toward defining the autoimmune microbiome for type 1 diabetes

(2010) Adriana Giongo et al.   ISME Journal

Regulatory crosstalk of the metabolic network

(2010) Nana-Maria Grüning et al.   TRENDS IN BIOCHEMICAL SCIENCES