Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability

Microbiota-derived 3-IAA influences chemotherapy efficacy in pancreatic cancer

(2023) Joseph Tintelnot et al.   NATURE

Cooperation increases robustness to ecological disturbance in microbial cross‐feeding networks

(2022) Leonardo Oña et al.   ECOLOGY LETTERS

Bacterial species rarely work together

(2022) Jacob D. Palmer et al.   SCIENCE

Global dynamics of microbial communities emerge from local interaction rules

(2022) Simon van Vliet et al.   PLoS Computational Biology

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

(2022) German A. Ashniev et al.   Microorganisms

Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties

(2022) Sudarshan A. Shetty et al.   ISME Journal

Long‐Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis

(2022) Alba Troci et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Gut bacterial nutrient preferences quantified in vivo

(2022) Xianfeng Zeng et al.   CELL

The long-term genetic stability and individual specificity of the human gut microbiome

(2021) Lianmin Chen et al.   CELL

Human and preclinical studies of the host–gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health

(2021) François Brial et al.   GUT

A metabolomics pipeline for the mechanistic interrogation of the gut microbiome

(2021) Shuo Han et al.   NATURE

Obligate cross-feeding expands the metabolic niche of bacteria

(2021) Leonardo Oña et al.   Nature Ecology & Evolution

Ecology impacts the decrease of Spirochaetes and Prevotella in the fecal gut microbiota of urban humans

(2021) Louise B. Thingholm et al.   BMC MICROBIOLOGY

Microbial regulation of hexokinase 2 links mitochondrial metabolism and cell death in colitis

(2021) Finn Hinrichsen et al.   Cell Metabolism

Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria

(2021) Samir Giri et al.   CURRENT BIOLOGY

In vitro interaction network of a synthetic gut bacterial community

(2021) Anna S. Weiss et al.   ISME Journal

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

(2020) Silas Kieser et al.   BMC BIOINFORMATICS

Microbial butyrate synthesis indicates therapeutic efficacy of azathioprine in IBD patients

(2020) M Effenberger et al.   Journal of Crohns & Colitis

A unified catalog of 204,938 reference genomes from the human gut microbiome

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

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

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

GapMind: Automated Annotation of Amino Acid Biosynthesis

(2020) Morgan N. Price et al.   mSystems

Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health

(2020) Marina Fassarella et al.   GUT

Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction and alter host behaviour

(2020) Sílvia F. Henriques et al.   Nature Communications

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

Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy

(2019) Rosina Pryor et al.   CELL

The biology of mucus: Composition, synthesis and organization

(2018) Rama Bansil et al.   ADVANCED DRUG DELIVERY REVIEWS

Microbial communities as dynamical systems

(2018) Didier Gonze et al.   CURRENT OPINION IN MICROBIOLOGY

Aryl hydrocarbon receptor and intestinal immunity

(2018) Bruno Lamas et al.   Mucosal Immunology

Ecology and evolution of metabolic cross-feeding interactions in bacteria

(2018) Glen D'Souza et al.   NATURAL PRODUCT REPORTS

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

(2018) Melanie Tramontano et al.   Nature Microbiology

Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation

(2018) Kees C. H. van der Ark et al.   Microbial Biotechnology

Microbial tryptophan catabolites in health and disease

(2018) Henrik M. Roager et al.   Nature Communications

Increased Tryptophan Metabolism Is Associated With Activity of Inflammatory Bowel Diseases

(2017) Susanna Nikolaus et al.   GASTROENTEROLOGY

Amino Acid Absorption in the Large Intestine of Humans and Porcine Models

(2017) Nikkie van der Wielen et al.   JOURNAL OF NUTRITION

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes

(2017) Joana C. Xavier et al.   METABOLIC ENGINEERING

A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites

(2017) Dylan Dodd et al.   NATURE

Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention

(2017) Ruixin Liu et al.   NATURE MEDICINE

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Physiology of Intestinal Absorption and Secretion

(2016) Pawel R. Kiela et al.   BEST PRACTICE & RESEARCH IN CLINICAL GASTROENTEROLOGY

Metabolic network architecture and carbon source determine metabolite production costs

(2016) Silvio Waschina et al.   FEBS Journal

Mutual Cross-Feeding Interactions between Bifidobacterium longum subsp. longum NCC2705 and Eubacterium rectale ATCC 33656 Explain the Bifidogenic and Butyrogenic Effects of Arabinoxylan Oligosaccharides

(2015) Audrey Rivière et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community

(2015) Sarahi L. Garcia et al.   MOLECULAR ECOLOGY

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Metabolic cross-feeding via intercellular nanotubes among bacteria

(2015) Samay Pande et al.   Nature Communications

The Role of Microbial Amino Acid Metabolism in Host Metabolism

(2015) Evelien Neis et al.   Nutrients

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

(2014) Glen D'Souza et al.   EVOLUTION

Metabolic Alterations to the Mucosal Microbiota in Inflammatory Bowel Disease

(2014) Michael Davenport et al.   INFLAMMATORY BOWEL DISEASES

Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe

(2014) A. Heinken et al.   JOURNAL OF BACTERIOLOGY

The gut microbiota, bacterial metabolites and colorectal cancer

(2014) Petra Louis et al.   NATURE REVIEWS MICROBIOLOGY

Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients With Psoriatic Arthritis, Resembling Dysbiosis in Inflammatory Bowel Disease

(2014) Jose U. Scher et al.   Arthritis & Rheumatology

sybil – Efficient constraint-based modelling in R

(2013) Gabriel Gelius-Dietrich et al.   BMC Systems Biology

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria

(2013) Samay Pande et al.   ISME Journal

Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein

(2013) Wendy R. Russell et al.   MOLECULAR NUTRITION & FOOD RESEARCH

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

(2012) J. J. Morris et al.   mBio

Twin Study Indicates Loss of Interaction Between Microbiota and Mucosa of Patients With Ulcerative Colitis

(2011) Patricia Lepage et al.   GASTROENTEROLOGY

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY