Short-Chain Fatty Acids Modulate Healthy Gut Microbiota Composition and Functional Potential

Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities

(2021) Stanislav N. Iablokov et al.   Frontiers in Microbiology

Controversial Roles of Gut Microbiota-Derived Short-Chain Fatty Acids (SCFAs) on Pancreatic β-Cell Growth and Insulin Secretion

(2020) Jun-Li Liu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Unravelling lactate‐acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics

(2020) Sudarshan A. Shetty et al.   ENVIRONMENTAL MICROBIOLOGY

16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics

(2019) Christine Tara Peterson et al.   PLoS One

Prebiotic Potential of Culinary Spices Used to Support Digestion and Bioabsorption

(2019) Christine T. Peterson et al.   Evidence-based Complementary and Alternative Medicine

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome

(2019) Dmitry A. Rodionov et al.   Frontiers in Microbiology

Bifidobacterial Dialogue With Its Human Host and Consequent Modulation of the Immune System

(2019) Giulia Alessandri et al.   Frontiers in Immunology

The Short-Chain Fatty Acid Acetate in Body Weight Control and Insulin Sensitivity

(2019) Hernández et al.   Nutrients

Varied Pathways of Infant Gut-Associated Bifidobacterium to Assimilate Human Milk Oligosaccharides: Prevalence of the Gene Set and Its Correlation with Bifidobacteria-Rich Microbiota Formation

(2019) Mikiyasu Sakanaka et al.   Nutrients

Prebiotic Potential of Herbal Medicines Used in Digestive Health and Disease

(2018) Christine Tara Peterson et al.   JOURNAL OF ALTERNATIVE AND COMPLEMENTARY MEDICINE

Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation

(2018) Katri Korpela   Annual Review of Food Science and Technology

Formate cross-feeding and cooperative metabolic interactions revealed by transcriptomics in co-cultures of acetogenic and amylolytic human colonic bacteria

(2018) Jenny A. Laverde Gomez et al.   ENVIRONMENTAL MICROBIOLOGY

Colonocyte metabolism shapes the gut microbiota

(2018) Yael Litvak et al.   SCIENCE

Specific substrate-driven changes in human faecal microbiota composition contrast with functional redundancy in short-chain fatty acid production

(2017) Nicole Reichardt et al.   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut

(2016) Audrey Rivière et al.   Frontiers in Microbiology

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

Tryptophan Catabolites from Microbiota Engage Aryl Hydrocarbon Receptor and Balance Mucosal Reactivity via Interleukin-22

(2013) Teresa Zelante et al.   IMMUNITY

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

(2013) Nicholas Arpaia et al.   NATURE

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

An In Vitro Model of the Horse Gut Microbiome Enables Identification of Lactate-Utilizing Bacteria That Differentially Respond to Starch Induction

(2013) Amy S. Biddle et al.   PLoS One

Metabolic niche of a prominent sulfate-reducing human gut bacterium

(2013) F. E. Rey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

(2012) Xiaolei Ze et al.   ISME Journal

Characterization of Phascolarctobacterium succinatutens sp. nov., an Asaccharolytic, Succinate-Utilizing Bacterium Isolated from Human Feces

(2011) Yohei Watanabe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fermentation in the Human Large Intestine

(2011) George T. Macfarlane et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

Natural Aryl Hydrocarbon Receptor Ligands Control Organogenesis of Intestinal Lymphoid Follicles

(2011) E. A. Kiss et al.   SCIENCE

Intestinal health functions of colonic microbial metabolites: a review

(2011) R. Havenaar   Beneficial Microbes

Central Role of the Early Colonizer Veillonella sp. in Establishing Multispecies Biofilm Communities with Initial, Middle, and Late Colonizers of Enamel

(2010) S. Periasamy et al.   JOURNAL OF BACTERIOLOGY

Resistant starch, large bowel fermentation and a broader perspective of prebiotics and probiotics

(2010) A. Bird et al.   Beneficial Microbes

A Quick Guide to Teaching R Programming to Computational Biology Students

(2009) Stephen J. Eglen   PLoS Computational Biology