Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

Cell factories converting lactate and acetate to butyrate: Clostridium butyricum and microbial communities from dark fermentation bioreactors

(2019) Anna Detman et al.   Microbial Cell Factories

The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease

(2018) Kassem Makki et al.   Cell Host & Microbe

Pro- and anti-inflammatory effects of short chain fatty acids on immune and endothelial cells

(2018) Meng Li et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Anti-inflammatory effect of microbial consortia during the utilization of dietary polysaccharides

(2018) Pamela Thomson et al.   FOOD RESEARCH INTERNATIONAL

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

(2018) Eugen Bauer et al.   mSystems

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

(2018) Kevin D'hoe et al.   eLife

Prebiotic inulin-type fructans induce specific changes in the human gut microbiota

(2017) Doris Vandeputte et al.   GUT

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

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

Influence of diet on the gut microbiome and implications for human health

(2017) Rasnik K. Singh et al.   Journal of Translational Medicine

Dysbiosis and Its Discontents

(2017) Katarzyna B. Hooks et al.   mBio

Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis

(2017) Jaeyun Sung et al.   Nature Communications

Modeling Metabolic Interactions in a Consortium of the Infant Gut Microbiome

(2017) Francisco Pinto et al.   Frontiers in Microbiology

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

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

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

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

Distinct patterns in the gut microbiota after surgical or medical therapy in obese patients

(2017) Daniel A. Medina et al.   PeerJ

Butyrate-producing bacteria supplemented in vitro to Crohn’s disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity

(2017) Annelies Geirnaert et al.   Scientific Reports

Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases

(2016) Mingming Sun et al.   JOURNAL OF GASTROENTEROLOGY

Diet–microbiota interactions as moderators of human metabolism

(2016) Justin L. Sonnenburg et al.   NATURE

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

Revised Estimates for the Number of Human and Bacteria Cells in the Body

(2016) Ron Sender et al.   PLOS BIOLOGY

On the Origins and Control of Community Types in the Human Microbiome

(2016) Travis E. Gibson et al.   PLoS Computational Biology

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

(2016) David Ríos-Covián et al.   Frontiers in Microbiology

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

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

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

Inulin-type fructans modulate intestinal Bifidobacterium species populations and decrease fecal short-chain fatty acids in obese women

(2015) Nuria Salazar et al.   CLINICAL NUTRITION

Pathways and functions of gut microbiota metabolism impacting host physiology

(2015) Smitha Krishnan et al.   CURRENT OPINION IN BIOTECHNOLOGY

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

Diversity of key players in the microbial ecosystems of the human body

(2015) Ferenc Jordán et al.   Scientific Reports

Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa

(2015) Pål Trosvik et al.   Microbiome

Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

(2014) Nicole Reichardt et al.   ISME Journal

The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts

(2014) Laurens Kraal et al.   PLoS One

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

The Impact of Diet and Lifestyle on Gut Microbiota and Human Health

(2014) Michael Conlon et al.   Nutrients

An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts

(2013) Seth Rakoff-Nahoum et al.   CURRENT BIOLOGY

A Stand-Alone Synbiotic Treatment for the Prevention of D-Lactic Acidosis in Short Bowel Syndrome

(2013) Kazuhiro Takahashi et al.   INTERNATIONAL SURGERY

Faecal D/L Lactate Ratio Is a Metabolic Signature of Microbiota Imbalance in Patients with Short Bowel Syndrome

(2013) Camille Mayeur et al.   PLoS One

The Interplay Between Fiber and the Intestinal Microbiome in the Inflammatory Response

(2013) Shiu-Ming Kuo   Advances in Nutrition

A review of the potential mechanisms for the lowering of colorectal oncogenesis by butyrate

(2012) Kim Y. C. Fung et al.   BRITISH JOURNAL OF NUTRITION

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

(2012) C. Lozupone et al.   GENOME RESEARCH

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

(2012) Pieter Van den Abbeele et al.   ISME Journal

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

Production of Lactate in Escherichia coli by Redox Regulation Genetically and Physiologically

(2010) Huimin Liu et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Inulin-Type Fructans Stimulated the Growth of Exogenously AdministeredLactobacillus plantarumNo. 14 in the Mouse Gastrointestinal Tract

(2010) Naoki TAKEMURA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Seguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov.

(2009) J.-P. Carlier et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Keystone species and food webs

(2009) F. Jordan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii

(2008) Carlett Ramirez-Farias et al.   BRITISH JOURNAL OF NUTRITION