Microbial nutrient niches in the gut

Stochastic neutral modelling of the Gut Microbiota’s relative species abundance from next generation sequencing data

(2016) Claudia Sala et al.   BMC BIOINFORMATICS

Modulation of the human gut microbiota by dietary fibres occurs at the species level

(2016) Wing Sun Faith Chung et al.   BMC BIOLOGY

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

(2016) María X. Maldonado-Gómez et al.   Cell Host & Microbe

Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid

(2016) Sylvia H. Duncan et al.   ENVIRONMENTAL MICROBIOLOGY

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance

(2016) Andrés Moya et al.   TRENDS IN MICROBIOLOGY

The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos

(2016) Felix Sommer et al.   Cell Reports

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium

(2016) Sandrine Brugiroux et al.   Nature Microbiology

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

(2016) Damian Rafal Plichta et al.   Nature Microbiology

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut

(2016) Henrik M. Roager et al.   Nature Microbiology

Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets

(2016) Lianwei Li et al.   Scientific Reports

Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

(2015) Tadashi Fukami   Annual Review of Ecology Evolution and Systematics

Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque

(2015) Koji Yasuda et al.   Cell Host & Microbe

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota

(2015) Rachel N. Carmody et al.   Cell Host & Microbe

Effects of Diurnal Variation of Gut Microbes and High-Fat Feeding on Host Circadian Clock Function and Metabolism

(2015) Vanessa Leone et al.   Cell Host & Microbe

Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers

(2015) A Lavelle et al.   GUT

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

(2015) Adam R Burns et al.   ISME Journal

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

(2015) M. Wu et al.   SCIENCE

Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome

(2015) Arvind Venkataraman et al.   mBio

The outer mucus layer hosts a distinct intestinal microbial niche

(2015) Hai Li et al.   Nature Communications

Detection of Sialic Acid-Utilising Bacteria in a Caecal Community Batch Culture Using RNA-Based Stable Isotope Probing

(2015) Wayne Young et al.   Nutrients

The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes

(2015) Inés Martínez et al.   Cell Reports

Mucin glycan foraging in the human gut microbiome

(2015) Louise E. Tailford et al.   Frontiers in Genetics

Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality

(2015) Rosemarie De Weirdt et al.   npj Biofilms and Microbiomes

Fermentable non-starch polysaccharides increases the abundance of Bacteroides–Prevotella–Porphyromonas in ileal microbial community of growing pigs

(2014) E. Ivarsson et al.   Animal

RNA–Stable-Isotope Probing Shows Utilization of Carbon from Inulin by Specific Bacterial Populations in the Rat Large Bowel

(2014) Gerald W. Tannock et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis

(2014) Christoph A. Thaiss et al.   CELL

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut

(2014) Henning Seedorf et al.   CELL

Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome

(2014) Amir Zarrinpar et al.   Cell Metabolism

Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

(2014) David Berry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary limits to cooperation in microbial communities

(2014) Nuno M. Oliveira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Innate lymphoid cells regulate intestinal epithelial cell glycosylation

(2014) Y. Goto et al.   SCIENCE

Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection

(2014) Casey M. Theriot et al.   Nature Communications

Gut microbiome of the Hadza hunter-gatherers

(2014) Stephanie L. Schnorr et al.   Nature Communications

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Nontoxigenic Clostridium difficile Protects Hamsters against Challenge with Historic and Epidemic Strains of Toxigenic BI/NAP1/027 C. difficile

(2013) Kristin J. Nagaro et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Glycobiome: Bacteria and mucus at the epithelial interface

(2013) Janneke P. Ouwerkerk et al.   BEST PRACTICE & RESEARCH IN CLINICAL GASTROENTEROLOGY

Probiotic Bacteria Reduce Salmonella Typhimurium Intestinal Colonization by Competing for Iron

(2013) Elisa Deriu et al.   Cell Host & Microbe

An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts

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

An Escherichia coli Nissle 1917 Missense Mutant Colonizes the Streptomycin-Treated Mouse Intestine Better than the Wild Type but Is Not a Better Probiotic

(2013) Jimmy Adediran et al.   INFECTION AND IMMUNITY

Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota

(2013) Zhigang Zhang et al.   ISME Journal

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

(2013) Katharine M. Ng et al.   NATURE

Bacterial colonization factors control specificity and stability of the gut microbiota

(2013) S. Melanie Lee et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Nutritional Basis for Colonization Resistance by Human Commensal Escherichia coli Strains HS and Nissle 1917 against E. coli O157:H7 in the Mouse Intestine

(2013) Rosalie Maltby et al.   PLoS One

Bacterial Community Mapping of the Mouse Gastrointestinal Tract

(2013) Shenghua Gu 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

Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing

(2013) D. Berry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota

(2013) P. C. Kashyap et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence

(2013) Benjamin Steeb et al.   PLoS Pathogens

Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure

(2012) Manuel Ferrer et al.   ENVIRONMENTAL MICROBIOLOGY

The Streptomycin-Treated Mouse Intestine SelectsEscherichia coli envZMissense Mutants That Interact with Dense and Diverse Intestinal Microbiota

(2012) Mary P. Leatham-Jensen et al.   INFECTION AND IMMUNITY

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

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

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

(2012) Erwin G Zoetendal et al.   ISME Journal

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

(2012) Xiaolei Ze et al.   ISME Journal

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes

(2012) P. Jeraldo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

The Evolution of Mutualism in Gut Microbiota Via Host Epithelial Selection

(2012) Jonas Schluter et al.   PLOS BIOLOGY

Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

(2012) Trevor D. Lawley et al.   PLoS Pathogens

Microbial pathways in colonic sulfur metabolism and links with health and disease

(2012) Franck Carbonero et al.   Frontiers in Physiology

Resource partitioning in relation to cohabitation of Lactobacillus species in the mouse forestomach

(2011) Gerald W Tannock et al.   ISME Journal

Disentangling the importance of ecological niches from stochastic processes across scales

(2011) J. M. Chase et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Pyrosequencing-Based Analysis of the Mucosal Microbiota in Healthy Individuals Reveals Ubiquitous Bacterial Groups and Micro-Heterogeneity

(2011) Pei-Ying Hong et al.   PLoS One

Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype

(2011) P. Rausch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice

(2011) J. J. Faith et al.   SCIENCE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

The Unified Neutral Theory of Biodiversity and Biogeography at Age Ten

(2011) James Rosindell et al.   TRENDS IN ECOLOGY & EVOLUTION

Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

(2010) Chin Wen Png et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

High temporal and inter-individual variation detected in the human ileal microbiota

(2010) Carien C. G. M. Booijink et al.   ENVIRONMENTAL MICROBIOLOGY

Postprandial remodeling of the gut microbiota in Burmese pythons

(2010) Elizabeth K Costello et al.   ISME Journal

Spatial organization of intestinal microbiota in the mouse ascending colon

(2010) Gerardo M Nava et al.   ISME Journal

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

(2010) Alan W Walker et al.   ISME Journal

Resistant Starches Types 2 and 4 Have Differential Effects on the Composition of the Fecal Microbiota in Human Subjects

(2010) Inés Martínez et al.   PLoS One

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Response of Gut Microbiota to Fasting and Hibernation in Syrian Hamsters

(2009) K. Sonoyama et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation

(2009) P. A. Crawford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

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

The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities

(2008) Alan W. Walker et al.   ENVIRONMENTAL MICROBIOLOGY

Biostructure of Fecal Microbiota in Healthy Subjects and Patients With Chronic Idiopathic Diarrhea

(2008) Alexander Swidsinski et al.   GASTROENTEROLOGY