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

Antibiotics-induced monodominance of a novel gut bacterial order

(2019) Falk Hildebrand et al.   GUT

Gut microbial metabolites in obesity, NAFLD and T2DM

(2019) Emanuel E. Canfora et al.   Nature Reviews Endocrinology

Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes

(2019) J. Alfredo Blakeley-Ruiz et al.   Microbiome

The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut

(2019) Janneke Elzinga et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Modelling microbiome recovery after antibiotics using a stability landscape framework

(2019) Liam P. Shaw et al.   ISME Journal

The Battle Within: Interactions of Bacteriophages and Bacteria in the Gastrointestinal Tract

(2019) Luisa De Sordi et al.   Cell Host & Microbe

Ecosystem tipping points in an evolving world

(2019) Vasilis Dakos et al.   Nature Ecology & Evolution

Precision Nutrition and the Microbiome, Part I: Current State of the Science

(2019) Mills et al.   Nutrients

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

(2019) Abigail J. Johnson et al.   Cell Host & Microbe

Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health

(2019) Kaitlyn Oliphant et al.   Microbiome

Dysbiosis: from fiction to function

(2019) Connor R Tiffany et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study

(2019) Matthias Willmann et al.   BMC BIOLOGY

Problems with the concept of gut microbiota dysbiosis

(2019) Harald Brüssow   Microbial Biotechnology

OUP accepted manuscript

(2018)   AMERICAN JOURNAL OF CLINICAL NUTRITION

The Human Gut Microbiome: From Association to Modulation

(2018) Thomas S.B. Schmidt et al.   CELL

Towards utilization of the human genome and microbiome for personalized nutrition

(2018) Stavros Bashiardes et al.   CURRENT OPINION IN BIOTECHNOLOGY

Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery

(2018) Michael Kriss et al.   CURRENT OPINION IN MICROBIOLOGY

The prebiotic inulin improves substrate metabolism and promotes short-chain fatty acid production in overweight to obese men

(2018) Christina M. van der Beek et al.   METABOLISM-CLINICAL AND EXPERIMENTAL

Healthy hosts rule within: ecological forces shaping the gut microbiota

(2018) Mariana X. Byndloss et al.   Mucosal Immunology

Current understanding of the human microbiome

(2018) Jack A Gilbert et al.   NATURE MEDICINE

Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes

(2018) Liping Zhao et al.   SCIENCE

Precision medicine using microbiota

(2018) Christian Jobin   SCIENCE

Lactobacillus paracasei CNCM I-3689 reduces vancomycin-resistant Enterococcus persistence and promotes Bacteroidetes resilience in the gut following antibiotic challenge

(2018) Laureen Crouzet et al.   Scientific Reports

OUP accepted manuscript

(2018)   Advances in Nutrition

The microbiome in precision medicine: the way forward

(2018) Joseph F. Petrosino   Genome Medicine

Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut

(2018) Siavash Atashgahi et al.   Frontiers in Physiology

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease

(2018) Ahmed Moustafa et al.   Clinical and Translational Gastroenterology

Potential of Fructooligosaccharides and Xylooligosaccharides as Substrates To Counteract the Undesirable Effects of Several Antibiotics on Elder Fecal Microbiota: A First in Vitro Approach

(2018) Beatriz Míguez et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Bacteroides thetaiotaomicron

(2018) Nathan T. Porter et al.   TRENDS IN MICROBIOLOGY

Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut?

(2018) Hanne L.P. Tytgat et al.   TRENDS IN MICROBIOLOGY

Recovery of gut microbiota of healthy adults following antibiotic exposure

(2018) Albert Palleja et al.   Nature Microbiology

Impact of antimicrobial therapy on the gut microbiome

(2018) Amira A Bhalodi et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Gut microbiota functions: metabolism of nutrients and other food components

(2017) Ian Rowland et al.   EUROPEAN JOURNAL OF NUTRITION

The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens

(2017) Sohn Kim et al.   IMMUNOLOGICAL REVIEWS

The evolution of the host microbiome as an ecosystem on a leash

(2017) Kevin R. Foster et al.   NATURE

Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics

(2017) Glenn R. Gibson et al.   Nature Reviews Gastroenterology & Hepatology

The resilience of the intestinal microbiota influences health and disease

(2017) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

Interindividual variability in gut microbiota and host response to dietary interventions

(2017) Genelle R Healey et al.   NUTRITION REVIEWS

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

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

(2017) Claire Duvallet et al.   Nature Communications

Functional Characterization of Novel Faecalibacterium prausnitzii Strains Isolated from Healthy Volunteers: A Step Forward in the Use of F. prausnitzii as a Next-Generation Probiotic

(2017) Rebeca Martín et al.   Frontiers in Microbiology

Enterotypes in the landscape of gut microbial community composition

(2017) Paul I. Costea et al.   Nature Microbiology

Oral supplementation of healthy adults with 2′-O-fucosyllactose and lacto-N-neotetraose is well tolerated and shifts the intestinal microbiota

(2016) Emma Elison et al.   BRITISH JOURNAL OF NUTRITION

Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans

(2016) Ron Sender et al.   CELL

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella

(2016) Fabian Rivera-Chávez et al.   Cell Host & Microbe

Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial

(2016) Dorien Reijnders et al.   Cell Metabolism

Microcins mediate competition among Enterobacteriaceae in the inflamed gut

(2016) Martina Sassone-Corsi et al.   NATURE

Quorum sensing signal–response systems in Gram-negative bacteria

(2016) Kai Papenfort et al.   NATURE REVIEWS MICROBIOLOGY

Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens

(2016) Eric G. Pamer   SCIENCE

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

Development of antimicrobial resistance in the normal anaerobic microbiota during one year after administration of clindamycin or ciprofloxacin

(2015) Mamun-Ur Rashid et al.   ANAEROBE

The initial state of the human gut microbiome determines its reshaping by antibiotics

(2015) Frédéric Raymond et al.   ISME Journal

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

(2015) K. Z. Coyte et al.   SCIENCE

Fat, fibre and cancer risk in African Americans and rural Africans

(2015) Stephen J. D. O’Keefe et al.   Nature Communications

Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut

(2015) Christian Milani et al.   Scientific Reports

Manipulation of the Quorum Sensing Signal AI-2 Affects the Antibiotic-Treated Gut Microbiota

(2015) Jessica Ann Thompson et al.   Cell Reports

The vocabulary of microbiome research: a proposal

(2015) Julian R. Marchesi et al.   Microbiome

The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome

(2015) DeAnna E. Beasley et al.   PLoS One

Exploring the effects of galacto-oligosaccharides on the gut microbiota of healthy adults receiving amoxicillin treatment

(2014) S. E. Ladirat et al.   BRITISH JOURNAL OF NUTRITION

Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates

(2014) Erica D. Sonnenburg et al.   Cell Metabolism

Effect of diet on the intestinal microbiota and its activity

(2014) Erwin G. Zoetendal et al.   CURRENT OPINION IN GASTROENTEROLOGY

Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants

(2014) Tanja Jaeggi et al.   GUT

Adhesion as a weapon in microbial competition

(2014) Jonas Schluter et al.   ISME Journal

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic

(2014) Colin Hill et al.   Nature Reviews Gastroenterology & Hepatology

Tipping elements in the human intestinal ecosystem

(2014) Leo Lahti et al.   Nature Communications

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

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

(2013) Els van Nood et al.   NEW ENGLAND JOURNAL OF MEDICINE

Long-Term Temporal Analysis of the Human Fecal Microbiota Revealed a Stable Core of Dominant Bacterial Species

(2013) Inés Martínez et al.   PLoS One

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

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

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

Gut microbiota disturbance during antibiotic therapy: a multi-omic approach

(2012) Ana Elena Pérez-Cobas et al.   GUT

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Early-warning signals for critical transitions

(2009) Marten Scheffer et al.   NATURE