Reconstruction and dynamics of the human intestinal microbiome observed In Situ

Mechanisms, Evaluation, and Management of Chronic Constipation

(2020) Adil E. Bharucha et al.   GASTROENTEROLOGY

Nod2 influences microbial resilience and susceptibility to colitis following antibiotic exposure

(2019) A. Goethel et al.   Mucosal Immunology

Fecal microbiota from patients with cirrhosis has a low capacity to ferment non‐digestible carbohydrates into short chain fatty acids

(2019) Mingliang Jin et al.   LIVER INTERNATIONAL

Long-Term Safety and Efficacy of Fecal Microbiota Transplant in Active Ulcerative Colitis

(2019) Xiao Ding et al.   DRUG SAFETY

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

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

Mapping human microbiome drug metabolism by gut bacteria and their genes

(2019) Michael Zimmermann et al.   NATURE

Microbiomes as sources of emergent host phenotypes

(2019) J. B. Lynch et al.   SCIENCE

The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3

(2019) Zheng Kuang et al.   SCIENCE

Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs

(2019) Katharine Michelle Ng et al.   Cell Host & Microbe

Understanding immune–microbiota interactions in the intestine

(2019) Philip P. Ahern et al.   IMMUNOLOGY

Efficacy of drugs in chronic idiopathic constipation: a systematic review and network meta-analysis

(2019) Pavit Luthra et al.   Lancet Gastroenterology & Hepatology

Antibiotic-induced microbiome perturbations are associated with significant alterations to colonic mucosal immunity in rhesus macaques

(2019) Jennifer A. Manuzak et al.   Mucosal Immunology

Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota

(2018) Carolina Tropini et al.   CELL

Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases

(2018) Rachel Fellows et al.   Nature Communications

Gut Microbiota-Derived Short Chain Fatty Acids Induce Circadian Clock Entrainment in Mouse Peripheral Tissue

(2018) Yu Tahara et al.   Scientific Reports

Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda

(2018) Yan Zeng et al.   Frontiers in Microbiology

Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling

(2018) Dorines Rosario et al.   Frontiers in Physiology

Stability of the human faecal microbiome in a cohort of adult men

(2018) Raaj S. Mehta et al.   Nature Microbiology

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Metagenomic insights into resistant starch degradation by human gut microbiota

(2018) Marius Vital et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Alterations and structural resilience of the gut microbiota under dietary fat perturbations

(2018) Cong Liu et al.   JOURNAL OF NUTRITIONAL BIOCHEMISTRY

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults

(2018) Chad W. MacPherson et al.   Scientific Reports

The circadian clock regulates the diurnal levels of microbial short-chain fatty acids and their rhythmic effects on colon contractility in mice

(2018) Anneleen Segers et al.   Acta Physiologica

Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study

(2018) Martin Steen Mortensen et al.   BMC MICROBIOLOGY

Resilience of human gut microbial communities for the long stay with multiple dietary shifts

(2018) Hong Liu et al.   GUT

Long-term impact of oral vancomycin, ciprofloxacin and metronidazole on the gut microbiota in healthy humans

(2018) Bastiaan W Haak et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

The intestinal microbiota regulates body composition through NFIL3 and the circadian clock

(2017) Yuhao Wang et al.   SCIENCE

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease

(2016) Kenichiro Takahashi et al.   DIGESTION

A strategy for the targeted metabolomics analysis of 11 gut microbiota-host co-metabolites in rat serum, urine and feces by ultra high performance liquid chromatography–tandem mass spectrometry

(2016) Waner Hou et al.   JOURNAL OF CHROMATOGRAPHY A

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Antibiotic-Induced Changes in the Intestinal Microbiota and Disease

(2016) Simone Becattini et al.   TRENDS IN MOLECULAR MEDICINE

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

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

Gut biogeography of the bacterial microbiota

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry

(2011) Warwick B Dunn et al.   Nature Protocols

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Bacterial biogeography of the human digestive tract

(2011) Jennifer C. Stearns et al.   Scientific Reports

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine

(2009) Petra Louis et al.   FEMS MICROBIOLOGY LETTERS

Inhibition of histone-deacetylase activity by short-chain fatty acids and some polyphenol metabolites formed in the colon

(2008) Markus Waldecker et al.   JOURNAL OF NUTRITIONAL BIOCHEMISTRY