The neuroactive potential of the human gut microbiota in quality of life and depression

Cerebrospinal fluid biomarkers of central dopamine deficiency predict Parkinson's disease

(2018) David S. Goldstein et al.   PARKINSONISM & RELATED DISORDERS

Evidence for PMAT- and OCT-like biogenic amine transporters in a probiotic strain of Lactobacillus: Implications for interkingdom communication within the microbiota-gut-brain axis

(2018) Mark Lyte et al.   PLoS One

Richness and ecosystem development across faecal snapshots of the gut microbiota

(2018) Gwen Falony et al.   Nature Microbiology

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

Differential effects of psychotropic drugs on microbiome composition and gastrointestinal function

(2018) Sofia Cussotto et al.   PSYCHOPHARMACOLOGY

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

(2017) J. R. Bedarf et al.   Genome Medicine

Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data

(2016) Gregory B. Gloor et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Transferring the blues: Depression-associated gut microbiota induces neurobehavioural changes in the rat

(2016) John R. Kelly et al.   JOURNAL OF PSYCHIATRIC RESEARCH

Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism

(2016) P Zheng et al.   MOLECULAR PSYCHIATRY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Gut microbes in correlation with mood: case study in a closed experimental human life support system

(2016) L. Li et al.   NEUROGASTROENTEROLOGY AND MOTILITY

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

The Neuro-endocrinological Role of Microbial Glutamate and GABA Signaling

(2016) Roberto Mazzoli et al.   Frontiers in Microbiology

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

(2016) Audrey Rivière et al.   Frontiers in Microbiology

Brief Report:Dialisteras a Microbial Marker of Disease Activity in Spondyloarthritis

(2016) Raul Y. Tito et al.   Arthritis & Rheumatology

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

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

A novel biomarker panel for irritable bowel syndrome and the application in the general population

(2016) Zlatan Mujagic et al.   Scientific Reports

Serotonin, tryptophan metabolism and the brain-gut-microbiome axis

(2015) S.M. O’Mahony et al.   BEHAVIOURAL BRAIN RESEARCH

Altered fecal microbiota composition in patients with major depressive disorder

(2015) Haiyin Jiang et al.   BRAIN BEHAVIOR AND IMMUNITY

Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis

(2015) Jessica M. Yano et al.   CELL

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics

(2015) Ettje F Tigchelaar et al.   BMJ Open

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

The gut microbiota, bacterial metabolites and colorectal cancer

(2014) Petra Louis et al.   NATURE REVIEWS MICROBIOLOGY

Correlation between the human fecal microbiota and depression

(2014) A. Naseribafrouei et al.   NEUROGASTROENTEROLOGY AND MOTILITY

The gut microbiota influences blood-brain barrier permeability in mice

(2014) V. Braniste et al.   Science Translational Medicine

LotuS: an efficient and user-friendly OTU processing pipeline

(2014) Falk Hildebrand et al.   Microbiome

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Psychobiotics: A Novel Class of Psychotropic

(2013) Timothy G. Dinan et al.   BIOLOGICAL PSYCHIATRY

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Functional γ-Aminobutyrate Shunt in Listeria monocytogenes: Role in Acid Tolerance and Succinate Biosynthesis

(2012) Conor Feehily et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties

(2012) Feixiong Cheng et al.   Journal of Chemical Information and Modeling

Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour

(2012) John F. Cryan et al.   NATURE REVIEWS NEUROSCIENCE

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence

(2009) Teresa Nogueira et al.   CURRENT BIOLOGY

Neuroimmune aspects of food intake

(2009) John Bienenstock et al.   INTERNATIONAL DAIRY JOURNAL