Associations between the gut microbiome and metabolome in early life

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages

(2019) Julie Schulthess et al.   IMMUNITY

Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study

(2019) Modupe O. Coker et al.   BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences

(2019) Himel Mallick et al.   Nature Communications

Disrupted Maturation of the Microbiota and Metabolome among Extremely Preterm Infants with Postnatal Growth Failure

(2019) Noelle E. Younge et al.   Scientific Reports

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

(2019) Kaitlyn Oliphant et al.   Microbiome

A Review and Tutorial of Machine Learning Methods for Microbiome Host Trait Prediction

(2019) Yi-Hui Zhou et al.   Frontiers in Genetics

Temporal development of the infant gut microbiome

(2019) Rebecca E. Moore et al.   Open Biology

Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem

(2019) Melissa A. E. Lawson et al.   ISME Journal

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

The fecal metabolome as a functional readout of the gut microbiome

(2018) Jonas Zierer et al.   NATURE GENETICS

Human Gut Microbiome: Function Matters

(2018) Anna Heintz-Buschart et al.   TRENDS IN MICROBIOLOGY

Human microbiota, blood group antigens, and disease

(2018) D. Rose Ewald et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Infant and Adult Gut Microbiome and Metabolome in Rural Bassa and Urban Settlers from Nigeria

(2018) Funmilola A. Ayeni et al.   Cell Reports

Urban Diets Linked to Gut Microbiome and Metabolome Alterations in Children: A Comparative Cross-Sectional Study in Thailand

(2018) Juma Kisuse et al.   Frontiers in Microbiology

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner

(2018) Sara N. Lundgren et al.   Microbiome

Function and functional redundancy in microbial systems

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

Temporal development of the gut microbiome in early childhood from the TEDDY study

(2018) Christopher J. Stewart et al.   NATURE

Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort

(2018) Maggie A. Stanislawski et al.   mBio

A Phylogeny-Regularized Sparse Regression Model for Predictive Modeling of Microbial Community Data

(2018) Jian Xiao et al.   Frontiers in Microbiology

Beneficial effects on host energy metabolism of short-chain fatty acids and vitamins produced by commensal and probiotic bacteria

(2017) Jean Guy LeBlanc et al.   Microbial Cell Factories

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

(2017) Christian Milani et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

First Foods and Gut Microbes

(2017) Martin F. Laursen et al.   Frontiers in Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort

(2017) Cian J. Hill et al.   Microbiome

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls

(2017) Christopher J. Stewart et al.   Microbiome

Bifidobacterial inulin-type fructan degradation capacity determines cross-feeding interactions between bifidobacteria and Faecalibacterium prausnitzii

(2016) Frédéric Moens et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Human gut microbes impact host serum metabolome and insulin sensitivity

(2016) Helle Krogh Pedersen et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Strain-level dissection of the contribution of the gut microbiome to human metabolic disease

(2016) Chenhong Zhang et al.   Genome Medicine

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

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

(2016) Audrey Rivière et al.   Frontiers in Microbiology

Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants

(2016) Juliette C. Madan et al.   JAMA Pediatrics

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

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

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

(2015) Aleksandar D. Kostic et al.   Cell Host & Microbe

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

Sparse canonical correlation analysis applied to -omics studies for integrative analysis and biomarker discovery

(2015) Dong-Sheng Cao et al.   JOURNAL OF CHEMOMETRICS

Sewage Reflects the Microbiomes of Human Populations

(2015) Ryan J. Newton et al.   mBio

Systems biology of host-microbe metabolomics

(2015) Almut Heinken et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

The Role of Microbial Amino Acid Metabolism in Host Metabolism

(2015) Evelien Neis et al.   Nutrients

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Precision High-Throughput Proton NMR Spectroscopy of Human Urine, Serum, and Plasma for Large-Scale Metabolic Phenotyping

(2014) Anthony C. Dona et al.   ANALYTICAL CHEMISTRY

The Intestinal Microbiome in Early Life: Health and Disease

(2014) Marie-Claire Arrieta et al.   Frontiers in Immunology

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects

(2014) Susan M Huse et al.   Microbiome

Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids

(2013) Gijs den Besten et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

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

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

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

(2013) Ian H McHardy et al.   Microbiome

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

Bacteria, Colonic Fermentation, and Gastrointestinal Health

(2012) George T. Macfarlane et al.   JOURNAL OF AOAC INTERNATIONAL

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Host-Gut Microbiota Metabolic Interactions

(2012) J. K. Nicholson et al.   SCIENCE

Microbiota-Targeted Therapies: An Ecological Perspective

(2012) K. P. Lemon et al.   Science Translational Medicine

Bacteroides in the Infant Gut Consume Milk Oligosaccharides via Mucus-Utilization Pathways

(2011) Angela Marcobal et al.   Cell Host & Microbe

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

Amino acid metabolism in intestinal bacteria: links between gut ecology and host health

(2010) Zhao-Lai Dai   Frontiers in Bioscience-Landmark

Sparse partial least squares regression for simultaneous dimension reduction and variable selection

(2010) Hyonho Chun et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Succession of microbial consortia in the developing infant gut microbiome

(2010) J. E. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Butyrate Enhances the Intestinal Barrier by Facilitating Tight Junction Assembly via Activation of AMP-Activated Protein Kinase in Caco-2 Cell Monolayers

(2009) Luying Peng et al.   JOURNAL OF NUTRITION

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Symbiotic gut microbes modulate human metabolic phenotypes

(2008) M. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA