A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function

Comparative assessment of faecal microbial composition and metabonome of swine, farmers and human control

(2020) Shiang Chiet Tan et al.   Scientific Reports

Integrated Metabolomics and Proteomics Analysis Revealed Second Messenger System Disturbance in Hippocampus of Chronic Social Defeat Stress Rat

(2019) Li-Ning Yang et al.   Frontiers in Neuroscience

Fecal Microbiota and Its Correlation With Fatty Acids and Free Amino Acids Metabolism in Piglets After a Lactobacillus Strain Oral Administration

(2019) Dongyan Zhang et al.   Frontiers in Microbiology

Core Gut Bacteria Analysis of Healthy Mice

(2019) Jingjing Wang et al.   Frontiers in Microbiology

Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria

(2019) Xiaofan Wang et al.   Microbiome

Experimental H1N1pdm09 infection in pigs mimics human seasonal influenza infections

(2019) Theresa Schwaiger et al.   PLoS One

Longitudinal Analysis of the Microbiota Composition and Enterotypes of Pigs from Post-Weaning to Finishing

(2019) Mathilde Le Sciellour et al.   Microorganisms

Immune regulation by microbiome metabolites

(2018) Chang H. Kim   IMMUNOLOGY

Microbiome profiling of commercial pigs from farrow to finish

(2018) Brenda De Rodas et al.   JOURNAL OF ANIMAL SCIENCE

iPath3.0: interactive pathways explorer v3

(2018) Youssef Darzi et al.   NUCLEIC ACIDS RESEARCH

A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection

(2018) Claudia Wylezich et al.   Scientific Reports

Pitfalls in short-chain fatty acid research: A methodological review

(2018) Takashi Sakata   ANIMAL SCIENCE JOURNAL

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets

(2018) Ann-Sofie Riis Poulsen et al.   PLoS One

Gut microbiota functions: metabolism of nutrients and other food components

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

Sample preparation optimization in fecal metabolic profiling

(2017) Olga Deda et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Microbiome-Modulated Metabolites at the Interface of Host Immunity

(2017) Eran Blacher et al.   JOURNAL OF IMMUNOLOGY

Meta-analysis To Define a Core Microbiota in the Swine Gut

(2017) Devin B. Holman et al.   mSystems

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

(2016) Ara Koh et al.   CELL

Using the mouse to model human disease: increasing validity and reproducibility

(2016) Monica J. Justice et al.   Disease Models & Mechanisms

Challenges of metabolomics in human gut microbiota research

(2016) Kirill S. Smirnov et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The production of multi-transgenic pigs: update and perspectives for xenotransplantation

(2016) Heiner Niemann et al.   TRANSGENIC RESEARCH

Metabolomics of fecal samples: A practical consideration

(2016) Silke Matysik et al.   TRENDS IN FOOD SCIENCE & TECHNOLOGY

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

(2016) Anna Heintz-Buschart et al.   Nature Microbiology

Intestinal Microbiota and Microbial Metabolites Are Changed in a Pig Model Fed a High-Fat/Low-Fiber or a Low-Fat/High-Fiber Diet

(2016) Sonja N. Heinritz et al.   PLoS One

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

How informative is the mouse for human gut microbiota research?

(2015) T. L. A. Nguyen et al.   Disease Models & Mechanisms

Stability of energy metabolites-An often overlooked issue in metabolomics studies: A review

(2015) Andres Gil et al.   ELECTROPHORESIS

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Human Microbiota-Associated Swine: Current Progress and Future Opportunities

(2015) M. Wang et al.   ILAR JOURNAL

Remaining Mysteries of Molecular Biology: The Role of Polyamines in the Cell

(2015) Leonor Miller-Fleming et al.   JOURNAL OF MOLECULAR BIOLOGY

Wheat and barley differently affect porcine intestinal microbiota

(2015) Eva Weiss et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

A Metaproteomics Approach to Elucidate Host and Pathogen Protein Expression during Catheter-Associated Urinary Tract Infections (CAUTIs)

(2015) Christian Lassek et al.   MOLECULAR & CELLULAR PROTEOMICS

Catching the tip of the iceberg - Evaluation of sample preparation protocols for metaproteomic studies of the rumen microbiota

(2015) Simon Deusch et al.   PROTEOMICS

News in livestock research — use of Omics -technologies to study the microbiota in the gastrointestinal tract of farm animals

(2015) Simon Deusch et al.   Computational and Structural Biotechnology Journal

Impact of Antibiotics with Various Target Sites on the Metabolome of Staphylococcus aureus

(2014) Kirsten Dörries et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations

(2014) Torey Looft et al.   ISME Journal

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

A straightforward and efficient analytical pipeline for metaproteome characterization

(2014) Alessandro Tanca et al.   Microbiome

Effect of inclusion of lactulose and Lactobacillus plantarum on the intestinal environment and performance of piglets at weaning

(2013) A.A. Guerra-Ordaz et al.   ANIMAL FEED SCIENCE AND TECHNOLOGY

The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism

(2013) Gijs den Besten et al.   JOURNAL OF LIPID RESEARCH

Use of pigs as a potential model for research into dietary modulation of the human gut microbiota

(2013) Sonja N. Heinritz et al.   NUTRITION RESEARCH REVIEWS

A biomolecular isolation framework for eco-systems biology

(2012) Hugo Roume et al.   ISME Journal

Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis

(2012) David Berry et al.   ISME Journal

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Comparative Metaproteomics and Diversity Analysis of Human Intestinal Microbiota Testifies for Its Temporal Stability and Expression of Core Functions

(2012) Carolin A. Kolmeder et al.   PLoS One

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

(2012) Alison R. Erickson et al.   PLoS One

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

(2012) H. Teeling et al.   SCIENCE

The intestinal microbiome of the pig

(2012) Richard Isaacson et al.   ANIMAL HEALTH RESEARCH REVIEWS

Role of the Commensal Microbiota in Normal and Pathogenic Host Immune Responses

(2011) Dan R. Littman et al.   Cell Host & Microbe

The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: contribution of germ-free and gnotobiotic animal models of human diseases

(2011) Helena Tlaskalová-Hogenová et al.   Cellular & Molecular Immunology

Human nutrition, the gut microbiome and the immune system

(2011) Andrew L. Kau et al.   NATURE

Genetics and pathogenesis of inflammatory bowel disease

(2011) Bernard Khor et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

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

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

Metaproteome analysis of sewage sludge from membrane bioreactors

(2011) Ramona Kuhn et al.   PROTEOMICS

The pig: a model for human infectious diseases

(2011) François Meurens et al.   TRENDS IN MICROBIOLOGY

Longitudinal investigation of the age-related bacterial diversity in the feces of commercial pigs

(2011) Hyeun Bum Kim et al.   VETERINARY MICROBIOLOGY

An optimised sample preparation method for NMR-based faecal metabonomic analysis

(2010) Junfang Wu et al.   ANALYST

Polyamines regulate E-cadherin transcription through c-Myc modulating intestinal epithelial barrier function

(2009) Lan Liu et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

Metabolite analysis of human fecal water by gas chromatography/mass spectrometry with ethyl chloroformate derivatization

(2009) Xianfu Gao et al.   ANALYTICAL BIOCHEMISTRY

Effects of the insoluble and soluble dietary fibre on the physicochemical properties of digesta and the microbial activity in early weaned piglets

(2008) F. Molist et al.   ANIMAL FEED SCIENCE AND TECHNOLOGY

Changes in Gut Microbiota Control Metabolic Endotoxemia-Induced Inflammation in High-Fat Diet-Induced Obesity and Diabetes in Mice

(2008) P. D. Cani et al.   DIABETES

Microbial Influences in Inflammatory Bowel Diseases

(2008) R. Balfour Sartor   GASTROENTEROLOGY