Early-life establishment of the swine gut microbiome and impact on host phenotypes

Effect of viable Lactobacillus fermentum on the growth performance, nutrient digestibility and immunity of weaned pigs

(2016) H. Yu et al.   JOURNAL OF ANIMAL AND FEED SCIENCES

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

Rethinking “Enterotypes”

(2014) Dan Knights et al.   Cell Host & Microbe

Mucosa-Associated Bacterial Microbiome of the Gastrointestinal Tract of Weaned Pigs and Dynamics Linked to Dietary Calcium-Phosphorus

(2014) Evelyne Mann et al.   PLoS One

Early-Life Environmental Variation Affects Intestinal Microbiota and Immune Development in New-Born Piglets

(2014) Dirkjan Schokker et al.   PLoS One

Transfer of gut microbiota from lean and obese mice to antibiotic-treated mice

(2014) Merete Ellekilde et al.   Scientific Reports

Changes in the gut microbiota of cloned and non-cloned control pigs during development of obesity: gut microbiota during development of obesity in cloned pigs

(2013) Rebecca Pedersen et al.   BMC MICROBIOLOGY

Vertical mother-neonate transfer of maternal gut bacteria via breastfeeding

(2013) Ted Jost et al.   ENVIRONMENTAL MICROBIOLOGY

Profiling the gastrointestinal microbiota in response to Salmonella: Low versus high Salmonella shedding in the natural porcine host

(2013) Shawn M.D. Bearson et al.   INFECTION GENETICS AND EVOLUTION

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Nutritional Basis for Colonization Resistance by Human Commensal Escherichia coli Strains HS and Nissle 1917 against E. coli O157:H7 in the Mouse Intestine

(2013) Rosalie Maltby et al.   PLoS One

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

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

Metabolic niche of a prominent sulfate-reducing human gut bacterium

(2013) F. E. Rey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

(2013) Falk Hildebrand et al.   GENOME BIOLOGY

Impact of chicory inclusion in a cereal-based diet on digestibility, organ size and faecal microbiota in growing pigs

(2012) E. Ivarsson et al.   Animal

High-Throughput Sequence-Based Analysis of the Intestinal Microbiota of Weanling Pigs Fed Genetically Modified MON810 Maize Expressing Bacillus thuringiensis Cry1Ab (Bt Maize) for 31 Days

(2012) Stefan G. Buzoianu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

IgA synthesis: a form of functional immune adaptation extending beyond gut

(2012) Duncan B Sutherland et al.   CURRENT OPINION IN IMMUNOLOGY

Microbial Composition and In Vitro Fermentation Patterns of Human Milk Oligosaccharides and Prebiotics Differ between Formula-Fed and Sow-Reared Piglets

(2012) Min Li et al.   JOURNAL OF NUTRITION

In-feed antibiotic effects on the swine intestinal microbiome

(2012) T. Looft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin

(2012) H. B. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Host-Gut Microbiota Metabolic Interactions

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

Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans

(2011) Reiner Jumpertz et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems

(2011) Kim-Anh Lê Cao et al.   BMC BIOINFORMATICS

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

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

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Unravelling the effects of the environment and host genotype on the gut microbiome

(2011) Aymé Spor et al.   NATURE REVIEWS MICROBIOLOGY

Establishment of Normal Gut Microbiota Is Compromised under Excessive Hygiene Conditions

(2011) Bettina Schmidt et al.   PLoS One

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

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

(2011) Hyeun Bum Kim et al.   VETERINARY MICROBIOLOGY

Structural Determination and Daily Variations of Porcine Milk Oligosaccharides

(2010) Nannan Tao et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Gut Microbial Gene Expression in Mother-Fed and Formula-Fed Piglets

(2010) Valeriy Poroyko et al.   PLoS One

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

integrOmics: an R package to unravel relationships between two omics datasets

(2009) Kim-Anh Lê Cao et al.   BIOINFORMATICS

Sparse canonical methods for biological data integration: application to a cross-platform study

(2009) Kim-Anh Lê Cao et al.   BMC BIOINFORMATICS

Differences in transcriptomic profile and IgA repertoire between jejunal and ileal Peyer's patches

(2009) Benoît Levast et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity

(2009) Marie A. Hildebrandt et al.   GASTROENTEROLOGY

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

Effect of dietary protein level on growth performance, indicators of enteric health, and gastrointestinal microbial ecology of weaned pigs induced with postweaning colibacillosis1,2

(2009) F. O. Opapeju et al.   JOURNAL OF ANIMAL SCIENCE

Real-time PCR quantification of the predominant bacterial divisions in the distal gut of Meishan and Landrace pigs

(2008) Xiulan Guo et al.   ANAEROBE

Plant Cell Wall Breakdown by Anaerobic Microorganisms from the Mammalian Digestive Tract

(2008) Harry J. Flint et al.   Annals of the New York Academy of Sciences

The immediate environment during postnatal development has long-term impact on gut community structure in pigs

(2008) Claire L Thompson et al.   ISME Journal

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH