Changes in the host transcriptome and microbial metatranscriptome of the ileum of dairy calves subjected to artificial dosing of exogenous rumen contents

Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow

(2019) Wenli Li et al.   Scientific Reports

CRISPR screening using an expanded toolkit of autophagy reporters identifies TMEM41B as a novel autophagy factor

(2019) Christopher J. Shoemaker et al.   PLOS BIOLOGY

Bacterial Community Dynamics across the Gastrointestinal Tracts of Dairy Calves during Preweaning Development

(2018) Juliana Dias et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effects of alpha-(1,2)-fucosyltransferase genotype variants on plasma metabolome, immune responses and gastrointestinal bacterial enumeration of pigs pre- and post-weaning

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

The composition of the perinatal intestinal microbiota in cattle

(2018) Mohammad Jaber Alipour et al.   Scientific Reports

Comparative study of rumen fermentation and microbial community differences between water buffalo and Jersey cows under similar feeding conditions

(2017) Muhammad Wasim Iqbal et al.   JOURNAL OF APPLIED ANIMAL RESEARCH

Baicalin promotes the bacteriostatic activity of lysozyme on S. aureus in mammary glands and neutrophilic granulocytes in mice

(2017) Xuejiao Gao et al.   Oncotarget

Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation

(2017) Kimberly A. Dill-McFarland et al.   Scientific Reports

Transcriptome analysis reveals regional and temporal differences in mucosal immune system development in the small intestine of neonatal calves

(2016) Guanxiang Liang et al.   BMC GENOMICS

Invited review: Transitioning from milk to solid feed in dairy heifers

(2016) M.A. Khan et al.   JOURNAL OF DAIRY SCIENCE

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Correction for Jabed et al., Targeted microRNA expression in dairy cattle directs production of β-lactoglobulin-free, high-casein milk

(2016)   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The maternal microbiota drives early postnatal innate immune development

(2016) M. Gomez de Aguero et al.   SCIENCE

Development of Ruminal and Fecal Microbiomes Are Affected by Weaning But Not Weaning Strategy in Dairy Calves

(2016) Sarah J. Meale et al.   Frontiers in Microbiology

Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency

(2015) Kelsea A. Jewell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fatty Acid-binding Proteins (FABPs) Are Intracellular Carriers for Δ9-Tetrahydrocannabinol (THC) and Cannabidiol (CBD)

(2015) Matthew W. Elmes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

(2015) Gemma Henderson et al.   Scientific Reports

Erratum to: Type 2 immunity-dependent reduction of segmented filamentous bacteria in mice infected with the helminthic parasite Nippostrongylus brasiliensis

(2015) W. Florian Fricke et al.   Microbiome

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

Effects of inoculation with rumen fluid on nutrient digestibility, growth performance and rumen fermentation of early weaned lambs

(2014) R.Z. Zhong et al.   Livestock Science

Uracil-DNA glycosylases-Structural and functional perspectives on an essential family of DNA repair enzymes

(2014) N. Schormann et al.   PROTEIN SCIENCE

An Antimethanogenic Nutritional Intervention in Early Life of Ruminants Modifies Ruminal Colonization by Archaea

(2014) Leticia Abecia et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

FABP5 deficiency enhances susceptibility to H1N1 influenza A virus-induced lung inflammation

(2013) Fabienne Gally et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

The use of direct-fed microbials for mitigation of ruminant methane emissions: a review

(2013) J. Jeyanathan et al.   Animal

Tight junction proteins: From barrier to tumorigenesis

(2013) E. Aaron Runkle et al.   CANCER LETTERS

Neonatal Immune Adaptation of the Gut and Its Role during Infections

(2013) Emilie Tourneur et al.   Clinical & Developmental Immunology

Glucocorticoids and microbiota regulate ontogeny of intestinal fucosyltransferase 2 requisite for gut homeostasis

(2013) N. N. Nanthakumar et al.   GLYCOBIOLOGY

Exploring the bovine rumen bacterial community from birth to adulthood

(2013) Elie Jami et al.   ISME Journal

Nutritional intervention in early life to manipulate rumen microbial colonization and methane output by kid goats postweaning1

(2013) L. Abecia et al.   JOURNAL OF ANIMAL SCIENCE

Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential

(2013) M. Rey et al.   JOURNAL OF APPLIED MICROBIOLOGY

Effect of calf starter feeding on gut microbial diversity and expression of genes involved in host immune responses and tight junctions in dairy calves during weaning transition

(2013) Nilusha Malmuthuge et al.   JOURNAL OF DAIRY SCIENCE

Immunosuppressive CD71+ erythroid cells compromise neonatal host defence against infection

(2013) Shokrollah Elahi et al.   NATURE

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

Knockdown of Myostatin Expression by RNAi Enhances Muscle Growth in Transgenic Sheep

(2013) Shengwei Hu et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Dynamic properties of the tight junction barrier

(2012) Christopher R. Weber   Annals of the New York Academy of Sciences

DAVID-WS: a stateful web service to facilitate gene/protein list analysis

(2012) X. Jiao et al.   BIOINFORMATICS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota

(2012) Hachung Chung et al.   CELL

Fatty acid-binding protein 4 (FABP4) and FABP5 modulate cytokine production in the mouse thymic epithelial cells

(2012) Yasuhiro Adachi et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Preweaning milk replacer intake and effects on long-term productivity of dairy calves

(2012) F. Soberon et al.   JOURNAL OF DAIRY SCIENCE

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Regional and age dependent changes in gene expression of Toll-like receptors and key antimicrobial defence molecules throughout the gastrointestinal tract of dairy calves

(2012) Nilusha Malmuthuge et al.   VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY

Development and genetic influence of the rectal bacterial flora of newborn calves

(2012) M. Mayer et al.   VETERINARY MICROBIOLOGY

Age-related changes in the distribution and frequency of myeloid and T cell populations in the small intestine of calves

(2011) Patrick N. Fries et al.   CELLULAR IMMUNOLOGY

Intestinal Bacterial Colonization Induces Mutualistic Regulatory T Cell Responses

(2011) Markus B. Geuking et al.   IMMUNITY

Epithelial barrier: an interface for the cross-communication between gut flora and immune system

(2011) Yoshiyuki Goto et al.   IMMUNOLOGICAL REVIEWS

Enterococci as probiotics and their implications in food safety

(2011) Charles M.A.P. Franz et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

RUMINANT NUTRITION SYMPOSIUM: OPTIMIZING PERFORMANCE OF THE OFFSPRING: Nourishing and managing the dam and postnatal calf for optimal lactation, reproduction, and immunity1,2

(2011) A. Bach   JOURNAL OF ANIMAL SCIENCE

Colon-specific delivery of a probiotic-derived soluble protein ameliorates intestinal inflammation in mice through an EGFR-dependent mechanism

(2011) Fang Yan et al.   JOURNAL OF CLINICAL INVESTIGATION

Production of transgenic calves expressing an shRNA targeting myostatin

(2011) K. Tessanne et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

The Toll-Like Receptor 2 Pathway Establishes Colonization by a Commensal of the Human Microbiota

(2011) J. L. Round et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Increased expression of epidermal fatty acid-binding protein by alveolar macrophages during acute rejection of rat lungs

(2010) JULIA HOLLER et al.   APMIS

The persistence of bacterial and methanogenic archaeal communities residing in the rumen of young lambs

(2010) David R. Yáñez-Ruiz et al.   FEMS MICROBIOLOGY ECOLOGY

Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease

(2010) Dermot P.B. McGovern et al.   HUMAN MOLECULAR GENETICS

Peptidoglycan Deacetylation in Helicobacter pylori Contributes to Bacterial Survival by Mitigating Host Immune Responses

(2010) G. Wang et al.   INFECTION AND IMMUNITY

Adipocyte Fatty Acid-binding Protein Modulates Inflammatory Responses in Macrophages through a Positive Feedback Loop Involving c-Jun NH2-terminal Kinases and Activator Protein-1

(2010) Xiaoyan Hui et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lysozymes in the animal kingdom

(2010) Lien Callewaert et al.   JOURNAL OF BIOSCIENCES

A prospective study of calf factors affecting first-lactation and lifetime milk production and age of cows when removed from the herd1

(2010) A.J. Heinrichs et al.   JOURNAL OF DAIRY SCIENCE

rRNA-based analysis to monitor succession of faecal bacterial communities in Holstein calves

(2010) Y. Uyeno et al.   LETTERS IN APPLIED MICROBIOLOGY

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The Glycobiome of the Rumen Bacterium Butyrivibrio proteoclasticus B316T Highlights Adaptation to a Polysaccharide-Rich Environment

(2010) William J. Kelly et al.   PLoS One

Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota

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

Regulation of Cellular Metabolism by Protein Lysine Acetylation

(2010) S. Zhao et al.   SCIENCE

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

Influence of early gut microbiota on the maturation of childhood mucosal and systemic immune responses

(2009) Y. M. Sjögren et al.   CLINICAL AND EXPERIMENTAL ALLERGY

Ecological Role of Lactobacilli in the Gastrointestinal Tract: Implications for Fundamental and Biomedical Research

(2008) J. Walter   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Changes in the expression of claudins in active ulcerative colitis

(2008) Tadayuki Oshima et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis

(2008) Harry J. Flint et al.   NATURE REVIEWS MICROBIOLOGY

Calf Nutrition from Birth to Breeding

(2008) James K. Drackley   VETERINARY CLINICS OF NORTH AMERICA-FOOD ANIMAL PRACTICE