Integrated multi-omics of the gastrointestinal microbiome and ruminant host reveals metabolic adaptation underlying early life development

Defining Fatty Acid Changes Linked to Rumen Development, Weaning and Growth in Holstein-Friesian Heifers

(2022) Emma N. Taylor et al.   Metabolites

Host genetics exerts lifelong effects upon hindgut microbiota and its association with bovine growth and immunity

(2021) Peixin Fan et al.   ISME Journal

Transcriptomic analysis reveals the molecular mechanisms of rumen wall morphological and functional development induced by different solid diet introduction in a lamb model

(2021) Daming Sun et al.   Journal of Animal Science and Biotechnology

Murine deficiency of peroxisomal l-bifunctional protein (EHHADH) causes medium-chain 3-hydroxydicarboxylic aciduria and perturbs hepatic cholesterol homeostasis

(2021) Pablo Ranea-Robles et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants

(2021) Fei Xie et al.   Microbiome

Epithelial argininosuccinate synthetase is dispensable for intestinal regeneration and tumorigenesis

(2021) Jonathan H. M. van der Meer et al.   Cell Death & Disease

Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics

(2020) Ori Furman et al.   Nature Communications

The Uniqueness of Tryptophan in Biology: Properties, Metabolism, Interactions and Localization in Proteins

(2020) Sailen Barik   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Taxonomic and functional composition of the small intestinal microbiome in neonatal calves provide a framework for understanding early life gut health

(2019) Nilusha Malmuthuge et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model

(2019) Limei Lin et al.   Microbiome

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Maternal Vertical Transmission Affecting Early-life Microbiota Development

(2019) Shaopu Wang et al.   TRENDS IN MICROBIOLOGY

Gadd45β promotes regeneration after injury through TGFβ-dependent restitution in experimental colitis

(2019) Jung Hwan Hwang et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Transcriptome Analysis Reveals That Alfalfa Promotes Rumen Development Through Enhanced Metabolic Processes and Calcium Transduction in Hu Lambs

(2019) Bin Yang et al.   Frontiers in Genetics

HMMER web server: 2018 update

(2018) Simon C Potter et al.   NUCLEIC ACIDS RESEARCH

Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract

(2018) Carl J. Yeoman et al.   Scientific Reports

The Development of Microbiota and Metabolome in Small Intestine of Sika Deer (Cervus nippon) from Birth to Weaning

(2018) Zhipeng Li et al.   Frontiers in Microbiology

Mitochondrial Fatty Acid Oxidation Disorders Associated with Short-Chain Enoyl-CoA Hydratase (ECHS1) Deficiency

(2018) Alice Sharpe et al.   Cells

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

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

Effect of age on nutritional properties of Iberian wild red deer meat

(2018) José M. Lorenzo et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Where less may be more: how the rare biosphere pulls ecosystems strings

(2017) Alexandre Jousset et al.   ISME Journal

The nitric oxide synthase 2 pathway is targeted by both pro- and anti-inflammatory treatments in the immature human intestine

(2017) Emanuela Ferretti et al.   NITRIC OXIDE-BIOLOGY AND CHEMISTRY

Emerging Roles for the Lysosome in Lipid Metabolism

(2017) Ashley M. Thelen et al.   TRENDS IN CELL BIOLOGY

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

Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants

(2016) Sheerli Kruger Ben Shabat et al.   ISME Journal

A branched-chain amino acid metabolite drives vascular fatty acid transport and causes insulin resistance

(2016) Cholsoon Jang et al.   NATURE MEDICINE

Hydroxycinnamic acid derivatives: a potential class of natural compounds for the management of lipid metabolism and obesity

(2016) Md Ashraful Alam et al.   Nutrition & Metabolism

Oscillospira : a Central, Enigmatic Component of the Human Gut Microbiota

(2016) Tom Konikoff et al.   TRENDS IN MICROBIOLOGY

edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test: Fig. 1.

(2015) Emmanuel Dimont et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

MetaboAnalyst 3.0—making metabolomics more meaningful

(2015) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

Nitric oxide synthase in innate and adaptive immunity: an update

(2015) Christian Bogdan   TRENDS IN IMMUNOLOGY

Phytonutrient diet supplementation promotes beneficial Clostridia species and intestinal mucus secretion resulting in protection against enteric infection

(2015) Marta Wlodarska et al.   Scientific Reports

Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves

(2014) Nilusha Malmuthuge et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Quality attributes and composition of meat from red deer (Cervus elaphus), fallow deer (Dama dama) and Aberdeen Angus and Holstein cattle (Bos taurus)

(2014) Daniel Bureš et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

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

Breast milk fatty acid profile in relation to infant growth and body composition: results from the INFAT study

(2013) Daniela Much et al.   PEDIATRIC RESEARCH

Establishment of ruminal enzyme activities and fermentation capacity in dairy calves from birth through weaning

(2012) M. Rey et al.   JOURNAL OF DAIRY SCIENCE

Dietary Triacylglycerol Structure and Its Role in Infant Nutrition

(2012) Sheila M. Innis   Advances in Nutrition

BCL2A1: the underdog in the BCL2 family

(2011) M Vogler   CELL DEATH AND DIFFERENTIATION

Autophagy in the Cellular Energetic Balance

(2011) Rajat Singh et al.   Cell Metabolism

Phenolic Acids Are in Vivo Atheroprotective Compounds Appearing in the Serum of Rats after Blueberry Consumption

(2011) Chenghui Xie et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Human HMGCS2 Regulates Mitochondrial Fatty Acid Oxidation andFGF21Expression in HepG2 Cell Line

(2011) Anna Vilà-Brau et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

The effects of dietary consumption of plants secondary compounds on small ruminants’ products quality

(2011) Valentina Vasta et al.   SMALL RUMINANT RESEARCH

Leucine and α-Ketoisocaproic Acid, but Not Norleucine, Stimulate Skeletal Muscle Protein Synthesis in Neonatal Pigs

(2010) Jeffery Escobar et al.   JOURNAL OF NUTRITION

Comparative Genome Analysis of Prevotella ruminicola and Prevotella bryantii: Insights into Their Environmental Niche

(2010) Janaki Purushe et al.   MICROBIAL ECOLOGY

The serum fatty acids myristic acid and linoleic acid are better predictors of serum cholesterol concentrations when measured as molecular percentages rather than as absolute concentrations

(2009) Kathryn E Bradbury et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Complement and its role in innate and adaptive immune responses

(2009) Jason R Dunkelberger et al.   CELL RESEARCH

Role for LAMP-2 in endosomal cholesterol transport

(2009) Alexander Schneede et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Acetyl-Coenzyme A acyltransferase 2 attenuates the apoptotic effects of BNIP3 in two human cell lines

(2008) Wei Cao et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH