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

Understanding the gut microbiome of dairy calves: Opportunities to improve early-life gut health 1

(2017) Nilusha Malmuthuge et al.   JOURNAL OF DAIRY SCIENCE

Early Postnatal Diets Affect the Bioregional Small Intestine Microbiome and Ileal Metabolome in Neonatal Pigs

(2017) Brian D Piccolo et al.   JOURNAL OF NUTRITION

Understanding host-microbial interactions in rumen: searching the best opportunity for microbiota manipulation

(2017) Nilusha Malmuthuge et al.   Journal of Animal Science and Biotechnology

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

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

Unique Bacteria Community Composition and Co-occurrence in the Milk of Different Ruminants

(2017) Zhipeng Li et al.   Scientific Reports

Formula diet alters small intestine morphology, microbial abundance and reduces VE-cadherin and IL-10 expression in neonatal porcine model

(2016) Laxmi Yeruva et al.   BMC GASTROENTEROLOGY

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

Microbial community profiles of the jejunum from steers differing in feed efficiency1,2,3

(2016) P. R. Myer et al.   JOURNAL OF ANIMAL SCIENCE

Changes in the intestinal bacterial community, short-chain fatty acid profile, and intestinal development of preweaned Holstein calves. 1. Effects of prebiotic supplementation depend on site and age

(2016) J.J. Castro et al.   JOURNAL OF DAIRY SCIENCE

Changes in the intestinal bacterial community, short-chain fatty acid profile, and intestinal development of preweaned Holstein calves. 2. Effects of gastrointestinal site and age 1

(2016) J.J. Castro et al.   JOURNAL OF DAIRY SCIENCE

Changes in the rumen microbiome and metabolites reveal the effect of host genetics on hybrid crosses

(2016) Zhipeng Li et al.   Environmental Microbiology Reports

Composition of Ileal Bacterial Community in Grazing Goats Varies across Non-rumination, Transition and Rumination Stages of Life

(2016) Jinzhen Jiao et al.   Frontiers in Microbiology

Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats

(2015) Jinzhen Jiao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Rumen development process in goats as affected by supplemental feeding v. grazing: age-related anatomic development, functional achievement and microbial colonisation

(2015) Jinzhen Jiao et al.   BRITISH JOURNAL OF NUTRITION

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

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

The composition of the zebrafish intestinal microbial community varies across development

(2015) W Zac Stephens et al.   ISME Journal

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

MetaboAnalyst 3.0—making metabolomics more meaningful

(2015) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

Response of the Rumen Microbiota of Sika Deer (Cervus nippon) Fed Different Concentrations of Tannin Rich Plants

(2015) Zhipeng Li et al.   PLoS One

The infant microbiome development: mom matters

(2015) Noel T. Mueller et al.   TRENDS IN MOLECULAR MEDICINE

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

(2015) Marta Wlodarska et al.   Scientific Reports

Manipulating rumen microbiome and fermentation through interventions during early life: a review

(2015) David R. Yáñez-Ruiz et al.   Frontiers in Microbiology

Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations

(2015) Paul J. Weimer   Frontiers in Microbiology

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

Recent advances in adherence and invasion of pathogenic Escherichia coli

(2014) Anjana Kalita et al.   CURRENT OPINION IN INFECTIOUS DISEASES

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production

(2014) Gary D Wu et al.   GUT

Bacterial Community Composition and Fermentation Patterns in the Rumen of Sika Deer (Cervus nippon) Fed Three Different Diets

(2014) Zhipeng Li et al.   MICROBIAL ECOLOGY

Agriculture: Steps to sustainable livestock

(2014) Mark C. Eisler et al.   NATURE

Bacteria and Methanogens Differ along the Gastrointestinal Tract of Chinese Roe Deer (Capreolus pygargus)

(2014) Zhipeng Li et al.   PLoS One

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

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

Pyrosequencing reveals diverse fecal microbiota in Simmental calves during early development

(2014) Daniela Klein-Jöbstl et al.   Frontiers in Microbiology

Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China

(2013) Zhi Li et al.   BMC MICROBIOLOGY

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

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Fecal Microbial Diversity in Pre-Weaned Dairy Calves as Described by Pyrosequencing of Metagenomic 16S rDNA. Associations of Faecalibacterium Species with Health and Growth

(2013) Georgios Oikonomou et al.   PLoS One

The immune modifying effects of amino acids on gut-associated lymphoid tissue

(2013) Megan R Ruth et al.   Journal of Animal Science and Biotechnology

Development of colonic microflora as assessed by pyrosequencing in dairy calves fed waste milk

(2012) T.S. Edrington et al.   JOURNAL OF DAIRY SCIENCE

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

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

Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice

(2012) Sahar El Aidy et al.   Mucosal Immunology

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools

(2011) Robert W. Li et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

(2011) Filipa Godoy-Vitorino et al.   ISME Journal

Host specificity of the ruminal bacterial community in the dairy cow following near-total exchange of ruminal contents1

(2010) P.J. Weimer et al.   JOURNAL OF DAIRY SCIENCE

Metagenomic analysis of the uterine bacterial microbiota in healthy and metritic postpartum dairy cows

(2010) T.M.A. Santos 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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Sulfur amino acid deficiency upregulates intestinal methionine cycle activity and suppresses epithelial growth in neonatal pigs

(2009) Caroline Bauchart-Thevret et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

FiehnLib: Mass Spectral and Retention Index Libraries for Metabolomics Based on Quadrupole and Time-of-Flight Gas Chromatography/Mass Spectrometry

(2009) Tobias Kind et al.   ANALYTICAL CHEMISTRY

Bacteria Associated with Immunoregulatory Cells in Mice

(2009) L. L. Presley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Calf Nutrition from Birth to Breeding

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