The bovine milk microbiota: insights and perspectives from -omics studies

Evaluation of milk cathelicidin for detection of dairy sheep mastitis

(2016) M.F. Addis et al.   JOURNAL OF DAIRY SCIENCE

Bovine Teat Microbiome Analysis Revealed Reduced Alpha Diversity and Significant Changes in Taxonomic Profiles in Quarters with a History of Mastitis

(2016) Hélène Falentin et al.   Frontiers in Microbiology

Ingestion of Milk Containing Very Low Concentration of Antimicrobials: Longitudinal Effect on Fecal Microbiota Composition in Preweaned Calves

(2016) Richard Van Vleck Pereira et al.   PLoS One

Trophoblast-microbiome interaction: a new paradigm on immune regulation

(2015) Gil Mor et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

The major acute phase proteins of bovine milk in a commercial dairy herd

(2015) Funmilola Clara Thomas et al.   BMC Veterinary Research

Intestinal Microbiota Development in Preterm Neonates and Effect of Perinatal Antibiotics

(2015) Silvia Arboleya et al.   JOURNAL OF PEDIATRICS

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota

(2015) Weili Xiong et al.   PROTEOMICS

Transfer of intestinal bacterial components to mammary secretions in the cow

(2015) Wayne Young et al.   PeerJ

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

Systems-based approaches to unravel multi-species microbial community functioning

(2015) Florence Abram   Computational and Structural Biotechnology Journal

Metatranscriptomic Analysis of Arctic Peat Soil Microbiota

(2014) Alexander T. Tveit et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences

(2014) Laura M. Cox et al.   CELL

Antibiotics and the gut microbiota

(2014) Sheetal R. Modi et al.   JOURNAL OF CLINICAL INVESTIGATION

Treatments of clinical mastitis occurring in cows on 51 large dairy herds in Wisconsin

(2014) L. Oliveira et al.   JOURNAL OF DAIRY SCIENCE

Early Empiric Antibiotic Use in Preterm Infants Is Associated with Lower Bacterial Diversity and Higher Relative Abundance of Enterobacter

(2014) Corryn Greenwood et al.   JOURNAL OF PEDIATRICS

Characterization of bacterial community of raw milk from dairy cows during subacute ruminal acidosis challenge by high-throughput sequencing

(2014) Ruiyang Zhang et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Microbiota of Cow’s Milk; Distinguishing Healthy, Sub-Clinically and Clinically Diseased Quarters

(2014) Georgios Oikonomou et al.   PLoS One

Novel High-Molecular Weight Fucosylated Milk Oligosaccharides Identified in Dairy Streams

(2014) Raj Mehra et al.   PLoS One

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Symbiosis, dysbiosis, and rebiosis-The value of metaproteomics in human microbiome monitoring

(2014) Lei Mao et al.   PROTEOMICS

Selection of antibiotic resistance at very low antibiotic concentrations

(2014) Linus Sandegren   UPSALA JOURNAL OF MEDICAL SCIENCES

The Origin of Human Milk Bacteria: Is There a Bacterial Entero-Mammary Pathway during Late Pregnancy and Lactation?

(2014) Juan M. Rodríguez   Advances in Nutrition

An introduction to the analysis of shotgun metagenomic data

(2014) Thomas J. Sharpton   Frontiers in Plant Science

A straightforward and efficient analytical pipeline for metaproteome characterization

(2014) Alessandro Tanca et al.   Microbiome

Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities

(2013) Robert L. Hettich et al.   ANALYTICAL CHEMISTRY

Antibiotic Administration Routes Significantly Influence the Levels of Antibiotic Resistance in Gut Microbiota

(2013) Lu Zhang et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Recent Advances in Studies on Milk Oligosaccharides of Cows and Other Domestic Farm Animals

(2013) Tadasu URASHIMA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Vertical mother-neonate transfer of maternal gut bacteria via breastfeeding

(2013) Ted Jost et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Annotation and structural elucidation of bovine milk oligosaccharides and determination of novel fucosylated structures

(2013) Danielle L Aldredge et al.   GLYCOBIOLOGY

Production and Release of Antimicrobial and Immune Defense Proteins by Mammary Epithelial Cells following Streptococcus uberis Infection of Sheep

(2013) Maria Filippa Addis et al.   INFECTION AND IMMUNITY

Exploring the bovine rumen bacterial community from birth to adulthood

(2013) Elie Jami et al.   ISME Journal

Metaproteomics of our microbiome — Developing insight in function and activity in man and model systems

(2013) Carolin A. Kolmeder et al.   Journal of Proteomics

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Bacterial Community Profiling of Milk Samples as a Means to Understand Culture-Negative Bovine Clinical Mastitis

(2013) Joanna S. Kuehn et al.   PLoS One

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

A New Method for Extracting Skin Microbes Allows Metagenomic Analysis of Whole-Deep Skin

(2013) Marc Garcia-Garcerà et al.   PLoS One

Evaluating the Impact of Different Sequence Databases on Metaproteome Analysis: Insights from a Lab-Assembled Microbial Mixture

(2013) Alessandro Tanca et al.   PLoS One

The human mycobiome in health and disease

(2013) Lijia Cui et al.   Genome Medicine

The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery

(2012) Raul Cabrera-Rubio et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Characterization of Lactobacillus salivarius CECT 5713, a strain isolated from human milk: from genotype to phenotype

(2012) Susana Langa et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

‘Omics’ of the mammalian gut – new insights into function

(2012) Regina Lamendella et al.   CURRENT OPINION IN BIOTECHNOLOGY

Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities

(2012) Robert L. Hettich et al.   CURRENT OPINION IN MICROBIOLOGY

Fluxomics - connecting ‘omics analysis and phenotypes

(2012) Gal Winter et al.   ENVIRONMENTAL MICROBIOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Feeding untreated and pasteurized waste milk and bulk milk to calves: effects on calf performance, health status and antibiotic resistance of faecal bacteria

(2012) V. Aust et al.   JOURNAL OF ANIMAL PHYSIOLOGY AND ANIMAL NUTRITION

Milk microbiome signatures of subclinical mastitis-affected cattle analysed by shotgun sequencing

(2012) V.D. Bhatt et al.   JOURNAL OF APPLIED MICROBIOLOGY

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

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

Behavioral changes in dairy cows with mastitis

(2012) C. Medrano-Galarza et al.   JOURNAL OF DAIRY SCIENCE

Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform

(2012) Andrew S. Whiteley et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Acute phase proteins in ruminants

(2012) F. Ceciliani et al.   Journal of Proteomics

Searching for a needle in a stack of needles: challenges in metaproteomics data analysis

(2012) Thilo Muth et al.   Molecular BioSystems

Antibiotics in early life alter the murine colonic microbiome and adiposity

(2012) Ilseung Cho et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Microbial contact during pregnancy, intestinal colonization and human disease

(2012) Samuli Rautava et al.   Nature Reviews Gastroenterology & Hepatology

Maternal weight and excessive weight gain during pregnancy modify the immunomodulatory potential of breast milk

(2012) Maria Carmen Collado et al.   PEDIATRIC RESEARCH

The human milk microbiota: Origin and potential roles in health and disease

(2012) Leónides Fernández et al.   PHARMACOLOGICAL RESEARCH

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

(2012)   PLoS One

Microbial Diversity of Bovine Mastitic Milk as Described by Pyrosequencing of Metagenomic 16s rDNA

(2012) Georgios Oikonomou et al.   PLoS One

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

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

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Tackling the Microbiome

(2012) L. Hood   SCIENCE

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

Bovine Milk as a Source of Functional Oligosaccharides for Improving Human Health

(2012) Angela M. Zivkovic et al.   Advances in Nutrition

Human milk: a source of more life than we imagine

(2012) P.V. Jeurink et al.   Beneficial Microbes

Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing

(2012) Nathan L. Yozwiak et al.   PLoS Neglected Tropical Diseases

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Host-defence-related proteins in cows’ milk

(2011) T. T. Wheeler et al.   Animal

Transmission of Intestinal Bifidobacterium longum subsp.longumStrains from Mother to Infant, Determined by Multilocus Sequencing Typing and Amplified Fragment Length Polymorphism

(2011) Hiroshi Makino et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Microbial Metabolomics

(2011) Jane Tang   CURRENT GENOMICS

Metagenomics and the protein universe

(2011) Adam Godzik   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Intestinal Bacterial Colonization Induces Mutualistic Regulatory T Cell Responses

(2011) Markus B. Geuking et al.   IMMUNITY

Proteomics and Pathway Analyses of the Milk Fat Globule in Sheep Naturally Infected by Mycoplasma agalactiae Provide Indications of theIn VivoResponse of the Mammary Epithelium to Bacterial Infection

(2011) Maria Filippa Addis et al.   INFECTION AND IMMUNITY

Molecular approaches to analysing the microbial composition of raw milk and raw milk cheese

(2011) Lisa Quigley et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

The fate of indigenous microbiota, starter cultures, Escherichia coli, Listeria innocua and Staphylococcus aureus in Danish raw milk and cheeses determined by pyrosequencing and quantitative real time (qRT)-PCR

(2011) Wafa Masoud et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Multiplex PCR assay for species identification of bovine mastitis pathogens

(2011) B.R. Shome et al.   JOURNAL OF APPLIED MICROBIOLOGY

Hot topic: Bovine milk samples yielding negative or nonspecific results in bacterial culturing—The possible role of PCR-single strand conformation polymorphism in mastitis diagnosis

(2011) K. Schwaiger et al.   JOURNAL OF DAIRY SCIENCE

Molecular Epidemiology of Mastitis Pathogens of Dairy Cattle and Comparative Relevance to Humans

(2011) Ruth N. Zadoks et al.   JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq

(2011) Hana Yi et al.   NUCLEIC ACIDS RESEARCH

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

(2011) María José Gosalbes et al.   PLoS One

Characterization of the Diversity and Temporal Stability of Bacterial Communities in Human Milk

(2011) Katherine M. Hunt et al.   PLoS One

Impact of probiotic administration on the health and fecal microbiota of young calves: A meta-analysis of randomized controlled trials of lactic acid bacteria

(2011) M.L. Signorini et al.   RESEARCH IN VETERINARY SCIENCE

The Gut's Clostridium Cocktail

(2011) M. J. Barnes et al.   SCIENCE

The mammalian intestinal epithelium as integral player in the establishment and maintenance of host–microbial homeostasis

(2011) Claudia U. Duerr et al.   SEMINARS IN IMMUNOLOGY

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

(2011) Thomas J. Sharpton et al.   PLoS Computational Biology

Development of biosensor-based assays to identify anti-infective oligosaccharides

(2010) Jonathan A. Lane et al.   ANALYTICAL BIOCHEMISTRY

Intestinal Bacteria and the Regulation of Immune Cell Homeostasis

(2010) David A. Hill et al.   Annual Review of Immunology

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

Variation of human milk oligosaccharides in relation to milk groups and lactational periods

(2010) Stephan Thurl et al.   BRITISH JOURNAL OF NUTRITION

Treatment of Infectious Mastitis during Lactation: Antibiotics versus Oral Administration of Lactobacilli Isolated from Breast Milk

(2010) Rebeca Arroyo et al.   CLINICAL INFECTIOUS DISEASES

Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing

(2010) Wafa Masoud et al.   INTERNATIONAL DAIRY JOURNAL

Natural variation in biomarkers indicating mastitis in healthy cows

(2010) Maria Åkerstedt et al.   JOURNAL OF DAIRY RESEARCH

Effects of clinical mastitis caused by gram-positive and gram-negative bacteria and other organisms on the probability of conception in New York State Holstein dairy cows

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

Field comparison of real-time polymerase chain reaction and bacterial culture for identification of bovine mastitis bacteria

(2010) M.T. Koskinen et al.   JOURNAL OF DAIRY SCIENCE

Breast Milk as the Gold Standard for Protective Nutrients

(2010) Allan Walker   JOURNAL OF PEDIATRICS

Milk-Derived Transforming Growth Factor-β and the Infant Immune Response

(2010) Irmeli A. Penttila   JOURNAL OF PEDIATRICS

Long-term impacts of antibiotic exposure on the human intestinal microbiota

(2010) C. Jernberg et al.   MICROBIOLOGY-SGM

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

(2010) Shaomei He et al.   NATURE METHODS

Generating and navigating proteome maps using mass spectrometry

(2010) Christian H. Ahrens et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome

(2010) Hedvig E. Jakobsson et al.   PLoS One

Human milk glycobiome and its impact on the infant gastrointestinal microbiota

(2010) A. M. Zivkovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging

(2010) F. Turroni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Succession of microbial consortia in the developing infant gut microbiome

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

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

(2010) M. G. Dominguez-Bello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential role of the intestinal microbiota of the mother in neonatal immune education

(2010) Anne Donnet-Hughes et al.   PROCEEDINGS OF THE NUTRITION SOCIETY

The human microbiome harbors a diverse reservoir of antibiotic resistance genes

(2010) Morten O.A. Sommer et al.   Virulence

The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies

(2010) Patrick D. Schloss   PLoS Computational Biology

Characterization of bacterial population of raw milk from bovine mastitis by culture-independent PCR–DGGE method

(2009) Ying Kuang et al.   BIOCHEMICAL ENGINEERING JOURNAL

Influence of antibiotic exposure in the early postnatal period on the development of intestinal microbiota

(2009) Shigemitsu Tanaka et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation

(2009) D. A. Antonopoulos et al.   INFECTION AND IMMUNITY

Effects of repeated gram-positive and gram-negative clinical mastitis episodes on milk yield loss in Holstein dairy cows

(2009) Y.H. Schukken et al.   JOURNAL OF DAIRY SCIENCE

Invited review: The role of contagious disease in udder health

(2009) H.W. Barkema et al.   JOURNAL OF DAIRY SCIENCE

Real-time polymerase chain reaction-based identification of bacteria in milk samples from bovine clinical mastitis with no growth in conventional culturing

(2009) S. Taponen et al.   JOURNAL OF DAIRY SCIENCE

Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research

(2009) Augustin Scalbert et al.   Metabolomics

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

(2009) Rotem Sorek et al.   NATURE REVIEWS GENETICS

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

(2009) N. Delmotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Oral Administration of Lactobacillus Strains Isolated from Breast Milk as an Alternative for the Treatment of Infectious Mastitis during Lactation

(2008) E. Jimenez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

(2008) Z. Liu et al.   NUCLEIC ACIDS RESEARCH

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

(2008) D. A. Sela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA