Weaning Age and Its Effect on the Development of the Swine Gut Microbiome and Resistome

Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome

(2021) Congying Chen et al.   Nature Communications

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage

(2020) Jolinda Pollock et al.   Scientific Reports

Metagenomic Characterization of Intestinal Regions in Pigs With Contrasting Feed Efficiency

(2020) Jianping Quan et al.   Frontiers in Microbiology

An improved pig reference genome sequence to enable pig genetics and genomics research

(2020) Amanda Warr et al.   GigaScience

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

(2020) David Wylensek et al.   Nature Communications

Development of piglet gut microbiota at the time of weaning influences development of postweaning diarrhea – A field study

(2020) Daniela Karasova et al.   RESEARCH IN VETERINARY SCIENCE

Probiotic Lactobacillus johnsonii BS15 Promotes Growth Performance, Intestinal Immunity, and Gut Microbiota in Piglets

(2019) Jinge Xin et al.   Probiotics and Antimicrobial Proteins

The MetaCyc database of metabolic pathways and enzymes - a 2019 update

(2019) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

(2019) Brian P Alcock et al.   NUCLEIC ACIDS RESEARCH

ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages

(2018) Chris M Rands et al.   ENVIRONMENTAL MICROBIOLOGY

Butyricicoccus porcorum sp. nov., a butyrate-producing bacterium from swine intestinal tract

(2018) Julian Trachsel et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Microbiome profiling of commercial pigs from farrow to finish

(2018) Brenda De Rodas et al.   JOURNAL OF ANIMAL SCIENCE

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Characterization of porcine milk oligosaccharides over lactation between primiparous and multiparous female pigs

(2018) Jinhua Wei et al.   Scientific Reports

Chlortetracycline enhances tonsil colonization and fecal shedding of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 without major alterations to the porcine tonsillar and intestinal microbiota

(2018) D. B. Holman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Gut Microbiota Dysbiosis in Postweaning Piglets: Understanding the Keys to Health

(2017) Raphaële Gresse et al.   TRENDS IN MICROBIOLOGY

Meta-analysis To Define a Core Microbiota in the Swine Gut

(2017) Devin B. Holman et al.   mSystems

Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition

(2016) Mark R. Charbonneau et al.   CELL

In Vitro Fermentation of Porcine Milk Oligosaccharides and Galacto-oligosaccharides Using Piglet Fecal Inoculum

(2016) Elisabetta Difilippo et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Milk Oligosaccharide Variation in Sow Milk and Milk Oligosaccharide Fermentation in Piglet Intestine

(2016) Elisabetta Difilippo et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Detection of cfxA2, cfxA3, and cfxA6 genes in beta-lactamase producing oral anaerobes

(2016) Buhle BINTA et al.   Journal of Applied Oral Science

Characterization of porcine milk oligosaccharides during early lactation and their relation to the fecal microbiome

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

Skin Microbiome Surveys Are Strongly Influenced by Experimental Design

(2016) Jacquelyn S. Meisel et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

The Probiotic Butyricicoccus pullicaecorum Reduces Feed Conversion and Protects from Potentially Harmful Intestinal Microorganisms and Necrotic Enteritis in Broilers

(2016) Venessa Eeckhaut et al.   Frontiers in Microbiology

Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut

(2016) Audrey Rivière et al.   Frontiers in Microbiology

Faecalibacterium prausnitzii prevents physiological damages in a chronic low-grade inflammation murine model

(2015) Rebeca Martín et al.   BMC MICROBIOLOGY

Quantification of short-chain fatty acids and energy production from hindgut fermentation in cannulated pigs fed graded levels of wheat bran1

(2015) E. A. Iyayi et al.   JOURNAL OF ANIMAL SCIENCE

Description of a novel pectin-degrading bacterial species Prevotella pectinovora sp. nov., based on its phenotypic and genomic traits

(2015) Brigita Nograšek et al.   JOURNAL OF MICROBIOLOGY

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

(2015) Núria Mach et al.   Environmental Microbiology Reports

Diet shapes the gut microbiome of pigs during nursing and weaning

(2015) Steven A. Frese et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Temporal changes and the effect of subtherapeutic concentrations of antibiotics in the gut microbiota of swine

(2014) Devin B. Holman et al.   FEMS MICROBIOLOGY ECOLOGY

A Perspective on the Complexity of Dietary Fiber Structures and Their Potential Effect on the Gut Microbiota

(2014) Bruce R. Hamaker et al.   JOURNAL OF MOLECULAR BIOLOGY

Effects of Lactobacillus johnsonii XS4 supplementation on reproductive performance, gut environment, and blood biochemical and immunological index in lactating sows

(2014) J. Wang et al.   Livestock Science

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Butyrate-Producing Bacteria, Including Mucin Degraders, from the Swine Intestinal Tract

(2013) Uri Y. Levine et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PCR-based detection of resistance genes in anaerobic bacteria isolated from intra-abdominal infections

(2013) Chau Minh Tran et al.   JOURNAL OF INFECTION AND CHEMOTHERAPY

A Diet High in Resistant Starch Modulates Microbiota Composition, SCFA Concentrations, and Gene Expression in Pig Intestine

(2013) Daniëlle Haenen et al.   JOURNAL OF NUTRITION

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

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

The biological stress of early weaned piglets

(2013) Joy M Campbell et al.   Journal of Animal Science and Biotechnology

Human milk oligosaccharide consumption by intestinal microbiota

(2012) A. Marcobal et al.   CLINICAL MICROBIOLOGY AND INFECTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Complex Carbohydrate Utilization by the Healthy Human Microbiome

(2012) Brandi L. Cantarel et al.   PLoS One

Consumption of Human Milk Oligosaccharides by Gut-Related Microbes

(2010) Angela Marcobal et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Selenomonas bovis sp. nov., isolated from yak rumen contents

(2009) K. Zhang et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY