Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes

Archaeal and Bacterial Metagenome-Assembled Genome Sequences Derived from Pig Feces

(2022) Matthew Crossfield et al.   Microbiology Resource Announcements

Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance

(2022) Yunyan Zhou et al.   Microbiome

Resistance determinants and their genetic context in enterobacteria from a longitudinal study of pigs reared under various husbandry conditions

(2021) Dominic Poulin-Laprade et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics

(2021) Paiboon Tunsagool et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2021) Congying Chen et al.   Nature Communications

Evolution of the Gut Microbiota and Its Fermentation Characteristics of Ningxiang Pigs at the Young Stage

(2021) Hao Li et al.   Animals

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Culturing Human Gut Microbiomes in the Laboratory

(2021) Simone Renwick et al.   Annual Review of Microbiology

Dysosmobacter welbionis is a newly isolated human commensal bacterium preventing diet-induced obesity and metabolic disorders in mice

(2021) Tiphaine Le Roy et al.   GUT

Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature

(2021) Lauren S. McKee et al.   Environmental Microbiology Reports

Microbial sulfate reduction by Desulfovibrio is an important source of hydrogen sulfide from a large swine finishing facility

(2021) Olga V. Karnachuk et al.   Scientific Reports

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

(2021) Fei Xie et al.   Microbiome

Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes

(2021) Daniela Gaio et al.   Microbial Genomics

Metagenomic Sequencing Analysis of the Effects of Colistin Sulfate on the Pig Gut Microbiome

(2021) Ling Guo et al.   Frontiers in Veterinary Science

Pathogenic investigations of Streptococcus pasteurianus , an underreported zoonotic pathogen, isolated from a diseased piglet with meningitis

(2021) Shuoyue Wang et al.   Transboundary and Emerging Diseases

Multivariable association discovery in population-scale meta-omics studies

(2021) Himel Mallick et al.   PLoS Computational Biology

Xylan alleviates dietary fiber deprivation-induced dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum in pigs

(2021) Zhenyu Wang et al.   Microbiome

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

(2021) Devin B. Holman et al.   mSystems

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

(2020) Jolinda Pollock et al.   Scientific Reports

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

(2020) Francesco Asnicar et al.   Nature Communications

DRAM for distilling microbial metabolism to automate the curation of microbiome function

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

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

(2020) Amanda Warr et al.   GigaScience

Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands

(2020) Finlay Maguire et al.   Microbial Genomics

Metagenomic reconstructions of gut microbial metabolism in weanling pigs

(2019) Weilan Wang et al.   Microbiome

Exploring the Fecal Microbial Composition and Metagenomic Functional Capacities Associated With Feed Efficiency in Commercial DLY Pigs

(2019) Jianping Quan et al.   Frontiers in Microbiology

Structures and characteristics of carbohydrates in diets fed to pigs: a review

(2019) Diego M. D. L. Navarro et al.   Journal of Animal Science and Biotechnology

Dysosmobacter welbionis gen. nov., sp. nov., isolated from human faeces and emended description of the genus Oscillibacter

(2019) Tiphaine Le Roy et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria

(2019) Xiaofan Wang et al.   Microbiome

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

(2019) Robert D. Stewart et al.   NATURE BIOTECHNOLOGY

Global trends in antimicrobial resistance in animals in low- and middle-income countries

(2019) Thomas P. Van Boeckel et al.   SCIENCE

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

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

Interactions between host and gut microbiota in domestic pigs: a review

(2019) Yadnyavalkya Patil et al.   Gut Microbes

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

Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

(2018) Patrick Munk et al.   Nature Microbiology

Global trends in infectious diseases of swine

(2018) Kimberly VanderWaal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of Diet-Modulated Butyrate Production on Intestinal Barrier Function and Inflammation

(2018) Knud Bach Knudsen et al.   Nutrients

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Probiotic roles ofLactobacillussp. in swine: insights from gut microbiota

(2017) V.D.V. Valeriano et al.   JOURNAL OF APPLIED MICROBIOLOGY

Polysaccharide Utilization Loci: Fueling Microbial Communities

(2017) Julie M. Grondin et al.   JOURNAL OF BACTERIOLOGY

Metagenomic Analysis of Cecal Microbiome Identified Microbiota and Functional Capacities Associated with Feed Efficiency in Landrace Finishing Pigs

(2017) Zhen Tan et al.   Frontiers in Microbiology

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

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

(2017) Devin B. Holman et al.   mSystems

Addition of arabinoxylan and mixed linkage glucans in porcine diets affects the large intestinal bacterial populations

(2016) John B. Gorham et al.   EUROPEAN JOURNAL OF NUTRITION

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

(2016) Audrey Rivière et al.   Frontiers in Microbiology

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

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

(2015) Dinghua Li et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

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

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

(2015) Núria Mach et al.   Environmental Microbiology Reports

Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations

(2015) Özgün C O Umu et al.   Microbiome

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) M. Vital et al.   mBio

Impact of subtherapeutic administration of tylosin and chlortetracycline on antimicrobial resistance in farrow-to-finish swine

(2013) Devin B. Holman et al.   FEMS MICROBIOLOGY ECOLOGY

The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism

(2013) Gijs den Besten et al.   JOURNAL OF LIPID RESEARCH

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Analysis of a Clostridium difficile PCR ribotype 078 100 kilobase island reveals the presence of a novel transposon, Tn6164

(2012) Jeroen Corver et al.   BMC MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Two Novel Antibiotic Resistance Genes, tet(44) and ant(6)-Ib, Are Located within a Transferable Pathogenicity Island in Campylobacter fetus subsp. fetus

(2010) C. Abril et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Transposases are the most abundant, most ubiquitous genes in nature

(2010) Ramy K. Aziz et al.   NUCLEIC ACIDS RESEARCH

tISCpe8, an IS1595-Family Lincomycin Resistance Element Located on a Conjugative Plasmid in Clostridium perfringens

(2009) D. Lyras et al.   JOURNAL OF BACTERIOLOGY