Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Metagenomic reconstructions of gut microbial metabolism in weanling pigs

(2019) Weilan Wang et al.   Microbiome

New approaches for metagenome assembly with short reads

(2019) Martin Ayling et al.   BRIEFINGS IN BIOINFORMATICS

Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes

(2019) Natalia Gutiérrez et al.   mSystems

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

(2019) M. Poyet et al.   NATURE MEDICINE

KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

(2019) Takuya Aramaki et al.   BIOINFORMATICS

UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction

(2018) Seong-In Na et al.   JOURNAL OF MICROBIOLOGY

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

(2018) Benjamin J. Tully et al.   Scientific Data

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

Pathogen elimination by probiotic Bacillus via signalling interference

(2018) Pipat Piewngam et al.   NATURE

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion

(2017) Mariana X. Byndloss et al.   SCIENCE

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

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

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

Natural Pig Plasma Immunoglobulins Have Anti-Bacterial Effects: Potential for Use as Feed Supplement for Treatment of Intestinal Infections in Pigs

(2016) Chris J. Hedegaard et al.   PLoS One

Adaptation of the Cecal Bacterial Microbiome of Growing Pigs in Response to Resistant Starch Type 4

(2015) Barbara U. Metzler-Zebeli et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu 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

Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs)

(2015) Jennifer M. Auchtung et al.   Microbiome

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

(2014) Elizabeth A. Rettedal et al.   Nature Communications

Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers

(2013) K. M. Singh et al.   JOURNAL OF APPLIED GENETICS

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Experimental test of the impacts of feral hogs on forest dynamics and processes in the southeastern US

(2009) Evan Siemann et al.   FOREST ECOLOGY AND MANAGEMENT