Characterization of Metagenome-Assembled Genomes and Carbohydrate-Degrading Genes in the Gut Microbiota of Tibetan Pig

The Role of Short-Chain Fatty Acids From Gut Microbiota in Gut-Brain Communication

(2020) Ygor Parladore Silva et al.   Frontiers in Endocrinology

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

Metagenomic reconstructions of gut microbial metabolism in weanling pigs

(2019) Weilan Wang et al.   Microbiome

Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome

(2019) Gherman Uritskiy et al.   Genes

Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space

(2019) William Helbert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

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

(2019) Dongwan D. Kang et al.   PeerJ

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

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

A Metataxonomic Tool to Investigate the Diversity of Treponema

(2019) Luisa K. Hallmaier-Wacker et al.   Frontiers in Microbiology

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health

(2019) Jillian L. Waters et al.   BMC BIOLOGY

Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates

(2019) Hannah Fehlner-Peach et al.   Cell Host & Microbe

High Altitude Adaptability and Meat Quality in Tibetan Pigs: A Reference for Local Pork Processing and Genetic Improvement

(2019) Mailin Gan et al.   Animals

The significance of the diversity and composition of the cecal microbiota of the Tibetan swine

(2018) Weiping Yang et al.   ANNALS OF MICROBIOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

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

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

(2018) Robert D. Stewart et al.   Nature Communications

A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation

(2018) Javad Gharechahi et al.   Biotechnology for Biofuels

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

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

(2018) Gherman V. Uritskiy et al.   Microbiome

Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes

(2018) Ana S Luis et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

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

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

(2017) Christian Milani et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets

(2017) Qi Xu et al.   PLoS One

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

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

CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems

(2016) Anne Abot et al.   BMC GENOMICS

Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum

(2016) Stefan Spring et al.   ISME Journal

A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres

(2016) Nurdyana Abdul Rahman 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

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

(2016) David Ríos-Covián et al.   Frontiers in Microbiology

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature 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

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

Automatic prediction of polysaccharide utilization loci in Bacteroidetes species

(2014) Nicolas Terrapon et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders

(2014) Sebastian GA Konietzny et al.   Biotechnology for Biofuels

Population history and genomic signatures for high-altitude adaptation in Tibetan pigs

(2014) Huashui Ai et al.   BMC GENOMICS

A Comparative Metagenome Survey of the Fecal Microbiota of a Breast- and a Plant-Fed Asian Elephant Reveals an Unexpectedly High Diversity of Glycoside Hydrolase Family Enzymes

(2014) Nele Ilmberger et al.   PLoS One

Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota

(2013) Sunghee Lee et al.   ISME Journal

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 abundance and variety of carbohydrate-active enzymes in the human gut microbiota

(2013) Abdessamad El Kaoutari et al.   NATURE REVIEWS MICROBIOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Commensal Clostridia: leading players in the maintenance of gut homeostasis

(2013) Loris R Lopetuso et al.   Gut Pathogens

Microbial carbohydrate esterases deacetylating plant polysaccharides

(2012) Peter Biely   BIOTECHNOLOGY ADVANCES

Effects of Gut Microbes on Nutrient Absorption and Energy Regulation

(2012) Rosa Krajmalnik-Brown et al.   NUTRITION IN CLINICAL PRACTICE

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

(2012) Nicola Segata et al.   GENOME BIOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Local Origin of the Tibetan Pig and Additional Insights into the Origin of Asian Pigs

(2011) Shuli Yang et al.   PLoS One

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Cellulosomes: Highly Efficient Nanomachines Designed to Deconstruct Plant Cell Wall Complex Carbohydrates

(2010) Carlos M.G.A. Fontes et al.   Annual Review of Biochemistry

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores

(2010) P. B. Pope et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA