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

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibacterium rodentium

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation

(2017) Olov Svartström et al.   ISME Journal

Differential effects of monensin and a blend of essential oils on rumen microbiota composition of transition dairy cows

(2017) M. Schären et al.   JOURNAL OF DAIRY SCIENCE

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

(2017) Supratim Mukherjee et al.   NATURE BIOTECHNOLOGY

Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs

(2017) Emma N. Bermingham et al.   PeerJ

A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data

(2017) Despoina D. Roumpeka et al.   Frontiers in Genetics

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

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

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids

(2016) Emily C Hoedt et al.   ISME Journal

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Breznakia blatticola gen. nov. sp. nov. and Breznakia pachnodae sp. nov., two fermenting bacteria isolated from insect guts, and emended description of the family Erysipelotrichaceae

(2016) Dorothee Tegtmeier et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

(2016) Rainer Roehe et al.   PLoS Genetics

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation

(2016) Janine Kamke et al.   Microbiome

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

(2015) Dinghua Li et al.   BIOINFORMATICS

The rumen microbial metagenome associated with high methane production in cattle

(2015) R. John Wallace et al.   BMC GENOMICS

Successful test launch for nanopore sequencing

(2015) Nicholas J Loman et al.   NATURE METHODS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Insights into the Role of Erysipelotrichaceae in the Human Host

(2015) Nadeem O. Kaakoush   Frontiers in Cellular and Infection Microbiology

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

(2015) Judith Risse et al.   GigaScience

Prepartum and Postpartum Rumen Fluid Microbiomes: Characterization and Correlation with Production Traits in Dairy Cows

(2014) Fabio S. Lima et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

(2014) Weibing Shi et al.   GENOME RESEARCH

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

Rumen Cellulosomics: Divergent Fiber-Degrading Strategies Revealed by Comparative Genome-Wide Analysis of Six Ruminococcal Strains

(2014) Bareket Dassa et al.   PLoS One

Illuminating the future of DNA sequencing

(2014) Mick Watson   GENOME BIOLOGY

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

(2014) Christopher W. Beitel et al.   PeerJ

Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle

(2013) J.-H. Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn 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

Meta4: a web application for sharing and annotating metagenomic gene predictions using web services

(2013) Emily J. Richardson et al.   Frontiers in Genetics

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

(2012) Andreas Wilke et al.   BMC BIOINFORMATICS

Genome Sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a Methanogenic Archaeon from the Human Gut Belonging to a Seventh Order of Methanogens

(2012) G. Borrel et al.   JOURNAL OF BACTERIOLOGY

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Rumen pH and fermentation characteristics in dairy cows supplemented with Megasphaera elsdenii NCIMB 41125 in early lactation

(2011) P.C. Aikman et al.   JOURNAL OF DAIRY SCIENCE

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Reclassification of Lactobacillus catenaformis (Eggerth 1935) Moore and Holdeman 1970 and Lactobacillus vitulinus Sharpe et al. 1973 as Eggerthia catenaformis gen. nov., comb. nov. and Kandleria vitulina gen. nov., comb. nov., respectively

(2010) E. Salvetti et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions

(2010) Sinead C. Leahy et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The characterization of lactic acid producing bacteria from the rumen of dairy cattle grazing on improved pasture supplemented with wheat and barley grain

(2008) J.D. Hernandez et al.   JOURNAL OF APPLIED MICROBIOLOGY