Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

Fusobacterium bloodstream infections: A literature review and hospital-based case series

(2020) Abdulellah Musaid Almohaya et al.   ANAEROBE

Etiology, epidemiology, pathology, and advances in diagnosis, vaccine development, and treatment of Gallibacterium anatis infection in poultry: a review

(2020) Dharanesha Narasinakuppe Krishnegowda et al.   VETERINARY QUARTERLY

Composition and Function of Chicken Gut Microbiota

(2020) Ivan Rychlik   Animals

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

(2020) Jinshui Zheng et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

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

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

(2020) Francesco Asnicar et al.   Nature Communications

Lists of names of prokaryotic Candidatus taxa

(2020) Aharon Oren et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Farm dust resistomes and bacterial microbiomes in European poultry and pig farms

(2020) Roosmarijn E.C. Luiken et al.   ENVIRONMENT INTERNATIONAL

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

(2020) Ebenezer Foster-Nyarko et al.   Microbial Genomics

Antibiotics-induced monodominance of a novel gut bacterial order

(2019) Falk Hildebrand et al.   GUT

Food in the Anthropocene: the EAT–Lancet Commission on healthy diets from sustainable food systems

(2019) Walter Willett et al.   LANCET

Use of 16S rRNA gene sequencing for prediction of new opportunistic pathogens in chicken ileal and cecal microbiota

(2019) Miloslava Kollarcikova et al.   POULTRY SCIENCE

The broiler chicken as a signal of a human reconfigured biosphere

(2019) Carys E. Bennett et al.   Royal Society Open Science

Diversity and Population Overlap between Avian and Human Escherichia coli Belonging to Sequence Type 95

(2019) Steffen L. Jørgensen et al.   mSphere

The Golden Egg: Nutritional Value, Bioactivities, and Emerging Benefits for Human Health

(2019) Sophie Réhault-Godbert et al.   Nutrients

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Genomic and molecular characterisation of Escherichia marmotae from wild rodents in Qinghai-Tibet plateau as a potential pathogen

(2019) Sha Liu et al.   Scientific Reports

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

(2019) Dongwan D. Kang et al.   PeerJ

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

(2019) Anuradha Ravi et al.   Microbial Genomics

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

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov.

(2019) Sudip Patel et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

(2018) Jongsik Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

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

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

(2018) Matej Medvecky et al.   BMC GENOMICS

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Evaluating the Information Content of Shallow Shotgun Metagenomics

(2018) Benjamin Hillmann et al.   mSystems

A plea for linguistic accuracy – also for Candidatus taxa

(2017) Aharon Oren   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

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

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

(2016) Daniel R. Mende et al.   NUCLEIC ACIDS RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach

(2016) Vipin Gupta et al.   Scientific Reports

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page 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

Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana

(2015) Sha Liu et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

International Code of Nomenclature of Prokaryotes

(2015) Charles T Parker et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies

(2015) Fernando Puente-Sánchez et al.   NUCLEIC ACIDS RESEARCH

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

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

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Aliicoccus persicus gen. nov., sp. nov., a halophilic member of the Firmicutes isolated from a hypersaline lake

(2014) M. A. Amoozegar et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

(2014) Chengwei Luo et al.   NUCLEIC ACIDS RESEARCH

Extensive Microbial and Functional Diversity within the Chicken Cecal Microbiome

(2014) Martin J. Sergeant et al.   PLoS One

Land, irrigation water, greenhouse gas, and reactive nitrogen burdens of meat, eggs, and dairy production in the United States

(2014) G. Eshel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LotuS: an efficient and user-friendly OTU processing pipeline

(2014) Falk Hildebrand et al.   Microbiome

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus)

(2012) M. Sakamoto et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Complete Genome Sequence of the Novel Escherichia coli Phage phAPEC8

(2012) J. Tsonos et al.   JOURNAL OF VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing

(2012) Anthony A. Fodor et al.   PLoS One

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

Characterization of the cryptic Escherichia lineages: rapid identification and prevalence

(2011) Olivier Clermont et al.   ENVIRONMENTAL MICROBIOLOGY

Poultry as a Host for the Zoonotic Pathogen Campylobacter jejuni

(2011) David Hermans et al.   VECTOR-BORNE AND ZOONOTIC DISEASES

Mugsy: fast multiple alignment of closely related whole genomes

(2010) Samuel V. Angiuoli et al.   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

Cryptic Lineages of the Genus Escherichia

(2009) S. T. Walk et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS