Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

Desulfurella amilsii sp. nov., a novel acidotolerant sulfur-respiring bacterium isolated from acidic river sediments

(2016) Anna P. Florentino et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Campylobacter geochelonis sp. nov. isolated from the western Hermann's tortoise (Testudo hermanni hermanni)

(2016) Alessandra Piccirillo et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota

(2016) Jessica A Kozlowski et al.   ISME Journal

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

(2016) Supratim Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Genome-Based Microbial Taxonomy Coming of Age

(2016) Philip Hugenholtz et al.   Cold Spring Harbor Perspectives in Biology

The ABC transporter YejABEF is required for resistance to antimicrobial peptides and the virulence of Brucella melitensis

(2016) Zhen Wang et al.   Scientific Reports

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

(2016) Kate L. Ormerod et al.   Microbiome

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

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

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

Cetia pacifica gen. nov., sp. nov., a chemolithoautotrophic, thermophilic, nitrate-ammonifying bacterium from a deep-sea hydrothermal vent

(2015) Ashley Grosche et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes

(2015) Aharon Oren et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

(2015) Chris Greening et al.   ISME Journal

Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage

(2015) Yun Kit Yeoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pathways for abiotic organic synthesis at submarine hydrothermal fields

(2015) Jill M. McDermott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial diversity and successional patterns during biofilm formation on freshly exposed basalt surfaces at diffuse-flow deep-sea vents

(2015) Lara K. Gulmann et al.   Frontiers in Microbiology

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

Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov.

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

Deep-sea hydrothermal vent Epsilonproteobacteria encode a conserved and widespread nitrate reduction pathway (Nap)

(2014) Costantino Vetriani et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria

(2014) Kai Schuchmann et al.   NATURE REVIEWS MICROBIOLOGY

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Novel Components of the Flagellar System in Epsilonproteobacteria

(2014) B. Gao et al.   mBio

The Archaeal Legacy of Eukaryotes: A Phylogenomic Perspective

(2014) L. Guy et al.   Cold Spring Harbor Perspectives in Biology

The plastid ancestor originated among one of the major cyanobacterial lineages

(2014) Jesús A. G. Ochoa de Alda et al.   Nature Communications

Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria

(2014) Ying Zhang et al.   Frontiers in Microbiology

Involvement of Intermediate Sulfur Species in Biological Reduction of Elemental Sulfur under Acidic, Hydrothermal Conditions

(2013) Eric S. Boyd et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past

(2013) Robert J.M. Eveleigh et al.   Genome Biology and Evolution

Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts

(2013) J G Sanders et al.   ISME Journal

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

LPSN—list of prokaryotic names with standing in nomenclature

(2013) Aidan C. Parte   NUCLEIC ACIDS RESEARCH

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

(2013) J. S. McLean et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

(2013) Jeremy A. Dodsworth et al.   Nature Communications

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

(2013) Sara C Di Rienzi et al.   eLife

Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids

(2013) Nancy H. Akerman et al.   Frontiers in Microbiology

Metagenomic evidence for sulfur lithotrophy by Epsilonproteobacteria as the major energy source for primary productivity in a sub-aerial arctic glacial deposit, Borup Fiord Pass

(2013) Katherine E. Wright et al.   Frontiers in Microbiology

Nitrate ammonification by Nautilia profundicola AmH: experimental evidence consistent with a free hydroxylamine intermediate

(2013) Thomas E. Hanson et al.   Frontiers in Microbiology

A Single-Cell Genome for Thiovulum sp.

(2012) Ian P. G. Marshall et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Thiofractor thiocaminus gen. nov., sp. nov., a novel hydrogen-oxidizing, sulfur-reducing epsilonproteobacterium isolated from a deep-sea hydrothermal vent chimney in the Nikko Seamount field of the northern Mariana Arc

(2012) Hiroko Makita et al.   ARCHIVES OF MICROBIOLOGY

Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations

(2012) Jörg Simon et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Respiratory proteins contribute differentially to Campylobacter jejuni’s survival and in vitro interaction with hosts’ intestinal cells

(2012) Issmat I Kassem et al.   BMC MICROBIOLOGY

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

(2012) Mark A Kozubal et al.   ISME Journal

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

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

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Lateral gene transfer as a support for the tree of life

(2012) S. S. Abby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Ecological Aspects of the Distribution of Different Autotrophic CO2Fixation Pathways

(2011) Ivan A. Berg   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Structural diversity of bacterial flagellar motors

(2011) Songye Chen et al.   EMBO JOURNAL

Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil

(2011) Casey R. J. Hubert et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge

(2011) Gilberto E. Flores et al.   ENVIRONMENTAL MICROBIOLOGY

The oxidative and nitrosative stress defence network of Wolinella succinogenes: cytochrome c nitrite reductase mediates the stress response to nitrite, nitric oxide, hydroxylamine and hydrogen peroxide

(2011) Melanie Kern et al.   ENVIRONMENTAL MICROBIOLOGY

The Wolinella succinogenes mcc gene cluster encodes an unconventional respiratory sulphite reduction system

(2011) Melanie Kern et al.   MOLECULAR MICROBIOLOGY

A framework for estimating niche metrics using the resemblance between qualitative resources

(2011) Miquel De Cáceres et al.   OIKOS

Pathways of Carbon and Energy Metabolism of the Epibiotic Community Associated with the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata

(2011) Michael Hügler et al.   PLoS One

Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones

(2011) J. Grote et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1T)

(2011) Iain Anderson et al.   Standards in Genomic Sciences

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts

(2010) Julie A. Huber et al.   FEMS MICROBIOLOGY ECOLOGY

Phylogeny of Gammaproteobacteria

(2010) K. P. Williams et al.   JOURNAL OF BACTERIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Electron transport chains and bioenergetics of respiratory nitrogen metabolism in Wolinella succinogenes and other Epsilonproteobacteria

(2009) Melanie Kern et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Individual hydrothermal vents at Axial Seamount harbor distinct subseafloor microbial communities

(2009) Andrew D. Opatkiewicz et al.   FEMS MICROBIOLOGY ECOLOGY

Zeta-ProteobacteriaDominate the Colonization and Formation of Microbial Mats in Low-Temperature Hydrothermal Vents at Loihi Seamount, Hawaii

(2009) Allen C. Rassa et al.   GEOMICROBIOLOGY JOURNAL

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Origin of the Sox multienzyme complex system in ancient thermophilic bacteria and coevolution of its constituent proteins

(2009) Wriddhiman Ghosh et al.   RESEARCH IN MICROBIOLOGY

Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola

(2009) Barbara J. Campbell et al.   PLoS Genetics

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nitrifier genomics and evolution of the nitrogen cycle

(2007) Martin G. Klotz et al.   FEMS MICROBIOLOGY LETTERS