Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

Illuminating Microbial Dark Matter in Meromictic Sakinaw Lake

(2014) Esther A. Gies et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic characterization of ‘Candidatus Defluviicoccus tetraformis strain TFO71’, a tetrad-forming organism, predominant in an anaerobic-aerobic membrane bioreactor with deteriorated biological phosphorus removal

(2014) Masaru K. Nobu et al.   ENVIRONMENTAL MICROBIOLOGY

Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’

(2014) Noha H Youssef et al.   ISME Journal

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

(2014) Kelly C Wrighton et al.   ISME Journal

A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere:geosphere interactions

(2014) R. John Parkes et al.   MARINE GEOLOGY

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

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Global Patterns of Abundance, Diversity and Community Structure of the Aminicenantes (Candidate Phylum OP8)

(2014) Ibrahim F. Farag et al.   PLoS One

The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic Features

(2014) Janine Kamke et al.   PLoS One

A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method

(2014) Seth D. Axen et al.   PLoS Computational Biology

Bacterial diversity and hydrography of Etoliko, an anoxic semi-enclosed coastal basin in Western Greece

(2013) Athina Chamalaki et al.   ANNALS OF MICROBIOLOGY

Clostridium acidurici Electron-Bifurcating Formate Dehydrogenase

(2013) Shuning Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evidence that a Metabolic Microcompartment Contains and Recycles Private Cofactor Pools

(2013) D. L. Huseby et al.   JOURNAL OF BACTERIOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

(2013) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Pyrosequencing Reveals High-Temperature Cellulolytic Microbial Consortia in Great Boiling Spring after In Situ Lignocellulose Enrichment

(2013) Joseph P. Peacock et al.   PLoS One

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

Genomes from Metagenomics

(2013) I. Sharon et al.   SCIENCE

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

(2013) R. S. Kantor et al.   mBio

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

Microbial Diversity and Biochemical Potential Encoded by Thermal Spring Metagenomes Derived from the Kamchatka Peninsula

(2013) Bernd Wemheuer et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

(2012) J Kirk Harris et al.   ISME Journal

Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities

(2012) Jessica K Cole et al.   ISME Journal

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

Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1

(2012) Sari Peura et al.   ISME Journal

A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

(2012) Hideto Takami et al.   PLoS One

The PduQ Enzyme Is an Alcohol Dehydrogenase Used to Recycle NAD+ Internally within the Pdu Microcompartment of Salmonella enterica

(2012) Shouqiang Cheng et al.   PLoS One

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

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

Succession of Deferribacteres and Epsilonproteobacteria through a nitrate-treated high-temperature oil production facility

(2012) Antje Gittel et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Ecophysiology of Uncultured Filamentous Anaerobes Belonging to the Phylum KSB3 That Cause Bulking in Methanogenic Granular Sludge

(2011) Takeshi Yamada et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Partial Genome Assembly for a Candidate Division OP11 Single Cell from an Anoxic Spring (Zodletone Spring, Oklahoma)

(2011) Noha H. Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokaryotic diversity, composition structure, and phylogenetic analysis of microbial communities in leachate sediment ecosystems

(2011) Jingjing Liu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Characteristic microbial community of a dry thermophilic methanogenic digester: its long-term stability and change with feeding

(2011) Yue-Qin Tang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Enrichment and cultivation of prokaryotes associated with the sulphate-methane transition zone of diffusion-controlled sediments of Aarhus Bay, Denmark, under heterotrophic conditions

(2011) Gordon Webster et al.   FEMS MICROBIOLOGY ECOLOGY

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

(2011) Priya Narasingarao et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Phylogenetic diversity of microbial communities associated with the crude-oil, large-insoluble-particle and formation-water components of the reservoir fluid from a non-flooded high-temperature petroleum reservoir

(2011) Hajime Kobayashi et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

(2011) B. N. Orcutt et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

New Abundant Microbial Groups in Aquatic Hypersaline Environments

(2011) Rohit Ghai et al.   Scientific Reports

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Bacterial Microcompartments

(2010) Cheryl A. Kerfeld et al.   Annual Review of Microbiology

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation

(2010) Jessica R. Sieber et al.   Annual Review of Microbiology

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes

(2010) Eva Biegel et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Phylogenetic diversity and metagenomics of candidate division OP3

(2010) Jana Glöckner et al.   ENVIRONMENTAL MICROBIOLOGY

Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf war

(2010) Iain C. Sutcliffe   ENVIRONMENTAL MICROBIOLOGY

Microbial diversity in Tunisian geothermal springs as detected by molecular and culture-based approaches

(2010) Raja Sayeh et al.   EXTREMOPHILES

Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges

(2010) Alexander Siegl et al.   ISME Journal

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group

(2010) Takuro Nunoura et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Characterisation of PduS, the pdu Metabolosome Corrin Reductase, and Evidence of Substructural Organisation within the Bacterial Microcompartment

(2010) Joshua B. Parsons et al.   PLoS One

Short N-terminal sequences package proteins into bacterial microcompartments

(2010) C. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enigmatic, ultrasmall, uncultivated Archaea

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

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Prokaryotic Community Structure and Sulfate Reducer Activity in Water from High-Temperature Oil Reservoirs with and without Nitrate Treatment

(2009) A. Gittel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin

(2009) Kyle C. Costa et al.   EXTREMOPHILES

Microbiology and geochemistry of Little Hot Creek, a hot spring environment in the Long Valley Caldera

(2009) T. J. VICK et al.   Geobiology

Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge

(2009) Delphine Rivière et al.   ISME Journal

The Iron-Hydrogenase of Thermotoga maritima Utilizes Ferredoxin and NADH Synergistically: a New Perspective on Anaerobic Hydrogen Production

(2009) G. J. Schut et al.   JOURNAL OF BACTERIOLOGY

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

(2008) M. S. Elshahed et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum)

(2008) Elizabeth Pierce et al.   ENVIRONMENTAL MICROBIOLOGY

Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods

(2008) Vinh D. Pham et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial community composition in thermophilic microbial mats from five hot springs in central Tibet

(2008) Maggie C. Y. Lau et al.   EXTREMOPHILES

A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells

(2008) Kelly C Wrighton et al.   ISME Journal

Microcompartments for B12-Dependent 1,2-Propanediol Degradation Provide Protection from DNA and Cellular Damage by a Reactive Metabolic Intermediate

(2008) E. M. Sampson et al.   JOURNAL OF BACTERIOLOGY

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

(2008) A. Dereeper et al.   NUCLEIC ACIDS RESEARCH

A korarchaeal genome reveals insights into the evolution of the Archaea

(2008) J. G. Elkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA