Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan

List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ

(2020) Aidan C. Parte et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide

(2019) Zahra F. Islam et al.   ISME Journal

Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures

(2019) Scott C. Thomas et al.   Frontiers in Microbiology

Tepidiforma bonchosmolovskayae gen. nov., sp. nov., a moderately thermophilic Chloroflexi bacterium from a Chukotka hot spring (Arctic, Russia), representing a novel class, Tepidiformia, which includes the previously uncultivated lineage OLB14

(2019) Tatiana V. Kochetkova et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs

(2019) Eva Spieck et al.   ISME Journal

MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes

(2018) Wataru Arai et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Convergent evolution of unusual complex I homologs with increased proton pumping capacity: energetic and ecological implications

(2018) Grayson L. Chadwick et al.   ISME Journal

Long-Term Cultivation and Metagenomics Reveal Ecophysiology of Previously Uncultivated Thermophiles Involved in Biogeochemical Nitrogen Cycle

(2018) Shingo Kato et al.   MICROBES AND ENVIRONMENTS

Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer

(2018) Lewis M. Ward et al.   Frontiers in Microbiology

Genome analysis, metabolic potential and predatory capabilities of Herpetosiphon llansteffanense sp. nov.

(2018) Paul G. Livingstone et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

(2018) Karen G. Lloyd et al.   mSystems

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

(2018) Chirag Jain et al.   Nature Communications

Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade

(2018) Kristina Bayer et al.   mSystems

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling

(2017) Maliheh Mehrshad 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

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

(2017) Neil D Rawlings et al.   NUCLEIC ACIDS RESEARCH

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Relative Importance of Chemoautotrophy for Primary Production in a Light Exposed Marine Shallow Hydrothermal System

(2017) Gonzalo V. Gomez-Saez et al.   Frontiers in Microbiology

An automated system for evaluation of the potential functionome: MAPLE version 2.1.0

(2016) Hideto Takami et al.   DNA RESEARCH

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2

(2016) Johan Bengtsson-Palme et al.   Ecological Informatics

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1Compound Oxidation

(2015) Vincent J. Denef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment

(2015) Leslie P Silva et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

Thermocrinis jamiesonii sp. nov., a thiosulfate-oxidizing, autotropic thermophile isolated from a geothermal spring

(2015) Jeremy A. Dodsworth et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

(2015) Johan Bengtsson-Palme et al.   Molecular Ecology Resources

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

(2015) Marcel Huntemann et al.   Standards in Genomic Sciences

Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China

(2015) Brian P. Hedlund et al.   Frontiers in Microbiology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

NCBI BLAST+ integrated into Galaxy

(2015) Peter J. A. Cock et al.   GigaScience

Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov.

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

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

(2014) Zheng-Shuang Hua et al.   ISME Journal

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Community Microrespirometry and Molecular Analyses Reveal a Diverse Energy Economy in Great Boiling Spring and Sandy's Spring West in the U.S. Great Basin

(2013) Caitlin N. Murphy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Acetate formation in the photoheterotrophic bacteriumChloroflexus aurantiacusinvolves an archaeal type ADP-forming acetyl-CoA synthetase isoenzyme I

(2013) Marcel Schmidt et al.   FEMS MICROBIOLOGY LETTERS

COMPLETE-MFA: Complementary parallel labeling experiments technique for metabolic flux analysis

(2013) Robert W. Leighty et al.   METABOLIC ENGINEERING

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

A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing

(2013) Weiguo Hou et al.   PLoS One

Evaluation method for the potential functionome harbored in the genome and metagenome

(2012) Hideto Takami et al.   BMC GENOMICS

Arsenite oxidase gene diversity amongChloroflexiandProteobacteriafrom El Tatio Geyser Field, Chile

(2012) Annette Summers Engel et al.   FEMS MICROBIOLOGY ECOLOGY

Dehalogenimonas alkenigignens sp. nov., a chlorinated-alkane-dehalogenating bacterium isolated from groundwater

(2012) K. S. Bowman et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi

(2012) F. E. Loffler et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

(2012) Jessica K Cole et al.   ISME Journal

Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

(2012) Dimitry Y Sorokin 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

Natural Niche for Organohalide-Respiring Chloroflexi

(2011) Mark J. Krzmarzick et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Coassimilation of Organic Substrates via the Autotrophic 3-Hydroxypropionate Bi-Cycle in Chloroflexus aurantiacus

(2011) Jan Zarzycki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea

(2011) Jeremy A. Dodsworth et al.   ENVIRONMENTAL MICROBIOLOGY

Potential role of Thermus thermophilus and T. oshimai in high rates of nitrous oxide (N2O) production in ∼80 °C hot springs in the US Great Basin

(2011) B. P. HEDLUND et al.   Geobiology

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Modeling soil metabolic processes using isotopologue pairs of position-specific 13C-labeled glucose and pyruvate

(2011) Paul Dijkstra et al.   SOIL BIOLOGY & BIOCHEMISTRY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

A review of the microbiology of the Rehai geothermal field in Tengchong, Yunnan Province, China

(2011) Brian P. Hedlund et al.   Geoscience Frontiers

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

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme

(2010) Rafael F. Say et al.   NATURE

The large-scale organization of the bacterial network of ecological co-occurrence interactions

(2010) Shiri Freilich et al.   NUCLEIC ACIDS RESEARCH

Probing carbon flux patterns through soil microbial metabolic networks using parallel position-specific tracer labeling

(2010) Paul Dijkstra et al.   SOIL BIOLOGY & BIOCHEMISTRY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

(2009) Kyle C. Costa et al.   EXTREMOPHILES

Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater

(2009) W. M. Moe et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS

The minimum information about a genome sequence (MIGS) specification

(2008) Dawn Field et al.   NATURE BIOTECHNOLOGY

Metabolic footprinting in microbiology: methods and applications in functional genomics and biotechnology

(2008) Valeria Mapelli et al.   TRENDS IN BIOTECHNOLOGY