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

Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process

(2017) Andrew R. J. Curson et al.   Nature Microbiology

Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea

(2016) Maliheh Mehrshad et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere

(2016) Heather Fullerton et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Distribution of Dehalococcoidia in the Anaerobic Deep Water of a Remote Meromictic Crater Lake and Detection of Dehalococcoidia-Derived Reductive Dehalogenase Homologous Genes

(2016) Corinne Biderre-Petit et al.   PLoS One

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Proteome Remodeling in Response to Sulfur Limitation in “ Candidatus Pelagibacter ubique”

(2016) Daniel P. Smith et al.   mSystems

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

(2015) Dinghua Li et al.   BIOINFORMATICS

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

(2015) Laura A. Hug et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Global diversity and biogeography of deep-sea pelagic prokaryotes

(2015) Guillem Salazar et al.   ISME Journal

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

Dehalococcoides mccartyi Strain DCMB5 Respires a Broad Spectrum of Chlorinated Aromatic Compounds

(2014) Marlén Pöritz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pangenome Evidence for Extensive Interdomain Horizontal Transfer Affecting Lineage Core and Shell Genes in Uncultured Planktonic Thaumarchaeota and Euryarchaeota

(2014) Philippe Deschamps et al.   Genome Biology and Evolution

Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi

(2014) D. Y. Sorokin et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

(2014) J Cameron Thrash et al.   ISME Journal

Prochlorococcus: the structure and function of collective diversity

(2014) Steven J. Biller et al.   NATURE REVIEWS MICROBIOLOGY

Isolation of two newDehalococcoides mccartyistrains with dissimilar dechlorination functions and their characterization by comparative genomics via microarray analysis

(2013) Patrick K. H. Lee et al.   ENVIRONMENTAL MICROBIOLOGY

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

(2013) Kenneth Wasmund et al.   ISME Journal

Kinetics of dechlorination by Dehalococcoides mccartyi using different carbon sources

(2013) Uwe Schneidewind et al.   JOURNAL OF CONTAMINANT HYDROLOGY

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

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

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

(2012) Y. Peng et al.   BIOINFORMATICS

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

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

(2012) Dimitry Y Sorokin et al.   ISME Journal

A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters

(2012) Timothy J Williams et al.   ISME Journal

Rhodanese Functions as Sulfur Supplier for Key Enzymes in Sulfur Energy Metabolism

(2012) Clément Aussignargues et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95T)

(2012) Hajnalka Kiss et al.   Standards in Genomic Sciences

High concentrations and turnover rates of DMS, DMSP and DMSO in Antarctic sea ice

(2011) Elizabeth C. Asher et al.   GEOPHYSICAL RESEARCH LETTERS

Microbial oceanography of the dark ocean's pelagic realm

(2011) Javier Arístegui et al.   LIMNOLOGY AND OCEANOGRAPHY

Bacterial Niche-Specific Genome Expansion Is Coupled with Highly Frequent Gene Disruptions in Deep-Sea Sediments

(2011) Yong Wang et al.   PLoS One

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

New Abundant Microbial Groups in Aquatic Hypersaline Environments

(2011) Rohit Ghai et al.   Scientific Reports

Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21T)

(2011) Yun-juan Chang et al.   Standards in Genomic Sciences

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   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

CO Dehydrogenase Genes Found in Metagenomic Fosmid Clones from the Deep Mediterranean Sea

(2009) A.-B. Martin-Cuadrado et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification of ribosomal RNA genes in metagenomic fragments

(2009) Ying Huang et al.   BIOINFORMATICS

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

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

Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean

(2009) Martha Schattenhofer et al.   ENVIRONMENTAL MICROBIOLOGY

The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity

(2009) M. S. Schwalbach et al.   ENVIRONMENTAL MICROBIOLOGY

Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum

(2009) Dongying Wu et al.   PLoS One

Occurrence and turnover of DMSP and DMS in deep waters of the Ross Sea, Antarctica

(2008) Alison N. Rellinger et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso- and bathypelagic waters of the (sub)tropical Atlantic

(2008) Marta M. Varela et al.   ENVIRONMENTAL MICROBIOLOGY

Isolation of novel bacteria within theChloroflexicapable of reductive dechlorination of 1,2,3-trichloropropane

(2008) J. Yan et al.   ENVIRONMENTAL MICROBIOLOGY

Dimethylsulfoniopropionate-Dependent Demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi

(2008) C. R. Reisch et al.   JOURNAL OF BACTERIOLOGY

SAR11 marine bacteria require exogenous reduced sulphur for growth

(2008) H. James Tripp et al.   NATURE

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Homology Modeling of Dissimilatory APS Reductases (AprBA) of Sulfur-Oxidizing and Sulfate-Reducing Prokaryotes

(2008) Birte Meyer et al.   PLoS One