Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota

The genome of an endosymbiotic methanogen is very similar to those of its free-living relatives

(2018) R.A. Beinart et al.   ENVIRONMENTAL MICROBIOLOGY

Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle

(2018) Anders E. Lind et al.   ISME Journal

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

(2018) Luis M Rodriguez-R et al.   NUCLEIC ACIDS RESEARCH

Detecting signatures of a sponge-associated lifestyle in bacterial genomes

(2018) Cristina Díez-Vives et al.   Environmental Microbiology Reports

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota

(2018) Zheng-Shuang Hua et al.   Nature Communications

“Candidatus Nitrosotenuis aquarius,” an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter

(2018) Laura A. Sauder et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems

(2017) Nathan A. Ahlgren et al.   ENVIRONMENTAL MICROBIOLOGY

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system

(2017) Laura A Sauder et al.   ISME Journal

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics

(2017) Lucas Moitinho-Silva et al.   ISME Journal

Uncultivated microbes in need of their own taxonomy

(2017) Konstantinos T Konstantinidis et al.   ISME Journal

DNA Adenine Methyltransferase (Dam) Overexpression Impairs Photorhabdus luminescens Motility and Virulence

(2017) Amaury Payelleville et al.   Frontiers in Microbiology

The sponge microbiome project

(2017) Lucas Moitinho-Silva et al.   GigaScience

Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge

(2017) Ren-Mao Tian et al.   mSystems

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

(2016) Jessica A Kozlowski et al.   ISME Journal

Evolution and function of eukaryotic-like proteins from sponge symbionts

(2016) David Reynolds et al.   MOLECULAR ECOLOGY

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

Proteomics and comparative genomics ofNitrososphaera viennensisreveal the core genome and adaptations of archaeal ammonia oxidizers

(2016) Melina Kerou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A hydrophobic ammonia-oxidizing archaeon of theNitrosocosmicusclade isolated from coal tar-contaminated sediment

(2016) Man-Young Jung et al.   Environmental Microbiology Reports

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes

(2016) Hannes Horn et al.   Frontiers in Microbiology

A catalogue of 136 microbial draft genomes from Red Sea metagenomes

(2016) Mohamed F. Haroon et al.   Scientific Data

A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics

(2016) Yuyang Li et al.   Scientific Reports

Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

(2016) Hsin-Hung Lin et al.   Scientific Reports

Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle

(2016) M. Aranda et al.   Scientific Reports

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

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

Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation

(2015) Barbara Bayer et al.   ISME Journal

Genomic and proteomic characterization of “CandidatusNitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

(2015) Alyson E. Santoro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges

(2015) Ilia Burgsdorf et al.   mBio

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

(2015) Dongwan D. Kang et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge

(2014) Ren-Mao Tian et al.   ENVIRONMENTAL MICROBIOLOGY

Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea

(2014) Michaela Stieglmeier et al.   ISME Journal

Host-specificity among abundant and rare taxa in the sponge microbiome

(2014) Julie Reveillaud et al.   ISME Journal

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

(2014) R. Louwen et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

Genome Sequence of Candidatus Nitrososphaera evergladensis from Group I.1b Enriched from Everglades Soil Reveals Novel Genomic Features of the Ammonia-Oxidizing Archaea

(2014) Kateryna V. Zhalnina et al.   PLoS One

The many faces of Fic: structural and functional aspects of Fic enzymes

(2014) Abel Garcia-Pino et al.   TRENDS IN BIOCHEMICAL SCIENCES

Symbiotic Adaptation Drives Genome Streamlining of the Cyanobacterial Sponge Symbiont "Candidatus Synechococcus spongiarum"

(2014) Z.-M. Gao et al.   mBio

Bacteriophage Orphan DNA Methyltransferases: Insights from Their Bacterial Origin, Function, and Occurrence

(2013) James Murphy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Intact Polar and Core Glycerol Dibiphytanyl Glycerol Tetraether Lipids of Group I.1a and I.1b Thaumarchaeota in Soil

(2012) Jaap S. Sinninghe Damsté et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2012) Y. Peng et al.   BIOINFORMATICS

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

(2012) Yuri I Wolf et al.   Biology Direct

Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community

(2012) Regina Radax et al.   ENVIRONMENTAL MICROBIOLOGY

The genome of the ammonia-oxidizingCandidatusNitrososphaera gargensis: insights into metabolic versatility and environmental adaptations

(2012) Anja Spang et al.   ENVIRONMENTAL MICROBIOLOGY

Metaproteogenomic analysis of a community of sponge symbionts

(2012) Michael Liu et al.   ISME Journal

Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle

(2012) S.-J. Park et al.   JOURNAL OF BACTERIOLOGY

Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from Marine Sediment

(2012) S.-J. Park et al.   JOURNAL OF BACTERIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genomic insights into the marine sponge microbiome

(2012) Ute Hentschel et al.   NATURE REVIEWS MICROBIOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts

(2012) L. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toxin-Antitoxin Systems Are Important for Niche-Specific Colonization and Stress Resistance of Uropathogenic Escherichia coli

(2012) J. Paul Norton et al.   PLoS Pathogens

Toxin-Antitoxin Systems Influence Biofilm and Persister Cell Formation and the General Stress Response

(2011) Xiaoxue Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference

(2011) Natalia Beloglazova et al.   EMBO JOURNAL

Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system

(2011) Tomas Sinkunas et al.   EMBO JOURNAL

Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms

(2011) Rachel L. Simister et al.   ENVIRONMENTAL MICROBIOLOGY

Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges

(2011) Regina Radax et al.   ENVIRONMENTAL MICROBIOLOGY

Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca2+-dependent Double-stranded DNA Binding Activity

(2011) Ki Hyun Nam et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil

(2011) L. E. Lehtovirta-Morley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil

(2011) M. Tourna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Marine Drugs from Sponge-Microbe Association—A Review

(2010) Tresa Remya A. Thomas et al.   Marine Drugs

Species boundaries and phylogenetic relationships between Atlanto-Mediterranean shallow-water and deep-sea coral associated Hexadella species (Porifera, Ianthellidae)

(2010) Julie Reveillaud et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

(2009) Miquel De Cáceres et al.   ECOLOGY

Bacterial genomic G+C composition-eliciting environmental adaptation

(2009) Scott Mann et al.   GENOMICS

Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont

(2009) John P. McCutcheon et al.   PLoS Genetics

Temperature thresholds for bacterial symbiosis with a sponge

(2008) Nicole S Webster et al.   ISME Journal

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH