A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

(2018) Panagiotis S. Adam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1)

(2017) Rosa León-Zayas et al.   ENVIRONMENTAL MICROBIOLOGY

Human embryos: Collect reliable data on embryo selection

(2017) Charis Thompson   NATURE

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

Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio

(2017) Anne-Catherine Ahn et al.   PLoS One

Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities

(2017) R. E. Danczak et al.   Microbiome

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis

(2017) Dimitry Y. Sorokin et al.   Nature Microbiology

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation

(2017) Cindy J. Castelle et al.   Scientific Reports

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2concentrations

(2016) Alexander J. Probst et al.   ENVIRONMENTAL MICROBIOLOGY

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

(2016) Kelly C Wrighton et al.   ISME Journal

Phylogenomic analysis of Candidatus ‘Izimaplasma’ species: free-living representatives from a Tenericutes clade found in methane seeps

(2016) Connor T Skennerton et al.   ISME Journal

Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen

(2016) Masaru Konishi Nobu et al.   ISME Journal

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

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

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

Small but mighty: how minor components drive major biogeochemical cycles

(2016) Colleen Hansel   Environmental Microbiology Reports

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

(2016) Karthik Anantharaman et al.   Nature Communications

Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines

(2016) Charlotte D. Vavourakis et al.   Frontiers in Microbiology

Genome-Based Taxonomic Classification of Bacteroidetes

(2016) Richard L. Hahnke et al.   Frontiers in Microbiology

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

(2016) Karthik Anantharaman et al.   PeerJ

A new view of the tree of life

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

Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia

(2015) William C. Nelson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2015) Dinghua Li et al.   BIOINFORMATICS

Functional microbiology of soda lakes

(2015) Dimitry Y Sorokin et al.   CURRENT OPINION IN MICROBIOLOGY

Desulfonatronobacter acetoxydans sp. nov.,: a first acetate-oxidizing, extremely salt-tolerant alkaliphilic SRB from a hypersaline soda lake

(2015) D. Y. Sorokin et al.   EXTREMOPHILES

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

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

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics

(2015) Tomàs Llorens-Marès et al.   ISME Journal

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Evidence for the presence of key chlorophyll-biosynthesis-related proteins in the genus Rubrobacter (Phylum Actinobacteria) and its implications for the evolution and origin of photosynthesis

(2015) Radhey S. Gupta et al.   PHOTOSYNTHESIS RESEARCH

Diverse uncultivated ultra-small bacterial cells in groundwater

(2015) Birgit Luef et al.   Nature Communications

Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome

(2015) Vímac Nolla-Ardèvol et al.   Frontiers in Microbiology

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking

(2015) Yuji Sekiguchi et al.   PeerJ

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

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine

(2014) Guillaume Borrel et al.   BMC GENOMICS

Microbial diversity and biogeochemical cycling in soda lakes

(2014) Dimitry Y. Sorokin et al.   EXTREMOPHILES

Algo-bacterial communities of the Kulunda steppe (Altai Region, Russia) Soda Lakes

(2014) O. S. Samylina et al.   MICROBIOLOGY

Sulfate-dependent acetate oxidation under extremely natron-alkaline conditions by syntrophic associations from hypersaline soda lakes

(2014) D. Y. Sorokin et al.   MICROBIOLOGY-SGM

Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat

(2014) Anna Hanke et al.   Frontiers in Microbiology

Disproportionation of elemental sulfur by haloalkaliphilic bacteria from soda lakes

(2013) Alexander Poser et al.   EXTREMOPHILES

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

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

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

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

(2013) R. S. Kantor et al.   mBio

Life at high salt concentrations, intracellular KCl concentrations, and acidic proteomes

(2013) Aharon Oren   Frontiers in Microbiology

Comparative structural and functional analysis of two octaheme nitrite reductases from closely relatedThioalkalivibriospecies

(2012) Tamara Tikhonova et al.   FEBS Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

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

Molecular aspects of bacterial pH sensing and homeostasis

(2011) Terry A. Krulwich et al.   NATURE REVIEWS MICROBIOLOGY

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

(2011) Lucie Zinger et al.   PLoS One

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

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

An integrative study of a meromictic lake ecosystem in Antarctica

(2010) Federico M Lauro et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Enzymology of the Wood-Ljungdahl Pathway of Acetogenesis

(2008) Stephen W. Ragsdale   Annals of the New York Academy of Sciences

Dethiobacter alkaliphilus gen. nov. sp. nov., and Desulfurivibrio alkaliphilus gen. nov. sp. nov.: two novel representatives of reductive sulfur cycle from soda lakes

(2008) D. Yu. Sorokin et al.   EXTREMOPHILES

An uncultivated crenarchaeota contains functional bacteriochlorophyll a synthase

(2008) Jun Meng et al.   ISME Journal

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH