Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria

Anaerobic degradation of paraffins by thermophilic Actinobacteria under methanogenic conditions

(2020) Yifan Liu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Older Than Genes: The Acetyl CoA Pathway and Origins

(2020) William F. Martin   Frontiers in Microbiology

Single-Cell Genomics of Novel Actinobacteria With the Wood–Ljungdahl Pathway Discovered in a Serpentinizing System

(2020) Nancy Merino et al.   Frontiers in Microbiology

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys

(2020) Jialin Hou et al.   Microbiome

Microbial dark matter coming to light: challenges and opportunities

(2020) Jian-Yu Jiao et al.   National Science Review

An evolving view of methane metabolism in the Archaea

(2019) Paul N. Evans et al.   NATURE REVIEWS MICROBIOLOGY

Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea

(2019) Guillaume Borrel et al.   Nature Microbiology

Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism

(2019) Anja Spang et al.   Nature Microbiology

Update on the classification of higher ranks in the phylum Actinobacteria

(2019) Nimaichand Salam et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments

(2019) William D. Orsi et al.   Nature Microbiology

Scaling read aligners to hundreds of threads on general-purpose processors

(2018) Ben Langmead et al.   BIOINFORMATICS

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

(2018) Jongsik Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

Structural absorption by barbule microstructures of super black bird of paradise feathers

(2018) Dakota E. McCoy et al.   Nature Communications

Abundant and Rare Microbial Biospheres Respond Differently to Environmental and Spatial Factors in Tibetan Hot Springs

(2018) Yanmin Zhang et al.   Frontiers in Microbiology

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

(2018) Charlotte D. Vavourakis et al.   Microbiome

Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea

(2018) Alexander L Jaffe et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Double-slit photoelectron interference in strong-field ionization of the neon dimer

(2018) Maksim Kunitski et al.   Nature Communications

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Energetics and Application of Heterotrophy in Acetogenic Bacteria

(2016) Kai Schuchmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

(2016) Kiley W Seitz et al.   ISME Journal

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

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

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard 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

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

(2015) Chris Greening et al.   ISME Journal

The two-domain tree of life is linked to a new root for the Archaea

(2015) Kasie Raymann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Dongwan D. Kang et al.   PeerJ

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

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

Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

(2014) Albert Leopold Müller 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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria

(2014) Kai Schuchmann et al.   NATURE REVIEWS MICROBIOLOGY

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

A missing link between complex I and group 4 membrane-bound [NiFe] hydrogenases

(2012) Bruno C. Marreiros et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

First insights into the syntrophic acetate-oxidizing bacteria - a genetic study

(2012) Bettina Müller et al.   MicrobiologyOpen

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

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

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

Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation

(2008) Stephen W. Ragsdale et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS