An archaeal origin of the Wood–Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy

Methanogenesis on Early Stages of Life: Ancient but Not Primordial

(2019) Israel Muñoz-Velasco et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

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

(2019) Guillaume Borrel et al.   Nature Microbiology

GeneSpy, a user-friendly and flexible genomic context visualizer

(2018) Pierre Simon Garcia et al.   BIOINFORMATICS

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

Current Trends in Methylotrophy

(2018) Ludmila Chistoserdova et al.   TRENDS IN MICROBIOLOGY

The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

(2017) Panagiotis S Adam et al.   ISME Journal

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO2fixation pathway

(2017) Israel A. Figueroa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The effect of widespread early aerobic marine ecosystems on methane cycling and the Great Oxidation

(2016) Stuart J. Daines et al.   EARTH AND PLANETARY SCIENCE LETTERS

Examining Archean methanotrophy

(2016) Sarah P. Slotznick et al.   EARTH AND PLANETARY SCIENCE LETTERS

Methanogenesis and the Wood–Ljungdahl Pathway: An Ancient, Versatile, and Fragile Association

(2016) Guillaume Borrel et al.   Genome Biology and Evolution

Dethiosulfatarculus sandiegensis gen. nov., sp. nov., isolated from a methanogenic paraffin-degrading enrichment culture and emended description of the family Desulfarculaceae

(2016) Irene A. Davidova et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

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

Computing the Internode Certainty and Related Measures from Partial Gene Trees

(2016) Kassian Kobert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Thermophilic archaea activate butane via alkyl-coenzyme M formation

(2016) Rafael Laso-Pérez et al.   NATURE

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters

(2016) T. Wagner et al.   SCIENCE

Wide Distribution of Genes for Tetrahydromethanopterin/Methanofuran-Linked C1 Transfer Reactions Argues for Their Presence in the Common Ancestor of Bacteria and Archaea

(2016) Ludmila Chistoserdova   Frontiers in Microbiology

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

(2016) Cristina N. Butterfield et al.   PeerJ

The physiology and habitat of the last universal common ancestor

(2016) Madeline C. Weiss et al.   Nature Microbiology

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

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

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

Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism

(2014) Filipa L. Sousa et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

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

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby et al.   PLoS One

Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines

(2014) Renxing Liang et al.   Frontiers in Microbiology

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

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

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

A Streamlined Strategy for Biohydrogen Production with Halanaerobium hydrogeniformans, an Alkaliphilic Bacterium

(2012) Matthew B. Begemann et al.   Frontiers in Microbiology

Modularity of methylotrophy, revisited

(2011) Ludmila Chistoserdova   ENVIRONMENTAL MICROBIOLOGY

Description of Anaerobaculum hydrogeniformans sp. nov., an anaerobe that produces hydrogen from glucose, and emended description of the genus Anaerobaculum

(2011) M. W. Maune et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A survey of carbon fixation pathways through a quantitative lens

(2011) Arren Bar-Even et al.   JOURNAL OF EXPERIMENTAL BOTANY

Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?

(2010) Georg Fuchs   Annual Review of Microbiology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

(2010) Katharina F. Ettwig et al.   NATURE

Microorganisms and climate change: terrestrial feedbacks and mitigation options

(2010) Brajesh K. Singh et al.   NATURE REVIEWS MICROBIOLOGY

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Oceanic nickel depletion and a methanogen famine before the Great Oxidation Event

(2009) Kurt O. Konhauser et al.   NATURE

A Revised, Hazy Methane Greenhouse for the Archean Earth

(2008) Jacob D. Haqq-Misra et al.   ASTROBIOLOGY

Formate as the Main Branch Point for Methylotrophic Metabolism in Methylobacterium extorquens AM1

(2008) G. J. Crowther et al.   JOURNAL OF BACTERIOLOGY

A Major Clade of Prokaryotes with Ancient Adaptations to Life on Land

(2008) F. U. Battistuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION