Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)

Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria

(2019) Maxim Rubin-Blum et al.   mSphere

Chemosynthetic ectosymbionts associated with a shallow-water marine nematode

(2019) Laure Bellec et al.   Scientific Reports

A short history of RubisCO: the rise and fall (?) of Nature's predominant CO 2 fixing enzyme

(2018) Tobias J Erb et al.   CURRENT OPINION IN BIOTECHNOLOGY

Endosymbiont genomes yield clues of tubeworm success

(2018) Yuanning Li et al.   ISME Journal

Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

(2018) Manuel Kleiner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reversibility of citrate synthase allows autotrophic growth of a thermophilic bacterium

(2018) Achim Mall et al.   SCIENCE

A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile

(2018) Takuro Nunoura et al.   SCIENCE

Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

(2018) Petra Pjevac et al.   Frontiers in Microbiology

Addendum: Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

(2018) David W. Waite et al.   Frontiers in Microbiology

Success of chemolithoautotrophic SUP05 and Sulfurimonas GD17 cells in pelagic Baltic Sea redox zones is facilitated by their lifestyles as K- and r -strategists

(2017) Andreas Rogge et al.   ENVIRONMENTAL MICROBIOLOGY

Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents

(2017) Dimitri V Meier et al.   ISME Journal

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

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents

(2017) Rika E. Anderson et al.   Nature Communications

Assessing species biomass contributions in microbial communities via metaproteomics

(2017) Manuel Kleiner et al.   Nature Communications

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

(2017) David W. Waite et al.   Frontiers in Microbiology

Short-chain alkanes fuel mussel and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps

(2017) Maxim Rubin-Blum et al.   Nature Microbiology

Sugar Synthesis from CO2 in Escherichia coli

(2016) Niv Antonovsky et al.   CELL

Ecological succession leads to chemosynthesis in mats colonizing wood in sea water

(2016) Dimitri Kalenitchenko et al.   ISME Journal

Trophic plasticity of the methanotrophic mussel Bathymodiolus childressi in the Gulf of Mexico

(2016) PM Riekenberg et al.   MARINE ECOLOGY PROGRESS SERIES

Environmental Breviatea harbour mutualistic Arcobacter epibionts

(2016) Emmo Hamann et al.   NATURE

A synthetic pathway for the fixation of carbon dioxide in vitro

(2016) Thomas Schwander et al.   SCIENCE

A specific and widespread association between deep-seaBathymodiolusmussels and a novel family of Epsilonproteobacteria

(2016) Adrien Assié et al.   Environmental Microbiology Reports

Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions

(2016) Matthias Winkel et al.   Frontiers in Microbiology

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

(2016) Beverly E. Flood et al.   Frontiers in Microbiology

Trophic plasticity of the methanotrophic mussel Bathymodiolus childressi in the Gulf of Mexico

(2016) PM Riekenberg et al.   MARINE ECOLOGY PROGRESS SERIES

Improved ultrastructure of marine invertebrates using non-toxic buffers

(2016) Jacqueline Montanaro et al.   PeerJ

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation

(2016) Jillian M. Petersen et al.   Nature 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

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

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

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Microbial lipids reveal carbon assimilation patterns on hydrothermal sulfide chimneys

(2014) Eoghan P. Reeves et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial consumption of zero-valence sulfur in marine benthic habitats

(2014) Petra Pjevac et al.   ENVIRONMENTAL MICROBIOLOGY

Epsilonproteobacteria as gill epibionts of the hydrothermal vent gastropod Cyathermia naticoides (North East-Pacific Rise)

(2014) Magali Zbinden et al.   MARINE BIOLOGY

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Linking regional variation of epibiotic bacterial diversity and trophic ecology in a new species of Kiwaidae (Decapoda, Anomura) from East Scotia Ridge (Antarctica) hydrothermal vents

(2014) Katrin Zwirglmaier et al.   MicrobiologyOpen

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria

(2013) Ida Porcelli et al.   BMC GENOMICS

Sulfide oxidation, nitrate respiration, carbon acquisition, and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) sp. filament

(2013) Barbara J. MacGregor et al.   Marine Genomics

Rapid Embedding Methods into Epoxy and LR White Resins for Morphological and Immunological Analysis of Cryofixed Biological Specimens

(2013) Kent L. McDonald   MICROSCOPY AND MICROANALYSIS

Rubisco: still the most abundant protein of Earth?

(2013) John A. Raven   NEW PHYTOLOGIST

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Metaproteomics Reveals Abundant Transposase Expression in Mutualistic Endosymbionts

(2013) M. Kleiner et al.   mBio

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Isolation of an aerobic sulfur oxidizer from the SUP05/Arctic96BD-19 clade

(2012) Katharine T Marshall et al.   ISME Journal

Bioengineering of carbon fixation, biofuels, and biochemicals in cyanobacteria and plants

(2012) Lisa Rosgaard et al.   JOURNAL OF BIOTECHNOLOGY

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

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

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Chemoautotrophy at Deep-Sea Vents: Past, Present, and Future

(2012) Stefan Sievert et al.   OCEANOGRAPHY

Evidence for the role of endosymbionts in regional-scale habitat partitioning by hydrothermal vent symbioses

(2012) R. A. Beinart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Ecological Aspects of the Distribution of Different Autotrophic CO2Fixation Pathways

(2011) Ivan A. Berg   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Analysis of codon usage in type 1 and the new genotypes of duck hepatitis virus

(2011) Meng Wang et al.   BIOSYSTEMS

Change Is Good: Variations in Common Biological Mechanisms in the Epsilonproteobacterial Genera Campylobacter and Helicobacter

(2011) J. J. Gilbreath et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Hydrogen is an energy source for hydrothermal vent symbioses

(2011) Jillian M. Petersen et al.   NATURE

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Sulfur Metabolisms in Epsilon- and Gamma-Proteobacteria in Deep-Sea Hydrothermal Fields

(2011) Masahiro Yamamoto et al.   Frontiers in Microbiology

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

(2010) Michael Hügler et al.   Annual Review of Marine Science

Design and analysis of synthetic carbon fixation pathways

(2010) A. Bar-Even et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Contributions of anoxygenic and oxygenic phototrophy and chemolithotrophy to carbon and oxygen fluxes in aquatic environments

(2009) JA Raven   AQUATIC MICROBIAL ECOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Macrobenthos community structure and trophic relationships within active and inactive Pacific hydrothermal sediments

(2009) Lisa A. Levin et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Symbioses between deep-sea mussels (Mytilidae: Bathymodiolinae) and chemosynthetic bacteria: diversity, function and evolution

(2008) Sébastien Duperron et al.   COMPTES RENDUS BIOLOGIES

Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics

(2008) Julie C. Robidart et al.   ENVIRONMENTAL MICROBIOLOGY

Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance

(2008) Satoshi Nakagawa et al.   FEMS MICROBIOLOGY ECOLOGY

Stable Isotope Variation Among the Mussel Bathymodiolus childressi and Associated Heterotrophic Fauna at Four Cold-Seep Communities in the Gulf of Mexico

(2008) S. E. MacAvoy et al.   JOURNAL OF SHELLFISH RESEARCH

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis

(2008) Nicole Dubilier et al.   NATURE REVIEWS MICROBIOLOGY

The evolution of modularity in bacterial metabolic networks

(2008) A. Kreimer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY