New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification of Complex Rumen Microbiome Interaction Within Diverse Functional Niches as Mechanisms Affecting the Variation of Methane Emissions in Bovine

(2020) Marina Martínez-Álvaro et al.   Frontiers in Microbiology

The host-associated archaeome

(2020) Guillaume Borrel et al.   NATURE REVIEWS MICROBIOLOGY

Microbial Community Composition and Function in Sediments from the Pearl River Mouth Basin

(2020) Ye Chen et al.   Journal of Ocean University of China

Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments

(2020) Cui-Jing Zhang et al.   Microbiome

Evidence for non‐methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales

(2020) Laura A. Zinke et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic insights into the metabolism and evolution of a new Thermoplasmata order ( Candidatus Gimiplasmatales)

(2020) Wenzhe Hu et al.   ENVIRONMENTAL MICROBIOLOGY

Genome of the candidate phylum Aminicenantes bacterium from a deep subsurface thermal aquifer revealed its fermentative saccharolytic lifestyle

(2019) Vitaly V. Kadnikov et al.   EXTREMOPHILES

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

Active prokaryotic population dynamics exhibit high correlation to reactor performance during methane production from acid hydrolysates of Agave tequilana var. azul bagasse

(2019) R. Snell‐Castro et al.   JOURNAL OF APPLIED MICROBIOLOGY

Methane Emission, Rumen Fermentation, and Microbial Community Response to a Nitrooxy Compound in Low-Quality Forage Fed Hu Sheep

(2019) Fei Xie et al.   CURRENT MICROBIOLOGY

Mercury methylation by anaerobic microorganisms: A review

(2019) Ming Ma et al.   CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY

Energy conservation in the gut microbe Methanomassiliicoccus luminyensis is based on membrane‐bound ferredoxin oxidation coupled to heterodisulfide reduction

(2019) Lena Kröninger et al.   FEBS Journal

Magnetite as an enhancer in methanogenic degradation of volatile fatty acids under ammonia-stressed condition

(2019) Joonyeob Lee et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health

(2019) Jillian L. Waters et al.   BMC BIOLOGY

Seasonal dynamics of bacterial communities in a Betula albosinensis forest

(2018) C. Du et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Structure of microbial communities of peat soils in two bogs in Siberian tundra and forest zones

(2018) I. D. Grodnitskaya et al.   MICROBIOLOGY

Temperature effects on structure and function of the methanogenic microbial communities in two paddy soils and one desert soil

(2018) Pengfei Liu et al.   SOIL BIOLOGY & BIOCHEMISTRY

Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages

(2018) Xiaobo Liu et al.   Microbiome

Metagenomic analyses highlight the symbiotic association between the glacier stonefly Andiperla willinki and its bacterial gut community

(2018) Takumi Murakami et al.   ENVIRONMENTAL MICROBIOLOGY

Polyamine function in archaea and bacteria

(2018) Anthony J. Michael   JOURNAL OF BIOLOGICAL CHEMISTRY

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome

(2017) Guillaume Borrel et al.   ISME Journal

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

(2017) Panagiotis S Adam et al.   ISME Journal

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

Growth Characteristics of Methanomassiliicoccus luminyensis and Expression of Methyltransferase Encoding Genes

(2017) Lena Kröninger et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

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

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

Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens

(2016) Kevin W. Becker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

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

(2016) Masaru Konishi Nobu et al.   ISME Journal

A Novel Putrescine Exporter SapBCDF ofEscherichia coli

(2016) Yuta Sugiyama et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Archaeal communities in the sediments of different mangrove stands at Dongzhaigang, China

(2016) Wei Li et al.   JOURNAL OF SOILS AND SEDIMENTS

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Diversity of methanogenic archaea from the 2012 terrestrial hot spring (Valley of Geysers, Kamchatka)

(2016) A. Y. Merkel et al.   MICROBIOLOGY

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

(2016) David Vallenet et al.   NUCLEIC ACIDS RESEARCH

Methane production from coal by a single methanogen

(2016) D. Mayumi et al.   SCIENCE

Comparison of microbial communities during the anaerobic digestion of Gracilaria under mesophilic and thermophilic conditions

(2016) Aqil Azizi et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the Methanomassiliicoccales

(2016) Yang Li et al.   Standards in Genomic Sciences

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

(2016) Inka Vanwonterghem et al.   Nature Microbiology

Archaea and the human gut: New beginning of an old story

(2016) Nadia Gaci et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison

(2015) Michael Richter et al.   BIOINFORMATICS

Microbial community of the deep-sea brine LakeKryosseawater-brine interface is active below the chaotropicity limit of life as revealed by recovery of mRNA

(2015) Michail M. Yakimov et al.   ENVIRONMENTAL MICROBIOLOGY

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Evidence for the involvement of two heterodisulfide reductases in the energy-conserving system ofMethanomassiliicoccus luminyensis

(2015) Lena Kröninger et al.   FEBS Journal

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

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

Noteworthy Facts about a Methane-Producing Microbial Community Processing Acidic Effluent from Sugar Beet Molasses Fermentation

(2015) Aleksandra Chojnacka et al.   PLoS One

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

(2015) P. N. Evans et al.   SCIENCE

Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes

(2015) Zhichao Zhou et al.   Frontiers in Microbiology

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

(2015) Dongwan D. Kang et al.   PeerJ

The microbiome of uncontacted Amerindians

(2015) J. C. Clemente et al.   Science Advances

Global prevalence and distribution of genes and microorganisms involved in mercury methylation

(2015) M. Podar et al.   Science Advances

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Illuminating Microbial Dark Matter in Meromictic Sakinaw Lake

(2014) Esther A. Gies et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

New Mode of Energy Metabolism in the Seventh Order of Methanogens as Revealed by Comparative Genome Analysis of “Candidatus Methanoplasma termitum”

(2014) Kristina Lang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   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

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Reclassification of Desulfobacterium anilini as Desulfatiglans anilini comb. nov. within Desulfatiglans gen. nov., and description of a 4-chlorophenol-degrading sulfate-reducing bacterium, Desulfatiglans parachlorophenolica sp. nov.

(2014) D. Suzuki et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere:geosphere interactions

(2014) R. John Parkes et al.   MARINE GEOLOGY

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

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette

(2014) Guillaume Borrel et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

AlienTrimmer removes adapter oligonucleotides with high sensitivity in short-insert paired-end reads. Commentary on Turner (2014) Assessment of insert sizes and adapter content in FASTQ data from NexteraXT libraries

(2014) Alexis Criscuolo et al.   Frontiers in Genetics

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia

(2013) Natalya Yutin et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogenomic Data Support a Seventh Order of Methylotrophic Methanogens and Provide Insights into the Evolution of Methanogenesis

(2013) Guillaume Borrel et al.   Genome Biology and Evolution

Candidatus Methanogranum caenicola: a Novel Methanogen from the Anaerobic Digested Sludge, and Proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a Methanogenic Lineage of the Class Thermoplasmata

(2013) Takao Iino et al.   MICROBES AND ENVIRONMENTS

Three decades of global methane sources and sinks

(2013) Stefanie Kirschke et al.   Nature Geoscience

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

The Genetic Basis for Bacterial Mercury Methylation

(2013) J. M. Parks et al.   SCIENCE

Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park

(2013) Kara Bowen De León et al.   Frontiers in Microbiology

Choline andN,N-Dimethylethanolamine as Direct Substrates for Methanogens

(2012) Andrew J. Watkins et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

“Methanoplasmatales,” Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens

(2012) Kristina Paul et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces

(2012) B. Dridi et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Genome Sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a Methanogenic Archaeon from the Human Gut Belonging to a Seventh Order of Methanogens

(2012) G. Borrel et al.   JOURNAL OF BACTERIOLOGY

Identification of microbial communities involved in the methane cycle of a freshwater meromictic lake

(2011) Corinne Biderre-Petit et al.   FEMS MICROBIOLOGY ECOLOGY

Methanolinea mesophila sp. nov., a hydrogenotrophic methanogen isolated from rice field soil, and proposal of the archaeal family Methanoregulaceae fam. nov. within the order Methanomicrobiales

(2011) S. Sakai et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Description of Christensenella minuta gen. nov., sp. nov., isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal of Christensenellaceae fam. nov.

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

Arsenic: toxicity, oxidative stress and human disease

(2011) K. Jomova et al.   JOURNAL OF APPLIED TOXICOLOGY

Biogeography Revisited with Network Theory: Retracing the History of Hydrothermal Vent Communities

(2011) Yann Moalic et al.   SYSTEMATIC BIOLOGY

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation

(2010) Jessica R. Sieber et al.   Annual Review of Microbiology

Prokaryotic functional diversity in different biogeochemical depth zones in tidal sediments of  the Severn Estuary, UK, revealed by stable-isotope probing

(2010) Gordon Webster et al.   FEMS MICROBIOLOGY ECOLOGY

Syntrophic butyrate and propionate oxidation processes: from genomes to reaction mechanisms

(2010) Nicolai Müller et al.   Environmental Microbiology Reports

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

Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity

(2009) Agnès Mihajlovski et al.   Environmental Microbiology Reports

Physiology, Ecology, Phylogeny, and Genomics of Microorganisms Capable of Syntrophic Metabolism

(2008) Michael J. McInerney et al.   Annals of the New York Academy of Sciences

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT