Metagenomics of microbial and viral life in terrestrial geothermal environments

Thermus thermophilus as source of thermozymes for biotechnological applications: homologous expression and biochemical characterization of an α-galactosidase

(2017) Martina Aulitto et al.   Microbial Cell Factories

High-level expression of thermostable cellulolytic enzymes in tobacco transplastomic plants and their use in hydrolysis of an industrially pretreated Arundo donax L. biomass

(2016) Daniela Castiglia et al.   Biotechnology for Biofuels

High-throughput pyrosequencing used for the discovery of a novel cellulase from a thermophilic cellulose-degrading microbial consortium

(2016) Chao Zhao et al.   BIOTECHNOLOGY LETTERS

ViromeScan: a new tool for metagenomic viral community profiling

(2016) Simone Rampelli et al.   BMC GENOMICS

Microbial community analysis of pH 4 thermal springs in Yellowstone National Park

(2016) Xiaoben Jiang et al.   EXTREMOPHILES

Microbial diversity and autotrophic activity in Kamchatka hot springs

(2016) Alexander Yu. Merkel et al.   EXTREMOPHILES

Life Cycle Characterization of Sulfolobus Monocaudavirus 1, an Extremophilic Spindle-Shaped Virus with Extracellular Tail Development

(2016) Kristine B. Uldahl et al.   JOURNAL OF VIROLOGY

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

(2016) Emiley A. Eloe-Fadrosh et al.   Nature Communications

Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes

(2016) María-Eugenia DeCastro et al.   Frontiers in Microbiology

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

(2016) Adam G. Clooney et al.   PLoS One

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

(2015) Jacob H. Munson-McGee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transcriptome analysis of Sulfolobus solfataricus infected with two related fuselloviruses reveals novel insights into the regulation of CRISPR-Cas system

(2015) Salvatore Fusco et al.   BIOCHIMIE

The CRISPR-Cas immune system: Biology, mechanisms and applications

(2015) Devashish Rath et al.   BIOCHIMIE

Metagenomics of extreme environments

(2015) DA Cowan et al.   CURRENT OPINION IN MICROBIOLOGY

Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs

(2015) Sóley Ruth Gudbergsdóttir et al.   ENVIRONMENTAL MICROBIOLOGY

Novel thermophilic hemicellulases for the conversion of lignocellulose for second generation biorefineries

(2015) Beatrice Cobucci-Ponzano et al.   ENZYME AND MICROBIAL TECHNOLOGY

Microbial life in Bourlyashchy, the hottest thermal pool of Uzon Caldera, Kamchatka

(2015) Nikolay A. Chernyh et al.   EXTREMOPHILES

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis

(2015) Benjamin Bolduc et al.   ISME Journal

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories

(2015) Christine L Sun et al.   ISME Journal

Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs

(2015) Peter Menzel et al.   MICROBIAL ECOLOGY

Archaeal Extrachromosomal Genetic Elements

(2015) Haina Wang et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

40 Years of archaeal virology: Expanding viral diversity

(2015) Jamie C. Snyder et al.   VIROLOGY

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

(2015) Simon Roux et al.   eLife

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

(2015) Young-Mo Kim et al.   Frontiers in Microbiology

Synergistic function of four novel thermostable glycoside hydrolases from a long-term enriched thermophilic methanogenic digester

(2015) Meng Wang et al.   Frontiers in Microbiology

Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing

(2015) Chia Sing Chan et al.   Frontiers in Microbiology

Diversity of putative archaeal RNA viruses in metagenomic datasets of a yellowstone acidic hot spring

(2015) Hongming Wang et al.   SpringerPlus

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

(2014) Simon Roux et al.   BMC BIOINFORMATICS

New Extremophilic Lipases and Esterases from Metagenomics

(2014) Olalla Lopez-Lopez et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

A standardized protocol for the UV induction of Sulfolobus spindle-shaped virus 1

(2014) Salvatore Fusco et al.   EXTREMOPHILES

Molecular biology of fuselloviruses and their satellites

(2014) Patrizia Contursi et al.   EXTREMOPHILES

Microbial diversity in Los Azufres geothermal field (Michoacán, Mexico) and isolation of representative sulfate and sulfur reducers

(2014) Elcia M. S. Brito et al.   EXTREMOPHILES

Versatile broad-host-range cosmids for construction of high quality metagenomic libraries

(2014) Jiujun Cheng et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Adding genomic 'foliage' to the tree of life

(2014) Alan Walker   NATURE REVIEWS MICROBIOLOGY

Structural and functional studies of Stf76 from the Sulfolobus islandicus plasmid–virus pSSVx: a novel peculiar member of the winged helix–turn–helix transcription factor family

(2014) Patrizia Contursi et al.   NUCLEIC ACIDS RESEARCH

Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

(2014) Rachel Poretsky et al.   PLoS One

Archaeal and bacterial diversity in five different hydrothermal ponds in the Copahue region in Argentina

(2014) M. Sofía Urbieta et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Unveiling viral–host interactions within the ‘microbial dark matter’

(2014) Manuel Martínez-García et al.   Nature Communications

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China

(2014) Shang Wang et al.   Scientific Reports

The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem

(2014) William Inskeep   Frontiers in Microbiology

Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand

(2014) Katrin Hug et al.   Frontiers in Microbiology

Archaeal Viruses: Diversity, Replication, and Structure

(2014) Nikki Dellas et al.   Annual Review of Virology

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

The Wonderful World of Archaeal Viruses

(2013) David Prangishvili   Annual Review of Microbiology

Comparative Genomic Analysis of Phylogenetically Closely Related Hydrogenobaculum sp. Isolates from Yellowstone National Park

(2013) Christine Romano et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Lytic viruses infecting organisms from the three domains of life

(2013) Jamie C. Snyder et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China

(2013) Brandon R. Briggs et al.   ENVIRONMENTAL MICROBIOLOGY

High abundance of heterotrophic prokaryotes in hydrothermal springs of the Azores as revealed by a network of 16S rRNA gene-based methods

(2013) Kerstin Sahm et al.   EXTREMOPHILES

Responding to toxic compounds: a genomic and functional overview of Archaea

(2013) Patrizia Contursi   Frontiers in Bioscience-Landmark

Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park

(2013) Jacob P Beam et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Dissecting genomic diversity, one cell at a time

(2013) Paul C Blainey et al.   NATURE METHODS

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

(2013) Connor T. Skennerton et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing

(2013) Weiguo Hou et al.   PLoS One

Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota

(2013) Laura Eme et al.   RESEARCH IN MICROBIOLOGY

CRISPRTarget

(2013) Ambarish Biswas et al.   RNA Biology

Microbial Diversity and Biochemical Potential Encoded by Thermal Spring Metagenomes Derived from the Kamchatka Peninsula

(2013) Bernd Wemheuer et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry

(2013) William P. Inskeep et al.   Frontiers in Microbiology

Metagenome Sequence Analysis of Filamentous Microbial Communities Obtained from Geochemically Distinct Geothermal Channels Reveals Specialization of Three Aquificales Lineages

(2013) Cristina Takacs-Vesbach et al.   Frontiers in Microbiology

Yellowstone Lake Nanoarchaeota

(2013) Scott Clingenpeel et al.   Frontiers in Microbiology

A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses

(2012) Geoffrey S Diemer et al.   Biology Direct

Glycoside Hydrolases from a targeted Compost Metagenome, activity-screening and functional characterization

(2012) Michael J Dougherty et al.   BMC BIOTECHNOLOGY

Microbial community structure and sulfur biogeochemistry in mildly-acidic sulfidic geothermal springs in Yellowstone National Park

(2012) R.E. Macur et al.   Geobiology

Subsurface structure of the Solfatara volcano (Campi Flegrei caldera, Italy) as deduced from joint seismic-noise array, volcanological and morphostructural analysis

(2012) Simona Petrosino et al.   GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

(2012) Mark A Kozubal et al.   ISME Journal

Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs

(2012) B. Bolduc et al.   JOURNAL OF VIROLOGY

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   NATURE REVIEWS MICROBIOLOGY

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

(2012) Chengwei Luo et al.   PLoS One

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

Archaeal viruses—novel, diverse and enigmatic

(2012) Xu Peng et al.   Science China-Life Sciences

Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass

(2011) John M. Gladden et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Acidophilic bacteria and archaea: acid stable biocatalysts and their potential applications

(2011) Archana Sharma et al.   EXTREMOPHILES

Metagenomic comparison of direct and indirect soil DNA extraction approaches

(2011) Tom O. Delmont et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Sulfolobus Turreted Icosahedral Virus c92 Protein Responsible for the Formation of Pyramid-Like Cellular Lysis Structures

(2011) J. C. Snyder et al.   JOURNAL OF VIROLOGY

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

(2011) M. Krupovic et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Identification and characterization of a multidomain hyperthermophilic cellulase from an archaeal enrichment

(2011) Joel E. Graham et al.   Nature Communications

Use of Cellular CRISPR (Clusters of Regularly Interspaced Short Palindromic Repeats) Spacer-Based Microarrays for Detection of Viruses in Environmental Samples

(2010) J. C. Snyder et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

RNA-Based Investigation of Ammonia-Oxidizing Archaea in Hot Springs of Yunnan Province, China

(2010) H. Jiang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The molecular characterization of a novel GH38 α-mannosidase from the crenarchaeon Sulfolobus solfataricus revealed its ability in de-mannosylating glycoproteins

(2010) Beatrice Cobucci-Ponzano et al.   BIOCHIMIE

The phage-host arms race: Shaping the evolution of microbes

(2010) Adi Stern et al.   BIOESSAYS

Microwave-assisted pretreatment of cellulose in ionic liquid for accelerated enzymatic hydrolysis

(2010) Sung Ho Ha et al.   BIORESOURCE TECHNOLOGY

Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles

(2010) Roger A. Garrett et al.   ENVIRONMENTAL MICROBIOLOGY

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Transcription termination in the plasmid/virus hybrid pSSVx from Sulfolobus islandicus

(2010) Patrizia Contursi et al.   EXTREMOPHILES

Diversity of Crenarchaeota in terrestrial hot springs in Tengchong, China

(2010) Zhao-Qi Song et al.   EXTREMOPHILES

A New Archaeal β-Glycosidase fromSulfolobus solfataricus

(2010) Beatrice Cobucci-Ponzano et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

(2010) Luciano A. Marraffini et al.   NATURE REVIEWS GENETICS

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

(2010) William P. Inskeep et al.   PLoS One

Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community

(2010) Martin Allgaier et al.   PLoS One

CRISPR-mediated phage resistance and the ghost of coevolution past

(2010) P. F. Vale et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A simple and efficient method for concentration of ocean viruses by chemical flocculation

(2010) Seth G. John et al.   Environmental Microbiology Reports

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys

(2009) N. Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogenetic Diversity and Metabolic Potential Revealed in a Glacier Ice Metagenome

(2009) C. Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Toward Plant Cell Wall Degradation Under Thermophilic Condition: A Unique Microbial Community Developed Originally from Swine Waste

(2009) Yanna Liang et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

CRISPI: a CRISPR interactive database

(2009) C. Rousseau et al.   BIOINFORMATICS

Ionic Liquids and Their Interaction with Cellulose

(2009) André Pinkert et al.   CHEMICAL REVIEWS

Expanding the Repertoire of Glycosynthases

(2009) Lai-Xi Wang   CHEMISTRY & BIOLOGY

Caldera unrest prior to intense volcanism in Campi Flegrei (Italy) at 4.0 ka B.P.: Implications for caldera dynamics and future eruptive scenarios

(2009) Roberto Isaia et al.   GEOPHYSICAL RESEARCH LETTERS

Systematic artifacts in metagenomes from complex microbial communities

(2009) Vicente Gomez-Alvarez et al.   ISME Journal

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

A two-host fosmid system for functional screening of (meta)genomic libraries from extreme thermophiles

(2009) Angel Angelov et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

CRISPR-based adaptive and heritable immunity in prokaryotes

(2009) John van der Oost et al.   TRENDS IN BIOCHEMICAL SCIENCES

Replication of porcine circoviruses

(2009) Florence Faurez et al.   Virology Journal

Assembly of Viral Metagenomes from Yellowstone Hot Springs

(2008) T. Schoenfeld et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity of algal viruses in various North American freshwater environments

(2008) SM Short et al.   AQUATIC MICROBIAL ECOLOGY

Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures

(2008) David T Pride et al.   BMC GENOMICS

Molecular modeling and functional characterization of the monomeric primase-polymerase domain from the Sulfolobus solfataricus plasmid pIT3

(2008) Santina Prato et al.   FEBS Journal

Viruses in acidic geothermal environments of the Kamchatka Peninsula

(2008) Ariane Bize et al.   RESEARCH IN MICROBIOLOGY

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

(2008) S. J. J. Brouns et al.   SCIENCE