List of works - Gene W. Tyson

A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres

scientific article

A genomic view of the reef-building coral Porites lutea and its microbial symbionts

scientific article published on 23 September 2019

A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments

scientific article

A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction.

scientific article published on 16 April 2018

A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities.

scientific article

A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)

scientific article published in 2018

Accelerating microbial iron cycling promotes re-cementation of surface crusts in iron ore regions

scientific article published on 19 August 2020

Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities

scientific article

Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling

article

An evolving view of methane metabolism in the Archaea

scientific article published on 21 January 2019

An expanded genomic representation of the phylum cyanobacteria

scientific article

Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae

scientific article published on 27 January 2020

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

scientific article

Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes

scientific article published on 19 December 2016

Application of metatranscriptomics to soil environments

scientific article

Archaeal and bacterial communities across a chronosequence of drained lake basins in Arctic Alaska.

scientific article published on 18 December 2015

Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

scientific article published on 12 December 2017

Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus

scientific article published on 21 May 2015

Biogenic Methane Cycling in a Laboratory Model of an Abandoned Bituminous Coal Mine

article

Biomass retention on electrodes rather than electrical current enhances stability in anaerobic digestion.

scientific article published on 3 February 2014

Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community.

scientific article

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

scientific article published on 14 May 2015

Chemotaxis by natural populations of coral reef bacteria

scientific article

Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean

scientific article published in 2022

Community proteomics of a natural microbial biofilm

scientific article published on 5 May 2005

Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

scientific article published on 05 January 2022

Comparison of microbial communities across sections of a corroding sewer pipe and the effects of wastewater flooding.

scientific article published on 28 September 2017

Consent insufficient for data release-Response

scientific article published on 01 May 2019

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.

scientific article published on 7 April 2014

Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

scientific article

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

scientific article published in February 2018

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

article

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

scientific article

Cultivating the uncultivated: a community genomics perspective

scientific article

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size

article

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

scientific article

Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., ...

scholarly article published on 14 December 2018

Discovery of a novel methanogen prevalent in thawing permafrost

scientific article

Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon

scientific article published on 8 March 2016

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

scientific article published on 16 January 2019

Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients

scientific article published on 21 March 2013

Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome

scientific article published on May 2015

Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors

scientific article

Dynamics of cathode-associated microbial communities and metabolite profiles in a glycerol-fed bioelectrochemical system

scientific article

Effects of nitrate dosing on sulfidogenic and methanogenic activities in sewer sediment.

scientific article

Erratum for Skennerton et al., "Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea".

scientific article

Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

scientific article published in Nature

Erratum: Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

article

Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome

scientific article published on 20 April 2021

Expanding our view of genomic diversity in Candidatus Accumulibacter clades

scientific article published on 27 August 2014

Fast, accurate error-correction of amplicon pyrosequences using Acacia

scientific article published on 27 April 2012

Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal

scientific article

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking.

scientific article

Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations

scientific article published on 27 May 2010

Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation

scientific article published on 25 February 2021

Future reef decalcification under a business-as-usual CO2 emission scenario

scientific article

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion.

scientific article published on 16 November 2017

Genetic exchange across a species boundary in the archaeal genus ferroplasma

scientific article

Genome dynamics in a natural archaeal population

scientific article

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

scientific article

Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well

scientific article

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.

scientific article published on 18 June 2016

Genome-centric view of carbon processing in thawing permafrost

scientific article published in Nature

Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community

scientific article

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

scientific article published on 19 March 2018

Grinder: a versatile amplicon and shotgun sequence simulator

scientific article

GroopM: an automated tool for the recovery of population genomes from related metagenomes.

scientific article

Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix

scientific article published on 10 February 2015

High-throughput amplicon sequencing reveals distinct communities within a corroding concrete sewer system

scientific article

Host-linked soil viral ecology along a permafrost thaw gradient

article

In-Solution Fluorescence In Situ Hybridization and Fluorescence-Activated Cell Sorting for Single Cell and Population Genome Recovery

article

Insights into the diversity of eukaryotes in acid mine drainage biofilm communities.

scientific article

Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea

scientific article published on 08 October 2019

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

scientific article

Lineages of acidophilic archaea revealed by community genomic analysis

scientific article

Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques

scientific article

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events

scientific article published on 5 January 2016

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm

scientific article

Metagenomics using next-generation sequencing

scientific article published in January 2014

Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column

scientific article

Methane dynamics regulated by microbial community response to permafrost thaw

scientific article published in October 2014

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

scientific article

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea

scientific article published on August 2017

Methanotrophy across a natural permafrost thaw environment

article

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

scientific article

Microbial community gene expression in ocean surface waters

scientific article

Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle

scientific article published on 28 May 2024

Microbiology: metagenomics

scientific article published in September 2008

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

scientific article

OrfM: a fast open reading frame predictor for metagenomic data

scientific article

Phage encoded H-NS: a potential achilles heel in the bacterial defence system

scientific article

Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps

scientific article published on 8 April 2016

Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses.

scientific article

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

scientific article published on 11 September 2017

Redefining the sponge-symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host-derived compounds.

scientific article

Rhizosphere Metatranscriptomics: Challenges and Opportunities

article

STAMP: statistical analysis of taxonomic and functional profiles.

scientific article

Selective Enrichment Establishes a Stable Performing Community for Microbial Electrosynthesis of Acetate from CO₂.

scientific article published on 30 June 2015

Sequencing platform and library preparation choices impact viral metagenomes

scientific article

Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data

scientific article

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

article

Spatial uniformity of microbial diversity in a continuous bioelectrochemical system

scientific article

Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.

scientific article published on 7 March 2007

Strainer: software for analysis of population variation in community genomic datasets.

scientific article

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years

scientific article published on 06 October 2021

Systems Level Dissection of Anaerobic Methane Cycling: Quantitative Measurements of Single Cell Ecophysiology, Genetic Mechanisms, and Microbial Interactions

article

Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters

scientific article published on 16 February 2015

Temporal changes in microbial community composition during culture enrichment experiments with Indonesian coals

article

The Bio-Community Perl toolkit for microbial ecology

scientific article

The Opportunity for High-Performance Biomaterials from Methane

scientific article

The effect of bituminous coal on methanogenic mixed cultures and pure cultures of Methanococcus and Methanosarcina

article

The effect of coal rank on biogenic methane potential and microbial composition

article

The importance of designating type material for uncultured taxa

article

The influence of hydrogeological disturbance and mining on coal seam microbial communities.

scientific article published on 6 November 2015

Toward unrestricted use of public genomic data:

scientific article

Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidal

scientific article published on 30 January 2019

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

scientific article

Where next for microbiome research?

scientific article

Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses

scientific article

[Are divergent viral communities controlling individual gut microbiota?]

scientific article published on 30 March 2011

pH and Organic Carbon Dose Rates Control Microbially Driven Bioremediation Efficacy in Alkaline Bauxite Residue

scientific article published on 28 September 2016

List of works by Gene W. Tyson

A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres

A genomic view of the reef-building coral Porites lutea and its microbial symbionts

A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments

A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction.

A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities.

A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)

Accelerating microbial iron cycling promotes re-cementation of surface crusts in iron ore regions

Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities

Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling

An evolving view of methane metabolism in the Archaea

An expanded genomic representation of the phylum cyanobacteria

Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes

Application of metatranscriptomics to soil environments

Archaeal and bacterial communities across a chronosequence of drained lake basins in Arctic Alaska.

Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus

Biogenic Methane Cycling in a Laboratory Model of an Abandoned Bituminous Coal Mine

Biomass retention on electrodes rather than electrical current enhances stability in anaerobic digestion.

Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community.

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

Chemotaxis by natural populations of coral reef bacteria

Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean

Community proteomics of a natural microbial biofilm

Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

Comparison of microbial communities across sections of a corroding sewer pipe and the effects of wastewater flooding.

Consent insufficient for data release-Response

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.

Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

Cultivating the uncultivated: a community genomics perspective

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., ...

Discovery of a novel methanogen prevalent in thawing permafrost

Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients

Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome

Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors

Dynamics of cathode-associated microbial communities and metabolite profiles in a glycerol-fed bioelectrochemical system

Effects of nitrate dosing on sulfidogenic and methanogenic activities in sewer sediment.

Erratum for Skennerton et al., "Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea".

Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

Erratum: Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome

Expanding our view of genomic diversity in Candidatus Accumulibacter clades

Fast, accurate error-correction of amplicon pyrosequences using Acacia

Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking.

Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations

Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation

Future reef decalcification under a business-as-usual CO2 emission scenario

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion.

Genetic exchange across a species boundary in the archaeal genus ferroplasma

Genome dynamics in a natural archaeal population

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.

Genome-centric view of carbon processing in thawing permafrost

Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

Grinder: a versatile amplicon and shotgun sequence simulator

GroopM: an automated tool for the recovery of population genomes from related metagenomes.

Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix

High-throughput amplicon sequencing reveals distinct communities within a corroding concrete sewer system

Host-linked soil viral ecology along a permafrost thaw gradient

In-Solution Fluorescence In Situ Hybridization and Fluorescence-Activated Cell Sorting for Single Cell and Population Genome Recovery

Insights into the diversity of eukaryotes in acid mine drainage biofilm communities.

Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

Lineages of acidophilic archaea revealed by community genomic analysis

Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm

Metagenomics using next-generation sequencing