List of works - Brian C. Thomas

A new view of the tree of life

scientific article (publication date: 11 April 2016)

A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges.

scientific article

A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes

scientific article

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

scientific article

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum.

scientific article published on 28 January 2016

Aquifer environment selects for microbial species cohorts in sediment and groundwater

scientific article published on 3 February 2015

Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

scientific article published on 26 March 2019

Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface

scientific article published on 26 November 2014

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics.

scientific article published in June 2015

Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community

scientific article published on 29 November 2012

CRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus

scientific article

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

scientific article published on 05 August 2013

Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities

scientific article

Community-wide analysis of microbial genome sequence signatures

scientific article

Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

scientific article

Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms

scientific article

Complete 4.55-Megabase-Pair Genome of "Candidatus Fluviicola riflensis," Curated from Short-Read Metagenomic Sequences

scientific article

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

scientific article

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface.

scientific article published on 29 January 2018

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.

scientific article

Diverse uncultivated ultra-small bacterial cells in groundwater

scientific article

Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly

scientific article

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

scientific article

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment.

scientific article published on 8 September 2017

Ecological distribution and population physiology defined by proteomics in a natural microbial community.

scientific article

Elevated temperature alters proteomic responses of individual organisms within a biofilm community.

scientific article

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants.

scientific article published on 3 June 2016

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

scientific article published on 21 February 2018

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment.

scientific article published on January 2013

Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla

scientific article published in September 2012

Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life

scientific article published on 17 December 2013

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation.

scientific article

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs.

scientific article published on 19 January 2016

Genome-reconstruction for eukaryotes from complex natural microbial communities.

scientific article published in March 2018

Genome-resolved metagenomics and detailed geochemical speciation analyses yield new insights into microbial mercury cycling in geothermal springs

scientific article published on 15 May 2020

Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings

scientific article

Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.

scientific article

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations.

scientific article published on 26 April 2016

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development.

scientific article

Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities

scientific article

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles.

scientific article published on 10 April 2018

Hydrogen-based metabolism - An ancestral trait in lineages sibling to the Cyanobacteria

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

scientific article published in Nature Communications

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

scientific article published on 10 January 2017

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

scientific article published on 3 February 2016

Measurement of bacterial replication rates in microbial communities.

scientific article

Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

scientific article published on 20 May 2019

Megaphages infect Prevotella and variants are widespread in gut microbiomes

scientific article published on 28 January 2019

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

scientific article

Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics

scientific article published on 12 March 2013

Metabolome-proteome differentiation coupled to microbial divergence

scientific article

Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla

scientific article

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

scientific article published in October 2018

Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem

scientific article published on 28 April 2015

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories.

scientific article published on 22 September 2015

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants.

scientific article

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics.

scientific article published on 28 July 2017

Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock

scientific article published on 13 June 2019

New CRISPR-Cas systems from uncultivated microbes.

scientific article

New approaches indicate constant viral diversity despite shifts in assemblage structure in an Australian hypersaline lake

scientific article

New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species "Leptospirillum group IV UBA BS".

scientific article

Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome

scientific article published on 8 November 2017

Novel Type V-A CRISPR Effectors Are Active Nucleases with Expanded Targeting Capabilities

scientific article published on 03 November 2020

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

scientific article published in Nature

Persisting viral sequences shape microbial CRISPR-based immunity

scientific article

Phage mutations in response to CRISPR diversification in a bacterial population

scientific article

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments.

scientific article

Processing of grassland soil C-N compounds into soluble and volatile molecules is depth stratified and mediated by genomically novel bacteria and archaea

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

scientific article

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities.

scientific article

Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation

scientific article published on 28 August 2009

Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community

scientific article published on 25 April 2011

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

scientific article published on 28 May 2018

Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea.

scientific article published on 3 April 2017

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

scientific article published on 03 May 2016

Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments

scientific article

Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla

scientific article

Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome.

scientific article

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

scientific article

Strong bias in the bacterial CRISPR elements that confer immunity to phage.

scientific article

Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph

scientific article published on 06 July 2020

The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis

scientific article published on 21 February 2017

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms.

scientific article published on 20 June 2018

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

scientific article

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.

scientific article published on 24 October 2016

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

scientific article

Unusual biology across a group comprising more than 15% of domain Bacteria.

scientific article

Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation

scientific article published on 09 January 2017

Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia

scientific article

List of works by Brian C. Thomas

A new view of the tree of life

A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges.

A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum.

Aquifer environment selects for microbial species cohorts in sediment and groundwater

Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics.

Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community

CRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities

Community-wide analysis of microbial genome sequence signatures

Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms

Complete 4.55-Megabase-Pair Genome of "Candidatus Fluviicola riflensis," Curated from Short-Read Metagenomic Sequences

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface.

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.

Diverse uncultivated ultra-small bacterial cells in groundwater

Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment.

Ecological distribution and population physiology defined by proteomics in a natural microbial community.

Elevated temperature alters proteomic responses of individual organisms within a biofilm community.

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants.

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment.

Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla

Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation.

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs.

Genome-reconstruction for eukaryotes from complex natural microbial communities.

Genome-resolved metagenomics and detailed geochemical speciation analyses yield new insights into microbial mercury cycling in geothermal springs

Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings

Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations.

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development.

Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles.

Hydrogen-based metabolism - An ancestral trait in lineages sibling to the Cyanobacteria

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

Measurement of bacterial replication rates in microbial communities.

Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

Megaphages infect Prevotella and variants are widespread in gut microbiomes

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics

Metabolome-proteome differentiation coupled to microbial divergence

Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories.

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants.

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics.

Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock

New CRISPR-Cas systems from uncultivated microbes.

New approaches indicate constant viral diversity despite shifts in assemblage structure in an Australian hypersaline lake

New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species "Leptospirillum group IV UBA BS".

Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome

Novel Type V-A CRISPR Effectors Are Active Nucleases with Expanded Targeting Capabilities

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

Persisting viral sequences shape microbial CRISPR-based immunity

Phage mutations in response to CRISPR diversification in a bacterial population

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments.

Processing of grassland soil C-N compounds into soluble and volatile molecules is depth stratified and mediated by genomically novel bacteria and archaea

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

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities.

Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation

Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea.

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments

Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla

Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome.

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant