Search filters

List of works by Konstantinos T. Konstantinidis

"Candidatus Macondimonas diazotrophica", a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments

scientific article published on 05 April 2019

'Candidatus Dichloromethanomonas elyunquensis' gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family.

scientific article

A Rieske-Type Oxygenase of Pseudomonas sp. BIOMIG1 Converts Benzalkonium Chlorides to Benzyldimethyl Amine

scientific article published on 28 October 2016

A novel droplet digital PCR human mtDNA assay for fecal source tracking

scientific article published on 26 June 2020

A novel, divergent alkane monooxygenase ( alkB ) clade involved in crude oil biodegradation

scientific article

A user's guide to quantitative and comparative analysis of metagenomic datasets

scientific article published in January 2013

Advantages outweigh concerns about using genome sequence as type material for prokaryotic taxonomy

scientific article published on 06 February 2020

Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment

scientific article published in Scientific Reports

Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics.

scientific article

Author Correction: Roadmap for naming uncultivated Archaea and Bacteria

scientific article published on 12 November 2020

Bacterial species may exist, metagenomics reveal ⬇️

scientific article published on December 12, 2011

Beach sand oil spills select for generalist microbial populations

scientific article published in November 2021

Beyond denitrification: The role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

scientific article

Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra

article

Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility

scholarly article

Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal

scientific article

Comparative Genomics and Phylogenomic Analysis of the Genus Salinivibrio

scientific article published on 11 September 2019

Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre

scientific article

Comparative systems biology across an evolutionary gradient within the Shewanella genus.

scientific article published in September 2009

Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer

scientific article published on 26 November 2019

Comparison of closely related, uncultivated Coxiella tick endosymbiont population genomes reveals clues about the mechanisms of symbiosis.

scientific article published on 24 March 2018

Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women

scientific article published on 01 April 2020

Consent insufficient for data release-Response

scientific article published on 01 May 2019

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

scientific article published in PLoS ONE

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

DNA-DNA hybridization values and their relationship to whole-genome sequence similarities

scientific article (publication date: 2007)

Decomposition of sediment-oil-agglomerates in a Gulf of Mexico sandy beach

scientific article published on 11 July 2019

Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. ...

scientific article

Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. a...

erratum

Design and testing of 'genome-proxy' microarrays to profile marine microbial communities

scientific article

Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils

scientific article

Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample

scientific article

Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps

scientific article published on 20 December 2020

Divergence in gene regulation contributes to sympatric speciation of Shewanella baltica strains

scientific article published on 8 December 2017

Do airborne microbes matter for atmospheric chemistry and cloud formation?

scientific article

Draft Genome Sequence of Bacillus cereus LA2007, a Human-Pathogenic Isolate Harboring Anthrax-Like Plasmids

scientific article

Draft Genome Sequence of Catellicoccus marimammalium, a Novel Species Commonly Found in Gull Feces

scientific article published on January 2013

Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium

scientific article published on 3 March 2016

Drinking Water Microbiome Project: Is it Time?

scientific article published on 25 April 2019

Dynamic models of the complex microbial metapopulation of lake mendota

scientific article

Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus "Candidatus Fonsibacter" and proposal of Ca. Fonsibacter lacus sp. nov

scientific article published on 06 May 2019

Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones.

scientific article published on 16 February 2018

Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity

scientific article published on 04 September 2020

Erratum to "First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarod is sp. nov" [Syst. Appl. Microbiol. 42 (2019) 457-467]

scientific article published on 04 November 2019

Estimating coverage in metagenomic data sets and why it matters

scientific article

Evaluating the performance of oligonucleotide microarrays for bacterial strains with increasing genetic divergence from the reference strain

scientific article

Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities

scientific article published on December 2014

Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe

scientific article

First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov

scientific article published on 12 April 2019

Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification

scientific article published on 24 October 2014

Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming

scientific article published on 29 September 2020

Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes

scientific article published on 01 March 2020

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species ⬇️

scientific article published on April 11, 2011

Genome sequencing of five Shewanella baltica strains recovered from the oxic-anoxic interface of the Baltic Sea.

scientific article published on March 2012

Genome sequencing reveals the environmental origin of enterococci and potential biomarkers for water quality monitoring

scientific article published on 12 March 2014

Genomic Characterization and Copy Number Variation of Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains

scientific article published on 01 July 2018

Genomic Variations Underlying Speciation and Niche Specialization of Shewanella baltica

scientific article published on 15 October 2019

Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum

scientific article

Genomic and Transcriptomic Insights into How Bacteria Withstand High Concentrations of Benzalkonium Chloride Biocides

scientific article published on 31 May 2018

Genomic comparison between members of the Salinibacteraceae family, and description of a new species of Salinibacter (Salinibacter altiplanensis sp. nov.) isolated from high altitude hypersaline environments of the Argentinian Altiplano

scientific article published on 31 January 2018

Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae

scientific article

Genomic diversity of Escherichia isolates from diverse habitats

scientific article

Genomic insights into the convergence and pathogenicity factors of Campylobacter jejuni and Campylobacter coli species

scientific article published on 17 July 2009

Genomic insights that advance the species definition for prokaryotes

scientific article

Genomic patterns of recombination, clonal divergence and environment in marine microbial populations

scientific article

Giant virus diversity and host interactions through global metagenomics

scientific article published on 22 January 2020

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations

scientific article

Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion

scientific article published in 2023

Gut microbiome, enteric infections and child growth across a rural-urban gradient: protocol for the ECoMiD prospective cohort study

publication published on 22 October 2021

Hidden Diversity within Common Protozoan Parasites Revealed by a Novel Genomotyping Scheme

scientific article published on 04 January 2021

High Arsenic Levels Increase Activity Rather than Diversity or Abundance of Arsenic Metabolism Genes in Paddy Soils

scientific article published on 11 August 2021

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

scientific article published in Nature Communications

How Systematic and Applied Microbiology will deal with two nomenclature codes (ICNP and SeqCode) for prokaryotes, and which classification standards are recommended for new taxa descriptions

scientific article published in 2023

How much do rRNA gene surveys underestimate extant bacterial diversity?

scientific article published on 5 January 2018

Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics

scientific article

Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy

scientific article published on 5 June 2015

Individual genome assembly from complex community short-read metagenomic datasets

scientific article published on 27 October 2011

Integrated omics elucidate the mechanisms driving the rapid biodegradation of Deepwater Horizon oil in intertidal sediments undergoing oxic-anoxic cycles

scientific article published on 15 July 2020

Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics

article

Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria

scientific article published on 17 March 2015

Iterative Subtractive Binning of Freshwater Chronoseries Metagenomes Identifies over 400 Novel Species and their Ecologic Preferences

scientific article published on 04 June 2020

Judicial Opinion 128

scientific article published in 2023

Judicial Opinions 112–122 ⬇️

scientific article published on 10 August 2022

Long-Term Exposure to Benzalkonium Chloride Disinfectants Results in Change of Microbial Community Structure and Increased Antimicrobial Resistance ⬇️

scientific article published on August 19, 2013

Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils

article

Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015).

scientific article published on 9 February 2016

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

scientific article published on 15 March 2022

Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling

scientific article published on 26 May 2021

Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem ⬇️

scientific article published on July 15, 2011

Metagenomic Signatures of Gut Infections Caused by Different Escherichia coli Pathotypes

scientific article published on 27 November 2019

Metagenomic insights into the effect of sulfate on enhanced biological phosphorus removal

scientific article published on 8 February 2021

Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

scientific article (publication date: 2016)

Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations

scientific article published on 02 March 2020

Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods

scientific article

Methods for estimating temperature sensitivity of soil organic matter based on incubation data: A comparative evaluation

article

MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes

scientific article published on 06 January 2021

Microbial community adaptation to quaternary ammonium biocides as revealed by metagenomics ⬇️

scientific article published on June 3, 2013

Microbial community degradation of widely used quaternary ammonium disinfectants

scientific article

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill ⬇️

scientific article published on 17 February 2015

Microbial diversity in a military impacted lagoon (Vieques, Puerto Rico) and description of “Candidatus Biekeibacterium resiliens” gen. nov., sp. nov. comprising a new bacterial family

scholarly article published in 2022

Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil

scientific article

Microbial species delineation using whole genome sequences

scientific article

Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications

scientific article

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

scientific article

Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes

scientific article published on 12 February 2020

More replenishment than priming loss of soil organic carbon with additional carbon input

scientific article published in Nature Communications

Moving the cataloguing of the "uncultivated majority" forward

scientific article published on 10 December 2018

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

scientific article

New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

scientific article published on 24 February 2020

Niche differentiation among annually recurrent coastal Marine Group II Euryarchaeota

scientific article published on 26 August 2019

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

scientific article published on 10 April 2018

Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

scientific article

Opinion: Response to concerns about the use of DNA sequences as types in the nomenclature of prokaryotes

scientific article published on 11 February 2020

Phosphorus-related gene content is similar in Prochlorococcus populations from the North Pacific and North Atlantic Oceans ⬇️

scientific article published on April 7, 2011

Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre

scientific article

Predicting sigma28 promoters in eleven Shewanella genomes

scientific article published on 19 April 2008

Predominance of deterministic microbial community dynamics in salterns exposed to different light intensities

scientific article published on 18 October 2019

Prevalence of viral photosynthesis genes along a freshwater to saltwater transect in Southeast USA

scientific article published on 16 July 2019

Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead

scientific article published on 17 October 2007

Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.

scientific article

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient

scientific article published in 2018

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

scientific article

Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables

scientific article published on 18 June 2022

Reply to Smith and Griffin: Methods, air flows, and conclusions are robust in the DeLeon-Rodriguez et al. study

scientific article published in June 2013

Reply to the commentary "Uncultivated microbes-in need of their own nomenclature?"

scientific article published on 15 January 2018

Reply to: "Re-evaluating the evidence for a universal genetic boundary among microbial species"

publication published on 07 July 2021

Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths

scientific article published on 08 July 2019

Roadmap for naming uncultivated Archaea and Bacteria

scientific article published on 08 June 2020

SAR11 bacteria linked to ocean anoxia and nitrogen loss.

scientific article

SeqCode: a nomenclatural code for prokaryotes described from sequence data

scientific article published in 2022

Sequencing platform and library preparation choices impact viral metagenomes

scientific article

Similar Microbial Consortia and Genes Are Involved in the Biodegradation of Benzalkonium Chlorides in Different Environments

scientific article

Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria

scientific article published on 10 July 2018

Soil microbial community responses to a decade of warming as revealed by comparative metagenomics

scientific article

Solar salterns as model systems to study the units of bacterial diversity that matter for ecosystem functioning

scientific article published in 2022

Stability, genotypic and phenotypic diversity of Shewanella baltica in the redox transition zone of the Baltic Sea.

scientific article

Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics.

scientific article

Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora

scientific article published in 2024

Temperature sensitivity of organic matter decomposition of permafrost-region soils during laboratory incubations

article

The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails With Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content

scientific article published on 14 August 2019

The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling

scientific article published on 29 April 2020

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.

scientific article published in July 2018

The bacterial species definition in the genomic era.

scientific article

The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes

The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes

article published in 2016

The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa

scientific article published on 17 April 2017

Thousands of small, novel genes predicted in global phage genomes

scientific article published in 2022

Toward a more robust assessment of intraspecies diversity, using fewer genetic markers

scientific article

Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations

scientific article published in 2021

Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms

scientific article published in 2022

Toward unrestricted use of public genomic data:

scientific article

Towards a genome-based taxonomy for prokaryotes

scientific article

Transcriptomic and rRNA:rDNA Signatures of Environmental versus Enteric Enterococcus faecalis Isolates under Oligotrophic Freshwater Conditions

Trends between gene content and genome size in prokaryotic species with larger genomes

scholarly article

Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon

scientific article published on 05 August 2019

Uncultivated microbes in need of their own taxonomy.

scientific article published on 21 July 2017

Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils ⬇️

scientific article (publication date: 27 November 2012)

Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea.

scientific article

Using flow cytometry and light-induced fluorescence to characterize the variability and characteristics of bioaerosols in springtime in Metro Atlanta, Georgia

Warming enhances old organic carbon decomposition through altering functional microbial communities

scientific article

Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community

scientific article published on 17 January 2020

Widely Used Benzalkonium Chloride Disinfectants Can Promote Antibiotic Resistance

scientific article published on 17 August 2018

Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria

scientific article published on 05 June 2020

Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization.

scientific article published on 3 November 2017

imGLAD: Accurate detection and quantification of target organisms in metagenomes

imGLAD: Accurate detection and quantification of target organisms in metagenomes

imGLAD: accurate detection and quantification of target organisms in metagenomes

article

‘Candidatus ferrigenium straubiae’ sp. nov., ‘Candidatus ferrigenium bremense’ sp. nov., ‘Candidatus ferrigenium altingense’ sp. nov., are autotrophic Fe(II)-oxidizing bacteria of the family Gallionellaceae

scientific article published in May 2022

Paulina is supported by:

About Paulina

Help