Konstantinos T. Konstantinidis

The paper analyzes whole-genome sequences of E. coli isolates to show rapid pathotype switching and genomovar-specific disease potential in northern Ecuador.

The paper describes three new species of the Microbulbifer genus using phylogenomic analysis of isolates from marine sponges and corals.

This study analyzes the gene content of Raskinella chloraquaticus to show that homologous recombination and geographic isolation shape its genetic diversity, with Lineage 1 showing more conserved genes and Lineage 2 showing greater diversity.

This study analyzes metagenomic data from the Gulf of Mexico to show unique microbial diversity and the long-range effects of freshwater input.

The paper uses metagenomics to compare microbial communities in coastal and inland hypersaline lakes, finding higher connectivity and allopatric speciation in coastal systems.

This study investigates microbial networks in northern peatlands under warming, finding resilience and alternative electron acceptor acquisition from soil organic matter.

This paper characterizes viral adsorption to Moore swabs using isotherm models, finding the Redlich-Peterson model best describes the relationship between viral concentration and swab uptake over time.

The paper introduces ROCker models for detecting and typing specific antibiotic resistance genes in short-read sequences, showing improved accuracy over existing methods.

This study examines the decay and solid-liquid partitioning of mpox and vaccinia viruses in wastewater to improve wastewater-based epidemiology practices.

The paper shows that uneven metagenome coverage can lead to misleading conclusions about feature differences and diversity comparisons, and proposes an approach to minimize this issue.

The paper defines rare biosphere and generalists using metagenomic and macroecological metrics, showing their roles in microbial resilience to disturbances like tropical cyclones and warming.

The paper shows SAR11 bacteria use promiscuous recombination to form sequence-discrete species with lower ANI thresholds than other microbes.

The paper identifies ecological cohesiveness and homologous recombination as mechanisms maintaining microbial species and genomovars in two bacterial species.

The paper identifies a 99.5% ANI gap in bacteriophage genomes that can define intra-species units, proposing 'genomovars' as a standardized classification.

GSearch efficiently searches and classifies microbial or viral genomes using k-mer hashing and HNSW graphs, achieving high speed and accuracy with low memory usage.

BinDash 2.0 improves genome comparison speed using new MinHash algorithms and SIMD optimizations, achieving faster and accurate large-scale genomic distance estimation.

This paper introduces an improved non-linear dimension reduction algorithm using HNSW for nearest neighbor search and applies it to visualize large-scale biological data with competitive accuracy.

This study evaluates the impact of a sanitation intervention on enteric pathogen detection in soils in Maputo, finding a 15% reduction in pathogen presence but persistent contamination.

MicrobeAnnotator provides a comprehensive, automated microbial genome annotation pipeline that integrates results from multiple databases to summarize metabolic potential using KEGG modules.

MetaPop analyzes and visualizes microbial and viral metagenome-derived populations at macro- and micro-diversity levels, revealing lower viral nucleotide diversity in autistic children.

The paper introduces an iterative subtractive binning pipeline to recover genomes from freshwater metagenomes, identifying over 400 novel species and their ecological preferences.

The paper introduces GROS, a database of microbial genomes from oiled environments, revealing niche specialization and highlighting the prevalence of novel species in oil-contaminated ecosystems.

FastANI accurately estimates average nucleotide identity (ANI) up to 782-fold faster than BLAST; across 90K prokaryotic genomes, an 83-95% ANI gap supports a 95% species boundary.

This study uses metagenomics to analyze microbial diversity in Anones Lagoon, Puerto Rico, showing increased diversity and changes in community composition after military activities ceased.