Ivan Erill
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View article: Parallel regulatory circuits orchestrate biofilm formation in response to c-di-GMP levels and growth phase
Parallel regulatory circuits orchestrate biofilm formation in response to c-di-GMP levels and growth phase Open
Biofilm formation is a highly regulated process that contributes to the environmental fitness of microorganisms, including pathogenic bacteria. The second messenger c-di-GMP is a critical regulator of biofilm formation whose cellular level…
View article: Determining the taxonomic and functional profile of marine bacterial copper systems involved in marine early copper surface colonization
Determining the taxonomic and functional profile of marine bacterial copper systems involved in marine early copper surface colonization Open
Copper-based antimicrobial paints are frequently used to inhibit the biofouling of marine vessels. However, some bacterial species can overcome this copper challenge and colonize the surfaces. The early adherent bacterial population of mar…
View article: Deciphering the Causes of IbfA-Mediated Abortive Infection in the P22-like Phage UAB_Phi20
Deciphering the Causes of IbfA-Mediated Abortive Infection in the P22-like Phage UAB_Phi20 Open
The study of bacterial defense mechanisms against phages is becoming increasingly relevant due to their impact on the effectiveness of phage therapy. Employing a multifaceted approach that combines bioinformatics, molecular microbiology, T…
View article: Information Theory of Composite Sequence Motifs: Mutational and Biophysical Determinants of Complex Molecular Recognition
Information Theory of Composite Sequence Motifs: Mutational and Biophysical Determinants of Complex Molecular Recognition Open
The recognition of nucleotide sequence patterns is a fundamental biological process that controls the start sites of replication, transcription and translation, as well as transcriptional and translational regulation. Foundational work on …
View article: Complete genome and characteristics of cluster BC bacteriophage SoJo, isolated using <i>Streptomyces mirabilis</i> NRRL B-2400 in Columbia, MD
Complete genome and characteristics of cluster BC bacteriophage SoJo, isolated using <i>Streptomyces mirabilis</i> NRRL B-2400 in Columbia, MD Open
Here, we present bacteriophage SoJo, a siphovirus infecting Streptomyces mirabilis , with a circularly permuted genome of 39 kbp and GC content of 71.5%. Its genome length and content are similar to that of other phages in the Actinobacter…
View article: Genomic analysis of<i>Staphylococcus aureus</i>isolates from bacteremia reveals genetic features associated with the COVID-19 pandemic
Genomic analysis of<i>Staphylococcus aureus</i>isolates from bacteremia reveals genetic features associated with the COVID-19 pandemic Open
Genomic analyses of bacterial isolates are necessary to monitor the prevalence of antibiotic resistance genes and virulence determinants. Herein, we provide a comprehensive genomic description of a collection of 339 Staphylococcus aureus s…
View article: Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting <i>Streptomyces</i> species
Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting <i>Streptomyces</i> species Open
Satellites are mobile genetic elements that are dependent upon the replication machinery of their helper viruses. Bacteriophages have provided many examples of satellite nucleic acids that utilize their helper morphogenic genes for propaga…
View article: Impact of mutagenesis and lateral gene transfer processes in bacterial susceptibility to phage in food biocontrol and phage therapy
Impact of mutagenesis and lateral gene transfer processes in bacterial susceptibility to phage in food biocontrol and phage therapy Open
Introduction The emergence of resistance and interference mechanisms to phage infection can hinder the success of bacteriophage-based applications, but the significance of these mechanisms in phage therapy has not been determined. This wor…
View article: TEM dataset for "Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species"
TEM dataset for "Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species" Open
Dataset of thirteen transmission electron micrographs of the Flayer satellite-helper phage system. Images of MindFlayer helper virions with MiniFlayer satellite attachment were taken on a Morgagni M268 Transmission Electron Microscope and …
View article: TEM dataset for "Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species"
TEM dataset for "Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species" Open
Dataset of thirteen transmission electron micrographs of the Flayer satellite-helper phage system. Images of MindFlayer helper virions with MiniFlayer satellite attachment were taken on a Morgagni M268 Transmission Electron Microscope and …
View article: The Rvv two-component regulatory system regulates biofilm formation and colonization in Vibrio cholerae
The Rvv two-component regulatory system regulates biofilm formation and colonization in Vibrio cholerae Open
The facultative human pathogen, Vibrio cholerae, employs two-component signal transduction systems (TCS) to sense and respond to environmental signals encountered during its infection cycle. TCSs consist of a sensor histidine kinase (HK) a…
View article: The Rvv two-component regulatory system regulates biofilm formation and colonization in Vibrio cholerae
The Rvv two-component regulatory system regulates biofilm formation and colonization in Vibrio cholerae Open
The facultative human pathogen, Vibrio cholerae , employs two-component signal transduction systems (TCS) to sense and respond to environmental signals encountered during its infection cycle. TCSs consist of a sensor histidine kinase (HK) …
View article: Linking Copper-Associated Signal Transduction Systems with Their Environment in Marine Bacteria
Linking Copper-Associated Signal Transduction Systems with Their Environment in Marine Bacteria Open
Copper is an essential trace element for living cells. However, copper can be potentially toxic for bacterial cells when it is present in excess amounts due to its redox potential. Due to its biocidal properties, copper is prevalent in mar…
View article: Systematic In Silico Assessment of Antimicrobial Resistance Dissemination across the Global Plasmidome
Systematic In Silico Assessment of Antimicrobial Resistance Dissemination across the Global Plasmidome Open
The emergence of pathogenic strains resistant to multiple antimicrobials is a pressing problem in modern healthcare. Antimicrobial resistance is mediated primarily by dissemination of resistance determinants via horizontal gene transfer. T…
View article: Evidence of a Set of Core-Function Genes in 16 Bacillus Podoviral Genomes with Considerable Genomic Diversity
Evidence of a Set of Core-Function Genes in 16 Bacillus Podoviral Genomes with Considerable Genomic Diversity Open
Bacteriophage genomes represent an enormous level of genetic diversity and provide considerable potential to acquire new insights about viral genome evolution. In this study, the genome sequences of sixteen Bacillus-infecting bacteriophage…
View article: Genome Sequences of <i>Streptomyces</i> Bacteriophages Fabian, FlowerPower, Geostin, RetrieverFever, and Vorvolakos
Genome Sequences of <i>Streptomyces</i> Bacteriophages Fabian, FlowerPower, Geostin, RetrieverFever, and Vorvolakos Open
This paper reports the genome sequences of five bacteriophages that were isolated using Streptomyces scabiei . Phages Fabian, FlowerPower, Geostin, RetrieverFever, and Vorvolakos were assigned to actinobacteriophage cluster BF based on sha…
View article: Complete Genome Sequences of <i>Streptomyces</i> Bacteriophages Annihilus, TonyStarch, Thiqqums, CricKo, ClubPenguin, RosaAsantewaa, and PherryCruz
Complete Genome Sequences of <i>Streptomyces</i> Bacteriophages Annihilus, TonyStarch, Thiqqums, CricKo, ClubPenguin, RosaAsantewaa, and PherryCruz Open
Seven siphoviruses were isolated from soil using Streptomyces hosts. Their genome sequences ranged from 42,730 to 57,624 bp long and had a GC content of approximately 60%. Based on their gene content similarity to actinobacteriophages, all…
View article: Editorial: Microbiome and microbial informatics
Editorial: Microbiome and microbial informatics Open
EDITORIAL article Front. Microbiol., 19 October 2022Sec. Evolutionary and Genomic Microbiology Volume 13 - 2022 | https://doi.org/10.3389/fmicb.2022.1054811
View article: The transcriptional regulator CtrA controls gene expression in Alphaproteobacteria phages: Evidence for a lytic deferment pathway
The transcriptional regulator CtrA controls gene expression in Alphaproteobacteria phages: Evidence for a lytic deferment pathway Open
Pilitropic and flagellotropic phages adsorb to bacterial pili and flagella. These phages have long been used to investigate multiple aspects of bacterial physiology, such as the cell cycle control in the Caulobacterales. Targeting cellular…
View article: Evidence for shared ancestry between Actinobacteria and Firmicutes bacteriophages
Evidence for shared ancestry between Actinobacteria and Firmicutes bacteriophages Open
Bacteriophages typically infect a small set of related bacterial strains. The transfer of bacteriophages between more distant clades of bacteria has often been postulated, but remains mostly unaddressed. In this work we leverage the sequen…
View article: Design of Machine Learning Models for the Prediction of Transcription Factor Binding Regions in Bacterial DNA
Design of Machine Learning Models for the Prediction of Transcription Factor Binding Regions in Bacterial DNA Open
Transcription Factors (TFs) are proteins that regulate the expression of genes by binding to their promoter regions. There is great interest in understanding in which regions TFs will bind to the DNA sequence of an organism and the possibl…
View article: Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO) Open
Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource fo…
View article: ECO: the Evidence and Conclusion Ontology, an update for 2022
ECO: the Evidence and Conclusion Ontology, an update for 2022 Open
The Evidence and Conclusion Ontology (ECO) is a community resource that provides an ontology of terms used to capture the type of evidence that supports biomedical annotations and assertions. Consistent capture of evidence information with…
View article: Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes
Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes Open
Lesions to DNA compromise chromosome integrity, posing a direct threat to cell survival. The bacterial SOS response is a widespread transcriptional regulatory mechanism to address DNA damage. This response is coordinated by the LexA transc…
View article: Enhanced copper-resistance gene repertoire in Alteromonas macleodii strains isolated from copper-treated marine coatings
Enhanced copper-resistance gene repertoire in Alteromonas macleodii strains isolated from copper-treated marine coatings Open
Copper is prevalent in coastal ecosystems due to its use as an algaecide and as an anti-fouling agent on ship hulls. Alteromonas spp. have previously been shown to be some of the early colonizers of copper-based anti-fouling paint but litt…