Biology subjects

Lood, C.

Publications and source records attributed to Lood, C..

10 recordsLinked to original sources

bioRxiv2026

Genomic Potential vs. Pathogenic Reality: Functional Virulence Variation in Pseudomonas aeruginosa

Despite the rapid expansion of bacterial genome sequencing, predicting pathogen virulence from genomic information remains a major challenge. To study this association, we integrate comparative genomics, functional phenotyping, host-pathogen interaction assays, and infection outcomes across a diverse collection of 28 Pseudomonas aeruginosa isolates, representing clinically relevant diversity in serotype, type IV pilus group, and flagellar type. While virulence-associated systems were broadly retained across the strain collection, isolates displayed substantial variation in phenotypic behavior and pathogenicity. Genotypic classifications based on pilus, flagellar, siderophore, or secretion system characteristics were poor predictors of virulence-associated phenotypes. Pathogenicity in a Galleria mellonella model varied markedly among strains and was most strongly associated with surface-associated motility, whereas other virulence traits and quorum-sensing genotypes showed limited predictive value. In a three-dimensional lung epithelial cell model, inflammatory responses were negatively correlated with activity of the type III secretion system effector ExoS, suggesting a role in modulation of host immune signaling. Together, these findings demonstrate that virulence emerges from functional deployment of conserved virulence repertoires, rather than their mere presence. By linking genomic diversity to phenotypic expression, pathogenicity, and host responses within a single strain collection, this study highlights fundamental limitations of gene-content-based virulence prediction and underscores the importance of integrating genomic and functional data to better understand P. aeruginosa virulence.

microbiology↗

bioRxiv2026

First community challenge for automated virus taxonomy

The rapid rate of virus discovery renders manual curation by taxonomy experts increasingly impractical, creating a need for reliable software that can reproducibly assign viral contigs to taxa at all fifteen ranks of the virus taxonomy. We led an open community challenge for the computational taxonomic classification of viruses and assembled a dataset of virus sequences combining expert-curated and metagenomic sequences. Seventeen teams contributed a total of thirty-four automated, fully reproducible classification pipelines. Most tools correctly assigned viruses belonging to established species, genera, or families, but viruses that are unclassified at those lower ranks remain challenging. This study provides datasets, open-source software, novel approaches, and recommendations to benchmark computational taxonomic classification of viruses, and support organizing the many viruses discovered in big omics data.

microbiology↗

bioRxiv2025

Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy

Plasmids are a ubiquitous feature of bacterial genomes, but the evolutionary forces driving genes to become associated with plasmids are poorly understood. To address this problem, we compared the fitness effects of chromosomal and plasmid genes in the plant symbiont Rhizobium leguminosarum. Here we show that plasmids are depleted in beneficial genes compared to the chromosome, and this effect is stronger for ancient plasmids compared to recently acquired plasmids. These findings support the hypothesis that evolution drives beneficial genes to become localized to the bacterial chromosome, resulting in a gradual decay in the ecological value of plasmids. These findings question the ecological importance of plasmids and highlight the challenge of understanding how plasmids persist over the long term.

evolutionary biology↗

bioRxiv2022

The paradoxical relationship between CRISPR-Cas and phage susceptibility in Pseudomonas aeruginosa

CRISPR-Cas systems are part of the pan-immune system of Pseudomonas aeruginosa and have been shown to limit horizontal gene transfers in that species. Indeed, isolates equipped with these systems tend to have smaller genomes and CRISPR spacers targeting integrative conjugative elements, phages, and plasmids. In this work, we investigate the genomic effects and phenotypic consequences of CRISPR-Cas systems in P. aeruginosa. First, we establish that the population structure is a confounding factor of the relation between genome sizes and the presence of CRISPR-Cas systems in P. aeruginosa as isolates from group II are, on average, 200 kbp larger than those from group I, and have a lower likelihood of possessing CRISPR-Cas systems. Second, we show that the impact on the genome size of CRISPR deactivation by anti-CRISPR proteins differs between the various CRISPR-Cas types found in this species (I-C, I-E, and I-F). Finally, we highlight a paradoxical, positive correlation between the presence of CRISPR-Cas systems and the chances of the host being infected by a set of distinct, strictly virulent Pseudomonas phages. We propose that this increased phage susceptibility in the presence of CRISPR-Cas is linked to a depletion of other accessory defense system genes in isolates with CRISPR-Cas systems. Note: This manuscript was published as a chapter in the doctoral dissertation of Cedric Lood [72]

microbiology↗

bioRxiv2022

Transcriptomics-driven characterisation of novel T7-like temperate Pseudomonas phage LUZ100

The Autographiviridae is a diverse yet distinct family of bacterial viruses marked by a strictly lytic lifestyle and a generally conserved genome organization. We here characterise Pseudomonas aeruginosa phage LUZ100, a distant relative of type phage T7. LUZ100 is a podovirus with a limited host range and identified LPS as the likely phage receptor. Interestingly, infection dynamics of LUZ100 indicated moderate adsorption rates and low virulence, hinting towards temperate behavior. This hypothesis was supported by genomic analysis, which showed that LUZ100 shares the conventional T7-like genome organization, yet encodes key genes associated with a temperate lifestyle. To unravel the peculiar characteristics of LUZ100, ONT-cappable-seq transcriptomics analysis was performed. This data generated a birds-eye view of the LUZ100 transcriptome and enabled the discovery of key regulatory elements, antisense RNA, and transcriptional unit structures. The transcriptional map of LUZ100 also allowed us to identify new RNAP-promoter pairs that can form the basis for biotechnological parts and tools for new synthetic transcription regulation circuitry. The ONT-cappable-seq data revealed that the LUZ100 integrase and a MarR-like regulator (proposed to be involved in the lytic/lysogeny decision), are actively co-transcribed in an operon. In addition, the presence of a phage-specific promoter transcribing the phage-encoded RNA polymerase, raises questions on the regulation of this polymerase, and suggests it is interwoven with the MarR-based regulation. This transcriptomics-driven characterisation of LUZ100 supports the increasing evidence that T7-like phages should not straightforwardly be marked as having a strictly lytic lifecycle. ImportanceBacteriophage T7, considered the model phage of the Autographiviridae family, is marked by a strictly lytic lifecycle and conserved genome organisation. Recently, novel phages of this clade are emerging and showing characteristics associated to a lysogenic lifecycle. Screening for temperate behaviour is of outmost importance in fields like phage therapy, where strictly lytic phages are generally required for therapeutic applications. In this study, weve used an omics-driven approach to characterise the T7-like Pseudomonas aeruginosa phage LUZ100. These results led to the identification of actively transcribed lysogeny-associated genes in the phage genome, pointing out that temperate T7-like phages are emerging more frequent than initially thought. In short, the combination of genomics and transcriptomics allowed us to obtain a better understanding of the biology of non-model Autographiviridae phages, which can be used to optimize the implementation of phages and their regulatory elements in phage therapy and biotechnological applications, respectively.

microbiology↗

bioRxiv2021

Unraveling protein interactions between the temperate virus Bam35 and its Bacillus host using an integrative yeast two hybrid-high throughput sequencing approach

AO_SCPLOWBSTRACTC_SCPLOWBacillus virus Bam35 is the model Betatectivirus and member of the Tectiviridae family, which is composed of tailless, icosahedral, and membrane-containing bacteriophages. The interest in these viruses has greatly increased in recent years as they are thought to be an evolutionary link between diverse groups of prokaryotic and eukaryotic viruses. Additionally, betatectiviruses infect bacteria of the Bacillus cereus group, known for their applications in industry and notorious since it contains many pathogens. Here, we present the first protein-protein interactions network for a tectivirus-host system by studying the Bam35-Bacillus thuringiensis model using a novel approach that integrates the traditional yeast two-hybrid system and Illumina high-throughput sequencing. We generated and thoroughly analyzed a genomic library of Bam35s host B. thuringiensis HER1410 and screened interactions with all the viral proteins using different combinations of bait-prey couples. In total, this screen resulted in the detection of over 4,000 potential interactions, of which 183 high-confidence interactions were defined as part of the core virus-host interactome. Overall, host metabolism proteins and peptidases are particularly enriched within the detected interactions, distinguishing this host-phage system from the other reported host-phage protein-protein interaction networks (PPIs). Our approach also suggests biological roles for several Bam35 proteins of unknown function, resulting in a better understanding of the Bam35-B. thuringiensis interaction at the molecular level. AO_SCPLOWUTHORC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSUMMARYC_SCPLOWMembers of the family Tectiviridae, composed of non-tailed icosahedral, membrane-containing bacteriophages, have been increasingly scrutinized in recent years for their possible role in the origin of dsDNA viruses. In particular, the genus Betatectivirus receives increased attention as these phages can infect clinical strains as well as industrially relevant members of the B. cereus group. However, little is known about the interactions between these temperate viruses and their hosts. Here, we present the first high-throughput study of tectivirus-host protein-protein interactions focusing on Bam35, model virus of betatectiviruses, and its host B. thuringiensis, an important entomopathogenic bacterium. We adapted the well-known technique yeast-two-hybrid and integrated high-throughput sequencing and bioinformatics for the downstream analysis of the results which enables large-scale analysis of protein-protein interactions. In total, 182 detected interactions show an enrichment in host metabolic proteins and peptidases, in contrast with the current knowledge on host-phage PPIs. Specific host-viral protein-protein interactions were also detected enabling us to propose functions for uncharacterized proteins.

microbiology↗

bioRxiv2021

Analyses of the complete genome sequence of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of (un)stable plasmids.

Aminobacter sp. MSH1 (CIP 110285) can use the pesticide dichlobenil and its transformation product, the recalcitrant groundwater micropollutant, 2,6-dichlorobenzamide (BAM) as sole source of carbon, nitrogen, and energy. The concentration of BAM in groundwater often exceeds the threshold limit for drinking water, resulting in the use of additional treatment in drinking water treatment plants (DWTPs) or closure of the affected abstraction wells. Biological treatment with MSH1 is considered a potential sustainable alternative to remediate BAM-contamination in drinking water production. Combining Illumina and Nanopore sequencing, we here present the complete genome of MSH1, which was determined independently in two different laboratories. Unexpectedly, divergences were observed between the two genomes, i.e. one of them lacked four plasmids compared to the other. Besides the circular chromosome and the two previously described plasmids involved in BAM catabolism pBAM1 (41 kb) and pBAM2 (54 kb), we observe that the genome of MSH1 contains two megaplasmids pUSP1 (367 kb) and pUSP2 (366 kb) and three smaller plasmids pUSP3 (97 kb), pUSP4 (64 kb), and pUSP5 (32 kb). The MSH1 substrain from KU Leuven showed a reduced genome lacking plasmids pUSP2 and the three smaller plasmids and was designated substrain MK1, whereas the variant with all plasmids was designated as substrain DK1. Results of a plasmid stability experiment, indicate that strain MSH1 may have a polyploid chromosome when growing in R2B medium with more chromosomes than plasmids per cell. Based on phylogenetic analyses, strain MSH1 is reassigned as Aminobacter niigataensis MSH1. ImportanceThe complete genomes of the two MSH1 substrains, DK1 and MK1, provide further insight into this already well-studied organism with bioremediation potential. The varying plasmid contents in the two substrains suggest that some of the plasmids are unstable, although this is not supported by the herein described plasmid stability experiment. Instead, results suggest that MSH1 is polyploid with respect to its chromosome, at least under some growth conditions. As the essential BAM-degradation genes are found on some of these plasmids, stable inheritance is essential for continuous removal of BAM. Finally, Aminobacter sp. MSH1 is reassigned as Aminobacter niigataensis MSH1, based on phylogenetic evidence.

microbiology↗

bioRxiv2020

The fully resolved genome of Bacillus thuringiensis HER1410 reveals a cry-containing chromosome, two megaplasmids & an integrative plasmidial prophage

Bacillus thuringiensis is the most used biopesticide in agriculture. Its entomopathogenic capacity stems from the possession of plasmid-borne insecticidal crystal genes (cry), traditionally used as discriminant taxonomic feature for that species. As such, crystal and plasmid identification are key to the characterization of this species. To date, about 600 B. thuringiensis genomes have been reported, but less than 5% have been resolved, while the other draft genomes are incomplete, precluding plasmid delineation. Here we present the complete genome of Bacillus thuringiensis HER1410, a strain closely related to B. thuringiensis entomocidus and a known host for a variety of Bacillus phages. The combination of short and long-reads techniques allowed fully resolving the genome and delineation of three plasmids. This enabled the accurate detection of an unusual location of a unique cry gene, cry1Ba4, located in a genomic island near the chromosome replication origin. Two megaplasmids, pLUSID1 and pLUSID2 could be delineated: pLUSID1 (368kb), a likely conjugative plasmid involved in virulence, and pLUSID2 potentially related to the sporulation process. A smaller plasmidial prophage pLUSID3, with a dual lifestyle whose integration within the chromosome, causes the disruption of a flagellar key component. Finally, phylogenetic analysis located this strain within a clade comprising members from the B. thuringiensis serovar thuringiensis and other serovars and with B.cereus s. s. This highlights the intermingled taxonomy of B. cereus sensu lato group, where genomics alone does not support the present taxonomy between B. cereus s. s. and B. thuringiensis as species designation currently relies solely on the presence of entomocidal genes. ImportanceBacillus cereus group species have been extensively studied due to their economical and clinical relevance. This importance originally set the basis for B. cereus group members classification which are commonly based on phenotypical criteria. Sequencing era has shed light about genomic characterization of these species, showing their chromosomal genomic similarity and highlighting the role of mobile genetic elements, especially megaplasmids, in the classification and characterization of this group. However, only the 5% of the sequenced B. thuringiensis genomes have been fully resolved. Thus, here we addressed efficiently the study B. thuringiensis HER1410 genomic features by the use of a combination of short and long-reads sequencing. This methodology resulted in the high-quality assembly, which led to the identification of an uncommon location of a cry gene close to the chromosomal origin, as well as three fully resolved extrachromosomal elements, two megaplasmids and an integrative plasmidial prophage.

microbiology↗

bioRxiv2019

Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

Pseudomonas virus vB_PaeM_PA5oct is a compelling model phage to investigate phage-bacteria interactions and is a potent candidate for phage therapy. Combining hybrid genome sequencing, RNA-Seq, and mass spectrometry of virion-associated proteins allowed us to accurately assemble and annotate PA5octs 286,783 bp genome. It encodes 461 coding regions, of which 93 were identified as virion-associated proteins using ESI-MS/MS. RNA-seq revealed twelve tRNA genes, four ncRNA regions, and a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. Although PA5oct is not organized into strictly contiguous regions of temporal transcription, defined genomic regions are expressed in early, middle, and late phases of infection. Interestingly, we observed distinct regions showing limited transcription activity throughout the infection cycle. The infection of Pseudomonas aeruginosa by PA5oct triggers the upregulation of bacterial operons related to NAD biosynthesis, Psl exopolysaccharide, and periplasmic nitrate reductase production and downregulates Type IV pili gene products, suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position this isolate amongst other phages using a protein-sharing network. This study expands our understanding of the molecular diversity of jumbo viruses and opens new questions towards cellular regulation and phage-encoded hijacking mechanisms.

molecular biology↗

bioRxiv2019

Megaplasmids on the rise: combining sequencing approaches to fully resolve a carbapenemase-encoding plasmid in a proposed novel Pseudomonas species

Horizontal transfer of plasmids plays a pivotal role in the dissemination of antibiotic resistance genes and emergence of multidrug-resistant bacteria. Sequencing of plasmids is thus paramount for the success of accurate epidemiological tracking strategies in the hospital setting and routine surveillance. Here, we combine Nanopore and Illumina sequencing to fully assemble a carbapenemase-encoding megaplasmid carried by a clinical isolate belonging to a putative novel Pseudomonas species. FFUP_PS_41 has a multidrug resistance phenotype and was initially identified as Pseudomonas putida, but an average nucleotide identity below the cut-off for species delineation suggests a new species related to the P. putida phylogenetic group. FFUP_PS_41 harbors a 498,516-bp untypable megaplasmid (pJBCL41) with low similarity compared with publicly available plasmids. pJBCL41 contains a full set of genes for self-transmission and genes predicted to be responsible for plasmid replication, partitioning, maintenance and heavy metal resistance. pJBCL41 carries a class 1 integron with the |aacA7|blaVIM-2|aacA4| cassette array (In103) located within a defective Tn402-like transposon that forms part of a 50,273-bp mosaic region bound by 38-bp inverted repeats typical of the Tn3 family and flanked by 5-bp direct repeats. This region is composed of different elements, including additional transposon fragments, five insertion sequences and a Tn3-Derived Inverted-Repeat Miniature Element. The hybrid Nanopore/Illumina approach resulted in contiguous assemblies and allowed us to fully resolve a carbapenemase-encoding megaplasmid from Pseudomonas spp. The identification of novel megaplasmids will shed a new light on the evolutionary effects of gene transfer and the selective forces driving AR.

microbiology↗