Vladimir Sentchilo

Vladimir Sentchilo
University of Lausanne | UNIL ·  Department of Fundamental Microbiology (DMF)

PhD

About

74
Publications
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984
Citations

Publications

Publications (74)
Article
The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here,...
Article
Full-text available
There is now a great awareness of the high diversity of most environmental (“free-living”) and host-associated microbiomes, but exactly how diverse microbial communities form and maintain is still highly debated. A variety of theories have been put forward, but testing them has been problematic because most studies have been based on synthetic comm...
Article
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Background Bioaugmentation aims to use the capacities of specific bacterial strains inoculated into sites to enhance pollutant biodegradation. Bioaugmentation results have been mixed, which has been attributed to poor inoculant growth and survival in the field, and, consequently, moderate catalytic performance. However, our understanding of biodegr...
Preprint
Full-text available
The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here,...
Preprint
Microbiomes are typically characterised by high species diversity but it is poorly understood how such system-level complexity can be generated and propagated. Here, we used soils as a relevant model to study microbiome development. Despite inherent stochastic variation in manipulating species-rich communities, both laboratory-mixed medium complexi...
Article
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The sewage sludge isolate Pseudomonas nitroreducens HBP-1 was the first bacterium known to completely degrade the fungicide 2-hydroxybiphenyl. PacBio and Illumina whole-genome sequencing revealed three circular DNA replicons: a chromosome and two plasmids. Plasmids were shown to code for putative adaptive functions such as heavy metal resistance, b...
Article
Full-text available
Understanding the adaptive responses of individual bacterial strains is crucial for microbiome engineering approaches that introduce new functionalities into complex microbiomes, such as xenobiotic compound metabolism for soil bioremediation. Adaptation requires metabolic reprogramming of the cell, which can be captured by multi-omics, but this dat...
Article
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
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Bacterial periplasmic-binding proteins have been acclaimed as general biosensing platform, but their range of natural ligands is too limited for optimal development of chemical compound detection. Computational redesign of the ligand-binding pocket of periplasmic-binding proteins may yield variants with new properties, but, despite earlier claims,...
Preprint
Full-text available
Understanding the adaptive responses of individual bacterial strains is crucial for microbiome engineering approaches that introduce new functionalities into complex microbiomes, such as xenobiotic compound metabolism for soil bioremediation. Adaptation requires metabolic reprogramming of the cell, which can be captured by multi-omics, but this dat...
Article
Bacteria that engage in longstanding associations with particular hosts are expected to evolve host‐specific adaptations that limit their capacity to thrive in other environments. Consistent with this, many gut symbionts seem to have a limited host range, based on community profiling and phylogenomics. However, few studies have experimentally inves...
Preprint
Full-text available
Bacterial periplasmic-binding proteins have been acclaimed as general biosensing platform, but their range of natural ligands is too limited for optimal development of chemical compound detection. Computational redesign of the ligand-binding pocket of periplasmic-binding proteins may yield variants with new properties, but, despite earlier claims,...
Preprint
Full-text available
Bacteria that engage in longstanding associations with particular hosts are expected to evolve host-specific adaptations that limit their capacity to strive in other environments. Consistent with this, many gut symbionts seem to have a limited host range, based on community profiling and phylogenomics. However, few studies have experimentally inves...
Article
Full-text available
Integrative and conjugative elements (ICEs) comprise ubiquitous large mobile regions in prokaryotic chromosomes that transmit vertically to daughter cells and transfer horizontally to distantly related lineages. Their evolutionary success originates in maximized combined ICE-host fitness trade-offs, but how the ICE impacts on the host metabolism an...
Article
Full-text available
The Escherichia coli RbsB ribose binding protein has been used as a scaffold for predicting new ligand binding functions through in silico modeling, yet with limited success and reproducibility. In order to possibly improve the success of predictive modeling on RbsB, we study here the influence of individual residues on RbsB-mediated signaling in a...
Article
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Microbacterium foliorum strain 122 is a bacterial endophyte isolated from a Dactylis glomerata plant growing in a natural oil seep soil located in Oil Springs, Ontario, Canada. We present here a draft genome sequence of an endophytic strain that has promising potential in hydrocarbon degradation and plant growth promotion.
Article
Full-text available
Plantibacter flavus isolate 251 is a bacterial endophyte isolated from an Achillea millefolium plant growing in a natural oil seep soil located in Oil Springs, Ontario, Canada. We present here a draft genome sequence of an infrequently reported genus Plantibacter , highlighting an endophytic lifestyle and biotechnological potential.
Article
Full-text available
The natural restoration of soils polluted by aromatic hydrocarbons such as benzene, tolu-ene, ethylbenzene and m-and p-xylene (BTEX) may be accelerated by inoculation of specific biodegraders (bioaugmentation). Bioaugmentation mainly involves introducing bacteria that deploy their metabolic properties and adaptation potential to survive and propaga...
Data
Figure A. Comparison of the linearized P. veronii chromosome 1 replicon (Pv) with its close relatives Pseudomonas sp. TKP (Ptkp Acc. No. CP006852.1) and P. trivialis IHBB745 (Ptri, CP011507.1). Figure B. Prediction of Cluster of Orthologous Group classification of coding regions in the P. veronii 1YdBTEX2 genome distributed across the three replico...
Data
Table A. Putative intact and incomplete prophages found in the genome of P. veronii strain 1YdBTEX2 and their differential gene expression. Table B. Putative regions of genome plasticity and genomic islands, and their differential gene expression. Table C. Differential expression of genes implicated in aerobic respiration and energy generation. Tab...
Article
Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study we determined...
Data
Full-text available
The clc element (ICEclc) is a mobile genetic element in the bacterium Pseudomonas knackmussii B13. ICEclc normally resides in the host’s chromosome but is capable of excising itself and forming a circularly closed DNA molecule, a process that happens during stationary phase in only 5% of all cells in a population. When a suitable recipient cell is...
Article
Plasmids have long been recognized as an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from the host's chromosome and their frequent self-transfer. It is thought that plasmids accumulate, rearrange and distribute nonessential genes, which may prov...
Article
We show proof of principle for assessing compound biodegradation at 1-2 mg C per L by measuring microbial community growth over time with direct cell counting by flow cytometry. The concept is based on the assumption that the microbial community will increase in cell number through incorporation of carbon from the added test compound into new cells...
Article
Full-text available
Integrative and conjugative elements (ICE) form a diverse group of DNA elements that are integrated in the chromosome of the bacterial host, but can occasionally excise and horizontally transfer to a new host cell. ICE come in different families, typically with a conserved core for functions controlling the element's behavior and a variable region...
Data
Full-text available
Supplementary tables. Location of ORFs in the ICEclc core region and bioinformatic predictions of protein function and transcription features. Primers used in this study. Probes produced for Northern hybridizations.
Article
Full-text available
Petroleum hydrocarbons are common contaminants in marine and freshwater aquatic habitats, often occurring as a result of oil spillage. Rapid and reliable on-site tools for measuring the bioavailable hydrocarbon fractions, i.e., those that are most likely to cause toxic effects or are available for biodegradation, would assist in assessing potential...
Article
Full-text available
Genomic islands are DNA elements acquired by horizontal gene transfer that are common to a large number of bacterial genomes, which can contribute specific adaptive functions, e.g. virulence, metabolic capacities or antibiotic resistances. Some genomic islands are still self-transferable and display an intricate life-style, reminiscent of both bact...
Article
Full-text available
Genomic islands (GEI) comprise a recently recognized large family of potentially mobile DNA elements and play an important role in the rapid differentiation and adaptation of bacteria. Most importantly, GEIs have been implicated in the acquisition of virulence factors, antibiotic resistances or toxic compound metabolism. Despite detailed informatio...
Article
Full-text available
Pseudomonas sp. strain B13 is a bacterium known to degrade chloroaromatic compounds. The properties to use 3- and 4-chlorocatechol are determined by a self-transferable DNA element, the clc element, which normally resides at two locations in the cell's chromosome. Here we report the complete nucleotide sequence of the clc element, demonstrating the...
Article
Full-text available
ed only one meta pathway operon, one upper pathway operon, and one copy each of xylS and xylR. The backbones of these two plasmids differed greatly from those of the others. Whereas these parts of the plasmids, carrying the xyl genes, were mostly conserved between plasmids of each group, the noncatabolic parts had undergone intensive DNA rearrangem...
Article
Full-text available
An unusual type of gene expression from an integrase promoter was found in cultures of the bacterium Pseudomonas sp. strain B13. The promoter controls expression of the intB13 integrase gene, which is present near the right end of a 105-kb conjugative genomic island (the clc element) encoding catabolism of aromatic compounds. The enzymatic activity...
Article
Full-text available
The clc genomic island is a 105 kb integrative and conjugative element (ICE) in Pseudomonas sp. strain B13, which encodes metabolism of 3-chlorocatechol. The clc island is integrated in a tRNAGly gene, but can excise and form a circular intermediate in which both ends are connected. The integrase gene (intB13) of the clc genomic island is located a...
Article
Full-text available
Genes for the degradation of organic pollutants have usually been allocated to plasmid DNAs in bacteria or considered non-mobile when detected in the chromosome. New discoveries have shown that catabolic genes can also be part of so-called integrative and conjugative elements (ICElands), a group of mobile DNA elements also known as genomic islands...
Article
Full-text available
Genes for metabolic pathways in bacteria that degrade aromatic or aliphatic pollutants have mostly been confined to either plasmid DNAs or to the chromosome. For a few pathways, including classical pathways for chlorocatechol and biphenyl degradation, recent evidence has been obtained for location of the pathway genes on mobile DNA elements which e...
Article
Full-text available
Twenty different Pseudomonas strains utilizingm-toluate were isolated from oil-contaminated soil samples near Minsk, Belarus. Seventeen of these isolates carried plasmids ranging in size from 78 to about 200 kb (assigned pSVS plasmids) and encoding the meta cleavage pathway for toluene metabolism. Most plasmids were conjugative but of unknown incom...
Article
Thesis (doctoral)--Swiss Federal Institute of Technology Zurich, 2003.

Questions

Questions (2)
Question
Does anyone know how to open an electronic pipette Picus Biohit without destroying it ;)
Question
In the general microbiology class E. coli phage enumeration is done using overlay soft agar containing among other ingredients 0.2% sodium citrate. Citrate is known to chelate Ca2+ thus it should prevent phage attachment to bacterial cells, and subsequently it should halt phage propagation and plaque formation/extension. Which is not the case--plaques are formed. Anyone knows why citrate is needed?

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