Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure

The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B. multivorans better predicts their genomic content and functionality. We identified four pairs of B. multivorans isolates, representing distinct STs and consisting of one CF and one environmental isolate each. All genomes were sequenced using the PacBio SMRT sequencing technology, which resulted in eight high-quality B. multivorans genome assemblies. The present study demonstrated that the genomic structure of the examined B. multivorans STs is highly conserved and that the B. multivorans genomic lineages are defined by their ST. Orthologous protein families were not uniformly distributed among chromosomes, with core orthologs being enriched on the primary chromosome and ST-specific orthologs being enriched on the second and third chromosome. The ST-specific orthologs were enriched in genes involved in defense mechanisms and secondary metabolism, corroborating the strain-specificity of these virulence characteristics. Finally, the same B. multivorans genomic lineages occur in both CF and environmental samples and on different continents, demonstrating their ubiquity and evolutionary persistence

Adaptations and evolution of a heritable leaf nodule symbiosis between Dioscorea sansibarensis and Orrella dioscoreae

Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species Orrella dioscoreae. Using whole-genome sequencing of plastids and bacteria from wild-collected samples, we show phylogenetic patterns consistent with a dominant vertical mode of transmission of the symbionts. Unique so far among leaf nodule symbioses, the bacteria can be cultured and are amenable to comparative transcriptomics, revealing a potential role in complementing the host’s arsenal of secondary metabolites. We propose a recent establishment of a vertical mode of transmission in this symbiosis which, together with a large effective population size explains the cultivability and apparent lack of genome reductive evolution in O. dioscoreae. We leverage these unique features to reveal pathways and functions under positive selection in these specialized endophytes, highlighting the candidate mechanisms enabling a permanent association in the phyllosphere

Introducing SPeDE : high-throughput dereplication and accurate determination of microbial diversity from matrix-assisted laser desorption-ionization time of flight mass spectrometry data

The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDE. IMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns

Comparative genomics of Burkholderia singularis sp. nov., a low G+C content, free-living bacterium that defies taxonomic dissection of the genus Burkholderia

Four Burkholderia pseudomallei-like isolates of human clinical origin were examined by a polyphasic taxonomic approach that included comparative whole genome analyses. The results demonstrated that these isolates represent a rare and unusual, novel Burkholderia species for which we propose the name B. singularis. The type strain is LMG 28154(T) (=CCUG 65685(T)). Its genome sequence has an average mol% G+C content of 64.34%, which is considerably lower than that of other Burkholderia species. The reduced G+C content of strain LMG 28154(T) was characterized by a genome wide AT bias that was not due to reduced GC-biased gene conversion or reductive genome evolution, but might have been caused by an altered DNA base excision repair pathway. B. singularis can be differentiated from other Burkholderia species by multilocus sequence analysis, MALDI-TOF mass spectrometry and a distinctive biochemical profile that includes the absence of nitrate reduction, a mucoid appearance on Columbia sheep blood agar, and a slowly positive oxidase reaction. Comparisons with publicly available whole genome sequences demonstrated that strain TSV85, an Australian water isolate, also represents the same species and therefore, to date, B. singularis has been recovered from human or environmental samples on three continents

The status of the energy calibration, polarization and monochromatization of the FCC-ee

The Future Circular electron-positron Collider, FCC- ee, is designed for unprecedented precision for particle physics experiments from the Z-pole up to above the top-pair-threshold, corresponding to a beam energy range from 45.6 to 182.5 GeV. Performing collisions at various particle-physics resonances requires precise knowledge of the centre-of-mass energy (ECM) and collision boosts at all four interaction points. Measurement of the ECM by resonant depolarization of transversely polarized pilot bunches in combination with a 3D polarimeter, aims to achieve a systematic uncertainty of 4 and 100 keV for the Z-pole and W-pair-threshold energies respectively. The ECM itself depends on the RF-cavity locations, beamstrahlung, longitudinal impedance, the Earth’s tides, opposite sign dispersion and possible collision offsets. Application of monochromatization schemes are envisaged at certain beam energies to reduce the energy spread. The latest results of studies of the energy calibration, polarization and monochromatization are reported here

Orrella

Cells are nonmotile, non‐spore‐forming coccobacilli (0.9–1.1 µm). Gram‐negative. Strictly respiratory with oxygen or nitrate as terminal electron acceptor. The optimal temperature for growth is 15–30°C, feeble at 40°C; no growth at 42°C. Optimal growth occurs between pH 7 and 9; no growth at pH 6 or less. Broth cultures form aggregates in stationary phase, and static broth cultures form a thick, brittle pellicle near the surface. Colonies on agar medium are low convex, nonpigmented, smooth, shiny, and mostly regular in shape, raised with a wrinkled surface upon extended incubation for more than 72 h. Catalase‐ and oxidase‐positive. A narrow range of substrates are oxidized, mostly organic acids, for example, malate, succinate, fumarate, citrate, and oxaloacetate and also l‐glutamate and l‐proline; d‐galactonate and d‐gluconate are oxidized by some strains. Strict endophytes found in the leaf glands of the tropical yam Dioscorea sansibarensis

Optimisation d'un éco-système de transport multimodal pour les grandes agglomérations urbaines

This thesis focuses on the optimal design of one-way station-based carsharing systems. We consider the system design through two structural aspects: the optimal system dimensioning (number of parking places, vehicles, battery capacities, etc.) and the identification of appropriate stations’ locations. Although the addressed problems do not directly concern the system management, some relevant aspects (like vehicle relocation operations) are nonetheless part of the models. The modelling approach uses graph theory to represent the system dynamics over time and various optimization models (ILPs and MILPs) are proposed. The objective is to deduce an optimal shape of the whole system (number of vehicles, parking places, jockeys, stations’ locations, etc.) allowing to capture the maximum number of estimated time-dependent requests. Electric vehicles and power supply are also included in an enhanced model version and context related constraints ensure the integrity of the whole model. The optimization allows to study the impact of different power supply technologies and settle the minimal autonomy a shared vehicle necessitate in this environment. Models are applied to realistic case studies, using both random generated data and real estimated outputs of simulation tools. Strategies including vehicle relocation operations managed by jockeys (employees of the carsharing operator) are considered. We propose some graph simplifications reducing the problem size and leading to greatly improve solver capabilities as well as computation times. A greedy heuristic helping to quickly find feasible solutions and initialize the solver is also proposed and illustrated.Cette thèse s'intéresse à la conception optimale d'un système d'autopartage de type one-way avec stations. Les problèmes abordés traitent de deux aspects structurels importants : le dimensionnement optimal du système (nombre de places de parking, de véhicules, de relocalisation de véhicules, etc.) et la localisation adéquate des stations. Bien que le management ou pilotage en temps réel du service ne soit pas l'objet de cette étude, certains aspects pertinents (relocalisation de véhicules, nombre de jockeys) ont toutefois été intégrés aux modèles. L'approche mathématique utilise des objets de la théorie des graphes pour représenter les systèmes dans le temps et les problèmes sont résolus grâce à la programmation linéaire en nombre entiers. L'objectif est d'identifier la structure du service permettant de capturer le plus de demandes possibles. L'introduction de véhicules électriques et de la puissance de charge en station sont étudiés dans un modèle dédié. Les expérimentations s'appuient sur des données réalistes, générées aléatoirement. Nous nous intéressons particulièrement aux pistes d'amélioration des temps de calculs et de réduction des graphes. Une heuristique gloutonne permettant d'identifier rapidement une solution réalisable est en particulier proposée. Enfin, une étude de dimensionnement des batteries confirme que des capacités deux fois inférieures à celles actuellement sur le marché sont viable dans le contexte urbain actuel

Optimization of a one-way carsharing system with relocation operations

International audienceCarsharing systems have gathered increasing attention and are now recognised as innovative and ecological solutions to transportation issues. Especially, one-way carsharing systems offer a high level of service because they exempt users from the obligation to return the vehicle at the same station where it was borrowed. Unfortunately, this flexibility comes with design complexity. This paper addresses a part of those design issues and deals with fleet dimensioning including vehicle relocation operations. We propose mathematical programming oriented approach and we introduce a simple linear model based on integer flow variables. This model is organized around three optimization criteria: maximizing satisfied carsharing demands while minimizing the fleet of vehicles and the relocation operations. From random generated benchmarks, we study the scalability of our method and we show that computation times remain acceptable for representative problem complexities

Mathematical Model for the Study of Relocation Strategies in One-way Carsharing Systems

International audienceCarsharing is today considered as an ecological and innovative solution to improve urban mobility. The one-way version, where vehicles can be drop-off in any station, brings however some challenging open questions. The system has to be design as part of the global transportation one and vehicle relocation operations must be included to get the higher level of service. In this paper, we consider a one-way carsharing system where stations and their location are fixed. The optimization problem consists in maximizing the total number of satisfied demands for a limited number of vehicles and relocation operations. We propose a formal definition and a mathematical model using Integer Linear Programming (ILP). We show that the problem size is strongly related to the number of possible relocation operations and a polynomial subcase is exhibited. Numerical results highlight that vehicle relocations can be drastically reduced without deteriorating the quality of solutions. Our method can thus be easily used in system management to evaluate possible implementation of vehicle relocation strategies