Rob Van Houdt

Rob Van Houdt
Belgian Nuclear Research Centre | SCK CEN · Interdisciplinary Biosciences

Ph.D. degree in Applied Biosciences and Engineering

About

258
Publications
27,109
Reads
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4,673
Citations
Introduction
In 2005, I obtained my Ph.D. at the KU Leuven (B). After one year as a Postdoctoral Fellow (KU Leuven, B), I joined the microbiology unit at the Belgian Nuclear Research Centre (SCK•CEN) in October 2006. Since January 2008, I have a permanent position and manage different projects that study the response and adaptation of microorganisms to stress conditions with emphasis on the Cupriavidus genus, metal resistance, and the role of mobile genetic elements.
Additional affiliations
October 2006 - present
Belgian Nuclear Research Centre
Position
  • Research Associate
October 2005 - September 2006
KU Leuven
Position
  • PostDoc Position
Education
October 2000 - September 2005
KU Leuven
Field of study
  • Bioscience Engineering
October 1995 - June 2000
KU Leuven
Field of study
  • Applied Biosciences and Engineering

Publications

Publications (258)
Article
Full-text available
The rise of metagenomics offers a leap forward for understanding the genetic diversity of microorganisms in many different complex environments by providing a platform that can identify potentially unlimited numbers of known and novel microorganisms. As such, it is impossible to imagine new major initiatives without metagenomics. Nevertheless, it r...
Article
Full-text available
Environmental uranium pollution due to industries producing naturally occurring radioactive material or nuclear accidents and releases is a global concern. Uranium is hazardous for ecosystems as well as for humans when accumulated through the food chain, through contaminated groundwater and potable water sources, or through inhalation. In particula...
Article
Full-text available
Bioregenerative life support systems (BLSS) are currently in development to tackle low recovery efficiencies, high energy demands, as well as food, water, and oxygen production challenges through the regeneration of nutrients from waste streams. The MELiSSA pilot plant has been developed as a testbed for regenerative life support system bioreactor...
Article
Full-text available
Background Although the total number of microbial taxa on Earth is under debate, it is clear that only a small fraction of these has been cultivated and validly named. Evidently, the inability to culture most bacteria outside of very specific conditions severely limits their characterization and further studies. In the last decade, a major part of...
Article
Full-text available
Maintaining crew health and safety are essential goals for long-term human missions to space. Attaining these goals requires the development of methods and materials for sustaining the crew’s health and safety. Paramount is microbiological monitoring and contamination reduction. Microbial biofilms are of special concern, because they can cause dama...
Conference Paper
Full-text available
As space agencies plan to expand human presence in space and to settle on the Moon first and Mars later, developing strategies to achieve this goal in a sustainable way is necessary. These include in situ resource utilization (ISRU) and recovering of materials by waste recycling (1). Microbe based technologies may be pivotal to the success of human...
Article
Full-text available
Cupriavidus metallidurans strains display a decreased viability when incubated in rich medium at a temperature of 37°C compared to their normal growth temperature of 30°C, a phenomenon coined “temperature-induced mortality and mutagenesis” (TIMM). To scrutinize this aberrant phenotype further, the contributions of specific inducers and protective a...
Article
Full-text available
Cupriavidus metallidurans is a model bacterium to study molecular metal resistance mechanisms and its use for the bioremediation of several metals has been shown. However, its mechanisms for radionuclide resistance are unexplored. We investigated the interaction with uranium and associated cellular response to uranium for Cupriavidus metallidurans...
Article
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Environmental bacteria belonging to various families were isolated from polluted water collected from ten different sites in Tunisia. Sites were chosen near industrial and urban areas known for their high degree of pollution. The aim of this study was to investigate cross-resistance between heavy metals (HM), i.e., silver, mercury and copper (Ag, H...
Article
Full-text available
Bacteria encounter elevated copper (Cu) concentrations in multiple environments, varying from mining wastes to antimicrobial applications of copper. As the role of the environment in the bacterial response to Cu ion exposure remains elusive, we used a tagRNA-seq approach to elucidate the disparate responses of two morphotypes of Caulobacter crescen...
Conference Paper
The EDEN ISS greenhouse, integrated in two joined containers, is a confined mobile test facility in Antarctica for the development and optimization of new plant cultivation techniques for future space programs. The EDEN ISS greenhouse was used successfully from February to November 2018 for fresh food production for the overwintering crew at the An...
Conference Paper
Long term human space missions require efficient strategies to sustain crew health and safety. This is why we need to develop improved spaceflight-suitable methods for microbiological monitoring and contamination control. Especially microbial biofilms are of concern in spaceflight because they can damage equipment by polymer deterioration, corrode...
Article
Full-text available
As humans explore and settle in space, they will need to mine elements to support industries such as manufacturing and construction. In preparation for the establishment of permanent human settlements across the Solar System, we conducted the ESA BioRock experiment on board the International Space Station to investigate whether biological mining co...
Article
Full-text available
The antimicrobial applications of copper (Cu) are exploited in several industries, such as agriculture and healthcare settings. While Cu is capable of efficiently killing microorganisms, sub-lethal doses can induce a viable-but-non-culturable (VBNC) state in bacteria of many distinct clades. VBNC cells cannot be detected by standard culture-based d...
Article
Full-text available
Cupriavidus metallidurans CH34 is a well-studied metal-resistant β-proteobacterium and contains a battery of genes participating in metal metabolism and resistance. Here, we generated a mutant (CH34ZnR) adapted to high zinc concentrations in order to study how CH34 could adaptively further increase its resistance against this metal. Characterizatio...
Article
Full-text available
Microbial communities are essential for a healthy soil ecosystem. Metals and radionuclides can exert a persistent pressure on the soil microbial community. However, little is known on the effect of long‐term co‐contamination of metals and radionuclides on the microbial community structure and functionality. We investigated the impact of historical...
Article
Cupriavidus metallidurans, and in particular type strain CH34, became a model bacterium to study bacterial resistance to metals. Although nowadays the routine use of a wide variety of omics and molecular techniques allow refining, deepening and expanding our knowledge on adaptation and resistance to metals, these were not available at the onset of...
Article
Full-text available
Microorganisms are employed to mine economically important elements from rocks, including the rare earth elements (REEs), used in electronic industries and alloy production. We carried out a mining experiment on the International Space Station to test hypotheses on the bioleaching of REEs from basaltic rock in microgravity and simulated Mars and Ea...
Article
Klebsiella pneumoniae, ubiquitously found in a variety of environmental sources, is an important pathogen in burn wounds and nosocomial infections. Burn wounds have been commonly treated with silver compounds, which are also used in a multitude of (non‐)medical products. As the latter increased silver discharge into different environments, we evalu...
Article
Full-text available
Microorganisms perform countless tasks on Earth and they are expected to be essential for human space exploration. Despite the interest in the responses of bacteria to space conditions, the findings on the effects of microgravity have been contradictory, while the effects of Martian gravity are nearly unknown. We performed the ESA BioRock experimen...
Article
Full-text available
Bacteria are increasingly used for biotechnological applications such as bioremediation, biorecovery, bioproduction, and biosensing. The development of strains suited for such applications requires a thorough understanding of their behavior, with a key role for their transcriptomic landscape. We present a thorough analysis of the transcriptome of C...
Article
Full-text available
Even though silver and silver nanoparticles at low concentrations are considered safe for human health, their steadily increasing use and associated release in nature is not without risk since it may result in the selection of silver-resistant microorganisms, thus impeding the utilization of silver as antimicrobial agent. Furthermore, increased res...
Article
Full-text available
Metallic copper to combat bacterial proliferation in drinking water systems is being investigated as an attractive alternative to existing strategies. A potential obstacle to this approach is the induction of metal resistance mechanisms in contaminating bacteria, that could severely impact inactivation efficacy. Thus far, the role of these resistan...
Article
Full-text available
The EDEN ISS greenhouse, integrated in two joined containers, is a confined mobile test facility in Antarctica for the development and optimization of new plant cultivation techniques for future space programs. The EDEN ISS greenhouse was used successfully from February to November 2018 for fresh food production for the overwintering crew at the An...
Article
Full-text available
Motivation: One of the most widespread methods used in taxonomy studies to distinguish between strains or taxa is the calculation of average nucleotide identity. It requires a computationally expensive alignment step, and is therefore not suitable for large-scale comparisons. Short-oligonucleotide-based methods do offer a faster alternative but at...
Chapter
An impaired immunity generally weakens the host defense against microbial challenges and increases the vulnerability to infection. Especially in space, the consequences of an impaired immune system can further aggravate as astronauts, spending 100% of their time enclosed, face multiple stressors in an artificial environment with its own microbial p...
Article
Full-text available
The uncontrolled and widespread use of (nano)silver compounds has led to the increased release of these compounds into the environment, raising concerns about their negative impact on ecosystems. Concomitantly, silver resistance determinants are widely spread among environmental and clinically relevant bacteria although the underlying mechanisms ar...
Article
Full-text available
The extensive anthropogenic use of platinum, a rare element found in low natural abundance in the Earth’s continental crust and one of the critical raw materials in the EU innovation partnership framework, has resulted in increased concentrations in surface environments. To minimize its spread and increase its recovery from the environment, biologi...
Article
Full-text available
For the past three decades, Cupriavidus metallidurans has been one of the major model organisms for bacterial tolerance to heavy metals. Its type strain CH34 contains at least 24 gene clusters distributed over four replicons, allowing for intricate and multilayered metal responses. To gain organic mercury resistance in CH34, broad-spectrum mer gene...
Article
Full-text available
Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to...
Article
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Background: Basalt is the most common igneous rock on the Earth's surface covering. Basalt-associated microorganisms drive the cycling and sequestration of different elements such as nitrogen, carbon and other nutrients, which facilitate subsequent pioneer and plant development, impacting long-term regulation of the Earth's temperature and biosphe...
Article
Full-text available
High levels of shear stress can prevent and disrupt Pseudomonas aeruginosa biofilm formation in vitro. Intrapulmonary percussive ventilation (IPV) could be used to introduce shear stress into the lungs of cystic fibrosis (CF) patients to disrupt biofilms in vivo. We performed a first-of-its-kind pilot clinical study to evaluate short-term IPV thera...
Article
The influence of different rock mineralogical compositions on element leaching and bio-weathering processes is poorly understood. Here, the role of basalt composition on nutrient leaching (calcium, iron, phosphorus or magnesium) and subsequent support of Cupriavidus metallidurans CH34 growth was evaluated. Seven different basalts were examined. In...
Article
Exposure to bioaerosols is one of the facets that affect indoor air quality, especially for people living in densely populated or confined habitats, and is associated to a wide range of health effects. Good indoor air quality is thus vital and a prerequisite for fully confined environments such as space habitats. Bioaerosols and microbial contamina...
Article
Full-text available
This study aimed to evaluate the suitability of two bioaerosol generation systems (dry and wet generation) for the aerosolization of microorganisms isolated from the International Space Station, and to calibrate the produced bioaerosols to fulfill the requirements of computational fluid dynamics model (CFD) validation. Concentration, stability, siz...
Article
In this paper, we describe the development of an International Space Station experiment, BioRock. The purpose of this experiment is to investigate biofilm formation and microbe–mineral interactions in space. The latter research has application in areas as diverse as regolith amelioration and extraterrestrial mining. We describe the design of a prot...
Article
Full-text available
Microbe-mineral interactions have become of interest for space exploration as microorganisms could be used to biomine from extra-terrestrial material and extract elements useful as micronutrients in life support systems. This research aimed to identify the impact of space flight on the long-term survival of Cupriavidus metallidurans CH34 in mineral...
Data
Statistical analysis of the planktonic, biofilm fractions as well as for the ICP-OES analysis.
Data
Wavelengths used for ICP-OES analysis.
Data
Scanning Electron Microscopy (SEM) image of basalt after preflight preparatory experiment with the same setup as the flight experiment.
Article
Full-text available
Transposable elements (TE), small mobile genetic elements unable to exist independently of the host genome, were initially believed to be exclusively deleterious genomic parasites. However, it is now clear that they play an important role as bacterial mutagenic agents, enabling the host to adapt to new environmental challenges and to colonize new n...
Article
Full-text available
In vitro models that mimic in vivo host-pathogen interactions are needed to evaluate candidate drugs that inhibit bacterial virulence traits. We established a new approach to study Pseudomonas aeruginosa biofilm susceptibility on biotic surfaces, using a three-dimensional (3-D) lung epithelial cell model. P. aeruginosa formed antibiotic resistant b...
Article
Full-text available
Flow cytometry is a rapid and quantitative method to determine bacterial viability. Although different stains can be used to establish viability, staining protocols are inconsistent and lack a general optimization approach. Very few “true” multicolor protocols, where dyes are combined in one sample, have been developed for microbiological applicati...
Article
Full-text available
Chronic colonization of the lungs by Pseudomonas aeruginosa is one of the major causes of morbidity and mortality in cystic fibrosis (CF) patients. To gain insights into the characteristic biofilm phenotype of P. aeruginosa in the CF lungs, mimicking the CF lung environment is critical. We previously showed that growth of the non-CF-adapted P. aeru...
Data
Relative abundances of the mucoid and nonmucoid morphotypes after growth of P. aeruginosa CF_PA39 in LB medium in culture tubes over time. Download
Data
Primers used for qRT-PCR amplification.
Data
Genes that are differentially expressed in P. aeruginosa CF_PA39 and P. aeruginosa PAO1 during growth under LS versus HS conditions.
Data
Analysis of the relative proportions of COG-functional classes that were represented among differentially expressed genes.
Data
Elongated P. aeruginosa cells observed under low fluid shear (A) and high fluid shear (B) conditions via scanning electron microscopy. Images are representative of different biological repeats. Elongated cells are indicated by white arrows. Red arrows indicate the putative septum that was formed during cell division. Download
Data
Bacterial strains used in this study.
Data
Relative abundances of the mucoid and nonmucoid morphotypes after growth of P. aeruginosa CF_PA39 in ASM in culture tubes over time. Download
Data
Overview of the RNA sequencing results for all coding sequences (CDS) and small RNA genes annotated in P. aeruginosa CF_PA39.
Article
Full-text available
Bacteria can respond to adverse environments by increasing their genomic variability and subsequently facilitating adaptive evolution. To demonstrate this, the contribution of Insertion Sequence (IS) elements to the genetic adaptation of Cupriavidus metallidurans AE126 to toxic zinc concentrations was determined. This derivative of type strain CH34...
Data
Schematic representation of the cnr operon of megaplasmid pMOL28 from C. metallidurans extracted from the MaGe platform (https://www.genoscope.cns.fr/agc/microscope/mage/) with cnrYX encoding two membrane-bound anti-sigma factors, cnrH a sigma factor, cnrCBA a RND efflux pump, and cnrT a cation diffusion facilitator. Black line represent the amplic...