A5073898339- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Genomics and Phylogenetic Studies
- Fungal and yeast genetics research
- Microbial Community Ecology and Physiology
- Enzyme Production and Characterization
- Anaerobic Digestion and Biogas Production
- Gut microbiota and health
- Fungal Biology and Applications
- Enzyme Catalysis and Immobilization
- Probiotics and Fermented Foods
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Algal biology and biofuel production
- Microbial Metabolites in Food Biotechnology
- Polysaccharides and Plant Cell Walls
- Biomedical Text Mining and Ontologies
- Plant-Microbe Interactions and Immunity
- Glycosylation and Glycoproteins Research
- Bacterial Genetics and Biotechnology
- Microbial Natural Products and Biosynthesis
- Tuberculosis Research and Epidemiology
- Plant Pathogenic Bacteria Studies
- Aquaculture Nutrition and Growth
- Bioeconomy and Sustainability Development
Wageningen University & Research
2016-2025
Delft University of Technology
2022-2024
Evides (Netherlands)
2023
TiFN
2013-2018
Institut de Biologie systémique et synthétique
2018
Hanze University of Applied Sciences
2018
John Wiley & Sons (United States)
2017
Bioengineering Center
2017
National Center for Genetic Engineering and Biotechnology
2017
Hudson Institute
2017
The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for production of enzymes and organic acids, particularly citric acid. We sequenced 33.9-megabase genome A. CBS 513.88, ancestor currently used enzyme strains. A high level synteny was observed with other aspergilli sequenced. Strong function predictions were made 6,506 14,165 open reading frames identified. detailed description components protein secretion pathway striking differences in hydrolytic...
The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces organic acids hydrolytic enzymes high amounts, some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. strain (CBS 513.88) has already been sequenced, versatility this species compel additional exploration. We therefore undertook whole-genome sequencing acidogenic wild-type (ATCC 1015) produced a...
ABSTRACT The composition and activity of the microbiota in human gastrointestinal tract are primarily shaped by nutrients derived from either food or host. Bacteria colonizing mucus layer have evolved to use mucin as a carbon energy source. One members mucosa-associated is Akkermansia muciniphila , which capable producing an extensive repertoire mucin-degrading enzymes. To further study substrate utilization abilities A. we constructed genome-scale metabolic model test amino acid auxotrophy,...
Background Massive high-throughput sequencing of short, hypervariable segments the 16S ribosomal RNA (rRNA) gene has transformed methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that methodology rather than biological variation is responsible for observed sample composition distribution. This compromises true meta-analyses, although this fact often disregarded. Results To facilitate meta-analysis microbiome studies,...
<ns4:p><ns4:bold>Background: </ns4:bold>Massive high-throughput sequencing of short, hypervariable segments the 16S ribosomal RNA (rRNA) gene has transformed methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that methodology rather than biological variation is responsible for observed sample composition distribution. This compromises meta-analyses, although this fact often disregarded.</ns4:p><ns4:p>...
Ten years of experience with molecular class-specific information systems (MCSIS) such as the hand-curated G protein-coupled receptor database (GPCRDB) or semiautomatically generated nuclear has made clear that a wide variety questions can be answered when protein-related data from many different origins flexibly combined. MCSISes revolve around multiple sequence alignment (MSA) includes "all" available sequences entire superfamily, and it been shown at occasions quality these alignments is...
Next generation sequencing (NGS) technologies can be applied in complex microbial ecosystems for metatranscriptome analysis by employing direct cDNA sequencing, which is known as RNA (RNA-seq). RNA-seq generates large datasets of great complexity, the comprehensive interpretation requires a reliable bioinformatic pipeline. In this study, we focus on development such pipeline, validate using Illumina derived from small intestine microbiota two individuals with an ileostomy.The pipeline...
NG-Tax 2.0 is a semantic framework for FAIR high-throughput analysis and classification of marker gene amplicon sequences including bacterial archaeal 16S ribosomal RNA (rRNA), eukaryotic 18S rRNA intergenic transcribed spacer sequences. It can directly use single or merged reads, paired-end reads unmerged from long range fragments as input to generate de novo sequence variants (ASV). Using the RDF data model, ASV's be automatically stored in graph database objects that link ASV with full...
Background The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates survive a complex highly competitive ecosystem. Understanding how these communities function requires elucidating role of its key players, interactions among them with environment/host. Methods genome gut bacterium Romboutsia ilealis CRIB T was sequenced multiple technologies (Illumina paired-end, mate-pair PacBio). transcriptome HiSeq) after growth three different...
Host glycans are paramount in regulating the symbiotic relationship between humans and their gut bacteria. The constant flux of host-secreted mucin at mucosal layer creates a steady niche for bacterial colonization. Mucin degradation by keystone species subsequently shapes microbial community. This study investigated transcriptional response during mucin-driven trophic interaction specialised mucin-degrader Akkermansia muciniphila butyrogenic commensal Anaerostipes caccae. A. monocultures...
The human pathogen Mycobacterium tuberculosis has the capacity to escape eradication by professional phagocytes. During infection, M. resists harsh environment of phagosomes and actively manipulates macrophages dendritic cells ensure prolonged intracellular survival. In contrast other pathogens, it remained difficult capture transcriptome mycobacteria during infection due an unfavorable host-to-pathogen ratio. We infected macrophage-like cell line THP-1 with attenuated surrogate bovis...
To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained available genome sequence of organisms has accelerated in many cases. black tiger shrimp (Penaeus monodon) is one the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production half a million tons last decade. However, its currently assemblies lack contiguity completeness required for accurate annotation due to highly...
Harnessing the power of microbial consortia is integral to a diverse range sectors, from healthcare biotechnology environmental remediation. To fully realize this potential, it critical understand mechanisms behind interactions that structure and determine their functions. Constraint-based reconstruction analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as state-of-the-art tool simulate behavior communities constituent genomes. In last decade, many...
In recent years, there has been growing interest in harnessing anaerobic digestion technology for resource recovery from waste streams. This approach evolved beyond its traditional role energy generation to encompass the production of valuable carboxylic acids, especially volatile fatty acids (VFAs) like acetic acid, propionic and butyric acid. VFAs hold great potential various industries biobased applications due their versatile properties. Despite increasing global demand, over 90% are...
Abstract Background Peptide spectrum matching (PSM) is the standard method in shotgun proteomics data analysis. It relies on availability of an accurate and complete sample proteome that used to make interpretation spectra feasible. Although this procedure has proven be effective many studies, approach limitations when applied complex samples microbial communities, such as those found human intestinal tract. Metagenome studies have indicated microbiome contains over 100 times more genes than...
Oxalate secretion by fungi is known to be associated with fungal pathogenesis. In addition, oxalate toxicity a concern for the commercial application of in food and drug industries. Although generated through several different biochemical pathways, oxaloacetate acetylhydrolase (OAH)-catalyzed hydrolytic cleavage appears an especially important route. Below, we report cloning Botrytis cinerea oahA gene demonstration that disruption this results loss formation. complementation have shown...
The oxygen reactivity of flavoproteins is poorly understood. Here we show that a single Ala to Gly substitution in l-galactono-γ-lactone dehydrogenase (GALDH) turns the enzyme into catalytically competent oxidase. GALDH an aldonolactone oxidoreductase with vanillyl-alcohol oxidase (VAO) fold. We found nearly all oxidases VAO family contain either or Pro at structurally conserved position near C4a locus isoalloxazine moiety flavin, whereas dehydrogenases prefer another residue this position....
Abstract Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering bioremediation. We analysed 432 sequenced strains by integrating results from large scale functional comparison using protein domains with data six metabolic models, nearly thousand transcriptome measurements four transposon mutagenesis experiments. Through heterogeneous integration we linked gene essentiality, persistence expression...
Global climate change and fossil fuels limitations have boosted the demand for robust efficient microbial factories manufacturing of bio-based products from renewable feedstocks. In this regard, efforts been done to enhance enzyme-secreting ability lignocellulose-degrading fungi, aiming improve protein yields while taking advantage their use lignocellulosic Access sugars in complex polysaccharides depends not only on release by specific hydrolytic enzymes, but also presence transporters...