A5007146856- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Bioinformatics and Genomic Networks
- Biofuel production and bioconversion
- Primate Behavior and Ecology
- Probiotics and Fermented Foods
- Animal Nutrition and Physiology
- Enzyme Production and Characterization
- Human-Animal Interaction Studies
- Metabolomics and Mass Spectrometry Studies
- SARS-CoV-2 and COVID-19 Research
- Historical and Archaeological Studies
- Gene Regulatory Network Analysis
- Mitochondrial Function and Pathology
- Protist diversity and phylogeny
- Evolution and Paleontology Studies
- Biomedical Text Mining and Ontologies
- Enzyme-mediated dye degradation
- Scientific Computing and Data Management
- Microbial Metabolic Engineering and Bioproduction
- Lichen and fungal ecology
- Bacterial Genetics and Biotechnology
- Advanced Proteomics Techniques and Applications
- SARS-CoV-2 detection and testing
Aalborg University
2024
Norwegian University of Life Sciences
2017-2023
University of Luxembourg
2020-2023
This study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans several domesticated species. The results obtained suggest that (paleo-)genomic data can be exploited to complement the fossil record support idea of self-domestication Homo sapiens, a process likely intensified as our species populated its niche. Our analysis lends attempts capture "domestication syndrome" terms alterations certain signaling pathways cell...
Abstract The efficiency of microorganisms to degrade lignified plants is great importance in the Earth’s carbon cycle, but also industrial biorefinery processes, such as for biofuel production. Here, we present a large-scale proteomics approach investigate and compare enzymatic response five filamentous fungi when grown on very different substrates: grass (sugarcane bagasse), hardwood (birch), softwood (spruce), cellulose glucose. included ascomycetes Aspergillus terreus , Trichoderma reesei...
While the field of microbiology has adapted to study complex microbiomes via modern meta-omics techniques, we have not updated our basic knowledge regarding quantitative levels DNA, RNA and protein molecules within a microbial cell, which ultimately control cellular function. Here report temporal measurements absolute per gene mixed bacterial-archaeal consortium. Our analysis this data reveals an protein-to-RNA ratio 102-104 for bacterial populations 103-105 archaeon, is more comparable...
Monitoring SARS-CoV-2 in wastewater has shown to be an effective tool for epidemiological surveillance. More specifically, RNA levels determined with RT-qPCR have been track the infection dynamics within population. However, surveillance of individual lineages circulating population based on genomic sequencing samples is challenging, as genetic material constitutes a mixture different viral haplotypes. Here, we identify specific signature mutations from estimate Luxembourg. We compare and...
The rapid development of the (meta-)omics fields has produced an unprecedented amount high-resolution and high-fidelity data. Through use these datasets we can infer role previously functionally unannotated proteins from single organisms consortia. In this context, protein function annotation be described as identification regions interest (i.e., domains) in sequences assignment biological functions. Despite existence numerous tools, challenges remain terms speed, flexibility,...
Abstract Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity, as well synergistic interactions between both cellulolytic non-cellulolytic microorganisms. Coprothermobacter proteolyticus frequently dominates thermophilic, lignocellulose-degrading with wide geographical distribution, which is in contrast to reports it ferments proteinaceous substrates incapable polysaccharide hydrolysis. Here we deconvolute a highly...
'Omics methods have empowered scientists to tackle the complexity of microbial communities on a scale not attainable before. Individually, omics analyses can provide great insight; while combined as "meta-omics", they enhance understanding which organisms occupy specific metabolic niches, how interact, and utilize environmental nutrients. Here we present three integrative meta-omics workflows, developed in Galaxy, for enhanced analysis integration metagenomics, metatranscriptomics,...
Abstract Background Network inference is an important aim of systems biology. It enables the transformation OMICs datasets into biological knowledge. consists reverse engineering gene regulatory networks from data, such as RNAseq or mass spectrometry-based proteomics through computational methods. This approach allows to identify signalling pathways involved in specific functions. The ability infer causality networks, addition correlation, crucial for several modelling approaches and...
Summary The last 20 years have witnessed unprecedented advances in revealing the microbiomes underpinning important processes natural and human associated environments. Recent large-scale metagenome surveys record variety of microbial life oceans 1 , wastewater 2 gut 3,4 earth 5,6 with compilations encompassing thousands public datasets 7–13 . So far, microbiome studies either miss functional information or consistency sample processing, although they may cover locations, these are missing...
Predicting the behaviour of complex microbial communities is challenging. However, this essential for biotechnological processes such as those in biological wastewater treatment plants (BWWTPs), which require sustainable operation. Here we summarize 14 months longitudinal meta-omics data from a BWWTP anaerobic tank into 17 temporal signals, explaining 91.1% variance, and link signals to ecological events within community. We forecast over subsequent five years use 21 extra samples collected...
<ns3:p>The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and influence collective genetic material (the ‘microbiome’) diversity patterns across habitats our planet. With evolution new sequencing technologies, researchers can now investigate microbiome map its on environment human health. Advances bioinformatics methods for next-generation (NGS) data analysis have helped to gain an in-depth knowledge about taxonomic composition communities....
Abstract Background The past decades have seen a rapid development of the (meta-)omics fields, producing an unprecedented amount data. Through use well-characterized datasets we can infer role previously functionally unannotated proteins from single organisms and consortia. In this context, protein function annotation allows identification regions interest (i.e. domains) in sequences assignment biological functions. Despite existence numerous tools, some challenges remain, specifically terms...
The porcine gut microbiome is central to animal health and growth as well it can be structurally or functionally reshaped by dietary interventions. microbiota composition in relation Cyberlindnera jadinii yeast a protein source weanling diet was studied previously. Also, there mounting body of knowledge regarding the response use rapeseed (Brassica napus subsp. napus) meal, faba beans (Vicia faba) sources during growing/finishing period. However, limited data on how respond combination C....
<ns4:p>The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and influence collective genetic material (the ‘microbiome’) human health disease. With evolution new sequencing technologies, researchers can now investigate microbiome map its on health. Advances bioinformatics methods for next-generation (NGS) data analysis have helped to gain an in-depth knowledge about taxonomic composition communities. Metagenomic-based been most commonly used approaches...
Abstract Genomes are fundamental to understanding microbial ecology and evolution. The emergence of high-throughput, long-read DNA sequencing has enabled recovery genomes from environmental samples at scale. However, expanding the genome catalogue soils sediments been challenging due enormous complexity these environments. Here, we performed deep, Nanopore 154 soil sediment collected across Denmark through an optimised bioinformatics pipeline, recovered 15,314 novel species, including 4,757...
ABSTRACT This study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans several domesticated species. The results obtained suggest that (paleo-) genomic data can be exploited to complement the fossil record support idea of self-domestication Homo sapiens, a process likely intensified as our species populated its niche. Our analysis lends attempts capture “domestication syndrome” terms alterations certain signaling pathways...
ABSTRACT Microbial communities are complex assemblages whose dynamics shaped by abiotic and biotic factors. A major challenge concerns correctly forecasting the community behaviour in future. In this context, biological wastewater treatment plants (BWWTPs) represent excellent model systems, because them is required to ultimately control operate a sustainable manner. Here, we forecast microbial from water-air interface of anaerobic tank BWWTP via longitudinal meta-omics (metagenomics,...
ABSTRACT Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity as well synergistic interactions between both cellulolytic non-cellulolytic microorganisms. Coprothermobacter proteolyticus frequently dominates thermophilic, lignocellulose-degrading with wide geographical distribution, which is in contrast to reports it ferments proteinaceous substrates incapable polysaccharide hydrolysis. Here we deconvolute a highly...
Abstract Microbiology is founded on well-known model organisms. For example, the majority of our fundamental knowledge regarding quantitative levels DNA, RNA, and protein backdates to keystone pure culture-based studies. Nowadays, meta-omic approaches allow us directly access molecules that constitute microbes microbial communities, however due a lack absolute measurements, many original culture-derived “microbiology statutes” have not been updated or adapted more complex microbiome...
The porcine gut microbiome is closely connected to diet and central animal health growth. microbiota composition in relation Cyberlindnera jadinii yeast as a protein source weanling was studied previously. Also, there mounting body of knowledge regarding the response use rapeseed ( Brassica napus subsp. ) meal, faba beans Vicia sources during growing/finishing period. However, limited data on how respond combination C. phase meal phase. This work investigated faecal changing novel with high...