A5023501398- Genomics and Phylogenetic Studies
- Fermentation and Sensory Analysis
- Horticultural and Viticultural Research
- Gut microbiota and health
- Microbial Community Ecology and Physiology
- RNA and protein synthesis mechanisms
- Gene expression and cancer classification
- Bacteriophages and microbial interactions
- Clostridium difficile and Clostridium perfringens research
- Phytochemicals and Antioxidant Activities
- Urinary Tract Infections Management
- Metabolomics and Mass Spectrometry Studies
- Plant Pathogens and Fungal Diseases
- Wine Industry and Tourism
- Antibiotic Resistance in Bacteria
- Forest Insect Ecology and Management
- Plant and Fungal Interactions Research
- Mycorrhizal Fungi and Plant Interactions
- Meat and Animal Product Quality
- Microbial Metabolism and Applications
- Research in Social Sciences
- Microbial Metabolic Engineering and Bioproduction
- Spectroscopy and Chemometric Analyses
- Machine Learning in Bioinformatics
- Probiotics and Fermented Foods
University of Copenhagen
2020-2023
Evolutionary Genomics (United States)
2021
Dienstleistungszentrum Ländlicher Raum Rheinpfalz
2018-2019
Dienstleistungszentrum Ländlicher Raum
2018-2019
University of Kaiserslautern
2018-2019
University of Helsinki
2010-2014
Genes of unknown function are among the biggest challenges in molecular biology, especially microbial systems, where 40-60% predicted genes unknown. Despite previous attempts, systematic approaches to include fraction into analytical workflows still lacking. Here, we present a conceptual framework, its translation computational workflow AGNOSTOS and demonstration on how can bridge known-unknown gap genomes metagenomes. By analyzing 415,971,742 from 1749 metagenomes 28,941 bacterial archaeal...
Abstract The widespread usage of antimicrobials has driven the evolution resistance in pathogenic microbes, both increased prevalence antimicrobial genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, impact on wider community commensal microbes associated with human body, microbiome, is less well understood. Small-scale studies have determined transient impacts antibiotic consumption but we conduct an extensive survey ARGs 8972 metagenomes to determine...
Abstract Prophages are phages that integrated into bacterial genomes and which key to understanding many aspects of biology. Their extreme diversity means they challenging detect using sequence similarity, yet this remains the paradigm thus remain unidentified. We present a novel, fast generalizing machine learning method based on feature space facilitate novel prophage discovery. To validate approach, we reanalyzed publicly available marine viromes single-cell our feature-based approaches...
Pinot Noir red wines made by malolactic fermentation were studied for studying differences in their chemical profiles with help of a wide spectrum grape-based and other compounds used winemaking. Determinations capillary electrophoresis, liquid chromatography, spectrometry to investigate carbohydrates, organic acids, aldehydes, anthocyanins, phenolic compounds, inorganic anions, metals. In addition, tot-N, tot-S, tot-P the examined. The wine products showed different minerals. Especially,...
Although there is an extensive tradition of research into the microbes that underlie winemaking process, much remains to be learnt. We combined high-throughput sequencing (HTS) tools metabarcoding and metagenomics, characterise how microbial communities Riesling musts sampled at four different vineyards, their subsequent spontaneously fermented derivatives, vary. specifically explored community variation related three points: i) vary by vineyard; ii) biodiversity changes during alcoholic...
Background: Fast and computationally efficient strategies are required to explore genomic relationships within an increasingly large diverse phage sequence space. Here, we present PhageClouds, a novel approach using graph database of sequences their intergenomic distances the Methods: A total 640,000 were retrieved from variety databases public virome assemblies. Intergenomic calculated with dashing, alignment-free method suitable for handling massive data sets. These used build Neo4j®...
One of the biggest challenges for dairy producers is substantial variability in final product properties caused by changes production environment. In cheese production, this variation influenced several factors, particularly milk base and its pretreatment, which shape microbiome throughout process ultimately affect cheese's organoleptic characteristics. To examine impact three different pre-treatments pasteurised milk- microfiltration, protein fortification, only pasteurisation (control)- on...
Abstract Genes of unknown function are among the biggest challenges in molecular biology, especially microbial systems, where 40%-60% predicted genes unknown. Despite previous attempts, systematic approaches to include fraction into analytical workflows still lacking. Here, we propose a conceptual framework and computational workflow that bridge known-unknown gap genomes metagenomes. We showcase our approach by exploring 415,971,742 from 1,749 metagenomes 28,941 bacterial archaeal genomes....
Non-targeted analysis is nowadays applied in many different domains of analytical chemistry such as metabolomics, environmental and food analysis. Conventional processing strategies for GC-MS data include baseline correction, feature detection, retention time alignment before multivariate modeling. These techniques can be prone to errors therefore time-consuming manual corrections are generally necessary. We introduce here a novel fully automated approach non-targeted processing. This new...
ABSTRACT Prophages are phages that integrated into bacterial genomes and which key to understanding many aspects of biology. Their extreme diversity means they challenging detect using sequence similarity, yet this remains the paradigm thus remain unidentified. We present a novel, fast generalizing machine learning method based on feature space facilitate novel prophage discovery. To validate approach, we reanalyzed publicly available marine viromes single-cell our feature-based approaches...
ABSTRACT The fungal pathogen Neonectria neomacrospora is of increasing concern in Europe where, within the last decade, it has caused substantial damage to forest stands and ornamental trees genus Abies (Mill.). Using whole-genome sequencing a comprehensive collection isolates, we show extent three major clades N. , which most likely diverged around end Ice Age. We find that current European epidemic was founded from population belonging east North American clade. All isolates (1957-2019)...
ABSTRACT The fungal plant pathogen Neonectria neomacrospora (C. Booth & Samuels) Mantiri Samuels (Ascomycota, Hypocreales) is a bark parasite causing twig blight, canker, and in severe cases, dieback fir ( Abies spp.). Although often described as mild pathogen, foresty phytosanitary agencies have expressed their concern for potential economic impact. Two epidemics caused by this species are known: one from eastern Canada current within Northern Europe. We present key genome features of...