Haris ZafeiropoulosKU Leuven | ku leuven · Rega Institute for Medical Research
Haris Zafeiropoulos
PhD
investigating microbial interactions using metabolic modeling approaches
About
24
Publications
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61
Citations
Citations since 2017
Introduction
Skills and Expertise
Publications
Publications (24)
The human gut is a complex ecosystem consisting of hundreds of microbial species interacting with each other and with the human host. Mathematical models of the gut microbiome integrate our knowledge of this system and help to formulate hypotheses to explain observations. The generalized Lotka-Volterra model has been widely used for this purpose, b...
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers h...
Microbial mats are vertically stratified communities of microorganisms characterised by pronounced physiochemical gradients allowing for high species diversity and a wide range of metabolic capabilities. High Throughput Sequencing has the potential to reveal the biodiversity and function of such ecosystems in the cycling of elements.
The present st...
Microbial interactions play a fundamental role in deciphering the underlying mechanisms that govern complex host-associated microbial communities. High throughput sequencing enables the taxonomic and functional characterization of such communities. Yet, new approaches are required to analyse sequencing data but also to exploit such information at a...
Microbial communities are established even in the most extreme environments where life, in human terms, would be inconceivable. To elucidate how microbial assemblages cope with environmental challenges, particularly such as low pH, high salinity or/and high temperature, we studied microbial mats in a hypersaline swamp exploiting reverse ecology and...
Historical biodiversity documents comprise an important link to the long-term data life cycle and provide useful insights on several aspects of biodiversity research and management. However, because of their historical context, they present specific challenges, primarily time- and effort-consuming in data curation. The data rescue process requires...
To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to mine such what-where-who associations f...
Microbial ecology investigates the interactions of microorganisms with each other and with the environment. Traditionally, culture-dependent techniques were used to investigate and evaluate microbial diversity. However, after the advent of pyrosequencing, isolation and culture of microorganisms is no more a limiting step.
One of the commonly used...
Presentation of a project about combining PREGO’s code base for corpus creation ("PREGO'' project http://prego.hcmr.gr/) with the spaCy NLP library to create a novel Named Entity Recognition (NER) tagger to detect chemicals in scientific text. The generated association rules indicate relationships of biological interest about hyperthermophiles and...
The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in environmental DNA (eDNA) metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units (OTUs) or/and amplicon sequence variants (ASVs) retrieved from such studies do not get a taxonomic assignment with a refer...
High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational cha...
The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in eDNA metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units or/and amplicon sequence variants are retrieved from such studies and referred to as “dark matter”, and do not get a taxonomic assignment with...
Scientific knowledge and methodology is undergoing transition from plain manuscript documents to multimedia-rich manuscripts linked to accompanying data. Organized datasets add value to a manuscript by being directly linked and available in reusable format [4]. The benefit of these add-on value could be multiplied once such data get repeatedly upda...
Marine microbial communities are an untapped reservoir of genetic and metabolic diversity and a valuable source for the discovery of new natural products of biotechnological interest. The newly discovered hydrothermal vent field of Santorini volcanic complex located in the Aegean Sea is gaining increasing interest for potential biotechnological exp...
Environmental DNA (eDNA) and metabarcoding have launched a new era in bio- and eco-assessment over the last years (Ruppert et al. 2019). The simultaneous identification, at the lowest taxonomic level possible, of a mixture of taxa from a great range of samples is now feasible; thus, the number of eDNA metabarcoding studies has increased radically (...
Environmental DNA (eDNA) metabarcoding has been commonly used in recent years (Jeunen et al. 2019) for the identification of the species composition of environmental samples. By making use of genetic markers anchored in conserved gene regions, universally present acrooss the species of large taxonomy groups, eDNA metabarcoding exploits both extra-...
An affiliation was missed in the initial publication and has been included.
Systems Biology is a fundamental field and paradigm that introduces a new era in Biology. The crux of its functionality and usefulness relies on metabolic networks that model the reactions occurring inside an organism and provide the means to understand the underlying mechanisms that govern biological systems. Even more, metabolic networks have a b...
Microorganisms are instrumental to the structure and functioning of marine ecosystems and to the chemistry of the ocean due to their essential part in the cycling of the elements and in the recycling of the organic matter. Sediments are considered as the “sink” of heavy metals and other pollutants as they enter the water column, thus sediment quali...
Background:
Environmental DNA and metabarcoding allow the identification of a mixture of species and launch a new era in bio- and eco-assessment. Many steps are required to obtain taxonomically assigned matrices from raw data. For most of these, a plethora of tools are available; each tool's execution parameters need to be tailored to reflect each...
PEMA alpha version.
PEMA is a metabarcoding pipeline that now supports four marker genes, 16S rRNA (Bacteria), 18S rRNA and COI (Metazoa) and ITS (Fungi). Furthermore, OTU clustering and ASV inference are both provided. Finally, a downstream amplicon analysis of the OTUs/ASVs retrieved, is facilitated by Phyloseq.
Thanks to container-based techno...
Organisms’ traits are increasingly being targeted to describe systems and their functionality. In ecological studies, analysis of traits’ as units are largely applied to communities, while the application of traits to taxonomic levels is receiving less attention. The project “Talitraits” was launched to target: 1) a relatively low taxonomic level,...
Background: Environmental DNA (eDNA) and metabarcoding, allow the identification of a mixture of individuals and launch a new era in bio- and eco-assessment. A number of steps are required to obtain taxonomically assigned (Molecular) Operational Taxonomic Unit ((M)OTU) tables from raw data. For most of these, a plethora of tools is available; each...
Metabarcoding is a genetics-NGS-based biodiversity assessment method, that uses marker genes to detect and determine environmental sample community composition. Depending on the targeted group of organisms, specific marker genes are employed. P.E.M.A. is a pipeline for two marker genes, 16S rRNA (microbes) and COI (eukaryotes). As input, P.E.M.A. a...
Projects
Project (1)
Regional cooperation for the transnational ecosystem sustainable development (RECONNECT) project aims to develop strategies for sustainable management of Marine Protected Areas (MPAs) and Natura 2000 sites. The study areas are characterised by similar habitats in different countries, which are threatened by common pressures. Creating a transnational cooperative network to confront under a common approach the environmental threats of ecosystems with a high natural and cultural interest, is the overall goal of this project. The establishment of common practices and a joint regional strategy are the main challenges of RECONNECT.
The overall objective of the project is to promote efficient management of natural systems which will enhance the competence of local management authorities through the development of a multidisciplinary Decision Support System (DSS). The new transnational holistic approach which will be developed, will change the current protection strategies in the Balkan-Mediterranean area promoting more efficient and accurate management practices. The main outputs of the RECONNECT project will provide information concerning habitat attributes, as well as the essential biodiversity, socio-economic and cultural variables, which will be freely available as tools through a web-based platform.
These outputs will be beneficial for
(a) local, regional and national authorities by promoting the sustainability of marine ecosystems;
(b) management agencies by enhancing their management toolbox;
(c) non-governmental organizations (NGOs) by improving their activities through the suggested strategies; and
(d) citizens, as their involvement during the project will increase their environmental awareness.
The transnational approach that will be used during the project will combine ecological and genetic methodologies for the biodiversity assessment, as well as socio-economic aspects, under the umbrella of a common DSS promoting joint policies and practices. The protection and conservation of areas with high ecological and economical value aims to harmonize the socio-economic and legal framework between the participating countries, something which could not be achieved individually at a national level. The design of new tools such as the DSS and the Handbook of management practices will be developed through the combination of multidisciplinary methodologies targeting to evaluate ecosystem quality and to promote the sustainable conservation of these vulnerable and fragile ecosystems. During its implementation, RECONNECT project will address consistently EU horizontal principles such as sustainable development, equal opportunities and non-discrimination and equality between men and women.
More information: http://www.interreg-balkanmed.eu/approved-project/9/
