A5073288820- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Gene Regulatory Network Analysis
- Cystic Fibrosis Research Advances
- Bioinformatics and Genomic Networks
- Evolution and Genetic Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Transplantation: Methods and Outcomes
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Environmental DNA in Biodiversity Studies
- Single-cell and spatial transcriptomics
- Mathematical Biology Tumor Growth
- Bacterial biofilms and quorum sensing
- Cancer-related molecular mechanisms research
- Respiratory viral infections research
- Renal Transplantation Outcomes and Treatments
- Yersinia bacterium, plague, ectoparasites research
- Viral Infections and Immunology Research
- interferon and immune responses
- Immune Response and Inflammation
- Forensic Anthropology and Bioarchaeology Studies
- Pneumonia and Respiratory Infections
- Protein Structure and Dynamics
- Species Distribution and Climate Change
Medical University of Vienna
2017-2025
Konrad Lorenz Institute for Evolution and Cognition Research
2017-2021
CeMM Research Center for Molecular Medicine
2017-2021
Austrian Academy of Sciences
2017-2021
University of Vienna
2006-2016
Isaac Newton Institute for Mathematical Sciences
2015
Institució Catalana de Recerca i Estudis Avançats
2009-2012
Barcelona Biomedical Research Park
2009-2012
Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential reveal ecological processes, it been insufficiently validated due the technical limitations inherent in studying complex ecosystems. Here, we simulate multi-species communities with known interaction patterns using generalized Lotka-Volterra dynamics, construct co-occurrence networks, and evaluate how well underlying...
Recent studies highlight linkages among the architecture of ecological networks, their persistence facing environmental disturbance, and related patterns biodiversity. A hitherto unresolved question is whether structure landscape inhabited by organisms leaves an imprint on networks. We analyzed, based pyrosequencing profiling biofilm communities in 114 streams, how features inherent to fluvial networks affect co-occurrence that microorganisms form these biofilms. Our findings suggest...
Growth rates, interactions between community members, stochasticity, and immigration are important drivers of microbial dynamics. In sequencing data analysis, such as network construction model parameterization, we make implicit assumptions about the nature these thereby restrict outcome. Despite apparent risk methodological bias, validity is rarely tested, comprehensive procedures lacking. Here, propose a classification scheme to determine processes that gave rise observed time series...
Abstract In the context of a polymicrobial infection, treating specific pathogen poses challenges because unknown consequences on other members community. The presence ecological interactions between microbes can change their physiology and response to treatment. For example, in cystic fibrosis lung antimicrobial susceptibility testing clinical isolates is often not predictive antibiotic efficacy. Novel approaches are needed identify interrelationships within microbial community better...
The systematic collection, integration and modelling of high-throughput molecular data (multi-omics) allows the detailed characterisation microbiomes in situ. Through metabolic trait inference, network reconstruction modelling, we are now able to define ecological interactions based on exchanges, identify keystone genes, functions species, resolve niches constituent microbial populations. resulting knowledge provides information ecosystem functioning. However, as communities dynamic nature...
Abstract The SBML ODE Solver Library (SOSlib) is a programming library for symbolic and numerical analysis of chemical reaction network models encoded in the Systems Biology Markup Language (SBML). It written ISO C distributed under open source LGPL license. package employs libSBML structures formula representation associated functions to construct system ordinary differential equations, their Jacobian matrix other derivatives. SUNDIALS' CVODES incorporated integration sensitivity analysis....
Abstract Polymicrobial infection of the airways is a hallmark obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic pulmonary disease. Pulmonary exacerbations (PEx) in these conditions are associated with accelerated function decline higher mortality rates. Understanding PEx ecology challenged by high inter-patient variability airway microbial community profiles. We analyze bacterial communities 880 CF sputum samples collected during an observational...
Sponges are well known for hosting dense and diverse microbial communities, but how these associations vary with biogeography environment is less clear. Here we compared the microbiome of an ecologically important sponge species, Carteriospongia foliascens , over a large geographic area identified environmental factors likely responsible driving community differences between inshore offshore locations using co-occurrence networks (NWs). The C. exhibited exceptionally high richness, more than...
Community-acquired pneumonia (CAP), often caused by Streptococcus pneumoniae, poses a significant global health challenge, especially among high-risk populations. This study investigates the temporal dynamics of pulmonary gene expression during S. pneumoniae-induced using murine model to elucidate host-pathogen interactions and identify potential biomarkers disease severity. Using bulk RNA sequencing, we analyzed lung tissues at early (1h, 8h) acute infection (2d, 3d), as well...
Listeria monocytogenes, a gram-positive pathogen, and causative agent of listeriosis, has become widely used model organism for intracellular infections. Recent studies have identified small non-coding RNAs (sRNAs) as important factors regulating gene expression pathogenicity L. monocytogenes. Increased speed reduced costs high throughput sequencing (HTS) techniques made RNA (RNA-Seq) the state-of-the-art method to study bacterial transcriptomes. We created large transcriptome dataset...
Cystic fibrosis (CF) is a genetic disorder causing poor mucociliary clearance in the airways and subsequent respiratory infection. The recently approved triple therapy Elexacaftor-Tezacaftor-Ivacaftor (ETI) has significantly improved lung function decreased airway infection persons with CF (pwCF). This improvement been shown to occur rapidly, within first few weeks of treatment. effects longer term ETI on dynamics, however, remain mostly unknown.
Network motifs are recurrent interaction patterns, which significantly more often encountered in biological graphs than expected from random nets. Their existence raises questions concerning their emergence and functional capacities. In this context, it has been shown that feed forward loops (FFL) composed of three genes capable processing external signals by responding a very specific, robust manner, either accelerating or delaying responses. Early studies suggested one-to-one mapping...
Ancient hominoid genome studies can be regarded by definition as metagenomic analyses since they represent a mixture of both and microbial sequences in an environment. Here, we report the molecular detection oral spirochete Treponema denticola ancient human tissue biopsies Iceman, 5,300-year-old Copper Age natural ice mummy. Initially, data Iceman's genomic survey was screened for bacterial ribosomal RNA (rRNA) specific reads. Through ranking reads abundance relatively high number rRNA most...
Rationale Lung transplantation is the ultimate treatment option for patients with end-stage respiratory diseases but bears highest mortality rate among all solid organ transplantations due to chronic lung allograft dysfunction (CLAD). The mechanisms leading CLAD remain elusive an insufficient understanding of complex post-transplant adaptation processes. Objectives To better understand these processes after and investigate their association future changes in function. Methods We performed...
Transcription networks define the core of regulatory machinery cellular life and are largely responsible for information processing decision making. At small scale, interaction motifs have been characterized based on their abundance some seemingly general patterns described. In particular, different feed-forward loop in gene displays systematic biases towards particular topologies, which much more common than others. The causative process this pattern is still matter debate.We analyzed...
Abstract Background The virome of lung transplant recipients (LTRs) under immunosuppressive therapy is dominated by non-pathogenic Anelloviridae and further includes several pathogenic viruses such as Herpesviruses or respiratory viruses. It unclear whether the donor-derived in transplanted influences recipient dynamics other body compartments if so, to which degree. Likewise, it unknown dependencies exist among virus populations that mutually shape viral loads kinetics. Results To address...
ABSTRACT Independent selection response of a trait is contingent on the availability genetic variation that not entangled with other traits. Mechanistically, such variational individuation in spite shared genome results from gene regulation. Changes increase traits are likely caused by regulatory changes. Yet effect evolution population understudied. Trait also occurs during development. Developmental differentiation involves two stages‐induction and maintenance differentiated fate. The...
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...