A5005498403- Pharmaceutical and Antibiotic Environmental Impacts
- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Antibiotic Resistance in Bacteria
- Genomics and Phylogenetic Studies
- Plant-Microbe Interactions and Immunity
- Bacteriophages and microbial interactions
- Soil Carbon and Nitrogen Dynamics
- Bacterial biofilms and quorum sensing
- Legume Nitrogen Fixing Symbiosis
- Bacterial Genetics and Biotechnology
- Microbial bioremediation and biosurfactants
- Evolution and Genetic Dynamics
- Nematode management and characterization studies
- Environmental DNA in Biodiversity Studies
- Plant Pathogens and Fungal Diseases
- Probiotics and Fermented Foods
- Plant Pathogenic Bacteria Studies
- Antibiotic Use and Resistance
- Plant tissue culture and regeneration
- Mycorrhizal Fungi and Plant Interactions
- Aquaculture disease management and microbiota
- Clostridium difficile and Clostridium perfringens research
- Plant Growth Enhancement Techniques
- Composting and Vermicomposting Techniques
University of Copenhagen
2017-2025
University of Washington
2023
Institute for Systems Biology
2023
InSysBio (Russia)
2023
Helmholtz Zentrum München
2016-2019
École Centrale de Lyon
2012-2016
Laboratoire Ampère
2013-2016
Université Claude Bernard Lyon 1
2012-2016
Centre National de la Recherche Scientifique
2014
OPINION article Front. Microbiol., 10 February 2016Sec. Terrestrial Microbiology Volume 7 - 2016 | https://doi.org/10.3389/fmicb.2016.00073
Aquaculture is on the rise worldwide, and use of antibiotics fostering higher production intensity. However, recent findings suggest that comes at price increased antibiotic resistance. Yet, effect oral administration mobility microbial resistance genes in fish gut not well understood. In present study, Piaractus mesopotamicus was used as a model to evaluate antimicrobial florfenicol diversity microbiome (ARGs) mobile genetic elements (MGEs) using metagenomic approach. The total relative...
Wastewater treatment plants (WWTPs) have been suggested as reservoirs and sources of antibiotic resistance genes (ARGs) in the environment. In a WWTP ecosystem, human enteric environmental bacteria are mixed exposed to pharmaceutical residues, potentially favoring genetic exchange thus ARG transmission. However, contribution microbial communities WWTPs dissemination remains poorly understood. Here, we examined for first time plasmid permissiveness an activated sludge community by utilizing...
Abstract Climate change alters frequencies and intensities of soil drying-rewetting freezing-thawing cycles. These fluctuations affect water availability, a crucial driver microbial activity. While these are leaving imprints on microbiome structures, the question remains if legacy one type weather fluctuation (e.g., drying-rewetting) affects community response to other freezing-thawing). As both phenomenons give similar availability fluctuations, we hypothesized that cycles have effects...
Abstract Many prokaryotes encode CRISPR-Cas systems as immune protection against mobile genetic elements (MGEs), yet a number of MGEs also harbor components. With few exceptions, loci encoded on are uncharted and comprehensive analysis their distribution, prevalence, diversity, function is lacking. Here, we systematically investigated across the largest curated collection natural bacterial archaeal plasmids. widely but heterogeneously distributed plasmids and, in comparison to host...
Abstract Drought severely restricts plant production and global warming is further increasing drought stress for crops. Much information reveals the ability of individual microbes affecting tolerance. However, effects emergent bacterial community properties on tolerance remain largely unexplored. Here, we inoculated Arabidopsis plants in vivo with a four-species consortium ( Stenotrophomonas rhizophila , Xanthomonas retroflexus Microbacterium oxydans Paenibacillus amylolyticus termed as...
Antibiotic-resistant pathogens constitute an escalating public health concern. Hence a better understanding of the underlying processes responsible for this expansion is urgently needed. Co-selection heavy metal/biocide and antibiotic resistance genes (ARGs) has been suggested as one potential mechanism promoting proliferation antimicrobial (AMR). This paper aims to elucidate interplay exploit differences in usage infer patterns co-selection by non-antibiotic factors metals biocides context...
A growing body of evidence demonstrates the potential various microbes to enhance plant productivity in cropping systems although their successful field application may be impaired by several biotic and abiotic constraints. In present work, we aimed at developing multifunctional synthetic microbial consortia used combination with suitable bioactive compounds for improving crop yield quality. Plant growth-promoting microorganisms (PGPMs) different functional attributes were identified a...
Abstract We investigated the effects of substrate (cellulose or starch) and different clay contents on production microbial extracellular polymeric substances (EPS) concomitant development stable soil aggregates. Soils were incubated with amounts montmorillonite (+ 0.1%, + 1%, 10%) both without two substrates contrasting quality (starch cellulose). Microbial respiration (CO 2 ), biomass carbon (C), EPS-protein, EPS-polysaccharide determined over experimental period. The diversity...
ABSTRACT Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well combination both. To assess pros cons these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations depth technology: (i) 20 Gbp Illumina (ii) 40 (iii) PacBio HiFi (iv)...
Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within communities established on roots. Here, a well-established four-species model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis study impact of growth community dynamics SPMX...
The capacity of microbes to degrade recalcitrant materials has been extensively explored for environmental remediation and industrial production. Significant achievements have made with single strains, but focus is now going towards the use microbial consortia owning their functional stability efficiency. However, assembly simplified (SMC) from complex communities still far trivial due large diversity effect biotic interactions. Here we propose a strategy, based on enrichment...
A soil column split-root experiment was designed to investigate the ability of apple replant disease (ARD)-causing agents spread in soil. 'M26' rootstocks grew into a top layer Control soil, followed by barrier-free split-soil (Control soil/ARD soil). We observed severely reduced root growth, concomitant with enhanced gene expression phytoalexin biosynthetic genes and content roots from ARD indicating pronounced local plant defense response. Amplicon sequencing (bacteria, archaea, fungi)...
Urban wastewater systems (UWSs) are a main receptacle of excreted antibiotic resistance genes (ARGs) and their host microorganisms. However, we lack integrated quantitative observations the occurrence ARGs in UWS to characterize sources identify processes that contribute fate. We sampled UWSs from three medium-size cities Denmark, Spain, United Kingdom quantified 70 clinically important extended-spectrum β-lactamase carbapenemase along with mobile genetic elements microbial communities....
Strains of Agrobacterium genomospecies 3 (i.e., genomovar G3 the tumefaciens species complex) have been previously isolated from diverse environments, including in association with plant roots, algae, as part a lignocellulose degrading community, hospital environment, human opportunistic pathogen, or reported this study, surface within International Space Station. Polyphasic taxonomic methods revealed relationship strains to other spp., which supports description novel species. The tested (...
Abstract Background In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with such as other ARGs, biocide genes, metal and virulence (VGs). The gut microbiome infants has been shown to contain numerous however, related ARGs is unknown during early life despite frequent exposures biocides metals from an age. Results We conducted a comprehensive analysis genetic in cohort 662 Danish children examined association...
Plasmids are small DNA molecules that enable bacteria to share beneficial traits, influencing microbial communities. However, their role within the human gut microbiome remains largely unknown. In this study, we investigate microbiomes of 34 mother-child cohorts, employing a plasmid analysis workflow understand impact plasmids on microbiome. We create phylogenetic tree, devise method for assigning hosts, and examine potential transfer networks. Our research discovers wide variety previously...