Biology subjects

Schoen, M. E.

Publications and source records attributed to Schoen, M. E..

2 recordsLinked to original sources

bioRxiv2026

Viral infection and virophage co-infection induce distinct remodeling of host lipidome

Virophages are small double-stranded DNA viruses that co-infect eukaryotic cells along with giant viruses. They are widespread in aquatic ecosystems and can influence microbial population dynamics by acting as an adaptive antiviral defense system, limiting production of giant virus progeny. Giant viruses extensively reprogram host metabolism to support their replication, yet little is known about how this process is altered by virophages. Characterizing these alterations may reveal the metabolic mechanisms underlying virophage-mediated changes in infection outcomes. Here, we used one of the few established host-giant virus-virophage experimental systems, consisting of the marine heterotrophic flagellate Cafeteria burkhardae, its giant virus CroV, and the virophage mavirus, to investigate lipid remodeling during viral infection and virophage co-infection. We found that infection by the giant virus strongly induced triacylglycerols containing furan fatty acids (FuFAs), a class of potent antioxidants that may protect infected cells and newly formed virions from oxidative damage. These lipids were also detected in purified giant virus particles, linking their accumulation to virus production. Co-infection with the virophage reduced the FuFA response and was instead characterized by pronounced accumulation of the betaine lipid diacylglyceryltrimethylhomoserine (DGTS). Most of the induced DGTS species were also present in the giant virus particles, suggesting that their accumulation during co-infection may be associated with altered giant virus production and lipid utilization. Together, these findings show that virophage co-infection reshapes giant virus-induced remodeling of the host lipidome, revealing a potential metabolic basis for their effects on virus production and infection outcomes.

microbiology↗

bioRxiv2019

PhyloMagnet: Fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics

MotivationMetagenomic and metatranscriptomic sequencing analyses have become increasingly popular tools for producing massive amounts of short-read data, often used for the reconstruction of draft genomes or the detection of (active) genes in microbial communities. Unfortunately, sequence assemblies of such datasets generally remain a computationally challenging task. Frequently, researchers are only interested in a specific group of organisms or genes; yet, the assembly of multiple datasets only to identify candidate sequences for a specific question is sometimes prohibitively slow, forcing researchers to select a subset of available datasets to address their question. Here we present PhyloMagnet, a workflow to screen meta-omics datasets for taxa and genes of interest using gene-centric assembly and phylogenetic placement of sequences.\n\nResultsUsing PhyloMagnet, we could identify up to 87% of the genera in an in vitro mock community with variable abundances, while the false positive predictions per single gene tree ranged from 0% to 23%. When applied to a group of metagenomes for which a set of MAGs have been published, we could detect the majority of the taxonomic labels that the MAGs had been annotated with. In a metatranscriptomic setting the phylogenetic placement of assembled contigs corresponds to that of transcripts obtained from transcriptome assembly.\n\nAvailabilityPhyloMagnet is built using Nextflow, available at github.com/maxemil/PhyloMagnet and is developed and tested on Linux. It is released under the open source GNU GPL license and documentation is available at phylomagnet.readthedocs.io. Version 0.5 of PhyloMagnet was used for all benchmarks experiments.

bioinformatics↗