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Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host.
PLoS One
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PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France.
Local co-circulation of multiple phylogenetic lineages is particularly likely for rapidly evolving pathogens in the current context of globalisation. When different phylogenetic lineages co-occur in the same fields, they may be simultaneously present in the same host plant (i.e.
View Article and Find Full Text PDFInsights into Within-Host Evolution and Dynamics of Oral and Intestinal Streptococci Unveil Niche Adaptation.
Int J Mol Sci
December 2024
Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule (RWTH) University Hospital, 52074 Aachen, Germany.
The oral-gut axis is a complex system linking the oral cavity and gastrointestinal tract, impacting host health and microbial composition. This study investigates genetic changes and adaptive mechanisms employed by streptococci-one of the few genera capable of colonizing oral and intestinal niches-within the same individual. We conducted whole-genome sequencing (WGS) on 218 streptococcal isolates from saliva and fecal samples of 14 inflammatory bowel disease (IBD) patients and 12 healthy controls.
View Article and Find Full Text PDF3D Cryo-Correlative Methods to Study Virus Structure and Dynamics Within Cells.
Subcell Biochem
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Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
Understanding the dynamic processes involving virus structural components within host cells is crucial for comprehending viral infection, as viruses rely entirely on host cells for replication. Viral infection involves various intracellular stages, including cell entry, genome uncoating, replication, transcription and translation, assembly of new virus particles in a complex morphogenetic process, and the release of new virions from the host cell. These events are dynamic and scarce and can be obscured by other cellular processes, necessitating novel approaches for their in situ characterization.
View Article and Find Full Text PDFPolyphonia: detecting inter-sample contamination in viral genomic sequencing data.
Bioinformatics
November 2024
Howard Hughes Medical Institute, Chevy Chase, MD 20815, United States.
Summary: In viral genomic research and surveillance, inter-sample contamination can affect variant detection, analysis of within-host evolution, outbreak reconstruction, and detection of superinfections and recombination events. While sample barcoding methods exist to track inter-sample contamination, they are not always used and can only detect contamination in the experimental pipeline from the point they are added. The underlying genomic information in a sample, however, carries information about inter-sample contamination occurring at any stage.
View Article and Find Full Text PDFStrain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series.
ISME J
January 2025
Université Paris Cité, INSERM, IAME, Paris 75018, France.
Escherichia coli is an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynamics in its primary commensal niche, the vertebrate gut. Using Illumina and/or Nanopore technologies, we sequenced whole genomes of 210 E.
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