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Recent advances in deep learning and language models for studying the microbiome.
Front Genet
January 2025
Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, United States.
Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a , enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data.
View Article and Find Full Text PDFWar and peace: exploring microbial defence systems as a source of new antimicrobial therapies.
Front Pharmacol
January 2025
Centre for Molecular Biosciences, Ulster University, Coleraine, United Kingdom.
The WHO has compiled a list of pathogens that urgently require new antibiotics in response to the rising reports of antibiotic resistance and a diminished supply of new antibiotics. At the top of this list is fluoroquinolone-resistant , fluoroquinolone-resistant spp. and vancomycin-resistant .
View Article and Find Full Text PDFNO-mediated DNA damage induced by polystyrene nanoparticles triggers program cell death in mesenchymal stem cells.
Drug Chem Toxicol
January 2025
Department of Genetics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.
Daily contact with considerable amounts of polystyrene nanoparticles (PSNPs) may cause harmful effects on the living organisms, through mechanisms that are not fully understood. The study aimed to evaluate the cytotoxic and genotoxic effects of PSNPs (size 200 nm and 40 nm) in mesenchymal stem cells (MSCs). In order to estimate cellular uptake and retention of nanoplastics, PSNP-treated cells have been analyzed by transmission electron microscopy.
View Article and Find Full Text PDFMetagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease.
Cell
January 2025
Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel; Division of Microbiome & Cancer, DKFZ, Heidelberg, Germany. Electronic address:
Host-microbiome-dietary interactions play crucial roles in regulating human health, yet their direct functional assessment remains challenging. We adopted metagenome-informed metaproteomics (MIM), in mice and humans, to non-invasively explore species-level microbiome-host interactions during commensal and pathogen colonization, nutritional modification, and antibiotic-induced perturbation. Simultaneously, fecal MIM accurately characterized the nutritional exposure landscape in multiple clinical and dietary contexts.
View Article and Find Full Text PDFPrecision and accuracy of the dynamic endocast method for measuring volume changes in XROMM studies.
J Exp Biol
January 2025
Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK.
The X-ray Reconstruction of Moving Morphology (XROMM) workflow enables precise and accurate measurement of the 3D skeletal kinematics underlying animal behaviors. The dynamic endocast method built upon that workflow to measure the rate of volume change within a bounded region of interest. We measured the precision and accuracy of the dynamic endocast method, using a fish oropharyngeal cavity as a case study.
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