Biology subjects

Ghanem, N.

Publications and source records attributed to Ghanem, N..

7 recordsLinked to original sources

bioRxiv2026

Crosstalk between Stromal cells and Macrophages Shapes Host Immunity to Mycobacteria

Granulomas are disease-defining heterocellular tissue structures in mycobacterial infections. They play a multifaceted role ranging from containing the pathogen to causing tissue destruction. Here, we established a mature peritoneal granuloma model in C57BL/6 mice to investigate the dynamic cell-cell interactions during mycobacterial infection, including long-term immune alterations in serous cavities as important sites of disease manifestation. We found that mycobacteria reside in stromal cells, which actively modulate the local tissue environment and shape macrophage responses, particularly through formation of chemokines and colony-stimulating factor 1. Chronic infection induces sustained reprogramming and diversification of stromal cells toward specialized, immune-like states, including active transfer of mycobacteria to macrophages and a pronounced interferon response. Consequently, stromal cells acquire immunoregulatory properties and support pathogen handling, monocyte recruitment and macrophage maturation, thereby playing a decisive role in granuloma formation and thus in the immune response to mycobacteria. HIGHLIGHTSO_LIA novel peritoneal mycobacterial infection model reveals heterocellular crosstalk in mature granulomas. C_LIO_LIMycobacterial infections persistently reshape immune architecture of serous cavities as important disease sites. C_LIO_LIStromal cells act as mycobacterial host cells and acquire immune effector functions. C_LIO_LIStromal cells co-organize the tissue host-pathogen interface by recruiting and directly communicating with bone marrow-derived monocytes. C_LI

immunology↗

bioRxiv2025

Neonatal BCG Vaccination Engages the Vasculature to Elicit γδ T Cell-Mediated Protection against Tuberculosis

The Bacillus Calmette-Guerin (BCG) vaccine remains the only approved vaccine against tuber-culosis (TB). Although its efficacy against pulmonary TB in adults is limited, BCG provides re-markable protection against miliary TB when administered during infancy. Despite more than 100 million infants worldwide receiving BCG annually, the mechanisms underlying its neonatal protective effects remain poorly defined. Here, we demonstrate that subcutaneous neonatal BCG vaccination (BCG-sc) induces a marked expansion of {gamma}{delta} T cells producing IL-17 and IL-22, which mediated protection against subsequent Mycobacterium tuberculosis (Mtb) experimental infection. A similar expansion of {gamma}{delta} T cells was observed in a longitudinal cohort of infants, from birth to three months of infants followed after intradermal BCG vaccination. Mechanistical-ly, BCG-mediated protection in neonates was linked to its early vascular dissemination through the distinct structure of neonatal skin, resembling the protective effects of intravenous BCG in adults. Moreover, neonatal BCG-sc vaccination generated a distinct BCG-induced microbiome signature, characterized by enrichment of Prevotellaceae, Tannerellaceae, and Bifidobacteriaceae, which was associated with protection. Together, these findings identify {gamma}{delta} T cells as key mediators of early-life BCG-induced immunity and highlight the role of the gut-lung axis in long-term protection against TB from infancy into adulthood.

immunology↗

bioRxiv2025

PHI: Prophage-Host Interaction toolkit for automated prediction and comprehensive profiling of prophages and their hosts via Galaxy

BackgroundViruses that infect bacteria, known as bacteriophages or phages, are widespread in nature and play important roles in shaping microbial communities and ecosystem functions. Some phages can integrate into bacterial genomes as "prophages", where they may influence the biology of their host by carrying genes that affect metabolism, virulence, or environmental adaptation. Despite their importance, studying prophages and their interactions with bacterial hosts remains challenging because it typically requires combining many complex computational tools and can be resource-intensive. ResultsIn this study, we introduce the Prophage-Host Interaction Toolkit (PHI), a user-friendly and automated workflow available through the Galaxy platform. PHI brings together multiple established tools into a single, reproducible pipeline that identifies candidate prophages, evaluates their quality, predicts host relationships, and characterizes key functional genes. Importantly, all results are summarized in an interactive report that simplifies interpretation. When applied to a mock community composed of 22 bacteria as a workflow demonstration, PHI detected 41 prophages across 14 hosts, classifying them into high- and medium-quality phage genomes. Host assemblies exhibited > 99 % completeness and < 1 % contamination for most genomes, while DefenseFinder revealed between 3 and 24 antiviral systems per genome. ConclusionsBy removing installation barriers and consolidating the outputs of multiple established tools, PHI lowers the barrier to advanced phage analysis, enabling both specialists and non-experts to explore phage-host interactions and their implications in areas such as microbiome research, biotechnology, and environmental science.

bioinformatics↗

bioRxiv2025

Effects of a novel Paraburkholderia phage IPK on the phenanthrene degradation efficiency of the PAH-degrading strain Paraburkholderia caledonica Bk.

Phages are a major cause of bacterial mortality, affecting bacterial diversity and ecosystem functioning. However, the impact of phage-host interactions in contaminated environments and their role in pollutant biodegradation have been largely overlooked. We isolated and characterized a novel phage from a polycyclic aromatic hydrocarbon (PAH)-contaminated soil that infects the PAH-degrading bacterium Paraburkholderia caledonica Bk, and investigated the effect of different multiplicity of infection (MOI) on the degradation efficiency of phenanthrene. The phage IPK is a temperate phage with a wide pH and temperature tolerance and a burst size of 80 PFC.ml{square}1. The IPK phage was classified as a member of the Caudoviricetes, related to Pseudomonas and Burkholderia phages; however, its low intergenomic similarity indicates that it belongs to a new species. Three AMGs related to amino acid metabolism and to bacterial growth regulation were identified in the phage genome. The highest multiplicity of infection (MOI 10) showed a rapid recovery of the host density abundance and greater phenanthrene degradation than MOIs ranging from 0.01 to 1. This work highlights the critical role of phage-host interactions in modulating pollutant degradation efficiency, which could be a key for improving the establishment of inoculants in bioremediation processes.

microbiology↗

bioRxiv2025

Unmapped reads from whole-genome sequencing data reveal pathogen diversity in European and African cattle breeds

Climate change is impacting the global spread of infectious diseases, altering pathogen distribution and transmission, threatening human and animal health. This study investigates the presence of potential pathogens in blood within unmapped reads obtained from whole-genome sequencing data of various cattle breeds across geographically diverse regions, including South Africa, Uganda, Egypt, Portugal, The Netherlands, and Finland. Unmapped reads were extracted, assembled into contigs, and subjected to taxonomic analysis based on an extensive literature search. The analysis revealed significant geographic variation in pathogen composition, with breeds in the Southern Hemisphere (Uganda, Egypt, and South Africa) showing higher alignment pathogen counts while northern breeds (particularly from Finland) exhibited lower diversity and counts. Portugal, representing a transition zone, exhibited a higher burden of parasites and tick-borne related pathogens which were also prevalent in Southern Hemisphere breeds such as Theileria parva, Anaplasma platys, Theileria orientalis, and Babesia bigemina, which is in line with the known capacity of these breeds to cope with local pathogens. Dutch breeds were found to harbor Escherichia coli O157, a known public health concern. The study provided key insights into emerging disease risks influenced by climate change and livestock management practices. This study highlights the potential for climate-driven variations in disease ecology and transmission, emphasizing the need for integrating genomic and environmental data and is currently the most comprehensive study to date investigating the microbial diversity present in unmapped reads obtained from WGS data of cattle populations. HighlightsO_LIUnmapped sequence reads analysis of blood reveals signatures of disease occurrence over time. C_LIO_LIBlood pathogens prevail in the Southern hemisphere, becoming less evident towards northern regions (i.e. we observed a gradient pattern), with Portugal (and partly the Netherlands) showing intermediate values. C_LIO_LIThe commercial Holstein cattle in the six countries exhibited lower pathogen sequence alignments than their native counterparts (i.e. the Netherlands). C_LI

bioinformatics↗

bioRxiv2025

Soil protist diversity enhances prokaryotic diversity, and regulates dominant prokaryotes and the abundance of key nitrogen cycling genes

Soil protists play crucial roles in soil microbial food-webs by preying on bacteria and other microorganisms. However, the effect of protist diversity on soil prokaryotic communities remains poorly understood. This study aimed to elucidate how different protist diversity treatments affect the composition and functionality of soil prokaryotic communities. We established soil microcosms with increasingly complex protist communities, including a control without protists, a medium diversity treatment with three small bacterivorous protists, and a high diversity treatment with seven protists of diverse trophic styles and sizes. Over 21 days, we monitored changes in the prokaryotic community using 16S rRNA gene sequencing and assessed the effects on nitrifiers and denitrifiers by qPCR of nitrogen-cycling genes. Protist diversity explained 23 % of the observed prokaryotic community differentiation over time, with the high-diversity treatment causing the greatest divergence from the control. The most abundant prokaryotes were preferentially predated in all protist treatments. Unexpectedly, the absolute abundance of the nirK gene, which is widely distributed among bacterial taxa and thus associated with high functional redundancy, decreased. The differential response of genes with lower distribution and redundancy, such as the bacterial and archaeal amoA and the Nitrospira-associated nxrB genes, to protist diversity indicated selective predation on archaea. High protist diversity systematically enhanced these effects compared to the medium diversity treatment. Overall, protist diversity was positively associated with prokaryotic diversity, which is crucial for maintaining ecosystem stability. These findings highlight the critical role of protist diversity and likely complementary predation in shaping soil prokaryotic communities and their functioning.

ecology↗

bioRxiv2025

Tissue imprinting defines functional mosaic of dermal macrophages

Dermal macrophages (macs) protect the skin from invading pathogens. They are derived from embryonic as well as hematopoietic progenitors. However, the functional impact of their diverse origin and the control networks defining different subsets remain unclear. Here, using multidimensional analysis of dermal macs, we reveal that the absence of circulating monocytes in interferon regulatory factor 8 (Irf8) deficient mice delays mac renewal during the steady state. Yet, the functional mosaic of dermal macs remains largely intact, i.e., major dermal mac subsets develop independently of monocyte replenishment. Thus, the tissue microenvironment is sufficient to induce alternative differentiation pathways and functional specialization of resident cells. Mycobacterial skin infection induces a steep increase in mac density due to monocyte-derived macs which execute urgent antibacterial functions and differentiate into site-adapted mac subsets in wildtype but not Irf8-/-mice, while long-term resident macs are required to initiate a tissue repair program already in early stages of infection. In summary, we introduce a model, where an intricate network of specialized mac subsets develops to meet microanatomical needs and external cellular input is required only during immunological emergency situations. HighlightsO_LIIrf8-/--driven monocytopenia has negligible impact on homeostatic dermal macrophage diversity. C_LIO_LIResident dermal macrophages have diverse specializations but remain flexible to adapt to challenges such as lacking monocyte influx C_LIO_LIBone marrow-derived macrophages differentiate into specialized resident cells, with microenvironmental cues overriding origin-dependent programming. C_LIO_LIIn chronic bacterial infections, distinct specialized bone-marrow-derived macrophages mount the defense, while resident macrophages activate a tissue-modifying program from early on. C_LI

immunology↗