Zaman, I. | bioRxiv Science

bioRxiv2026

SpatialBench: Comparative cross-platform benchmarking of high-resolution spatial transcriptomics using matched mouse lymphoid tissue

Spatial transcriptomics (ST) has rapidly expanded with the introduction of multiple high-resolution platforms, yet cross-platform benchmarking remains limited and largely focused on technical performance. Here we present SpatialBench, a matched multi-platform resource comprising Visium HD, Xenium and MERSCOPE data together with single-cell and single-nucleus references from a malaria-challenged wild-type and B cell-specific Tbx21 knockout mouse spleen model. In this system, loss of T-bet in B cells disrupts germinal center (GC) polarization and antibody maturation, providing a biologically grounded benchmark for technology comparison. We leveraged this system to systematically evaluate ST platform performance using technical and biological readouts. Across platforms, immune organization and Tbx21-associated programs were consistently recovered, indicating robustness of major biological signals. Platforms instead differed in the level of biological resolution accessible. Visium HD enabled transcriptome-scale GC characterization and, together with Xenium, resolved dark and light zone organization, whereas GC zonation was not resolved in MERSCOPE, consistent with differences in transcript detection sensitivity. SpatialBench provides a biologically defined reference dataset for evaluation of ST technologies, method development, computational benchmarking, and studies of GC spatial organization in lymphoid tissue.

bioinformatics↗

bioRxiv2025

Functional and genomic insights into landfill-isolated Brucella intermedia strains capable of degrading Linear Low-Density Polyethylene (LLDPE)

The global accumulation of linear low-density polyethylene (LLDPE) waste has created an urgent need for sustainable biodegradation strategies. Here, we report the identification and characterization of two landfill-derived Brucella intermedia isolates associated with LLDPE biodegradation. Soil samples collected from the Matuail landfill in Dhaka, Bangladesh, were screened on minimal salt medium supplemented with LLDPE. Both isolates demonstrated sustained growth under carbon-limited conditions in which LLDPE was the principal carbon source. LLDPE recovered from bacterial cultures showed chemical and surface morphological changes, as supported by Fourier-transform infrared (FTIR) spectroscopy, droplet-spreading analysis, and scanning electron microscopy (SEM). FTIR analysis revealed additional carbonyl, hydroxyl, and C-O bands consistent with oxidative modification of the polymer surface, while SEM showed roughening, fissures, and fragmentation-like surface features. Whole-genome sequencing identified both isolates as closely related but distinct strains of Brucella intermedia and revealed enrichment of candidate functions associated with oxidative activation, depolymerization, and downstream assimilation. Transcriptomic analysis under LLDPE growth further showed expression of multiple candidate plastic degradation- and biofilm-associated genes. Resistome, virulome, and phenotypic antimicrobial susceptibility analyses indicated that both isolates are environmentally resilient, low-pathogenic variants with a limited intrinsic resistome. Both strains also exhibited biofilm-associated growth under hydrocarbon-substituted and plastic-associated conditions. Collectively, these findings identify environmental B. intermedia as an unexpected plastic-associated lineage and expand current understanding of the ecological and genomic diversity of bacteria linked to LLDPE biodegradation. Environmental ImplicationThis study identifies landfill-derived Brucella intermedia strains that can support biodegradation of linear low-density polyethylene (LLDPE), a major persistent plastic pollutant in landfill environments. Functional, genomic, and transcriptomic evidence indicate that these isolates use coordinated oxidative, depolymerization, and biofilm-associated responses during growth under plastic-associated, carbon-limited conditions. Their low-pathogenic environmental profiles and limited intrinsic resistomes further support their relevance as candidates for future biodegradation-focused biotechnological research. Overall, these findings expand the known diversity of plastic-associated bacteria and highlight naturally adapted landfill microorganisms as promising resources for sustainable strategies to mitigate plastic accumulation in terrestrial ecosystems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/687417v2_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@5f84f2org.highwire.dtl.DTLVardef@111626dorg.highwire.dtl.DTLVardef@54f51eorg.highwire.dtl.DTLVardef@1a8910c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗