Biology subjects

Abbaszade, G.

Publications and source records attributed to Abbaszade, G..

3 recordsLinked to original sources

bioRxiv2025

biscot: an Optimal Transport framework for multimodal bacterial single-cell data analysis

Computational optimal transport-based approaches have emerged as promising tools for the integration and interpretation of complex single-cell data. In this study, we introduce an integrative Optimal Transport (OT) framework for spatiotemporal and multi-omics bacterial single-cell analysis using Gaussian Mixture Model (GMM) OT, termed biscot (bacterial integrative single-cell optimal transport). We show that biscot, equipped with a novel global-to-local GMM initialization, outperforms classical OT and entropically-regularized OT methods both in terms of speed and accuracy for disentangling complex bacterial communities mixtures from single-cell flow cytometry data. When applied to time-series flow cytometry data from Bacillus subtilis, our framework delivers robust and biologically meaningful results, effectively capturing subtle phenotypic shifts in spore populations transitioning from inactive to active growth states. biscot also allows multi-omics integration of flow cytometry and unpaired bacterial single-cell RNA sequencing (scRNA-seq) data, enabling the alignment of individual gene expression profiles to the cytometric data. For an unpaired flow cytometry/scRNA-seq dataset of Bacillus subtilis cells, we validate the biological plausibility of inferred gene expression patterns with relevant marker genes, including spoVID and nin, closely aligning with observed cellular states. Overall, our framework thus provides not only dynamic tracking of phenotypic cell states but aligns cell states with detailed transcriptomic information from scRNA-seq, demonstrating its potential to advance microbial single-cell research. biscot will be made publicly available on GitHub.

bioinformatics↗

bioRxiv2025

Cannibalism Shapes Biofilm Structure and Composition in Bacillus subtilis

In Bacillus subtilis colony biofilms, phenotypic diversification confers tissue-like properties and enhanced competitive fitness within a structural framework that allows both colony expansion and long-term survival via endospore formation. Cannibalism is thought to delay sporulation by enabling one subpopulation to produce the sporulation delay protein SDP, the sporulation killing factor SKF and the epipeptide EPE. These toxins are thought to lyse susceptible nonproducers, thereby releasing nutrients to prevent premature sporulation. However, the molecular mechanisms orchestrating this bacterial programmed cell death during biofilm development are poorly understood. Here, we comprehensively characterized mutants defective in either toxin production or the corresponding autoimmunity by a multiscale approach, combining luminescence reporters, colony biopsy, multi-parameter flow cytometry and MALDI-mass spectrometry imaging to resolve cannibalism function and distribution. The toxins are produced in distinct, only partially overlapping areas of the colony and interdepend in their spatial distribution. Both EPE and SDP, but not SKF, are crucial for delaying sporulation. Loss of EPE or SDP autoimmunity resulted in severe morphological changes and stress-induced occurrence of suppressor mutants. The absence of all three toxins led to small, hyper-sporulating colonies with excessive wrinkle formation, indicating that cannibalism is essential for maintaining biofilm structure and lateral expansion. Our results provide the first evidence for the complex interactions between the cannibalism toxins that shape biofilm architecture through bacterial programmed cell death. Localized toxin production and their spatial distribution affect the spatiotemporal organization, morphology and subpopulation dynamics within B. subtilis biofilms. ImportanceProgrammed cell death (PCD) is a ubiquitous and crucial mechanism to structure eukaryotic multicellular tissues. PCD-like processes have also been described in bacteria, but their contribution to the multicellular development is poorly understood. Cannibalism in Bacillus subtilis has been described as a sporulation delay strategy, in which one subpopulation produces antimicrobial peptides that kill susceptible nonproducing siblings. Their lysis is thought to release nutrients that delay the sporulation in the producing subpopulation. This study comprehensively analyses the role of the three cannibalism toxins in shaping colony biofilms. By combining MALDI-mass spectrometry imaging, colony biopsy, flow cytometry, and luminescence reporters, we demonstrate that cannibalism toxins are crucial for biofilm structure. They show a discrete and interdependent localization within the biofilm. While cannibalism inhibits sporulation and causes severe envelope stress within colonies, our data challenges the established role of cannibalism-dependent killing as the mechanism behind this sporulation delay.

microbiology↗

bioRxiv2024

Bacterial colony biopsies: spatial discrimination of heterogeneous cell types by cytometric fingerprinting

Colonies of pure bacterial strains are highly dense cell structures that are organized in distinct and typical arrangements. The size, shape and variability of bacterial colonies are strongly dependent on the species and also influenced by environmental conditions. However, the spatial organization of individual cells is unknown for most strains. How specific heterogeneous cell types at different locations in a colony contribute to the overall structure and how they may influence the overall function of a colony is largely unknown. The study aims to investigate the local diversification of bacterial colony structures by introducing a local biopsy technique. The biopsied cells were analyzed by microbial flow cytometry and cytometric fingerprinting, which diversified the biopsied samples into many heterogeneous cell states. This two-stage resolution insight into colony structure was performed on five bacterial strains: Bacillus subtilis, Paenibacillus polymyxa, Kocuria rhizophila, Stenotrophomonas rhizophila, and Pseudomonas citronellolis. The effects of biopsy tool size (27G needle and 10 {micro}L, 200 {micro}L, 1000 {micro}L pipette tips) and sampling location on the precision of the technique were tested by using both gates setting along Gaussian distributions of subpopulations and a grid gating tool as well as the t-distributed Stochastic Neighbor Embedding (t-SNE) method. The biopsy technique uncovered significant heterogeneity among the cells within bacterial colonies, identifying differences in cell cycle stages, the proportion of living and dead cells, and the abundance of spore types. Cells from different biopsy sites displayed distinct physiological states, revealing that colony structure is far more complex than previously understood. The techniques precision depends on the biopsy tool size, dye equilibration, and cell handling, underscoring the importance of method calibration. The biopsy method, combined with cytometric fingerprinting, provided insights within only 15 to 45 minutes and is universally applicable. The study provides a high-resolution biopsy technique that explores the spatial distribution of cell types and their heterogeneous physiological cell states, allowing conclusions to be drawn from biopsy composition at different locations to overarching functions of the entire bacterial colony. This method also facilitates downstream analysis through further cell sorting, offering a powerful approach for future functional investigations.

microbiology↗