Highly multiplexed spatial transcriptomics in bacteria

Tolerance and heteroresistance to echinocandins in Candida auris: conceptual issues, clinical implications, and outstanding questions

Candida auris is a significant public health threat due to its environmental persistence and multidrug resistance, with echinocandins being the preferred treatment. However, in addition to resistance, echinocandin tolerance and heteroresistance may contribute to treatment challenges. Echinocandin tolerance involves reduced drug-mediated killing, while heteroresistance is the ability of a small cell subset to grow at high drug concentrations. These phenomena may facilitate the emergence of full resistance and complicate clinical outcomes. The clinical significance of these mechanisms remains unclear, with limited data correlating them with treatment failures. Research is needed to understand their mechanisms and impact, develop streamlined and robust methods to detect them in clinical settings, and explore mitigation strategies. The pathogen's range of drug adaptations demands innovative approaches like spatial transcriptomics to dissect these complex responses and improve patient outcomes.

Microorganisms in Macroalgae Cultivation Ecosystems: A Systematic Review and Future Prospects Based on Bibliometric Analysis

Microorganisms play an essential role in the biogeochemical processes of macroalgal cultivation ecosystems by participating in a complex network of interactions, significantly influencing the growth and development of macroalgae. This study used bibliometric analysis and VOSviewer based on Web of Science data to provide an overview by tracing the developmental footprint of the technology. Countries, institutions, authors, keywords, and key phrases were tracked and mapped accordingly. From 1 January 2003 to 31 December 2023, 619 documents by 2516 authors from 716 institutions in 51 countries were analyzed. Keyword co-occurrence network analysis revealed five main areas of research on microbes in macroalgal cultivation ecosystems: (1) identification of microbial species and functional genes, (2) biogeochemical cycling of carbon in microbial communities, (3) microbial influences on macroalgae growth and development, (4) bioactivities, and (5) studies based on database. Thematic evolution and map research emphasized the centrality of microbial diversity research in this direction. Over time, the research hotspots and the core scientific questions of the microorganisms in the macroalgal cultivation ecosystems have evolved from single-organism interactions to the complex dynamics of microbial communities. The application of high-throughput techniques had become a hotspot, and the adoption of systems biology approaches had further facilitated the integrated analysis of microbial community composition and function. Our results provide valuable guidance and information for future researches on algal-bacterial interactions and microbe-driven carbon cycling in coastal ecosystems.

Molecule Differentiation Encoding Microscopy to Dissect Dense Biomolecules in Cellular Nanoenvironments below Spatial Resolution

Cellular biomolecules may exhibit dense distribution and organization at the nanoscale to govern vital biological processes. However, it remains a common challenge to digitize the spatially dense biomolecules under the spatial resolution of microscopies. Here, a proof-of-principle method, molecule differentiation encoding microscopy by orthogonal tandem repeat DNA identifiers is reported, to resolve the copy numbers of dense biomolecules in cellular nanoenvironments. The method encodes each copy of the same biomolecules into different types of DNA barcodes based on stochastic multiplexed reactions. It can transform the overlap of the same spectrum into the overlap of different spectra. Furthermore, an algorithm is developed to automatically quantitate overlapping spots and individual spots. Using this method, RNAs in the cytoplasm, DNA epigenetic modifications in the cell nucleus, and glycans and glycoRNAs on the cell surface are dissected, respectively. It is found that all these biomolecules present dense distribution with diverse degrees in crowded cellular nanoenvironments. Especially, an average 17% copies of U1 glycoRNA of single cells are gathered in various nano environments on the cell surface. The strategy provides a powerful tool for digitally quantitative visualization of dense biomolecules below the spatial resolution of microscopies and can provide insights into underlying functions and mechanisms of the dense distribution information.

Living on the edge: Mucus-associated microbes in the colon

The colonic mucus layer acts as a physicochemical barrier to pathogen invasion and as a habitat for mucus-associated microbes. This mucosal microbiome plays a crucial role in moderating mucus production, maintaining barrier integrity, and shaping the host immune response. However, unchecked mucin foraging may render the host vulnerable to disease. To better understand these dynamics in the mucus layer, it is essential to advance fundamental knowledge on how commensals bind to and utilize mucin as well as their interactions with both the host and their microbial neighbors. We present an overview of approaches for surveying mucus-associated bacteria and assessing their mucin-utilizing capacity, alongside a discussion of the limitations of existing methods. Additionally, we highlight how diet and host secretory immunoglobulin A interact with the mucosal bacterial community in the colon. Insights into this subset of the microbial community can guide therapeutic strategies to optimally support and modulate mucosal barrier integrity.