Dataset Information

High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing [Spatial transcriptomics]

ABSTRACT: Inter-microbial and host-microbial interactions are critical for the functioning of the gut microbiome, but few tools are available to measure these interactions in situ. Here, we report a method for broad spatial sampling of microbiome-host interactions in the gut at high resolution (1 µm). This method combines enzymatic in situ polyadenylation of both bacterial and host RNA with spatial RNA-sequencing to increase bacterial RNA recovery and enable transcriptomic analysis of low-abundance and spatially restricted microbial taxa. We benchmark the method against existing spatial transcriptomic workflows, demonstrating improved sensitivity and resolution. Application of this method in a mouse model of intestinal neoplasia revealed the biogeography of the mouse gut microbiome as function of location in the intestine, frequent strong inter-microbial interactions at short length scales, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with widely available commercial platforms for spatial RNA-sequencing and can therefore be readily adopted to study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.

ORGANISM(S): Mus musculus

PROVIDER: GSE316608 | GEO | 2026/01/21

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Background: Toll-like receptor 2 (TLR2) plays a pivotal role in innate immunity and has recently emerged as a criti-cal regulator of host-microbiome interactions. However, how TLR2 influences host transcriptional responses to colonized microbiome and microbial community dynamics remains largely unclear. Germ free (GF) and conven-tionalized zebrafish (Danio rerio) model provides a valuable system to study microbiome functions. Results: RNAseq analysis revealed that transcriptomic alterations resulted from tlr2 mutation were more extensive in the presence of the microbiome than under the GF condition, indicating that tlr2 mutation has a more pro-nounced impact on host transcriptional responses when microbial signals are present. KEGG enrichment analyses showed an enhanced host response to the energy metabolism in the presence of microbial stimuli resulting from tlr2 deficiency. In addition, microbiome colonization elicited a broader transcriptional response in tlr2 wild-type larvae than in the mutants, highlighting the essential role of tlr2 in regulating host transcriptomic programs in re-sponse to microbial signals. In terms of how tlr2 influences microbial composition, 16S rRNA gene sequencing showed that tlr2 mutants exhibited higher microbial diversity during early development, whereas adult microbial diversity was highest in wild-type males, indicating a developmental stage- and sex-specific restructuring of the gut microbiome. For larvae at the genus level, tlr2 mutant larvae showed increased Chryseobacterium and Flecto-bacillus but reduced Gracilibacteria abundance relative to wild-type controls. For adult gut samples, the relative abundance of Cetobacterium was lower, while genera such as Romboutsia, Aeromonas and Pseudarthrobacter were more abundant in tlr2 wild-type male group compared to other groups. Predicted functional analyses revealed that tlr2 deficiency induced complex alterations in microbial metabolic pathways, with distinct pathway enrichments observed between larval and adult stages. Conclusions: TLR2 not only modulates host transcriptional responses to microbial colonization but also shapes gut microbial diversity, composition, and metabolic potential. Our findings highlight the critical role of TLR2 in orchestrating immunometabolic homeostasis and provide new insights into its broader function in maintaining host-microbiota symbiosis across developmental stages.

Dataset Information

High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing [Spatial transcriptomics]

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets