ArticleProceedings of the National Academy of Sciences of the United States of America2022
Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Review
- Geometric ordering in bacterial communities.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Spatial mapping of microbial communities by an integrated automation platform of sequential FISH.Cell reports methods · 2026Article
- Uniform bacterial genetic diversity along the gut.Nature communications · 2026Article
- Strategies to control cellular spatial organization in microphysiological systems.Microsystems & nanoengineering · 2026Review
- Intestinal epithelial TLR5 signaling promotes barrier-supportive macrophages.Science immunology · 2026Article
- In situ visualization of Clostridioides difficile phenotypic heterogeneity and single-cell morphology during gut infection.Nature communications · 2026Article
- Visualizing C. difficile During Murine Infection.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Microbiogeographic insights as keys to understanding personalized gut microbiota responses: the role ofBioscience of microbiota, food and health · 2026Review
- Interrogation of imaging-based interspecies dynamics in the oral microbiome.Journal of oral microbiology · 2026Review
- Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota.FEMS microbiology ecology · 2025Article
- Hydrogel-based experimental models of the gastrointestinal tract.Microbiome · 2025Review
- Intravital imaging of translocated bacteria via fluorogenic labeling of gut microbiota in situ.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.Nature microbiology · 2025Article
- Oral bacteriophages and their potential as adjunctive treatments for periodontitis: a narrative review.Journal of oral microbiology · 2025Review
- SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.bioRxiv : the preprint server for biology · 2024Article
- Deciphering the Diversity in Bacterial Transporters That Salvage Queuosine Precursors.Epigenomes · 2024Article
- The gut microbiota and its biogeography.Nature reviews. Microbiology · 2024Review
- Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics.The ISME journal · 2024Article
- Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria.Nature ecology & evolution · 2023Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Improving our understanding of host–microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the three-dimensional (3D) spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 d after recovery when overall bacterial loads returned to preantibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern is resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that Lactobacilli were found closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae, regardless of antibiotic exposure. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.
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