Quantitative imaging of gut microbiota spatial organization
Open accessAbstract
Genomic technologies have significantly advanced our understanding of the composition and diversity of host-associated microbial populations. However, their spatial organization and functional interactions relative to the host have been more challenging to study. Here we present a pipeline for the assessment of intestinal microbiota localization within immunofluorescence images of fixed gut cross-sections that includes a flexible software package, BacSpace, for high-throughput quantification of microbial organization. Applying this pipeline to gnotobiotic and human microbiota-colonized mice, we demonstrate that elimination of microbiota-accessible carbohydrates (MACs) from the diet results in thinner mucus in the distal colon, increased proximity of microbes to the epithelium, and heightened expression of the inflammatory marker REG3β. Measurements of microbe-microbe proximity reveal that a MAC-deficient diet alters monophyletic spatial clustering. Furthermore, we quantify the invasion of Helicobacter pylori into the glands of the mouse stomach relative to host mitotic progenitor cells, illustrating the generalizability of this approach.
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Akkermansia has been positively associated with metabolic health, but also with low-fiber diets, and is rare in populations consuming traditional diets.
“Akkermansia has been positively associated with metabolic health (Derrien et al., 2017), but has also been associated with low-fiber diets and is rare in populations consuming traditional diets (Earle et al., 2015; Desai et al., 2016; Smits et al., 2017).”
From Gut-microbiota-targeted diets modulate human immune status (2021) · cites this paper as Earle et al., 2015
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- Authors
- Earle, K. A., Billings, G., Sigal, M., Lichtman, J. S., Hansson, G. C., Elias, J. E., Amieva, M. R., Huang, K. C., & Sonnenburg, J. L.
- Affiliations
- Stanford Medicine (US)
- Stanford University (US)
- University of Gothenburg (SE)
- Corresponding author
- Huang, Kerwyn Casey
- Sonnenburg, Justin L.
- ORCID
- Venue
- Cell Host & Microbe
- Publisher
- Elsevier BV
- Published
- 2015-10
- Volume
- 18
- Issue
- 4
- Pages
- 478-488
- ISSN
- 1931-3128 (ISSN-L)
- PMC
- PMC4628835
- OpenAlex
- W1961184135
- Cited by
- 433
- References
- 33
- Citations by year
- 2026: 28 · 2025: 31 · 2024: 35 · 2023: 50 · 2022: 38 · 2021: 47 · 2020: 45 · 2019: 41 · 2018: 35 · 2017: 37 · 2016: 41 · 2015: 5
- FWCI
- 17.09
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell Host & Microbe (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
- Funders
- National Institutes of Health (1dp2od006466-01, 1dp2od006515-01)
- National Institute of General Medical Sciences (P50GM107615)
- National Institute of Allergy and Infectious Diseases (U01AI095473)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK085025)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- Reg3β, Helicobacter pylori, gastric glands, gnotobiotic mice
- MeSH terms
- Gastrointestinal Microbiome, Animals, Bacteriological Techniques, Diet, Microscopy, Fluorescence, Helicobacter pylori, Gastrointestinal Tract, Carbohydrate Metabolism, Mice, Host-Pathogen Interactions, Optical Imaging
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