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3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa

Mondragón-Palomino, Octavio and Poceviciute, Roberta and Lignell, Antti and Griffiths, Jessica A. and Takko, Heli and Ismagilov, Rustem F. (2021) 3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa. . (Unpublished)

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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 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 days after recovery when overall bacterial loads returned to pre-antibiotic 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 was 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 bacterial taxa are distributed differently within crypts, with Lactobacilli laying closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper
Mondragón-Palomino, Octavio0000-0003-1129-4932
Poceviciute, Roberta0000-0002-6649-2170
Lignell, Antti0000-0001-7664-5583
Griffiths, Jessica A.0000-0002-5586-1567
Takko, Heli0000-0003-2544-409X
Ismagilov, Rustem F.0000-0002-3680-4399
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. This work was funded in part by a Burroughs Wellcome Fund Career Award at the Scientific Interface (#1016969, to O.M.P.), a Biology & Biological Engineering divisional fellowship (to O.M.P.), a seeding grant from Caltech’s Center for Environmental Microbial Interactions (CEMI), Army Research Office (ARO) Multidisciplinary University Research Initiative (MURI) contract #W911NF-17-1-0402, Defense Advanced Research Projects Agency (DARPA) award #HR0011-17-2-0037, an Innovator Award from the Kenneth Rainin Foundation (Grant 2018-1207), and the Jacobs Institute for Molecular Engineering for Medicine. We thank Said Bogatyrev for sharing his expertise and advice, and help with the administration of antibiotics to mice as well as processing fecal samples for quantitative sequencing. We acknowledge technical advice from Nick Flytzanis, Ben Deverman and Ken Chan. We thank Andres Collazo and Giada Spigolon at the Beckman Institute Biological Imaging Facility for help with imaging, and we thank Natasha Shelby for contributions to writing and editing this manuscript. OMP would like to thank Jeff Hasty and Lev Tsimring of the BioCircuits Institute at UC San Diego for the generous space and resources provided to complete this manuscript. Data availability: The data that support the findings of this study are available upon request to the corresponding author. Author contributions: Conceptualization, O.M.P. and R.F.I.; Investigation, O.M.P, R.P., A.L., J.G., H.T., and R.F.I.; Resources, A.L., L.C., and R.F.I.; Writing, O.M.P, R.P., A.L., J.G., and R.F.I.; Funding Acquisition, O.M.P, A.L., L.C., and R.F.I. A detailed list of contributions by non-corresponding authors is included at the end of the Supplemental Information. This work is the subject of a patent application filed by Caltech.
Group:Caltech Center for Environmental Microbial Interactions (CEMI), Jacobs Institute for Molecular Engineering for Medicine
Funding AgencyGrant Number
Burroughs Wellcome Fund1016969
Caltech Division of Biology and Biological EngineeringUNSPECIFIED
Caltech Center for Environmental Microbial Interactions (CEMI)UNSPECIFIED
Army Research Office (ARO)W911NF-17-1-0402
Defense Advanced Research Projects Agency (DARPA)HR0011-17-2-0037
Kenneth Rainin Foundation2018-1207
Joseph J. Jacobs Institute for Molecular Engineering for MedicineUNSPECIFIED
Record Number:CaltechAUTHORS:20211015-222210959
Persistent URL:
Official Citation:3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa Octavio Mondragón-Palomino, Roberta Poceviciute, Antti Lignell, Jessica A. Griffiths, Heli Takko, Rustem F. Ismagilov bioRxiv 2021.10.07.463215; doi:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:111487
Deposited By: George Porter
Deposited On:18 Oct 2021 16:56
Last Modified:18 Oct 2021 16:56

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