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Spatial metagenomic characterization of microbial biogeography in the gut

Abstract

Spatial structuring is important for the maintenance of natural ecological systems1,2. Many microbial communities, including the gut microbiome, display intricate spatial organization3,4,5,6,7,8,9. Mapping the biogeography of bacteria can shed light on interactions that underlie community functions10,11,12, but existing methods cannot accommodate the hundreds of species that are found in natural microbiomes13,14,15,16,17. Here we describe metagenomic plot sampling by sequencing (MaPS-seq), a culture-independent method to characterize the spatial organization of a microbiome at micrometer-scale resolution. Intact microbiome samples are immobilized in a gel matrix and cryofractured into particles. Neighboring microbial taxa in the particles are then identified by droplet-based encapsulation, barcoded 16S rRNA amplification and deep sequencing. Analysis of three regions of the mouse intestine revealed heterogeneous microbial distributions with positive and negative co-associations between specific taxa. We identified robust associations between Bacteroidales taxa in all gut compartments and showed that phylogenetically clustered local regions of bacteria were associated with a dietary perturbation. Spatial metagenomics could be used to study microbial biogeography in complex habitats.

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Fig. 1: MaPS-seq and quality control.
Fig. 2: Spatial organization of the microbiota in the mouse distal colon.
Fig. 3: Survey of spatial organization in the mouse gastrointestinal tract.
Fig. 4: Spatial organization in the colon after dietary perturbation.

Data availability

All sequencing data are available from the NCBI Sequence Read Archive under accession PRJNA541181.

Code availability

The code utilized in this study as well as microfluidic device designs and OTU tables can be accessed at http://github.com/ravisheth/mapsseq.

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Acknowledgements

We thank A. Kaufman for technical assistance, R. Rabadan and D. Vitkup for technical advice and discussions, and D. Pe’er and the CUMC Pathology Department for access to sequencing instruments. H.H.W. acknowledges specific funding from the NIH (1R01AI132403, 1R01DK118044), ONR (N00014-15-1-2704) and Burroughs Welcome Fund PATH (1016691) for this work. K.W.L. is partially supported by NIH R01GM110494. P.A.S. acknowledges support from NIH/NIBIB K01EB016071. R.U.S. is supported by a Fannie and John Hertz Foundation Fellowship and an NSF Graduate Research Fellowship (DGE-1644869).

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R.U.S. and H.H.W. developed the initial concept; R.U.S. developed the technique, performed experiments and analyzed data with input from P.A.S. and H.H.W.; and M.L., W.J. and K.W.L. assisted with prototypes of the microfluidic device. R.U.S. and H.H.W. wrote the manuscript. All authors discussed results and commented on and approved the manuscript.

Corresponding author

Correspondence to Harris H. Wang.

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Competing interests

H.H.W. and R.U.S. are inventors on a patent application filed by the Trustees of Columbia University in the City of New York regarding this work.

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Sheth, R.U., Li, M., Jiang, W. et al. Spatial metagenomic characterization of microbial biogeography in the gut. Nat Biotechnol 37, 877–883 (2019). https://doi.org/10.1038/s41587-019-0183-2

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