A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome

Alessandra Riva, Orest Kuzyk, Erica Forsberg, Gary Siuzdak, Carina Pfann, Craig Herbold, Holger Daims, Alexander Loy, Benedikt Warth and David Berry ()
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Alessandra Riva: University of Vienna
Orest Kuzyk: University of Vienna
Erica Forsberg: Scripps Center for Metabolomics and Mass Spectrometry
Gary Siuzdak: Scripps Center for Metabolomics and Mass Spectrometry
Carina Pfann: University of Vienna
Craig Herbold: University of Vienna
Holger Daims: University of Vienna
Alexander Loy: University of Vienna
Benedikt Warth: Scripps Center for Metabolomics and Mass Spectrometry
David Berry: University of Vienna

Nature Communications, 2019, vol. 10, issue 1, 1-11

Abstract: Abstract Compartmentalization of the gut microbiota is thought to be important to system function, but the extent of spatial organization in the gut ecosystem remains poorly understood. Here, we profile the murine colonic microbiota along longitudinal and lateral axes using laser capture microdissection. We found fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity along the length of the colon. Privation of fiber reduces the diversity of the microbiota and disrupts longitudinal and lateral gradients in microbiota composition. Both mucus-adjacent and luminal communities are influenced by the absence of dietary fiber, with the loss of a characteristic distal colon microbiota and a reduction in the mucosa-adjacent community, concomitant with depletion of the mucus layer. These results indicate that diet has not only global but also local effects on the composition of the gut microbiota, which may affect function and resilience differently depending on location.

Date: 2019
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DOI: 10.1038/s41467-019-12413-0

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