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Spatial structure of gut microbiota

Bacteria identified in the gnotobiotic mouse colon by fluorescence in situ hybridization.

The spatial organization of bacterial species within the gut is believed to influence the relationships among members of the gut microbial community and between community members and their hosts. However, the spatial structure of gut microbiota has been poorly characterized. Jessica Mark Welch et al. (pp. E9105–E9114) colonized adult germ-free mice with a mixture of 15 human gut-derived bacterial species, and used fluorescence in situ hybridization to simultaneously image multiple members of this consortium in cross-sections of mouse colon over scales ranging from a few micrometers to hundreds of micrometers. Bacteria were concentrated at the border between the intestinal mucosa and lumen and in mucus-rich patches in the interior of the lumen. At fine length scales, similar mixtures of bacterial species were observed in both luminal and mucosal habitats. Some spatial organization was observed within habitats; for example, Ruminococcus torques was depleted relative to other species in a narrow boundary region closest to host cells. According to the authors, the colon should not be considered as possessing sharply demarcated luminal and mucosal compartments, but instead might be described as an incompletely mixed bioreactor. Identifying host and microbial factors that contribute to …

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