Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice
Figure 5
Whole genome (maximum likelihood) phylogeny of intestinal bacteria demonstrating the phylogenetic placement of disease-resolving bacteriotherapy bacteria (MixB) and the dominant members of the supershedder microbiota.
Maximum likelihood phylogeny produced using FastTree from the concatenated protein sequence of 44 common genes (See methods). Species names marked in green indicate members of the suppressive MixB mixture, names marked in red indicate species that were commonly detected in the feces of supershedding mice, names in black are reference genomes from common intestinal bacteria that were included to provide phylogenetic context to the tree. Taxonomic designations are given at the relevant branch nodes. Adjacent pictures are transmission electron micrographs of sectioned bacterial strains that constitute MixB. Methods for sample processing and imaging have been described [33]. Scale bars are shown below bacteria.