PMC

Relative abundance of major phyla in cases (+) and controls (−). In both groups, the 2 dominant phyla were Bacteroidetes and Firmicutes, which made up >95% of each individual's microbiota, with the exception of case 9, who had an unusually high relative abundance of fusobacteria in lieu of Firmicutes.

Stool microbial community composition in cases, compared with that in controls. Community composition dissimilarity was analyzed using nonmetric dimensional scaling (NMDS) based on a Canberra community dissimilarity matrix. Each dot represents the microbiota of a single subject. Ellipses represent 95% confidence intervals for the standard error of weighted NDMS score means of cases and controls. Community differences were verified using Adonis (P = <.05).

Linear discriminant analysis (LDA) effect size (LEfSe) detects specific differentially abundant taxa in cases and controls. A, Cladogram showing differentially abundant taxonomic clades with an LDA score >2.0 among cases and controls. B, LDA scores of differentially abundant taxa among cases and controls. The LDA score indicates the effect size and ranking of each differentially abundant taxon. C, The relative abundance of taxa identified by LEfSe as being differentially abundant in cases and controls was compared using the Mann–Whitney test: Proteobacteria, P = <.05; Gammaproteobacteria, P = .04; Enterobacteriales, P = <.05; Enterobacteriaceae, P = <.05; Erysipelotrichi, P = .01; Erysipelotrichales, P = .01; Erysipelotrichaceae, P = .01; Barnesiella, P = .01; Alistipes, P = .01; and Rikenellaceae, P = .01.

Markers of microbial translocation and systemic inflammation in cases and controls. Levels of markers of microbial translocation (soluble CD14 [sCD14], endotoxin core antibody [EndoCAb], 16S ribosomal RNA [rRNA] gene, and lipopolysaccharide [LPS]) and systemic inflammation (interleukin 6 [IL-6], interferon γ [IFN-γ], interleukin 1β [IL-1β], tumor necrosis factor α [TNF-α], and high-sensitivity C-reactive protein [hsCRP]) were measured in cases and controls, as described in “Methods” section, and compared using the Mann–Whitney test. *P = <.01.