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Crohn’s disease causes chronic inflammation in the gastrointestinal tract and its pathogenesis remains unclear. In the intestine of Crohn’s disease patients, CD14 + CD11 + CD163 low  macrophages contribute to inflammation through the induction of Th17 cells and production of inflammatory cytokines; the CD14 + CD11c + 163 high  fraction is anti-inflammatory through the production of IL-10 in normal cases. In this report, the 16S rRNA gene amplicon sequencing method was used to identify bacteria that are specifically present in intestinal CD14 + CD11c +  macrophages of Crohn’s disease patients. Bacteria present in intestinal CD14 + CD11c +  macrophages and mucus of Crohn’s disease patients were separated into different clusters in principal coordinates analysis. There was a statistically significant increase in the relative composition of CD14 + CD11c +  macrophages from mucus in two phyla ( Proteobacteria  [p = 0.01] and  Actinobacteria  [p = 0.02]) and two families ( Moraxellaceae  [p < 0.001] and  Pseudomonadaceae  [p = 0.01]). In addition, OTU-1:  Acinetobacter  and OTU-8:  Pseudomonadaceae  tended to concentrate in the CD14 + CD11c + CD163 low  subset, whereas OTU-10:  Proteus , OTU-15:  Collinsella  tended to concentrate more in the CD14 + CD11c + CD163 high  subset than the other subset and mucus.

Some Gammaproteobacteria are enriched within CD14+ macrophages from intestinal lamina propria of Crohn’s disease patients versus mucus