A decrease in functional microbiomes represented as Faecalibacterium affects immune homeostasis in long-term stable liver transplant patients

Abstract

LT, liver transplantation; HCC, hepatocellular carcinoma; IS, immunosuppressants; DC, dendritic cells; Treg, regulatory T; Th17, T helper 17; AST, aspartate transaminase; ALT, alanine transaminase; OUT, operational taxonomic unit; LEfSe, linear discriminant analysis effect size; LDA, linear discriminant analysis; IL, interleukin; TGF, transforming growth factor; GM-CSF, granulocyte-macrophage colony-stimulating factor; IFN, interferon; TNF-α, tumor necrosis factor-α; MIP-1α, macrophage inflammatory protein-1α; IP-10, interferon γ-induced protein; MCP-1, monocyte chemoattractant protein-1; ACR, acute cellular rejection; NF-κB, nuclear factor κB; PT INR, prothrombin time; QC, quality check; PBMC, peripheral blood mononuclear cells; PBS, phosphate-buffered saline; ELISA, enzyme-linked immunosorbent assay.

Keywords: Faecalibacterium; Liver transplantation; bacteroides; gut dysbiosis; gut microbiome; immunosuppressant; regulatory T cells; tolerance.

Figure 1.

Comparisons of (a) alpha-diversity measured by observed OTUs and Shannon score and (b) beta-diversity using PCoA based on Bray-Curtis dissimilarity between long-term post-LT patients (n = 22) and healthy controls (n = 20). OTUs, operational taxonomic units; PCoA, principal coordinate analysis; LT, liver transplantation.

Figure 2.

Comparisons of fecal microbial composition and the proportion of Treg and Th17 cells between long-term post-LT patients and healthy controls. (a, b) Relative proportion of bacteria at the phylum, family and genus level. (c) The LDA effect size analysis to identify significantly different microbiome in the relative abundance between long-term post-LT patients and healthy controls. (d) The proportion of CD4+ Treg and CD4+ Th17 cells in PBMC of long-term post-LT patients and healthy controls. Treg, regulatory T cells; Th17, T helper 17 cells; LT, liver transplantation; LDA, linear discriminant analysis.

Figure 3.

Comparisons of relative abundance of specific bacteria between long-term post-LT patients and healthy controls, and the change of Treg cells, IL-17, and IL-10 after treated with bacteria and butyrate. (a) Comparisons of relative abundance of the Faecalibacterium, Bifidobacterium, Akkermansia, Bacteroides genus and F. prausnitzii species between long-term post-LT patients and healthy controls. (b-d) CD4 + T cells from PBMC of long-term post-LT patients were cultured in the absence or presence of B. bifidum, B. longum, F. prausnitzii, A. muciniphila , and butyrate under the anti-CD3 stimulation condition for 3 d. The proportion of Treg cells and Th17 cells were analyzed by flow cytometry and the level of level of IL-17, IL-10 and TGF-β were analyzed by ELISA. LT, liver transplantation.

Figure 4.

Comparisons of (a) alpha diversity measured by observed OTUs and Shannon score, (b) beta-diversity using PCoA based on Bray-Curtis dissimilarity, (c) microbial composition, and (d) relative abundance of specific bacteria between the higher, lower ratio and healthy groups. OTUs, operational taxonomic units; PCoA, principal coordinate analysis; the higher ratio group, the group with the ratio of tacrolimus level/dose > 1.6; the lower ratio group, the group with the ratio of tacrolimus level/dose ≤ 1.6.

Figure 5.

Comparisons of (a) alpha diversity measured by observed OTUs and Shannon score, (b) beta-diversity using PCoA based on Bray-Curtis dissimilarity, (c, d) microbial composition, (e) relative abundance of specific bacteria, and (f) the proportion of Treg and Th17 cells between long-term post-LT patients and tolerant patients. (g) Comparison of cytokine and chemokine expression in long-term post-LT patients and tolerant patients. Cytokines and chemokines were detected from plasma. OTUs, operational taxonomic units; PCoA, principal coordinate analysis; Treg, regulatory T cells; Th17, T helper 17 cells; LT, liver transplantation; GM-CFS, granulocyte-macrophage colony-stimulating factor; IL, interleukin; IFN, interferon.