| Literature DB >> 35733959 |
Ranxi Li1,2, Xinzhu Yi2, Junhao Yang2, Zhou Zhu1,2, Yifei Wang1,2, Xiaomin Liu2, Xili Huang1,2, Yu Wan3, Xihua Fu4, Wensheng Shu2, Wenjie Zhang5, Zhang Wang1,2.
Abstract
The gut microbiome is associated with hepatitis B virus (HBV)-induced liver disease, which progresses from chronic hepatitis B, to liver cirrhosis, and eventually to hepatocellular carcinoma. Studies have analyzed the gut microbiome at each stage of HBV-induced liver diseases, but a consensus has not been reached on the microbial signatures across these stages. Here, we conducted by a systematic meta-analysis of 486 fecal samples from publicly available 16S rRNA gene datasets across all disease stages, and validated the results by a gut microbiome characterization on an independent cohort of 15 controls, 23 chronic hepatitis B, 20 liver cirrhosis, and 22 hepatocellular carcinoma patients. The integrative analyses revealed 13 genera consistently altered at each of the disease stages both in public and validation datasets, suggesting highly robust microbiome signatures. Specifically, Colidextribacter and Monoglobus were enriched in healthy controls. An unclassified Lachnospiraceae genus was specifically elevated in chronic hepatitis B, whereas Bilophia was depleted. Prevotella and Oscillibacter were depleted in liver cirrhosis. And Coprococcus and Faecalibacterium were depleted in hepatocellular carcinoma. Classifiers established using these 13 genera showed diagnostic power across all disease stages in a cross-validation between public and validation datasets (AUC = 0.65-0.832). The identified microbial taxonomy serves as non-invasive biomarkers for monitoring the progression of HBV-induced liver disease, and may contribute to microbiome-based therapies.Entities:
Keywords: gut microbiome; hepatitis; hepatitis B virus; hepatocellular carcinoma; liver cirrhosis; meta-analysis
Year: 2022 PMID: 35733959 PMCID: PMC9208012 DOI: 10.3389/fmicb.2022.916061
Source DB: PubMed Journal: Front Microbiol ISSN: 1664-302X Impact factor: 6.064
Figure 1The analysis pipeline in this study, such as the flowchart of the meta-analysis for gut microbiome of public datasets, and the independent cohort validation. Each step is shown in the white box, and the statistical methods and software used are within. n denotes the number of datasets included in each step.
Summary of the public datasets included in the meta-analysis.
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| PRJNA558158 | 32265857 | Xiamen, | Illumina | V3–V4 | PE | 21 | 28 | 25 | |
| PRJNA382861 | 29180991 | Shanghai, | Illumina | V3–V4 | PE | 22 | 85 | ||
| PRJNA445763 | 29780327 | Harbin, | Illumina | V3–V4 | PE | 20 | 30 | ||
| PRJNA540574 | 32281295 | Jilin, | Illumina | V4 | PE | 20 | 8 | 8 | 35 |
| PRJEB32568 | NA | Yantai, | Illumina | V4–V5 | SE | 5 | 12 | 11 | 9 |
| PRJNA428932 | 30675188 | Nanjing, | Illumina | V4 | SE | 33 | 35 | ||
| PRJNA478823 | 31293562 | Guangzhou, | Illumina | V4–V5 | SE | 18 | 61 | ||
Figure 2Signature microbiome taxa identified in the meta-analysis. (A) The public datasets included for each pair wise comparison. (B) Mean proportion of each genus between groups of interest in each individual dataset, and the summary statistics for the random effect meta-analysis for each pair wise comparison. The genus was highlighted by red if it was consistently and significantly altered in both public and validation datasets. Shown are the genera at the p-value threshold of 0.05.
Figure 3Overview of the gut microbiome in the validation cohort. (A) Alpha diversity for each disease status concluding Chao1, ACE, Shannon and Simpson. The differences were calculated by Wilcoxon test on genus level. *p < 0.05; ***p < 0.001. (B) Principal Coordinates Analysis (PCoA) of microbiome beta-diversity based on Bray-Curtis dissimilarity index.
Figure 4The consistency of the 13 signature genera between public and validation datasets. For each genus, the gray box indicates the pair wise comparison that the genus was both significantly and consistently altered in public and validation datasets. The green and yellow box indicates the pair wise comparisons that the genus was consistently increased or decreased in public and validation datasets (but not necessarily significant). The 2 heat maps indicate the fold-change across the pair wise comparisons and the average relative abundance across the four subgroups in the validation dataset. ① CHB vs. Healthy; ② LC vs. Healthy; ③HCC vs. Healthy; ④ LC vs CHB; ⑤ HCC vs. CHB; ⑥ HCC vs. LC. *p < 0.05; **p < 0.01; ***p < 0.001.
Figure 5The consistent microbial signatures along the progression of the HBV-induced diseases based on results in this study. The genera in the “highest” box denote that their average relative abundances were most enriched in the corresponding subgroup compared to all other subgroups, whereas those in the “lowest” box represent that their abundance were most depleted in the corresponding subgroup. In the progression from 1 disease stage to another, ↑ denotes significantly increased abundance, ↓ denotes significantly decreased abundance.
Figure 6The receiver operating characteristic curves for classifiers based on the 13 signature genera. For each comparison between healthy and CHB, healthy and LC, healthy and HCC, CHB and LC, CHB and HCC, LC and HCC, the ROC curve and area under curve (AUC) were shown. The LASSO binary classifiers were trained by public dataset and validated in the independent cohort.