Operable hepatitis B virus-related hepatocellular carcinoma: gut microbiota profile of patients at different ages

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Abstract

Background

Age was important prognostic factors for operable hepatocellular carcinoma patients. The aim of the present study was to assess the difference in gut microbiota in patients with operable hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) at different ages ; to investigate the features of the microbiota and its function associated with different ages; to provide a preliminary look at effects of the gut microbiota dimension on prognostic.

Methods

From September 2020 to May 2021, patients with HBV-HCC were able to undergo liver resection and were recruited consecutively and divided into the younger age group (age <45 years) (Y.AG) (n=20), middle age group (age from 45 to 65 years) (M.AG) (n=13) 45–65 years, and older age group (age >65 years) (O.AG) (n=20). The relationships between gut microbiota and different ages were explored using 16S rRNA gene sequencing data. PICRUST2 was used to examine the metagenomic data in PHLF patients. Fisher’s exact and Mann-Whitney U-test were used for the data analysis.

Results

Pairwise comparison between the three groups showed that the α-diversity of Y.AG was significantly higher than that of O.AG (ACE Index, P=0.017; chao1 Index, P=0.031; observed_species Index, P=0.011; and goods_coverage Index, P=0.041). The β-diversity in the 3 groups differed significantly (stress =0.100), while the composition (β-diversity) differed significantly between the Y.AG and the M.AG (stress =0.090), the M.AG and the O.AG (stress =0.095), and the Y.AG and the O.AG (stress =0.099). At the genus level, 7 bacterial genera were significantly enriched in the O.AG compared with the Y.AG, of which Streptococcus, Blautia, Erysipelotrichaceae_UCG-003, and Fusicatenibacter represented the major variances in O.AG microbiomes. Eleven genera were significantly increased in the O.AG, of which Prevotella, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Ruminiclostridium, and Phascolarctobacterium represented the major variances in the O.AG. The Y.AG and the O.AG were predicted by PICRUSt2 analysis, which found 72 pathways related to differential gut microbiome at the genus level. Redundancy analysis showed that 7 environmental factors were significantly correlated with intestinal microorganisms, especially in the Y.AG compared with the O.AG.

Conclusions

Analysis of gut microbiota characteristics in patients of different ages could ultimately contribute to the development of novel avenues for the treatment of HCC at different ages.

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Most cited references 90

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QIIME allows analysis of high-throughput community sequencing data.

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FLASH: fast length adjustment of short reads to improve genome assemblies.

T. Magoc, S. L. Salzberg (2013)

Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.

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Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.

Qiong Wang, George Garrity, James Tiedje … (2007)

The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (> or = 95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.

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Author and article information

Journal

Journal ID (nlm-ta): Ann Transl Med

Journal ID (iso-abbrev): Ann Transl Med

Journal ID (publisher-id): ATM

Title: Annals of Translational Medicine

Publisher: AME Publishing Company

ISSN (Print): 2305-5839

ISSN (Electronic): 2305-5847

Publication date (Print and electronic): April 2022

Publication date (Print): April 2022

Volume: 10

Issue: 8

Electronic Location Identifier: 477

Affiliations

[1 ]deptDepartment of Hepatobiliary Surgery , Guangxi Medical University Cancer Hospital , Nanning, China;

[2 ]deptKey Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor , Ministry of Education , Nanning, China;

[3 ]Guangxi Liver Cancer Diagnosis and Treatment Engineering and Technology Research Center , Nanning, China

Author notes

Contributions: (I) Conception and design: YC Peng, LQ Li; (II) Administrative support: LQ Li; (III) Provision of study materials or patients: All authors; (IV) Collection and assembly of data: YC Peng, JX Xu, LN Qi; (V) Data analysis and interpretation: YC Peng, JX Xu, LN Qi; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors.

[#]

These authors contributed equally to this work.

Correspondence to: Dr. Lu-Nan Qi; Le-Qun Li. Department of Hepatobiliary Surgery, Guangxi Medical University Cancer Hospital, No. 71 Hedi Road, Nanning 530021, China. Email: qilunan_gxmu@ 123456163.com ; lilequn_gxmu@ 123456163.com .

[^]

ORCID: Yu-Chong Peng, 0000-0001-9287-8686; Jing-Xuan Xu, 0000-0002-5516-4948; Lu-Nan Qi, 0000-0003-2538-9748.

Article

Publisher ID: atm-10-08-477

DOI: 10.21037/atm-22-1572

PMC ID: 9096381

PubMed ID: 35571398

SO-VID: 74a2fc66-fccf-4cca-98e6-3563bfef620a

License:

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0.

History

Date received : 23 February 2022

Date accepted : 20 April 2022

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Operable hepatitis B virus-related hepatocellular carcinoma: gut microbiota profile of patients at different ages

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Abstract

Background

Methods

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Point-Of-Care Testing for Hepatitis

Most cited references 90

QIIME allows analysis of high-throughput community sequencing data.

FLASH: fast length adjustment of short reads to improve genome assemblies.

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.

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