Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis

Chen, Yaowen; Liao, Pu; Liu, Runyan; Hu, Shuofeng; He, Zhen; Dong, Guohua; Feng, Chao; An, Sijing; Ying, Xiaomin

doi:10.1128/msystems.00775-21

Cited by 6 publications

(6 citation statements)

References 55 publications

(56 reference statements)

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“…Correspondingly, some beneficial bacterial taxa were decreased in SBP patients, such as Faecalibacterium prausnitzii , Methanobrevibacter smithii and Lactobacillus reuteri . The species F. prausnitzii has been demonstrated to have a lower abundance in patients with liver cirrhosis than in healthy people, and is associated with the regression of acute-on-chronic liver failure (ACLF) ( Wang et al., 2021 ; Chen et al., 2021 ). F. prausnitzii is the main butyrate-producing bacterium, and its short-chain fatty acid (SCFA) metabolites have an important anti-inflammatory effect on the intestine and liver ( Lee et al., 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Alterations of gut microbiota in cirrhotic patients with spontaneous bacterial peritonitis: A distinctive diagnostic feature

Zhou

Liu

et al. 2022

Front. Cell. Infect. Microbiol.

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BackgroundSpontaneous bacterial peritonitis (SBP) is a severe infection in cirrhotic patients that requires early diagnosis to improve the long-term outcome. Alterations in the gut microbiota have been shown to correlate with the development and progression of liver cirrhosis. However, the relationship between SBP and gut microbiota remains unknown.MethodsIn this study, we applied 16S rRNA pyrosequencing of feces to ascertain possible links between the gut microbiota and SBP. We recruited 30 SBP patients, 30 decompensated cirrhotic patients without SBP (NSBP) and 30 healthy controls. Metagenomic functional prediction of bacterial taxa was achieved using PICRUSt. ResultsThe composition of the gut microbiota in the SBP patients differed remarkably from that in the NSBP patients and healthy individuals. The microbial richness was significantly decreased, while the diversity was increased in the SBP patients. Thirty-four bacterial taxa containing 15 species, mainly pathogens such as Klebsiella pneumoniae, Serratia marcescens and Prevotella oris, were dominant in the SBP group, while 42 bacterial taxa containing 16 species, especially beneficial species such as Faecalibacterium prausnitzii, Methanobrevibacter smithii and Lactobacillus reuteri, were enriched in the NSBP group. Notably, we found that 18 gene functions of gut microbiota were different between SBP patients and NSBP patients, which were associated with energy metabolism and functional substance metabolism. Five optimal microbial markers were determined using a random forest model, and the combination of Lactobacillus reuteri, Rothia mucilaginosa, Serratia marcescens, Ruminococcus callidus and Neisseria mucosa achieved an area under the curve (AUC) value of 0.8383 to distinguish SBP from decompensated cirrhosis.ConclusionsWe described the obvious dysbiosis of gut microbiota in SBP patients and demonstrated the potential of microbial markers as noninvasive diagnostic tools for SBP at an early stage.

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Section: Discussionmentioning

confidence: 99%

Alterations of gut microbiota in cirrhotic patients with spontaneous bacterial peritonitis: A distinctive diagnostic feature

Zhou

Liu

et al. 2022

Front. Cell. Infect. Microbiol.

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“…We show that the majority of high importance frequentmers originate from microorganisms known to be associated with liver cirrhosis, such as Prevotella copri, Faecalibacterium prausnitzii and Klebsiella pneumoniae , multiple of which have been previously associated with liver cirrhosis (Dong et al 2020; Y. Chen et al 2021; Yuan et al 2019). These results demonstrate the ability of the method to discover new associations between microbial species in the gut microbiome and disease.…”

Section: Discussionmentioning

confidence: 95%

Frequentmers - a novel way to look at metagenomic Next Generation Sequencing data and an application in detecting liver cirrhosis

Mouratidis,

Chantzi,

Khan

et al. 2023

Preprint

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Early detection of human disease is associated with improved clinical outcomes. However, many diseases are often detected at an advanced, symptomatic stage where patients are past efficacious treatment periods and can result in less favorable outcomes. Therefore, methods that can accurately detect human disease at a presymptomatic stage are urgently needed. Here, we introduce frequentmers; short sequences that are specific and recurrently observed in either patient or healthy control samples, but not in both. We showcase the utility of frequentmers for the detection of liver cirrhosis using metagenomic Next Generation Sequencing data from stool samples of patients and controls. We develop classification models for the detection of liver cirrhosis and achieve an AUC score of 0.91 using ten-fold cross-validation. A small subset of 200 frequentmers can achieve comparable results in detecting liver cirrhosis. Finally, we identify the microbial organisms in liver cirrhosis samples, which are associated with the most predictive frequentmer biomarkers.

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“…Faecalibacterium prausnitzii was the only species that appeared in more than 95 % of all individuals. F. prausnitzii , an important butyrate-producing bacterium found in the intestine, enhances gut barrier protection, exhibits anti-inflammatory effects [54] , [55] and strain-level genomic diversity, and SCFA metabolism may differ among strain clusters [56] . We found 13 species shared by more than 90 % of the investigated individuals (core species).…”

Section: Discussionmentioning

confidence: 99%

“…This study was conducted at the species level. Future studies between microbes and populations should be conducted at the strain level, as strains are the basic functional units that communicate with hosts, and different strains in the same species may exert different functions [56] . Another noteworthy aspect that requires further investigation is the abundance of bacteriocin biosynthetic gene clusters in the gut microbiome.…”

Section: Discussionmentioning

confidence: 99%

Combined analysis of cross-population healthy adult human microbiome reveals consistent differences in gut microbial characteristics between Western and non-Western countries

Sheng,

Wang,

Gao

et al. 2024

Computational and Structural Biotechnology Journal

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Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis

Cited by 6 publications

References 55 publications

Alterations of gut microbiota in cirrhotic patients with spontaneous bacterial peritonitis: A distinctive diagnostic feature

Alterations of gut microbiota in cirrhotic patients with spontaneous bacterial peritonitis: A distinctive diagnostic feature

Frequentmers - a novel way to look at metagenomic Next Generation Sequencing data and an application in detecting liver cirrhosis

Combined analysis of cross-population healthy adult human microbiome reveals consistent differences in gut microbial characteristics between Western and non-Western countries

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