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Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies

BACKGROUND: Liver cirrhosis is a major public health problem, accounting for high rates of morbidity and mortality worldwide. The cirrhosis etiology is a broad and essential step in planning a treatment strategy. Many recent studies have documented that gut microbiome alterations play a vital role i...

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Autores principales: Naseri, Mohadeseh, Palizban, Fahimeh, Yadegar, Abbas, Khodarahmi, Mohsen, Asadzadeh Aghdaei, Hamid, Houri, Hamidreza, Zahiri, Javad
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8845349/
https://www.ncbi.nlm.nih.gov/pubmed/35168645
http://dx.doi.org/10.1186/s13099-022-00482-4
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author Naseri, Mohadeseh
Palizban, Fahimeh
Yadegar, Abbas
Khodarahmi, Mohsen
Asadzadeh Aghdaei, Hamid
Houri, Hamidreza
Zahiri, Javad
author_facet Naseri, Mohadeseh
Palizban, Fahimeh
Yadegar, Abbas
Khodarahmi, Mohsen
Asadzadeh Aghdaei, Hamid
Houri, Hamidreza
Zahiri, Javad
author_sort Naseri, Mohadeseh
collection PubMed
description BACKGROUND: Liver cirrhosis is a major public health problem, accounting for high rates of morbidity and mortality worldwide. The cirrhosis etiology is a broad and essential step in planning a treatment strategy. Many recent studies have documented that gut microbiome alterations play a vital role in the development and progression of cirrhosis and its complications. Nevertheless, there is insufficient data on the correlation between liver cirrhosis and gut phageome alterations in patients with advanced liver diseases. This study aimed to analyze the taxonomic structure and functional attributes of the gut phageome in six different etiologies of advanced liver cirrhosis. METHODS: We first retrieved metagenomic sequencing data from three datasets of fecal samples taken from cirrhotic patients with various etiologies. Subsequently, several bioinformatics pipelines were used to analyze bacteriophage composition and determine their functionality. RESULTS: A gene catalog of 479,425 non-redundant genes was developed as a reference to measure gene prevalence. The results of the analysis revealed a few significant differences among the cohorts at the phage species level. However, the alternations were more evident as there were more in-depth analyses of the functional resolution of the gut phageome. CONCLUSIONS: Our findings suggest that the functional analysis of the gut phageome would provide meaningful markers to predict the progression of liver cirrhosis and facilitate the development of novel treatment approaches. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13099-022-00482-4.
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spelling pubmed-88453492022-02-16 Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies Naseri, Mohadeseh Palizban, Fahimeh Yadegar, Abbas Khodarahmi, Mohsen Asadzadeh Aghdaei, Hamid Houri, Hamidreza Zahiri, Javad Gut Pathog Research BACKGROUND: Liver cirrhosis is a major public health problem, accounting for high rates of morbidity and mortality worldwide. The cirrhosis etiology is a broad and essential step in planning a treatment strategy. Many recent studies have documented that gut microbiome alterations play a vital role in the development and progression of cirrhosis and its complications. Nevertheless, there is insufficient data on the correlation between liver cirrhosis and gut phageome alterations in patients with advanced liver diseases. This study aimed to analyze the taxonomic structure and functional attributes of the gut phageome in six different etiologies of advanced liver cirrhosis. METHODS: We first retrieved metagenomic sequencing data from three datasets of fecal samples taken from cirrhotic patients with various etiologies. Subsequently, several bioinformatics pipelines were used to analyze bacteriophage composition and determine their functionality. RESULTS: A gene catalog of 479,425 non-redundant genes was developed as a reference to measure gene prevalence. The results of the analysis revealed a few significant differences among the cohorts at the phage species level. However, the alternations were more evident as there were more in-depth analyses of the functional resolution of the gut phageome. CONCLUSIONS: Our findings suggest that the functional analysis of the gut phageome would provide meaningful markers to predict the progression of liver cirrhosis and facilitate the development of novel treatment approaches. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13099-022-00482-4. BioMed Central 2022-02-15 /pmc/articles/PMC8845349/ /pubmed/35168645 http://dx.doi.org/10.1186/s13099-022-00482-4 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Naseri, Mohadeseh
Palizban, Fahimeh
Yadegar, Abbas
Khodarahmi, Mohsen
Asadzadeh Aghdaei, Hamid
Houri, Hamidreza
Zahiri, Javad
Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies
title Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies
title_full Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies
title_fullStr Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies
title_full_unstemmed Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies
title_short Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies
title_sort investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8845349/
https://www.ncbi.nlm.nih.gov/pubmed/35168645
http://dx.doi.org/10.1186/s13099-022-00482-4
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