Functional analysis of the relationship between intestinal microbiota and the expression of hepatic genes and pathways during the course of liver regeneration

Hui Xin Liu, Clarissa Santos Rocha, Satya Dandekar, Yu-Jui Yvonne Wan

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23 Citations (Scopus)

Abstract

Background & Aims The pathways regulating liver regeneration have been extensively studied within the liver. However, the signaling contribution derived from the gut microbiota to liver regeneration is poorly understood. Methods Microbiota and expression of hepatic genes in regenerating livers obtained from mice at 0 h to 9 days post 2/3 partial hepatectomy were temporally profiled to establish their interactive relationships. Results Partial hepatectomy led to rapid changes in gut microbiota that was reflected in an increased abundance of Bacteroidetes S24-7 and Rikenellaceae and decreased abundance of Firmicutes Clostridiales, Lachnospiraceae, and Ruminococcaceae. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was used to infer biological functional changes of the shifted microbiota. RNA-sequencing data revealed 6125 genes with more than a 2-fold difference in their expression levels during regeneration. By analyzing their expression pattern, six uniquely expressed patterns were observed. In addition, there were significant correlations between hepatic gene expression profiles and shifted bacterial populations during regeneration. Moreover, hepatic metabolism and immune function were closely associated with the abundance of Ruminococcacea, Lachnospiraceae, and S24-7. Bile acid profile was analyzed because bacterial enzymes produce bile acids that significantly impact hepatocyte proliferation. The data revealed that specific bacteria were closely associated with the concentration of certain bile acids and expression of hepatic genes. Conclusions The presented data established, for the first time, an intimate relationship between intestinal microbiota and the expression of hepatic genes in regenerating livers.

Original languageEnglish (US)
Pages (from-to)641-650
Number of pages10
JournalJournal of Hepatology
Volume64
Issue number3
DOIs
StatePublished - Mar 1 2016

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Liver Regeneration
Gene Expression
Liver
Bile Acids and Salts
Microbiota
Hepatectomy
Regeneration
Bacteroidetes
RNA Sequence Analysis
Gastrointestinal Microbiome
Transcriptome
Hepatocytes
Bacteria
Enzymes

Keywords

  • Bile acid
  • Gutliver axis
  • Immune response
  • Metabolism
  • Partial hepatectomy

ASJC Scopus subject areas

  • Medicine(all)
  • Hepatology

Cite this

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title = "Functional analysis of the relationship between intestinal microbiota and the expression of hepatic genes and pathways during the course of liver regeneration",
abstract = "Background & Aims The pathways regulating liver regeneration have been extensively studied within the liver. However, the signaling contribution derived from the gut microbiota to liver regeneration is poorly understood. Methods Microbiota and expression of hepatic genes in regenerating livers obtained from mice at 0 h to 9 days post 2/3 partial hepatectomy were temporally profiled to establish their interactive relationships. Results Partial hepatectomy led to rapid changes in gut microbiota that was reflected in an increased abundance of Bacteroidetes S24-7 and Rikenellaceae and decreased abundance of Firmicutes Clostridiales, Lachnospiraceae, and Ruminococcaceae. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was used to infer biological functional changes of the shifted microbiota. RNA-sequencing data revealed 6125 genes with more than a 2-fold difference in their expression levels during regeneration. By analyzing their expression pattern, six uniquely expressed patterns were observed. In addition, there were significant correlations between hepatic gene expression profiles and shifted bacterial populations during regeneration. Moreover, hepatic metabolism and immune function were closely associated with the abundance of Ruminococcacea, Lachnospiraceae, and S24-7. Bile acid profile was analyzed because bacterial enzymes produce bile acids that significantly impact hepatocyte proliferation. The data revealed that specific bacteria were closely associated with the concentration of certain bile acids and expression of hepatic genes. Conclusions The presented data established, for the first time, an intimate relationship between intestinal microbiota and the expression of hepatic genes in regenerating livers.",
keywords = "Bile acid, Gutliver axis, Immune response, Metabolism, Partial hepatectomy",
author = "Liu, {Hui Xin} and Rocha, {Clarissa Santos} and Satya Dandekar and Wan, {Yu-Jui Yvonne}",
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language = "English (US)",
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T1 - Functional analysis of the relationship between intestinal microbiota and the expression of hepatic genes and pathways during the course of liver regeneration

AU - Liu, Hui Xin

AU - Rocha, Clarissa Santos

AU - Dandekar, Satya

AU - Wan, Yu-Jui Yvonne

PY - 2016/3/1

Y1 - 2016/3/1

N2 - Background & Aims The pathways regulating liver regeneration have been extensively studied within the liver. However, the signaling contribution derived from the gut microbiota to liver regeneration is poorly understood. Methods Microbiota and expression of hepatic genes in regenerating livers obtained from mice at 0 h to 9 days post 2/3 partial hepatectomy were temporally profiled to establish their interactive relationships. Results Partial hepatectomy led to rapid changes in gut microbiota that was reflected in an increased abundance of Bacteroidetes S24-7 and Rikenellaceae and decreased abundance of Firmicutes Clostridiales, Lachnospiraceae, and Ruminococcaceae. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was used to infer biological functional changes of the shifted microbiota. RNA-sequencing data revealed 6125 genes with more than a 2-fold difference in their expression levels during regeneration. By analyzing their expression pattern, six uniquely expressed patterns were observed. In addition, there were significant correlations between hepatic gene expression profiles and shifted bacterial populations during regeneration. Moreover, hepatic metabolism and immune function were closely associated with the abundance of Ruminococcacea, Lachnospiraceae, and S24-7. Bile acid profile was analyzed because bacterial enzymes produce bile acids that significantly impact hepatocyte proliferation. The data revealed that specific bacteria were closely associated with the concentration of certain bile acids and expression of hepatic genes. Conclusions The presented data established, for the first time, an intimate relationship between intestinal microbiota and the expression of hepatic genes in regenerating livers.

AB - Background & Aims The pathways regulating liver regeneration have been extensively studied within the liver. However, the signaling contribution derived from the gut microbiota to liver regeneration is poorly understood. Methods Microbiota and expression of hepatic genes in regenerating livers obtained from mice at 0 h to 9 days post 2/3 partial hepatectomy were temporally profiled to establish their interactive relationships. Results Partial hepatectomy led to rapid changes in gut microbiota that was reflected in an increased abundance of Bacteroidetes S24-7 and Rikenellaceae and decreased abundance of Firmicutes Clostridiales, Lachnospiraceae, and Ruminococcaceae. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was used to infer biological functional changes of the shifted microbiota. RNA-sequencing data revealed 6125 genes with more than a 2-fold difference in their expression levels during regeneration. By analyzing their expression pattern, six uniquely expressed patterns were observed. In addition, there were significant correlations between hepatic gene expression profiles and shifted bacterial populations during regeneration. Moreover, hepatic metabolism and immune function were closely associated with the abundance of Ruminococcacea, Lachnospiraceae, and S24-7. Bile acid profile was analyzed because bacterial enzymes produce bile acids that significantly impact hepatocyte proliferation. The data revealed that specific bacteria were closely associated with the concentration of certain bile acids and expression of hepatic genes. Conclusions The presented data established, for the first time, an intimate relationship between intestinal microbiota and the expression of hepatic genes in regenerating livers.

KW - Bile acid

KW - Gutliver axis

KW - Immune response

KW - Metabolism

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