Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis

Abstract

BackgroundHuman gut microbiota plays an important role in the pathogenesis of cirrhosis complications. Although the phylogenetic diversity of intestinal microbiota in patients with liver cirrhosis has been examined in several studies, little is known about their functional composition and structure.ResultsTo characterize the functional gene diversity of the gut microbiome in cirrhotic patients, we recruited a total of 42 individuals, 12 alcoholic cirrhosis patients, 18 hepatitis B virus (HBV)-related cirrhosis patients, and 12 normal controls. We determined the functional structure of these samples using a specific functional gene array, which is a combination of GeoChip for monitoring biogeochemical processes and HuMiChip specifically designed for analyzing human microbiomes. Our experimental data showed that the microbial community functional composition and structure were dramatically distinctive in the alcoholic cirrhosis. Various microbial functional genes involved in organic remediation, stress response, antibiotic resistance, metal resistance, and virulence were highly enriched in the alcoholic cirrhosis group compared to the control group and HBV-related cirrhosis group. Cirrhosis may have distinct influences on metabolic potential of fecal microbial communities. The abundance of functional genes relevant to nutrient metabolism, including amino acid metabolism, lipid metabolism, nucleotide metabolism, and isoprenoid biosynthesis, were significantly decreased in both alcoholic cirrhosis group and HBV-related cirrhosis group. Significant correlations were observed between functional gene abundances and Child-Pugh scores, such as those encoding aspartate-ammonia ligase, transaldolase, adenylosuccinate synthetase and IMP dehydrogenase.ConclusionsFunctional gene array was utilized to study the gut microbiome in alcoholic and HBV-related cirrhosis patients and controls in this study. Our array data indicated that the functional composition of fecal microbiomes was heavily influenced by cirrhosis, especially by alcoholic cirrhosis. This study provides new insights into the functional potentials and activity of gut microbiota in cirrhotic patients with different etiologies.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-753) contains supplementary material, which is available to authorized users.

Faecal microbiota from patients with cirrhosis has a low capacity to ferment non‐digestible carbohydrates into short‐chain fatty acids

“…Cirrhosis is associated with profound changes in the gut microbiota as compared to healthy controls . This ‘dysbiosis’ progresses as the liver disease evolves to advanced stages and is characterized by a reduced bacterial diversity and shifts in community structure and composition .…”

Community-Metabolome Correlations of Gut Microbiota from Child-Turcotte-Pugh of A and B Patients

“…Fecal samples were collected from 15 compensated cirrhotic patients and 15 age-matched controls to evaluate changes in stool microbiota composition and function in cirrhotic patients after omeprazole therapy, and they found that omeprazole was associated with a microbiota shift and functional change in the distal gut in compensated cirrhotic patients that could set the stage for bacterial overgrowth (Bajaj et al, 2014). Chen et al (2014) researched on fecal samples from 12 alcoholic cirrhosis patients, 18 hepatitis B virus related cirrhosis patients, and 12 normal controls using a specific functional gene array, which suggested that the functional composition of fecal microbiota was heavily influenced by cirrhosis, especially by alcoholic cirrhosis. Grąt et al (2014) confirmed the enrichment of lactobacilli in the gut microflora of liver transplant candidates with cirrhosis as revealed by intestinal flora component analysis.…”

Gut microbiota modulate the immune effect against hepatitis B virus infection

“…Chassaing et al also suggest that mechanisms by which HBV promotes liver disease is mediated, in part, via the gut microbiota [63]. Constantly, functional gene arrays data showed that the abundance of functional genes relevant to nutrient metabolism, including amino acid metabolism, lipid metabolism, nucleotide metabolism, and isoprenoid biosynthesis, were significantly decreased in both the alcoholic cirrhosis group and the HBV-related cirrhosis group compared to normal controls [64]. These studies suggested that antibiotics could influence the gut microbiota and its related liver immunity.…”