Application of next-generation sequencing to study ascitic microbiome in cirrhotic patients with or without spontaneous bacterial peritonitis

Background: Spontaneous bacterial peritonitis is an important cause of morbidity and mortality in cirrhotic patients with ascites. The key step in the pathogenesis of spontaneous bacterial peritonitis is bacterial translocation from intestinal lumen to mesenteric lymph nodes, and from there to the systemic circulation and ascitic fluid. We aimed to study the ascitic microbiota of cirrhotic patients with or without spontaneous bacterial peritonitis. Methods: Both the 16S polymerase chain reaction approach and the whole genome shotgun approach were adopted for the next-generation sequencing technology. We compared the results derived from the two methods. Results: The bacterial culture-negative ascites in cirrhotic patients, which even failed for amplification of 16S ribosomal DNA, were found to contain much less bacterial DNA than the culture-positive ones, indicating that the paucity of bacteria, instead of the difficulty of bacterial culture, was possibly the main reason for negative culture result of the ascites. Escherichia coli was the predominant species in all samples, and the bacteria of low abundance were also identified by the next-generation sequencing technology. Conclusion: Whole genome shotgun-based next-generation sequencing is an appropriate method for depicting the microbiome of ascites or of other specimens with a low abundance of bacterial DNA. Copyright (C) 2014, Taiwan Society of Microbiology. Published by Elsevier Taiwan LLC. All rights reserved.