Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori

Abstract

<p>Transient gut microbiota alterations have been reported after antibiotic therapy for <em>Helicobacter pylori</em>. However, alteration in the gut virome after <em>H. pylori</em> eradication remains uncertain. Here, we apply metagenomic sequencing to fecal samples of 44 <em>H. pylori</em>-infected patients at baseline, 6-week (<em>N</em> = 44), and 6-month (<em>N</em> = 33) after treatment. Following <em>H. pylori</em> eradication, we discover contraction of the gut virome diversity, separation of virome community with increased community difference, and shifting towards a higher proportion of core virus. While the gut microbiota is altered at 6-week and restored at 6-month, the virome community shows contraction till 6-month after the treatment with enhanced phage-bacteria interactions at 6-week. Multiple courses of antibiotic treatments further lead to lower virus community diversity when compared with treatment naive patients. Our results demonstrate that <em>H. pylori</em> eradication therapies not only result in transient alteration in gut microbiota but also significantly alter the previously less known gut virome community.</p>