Metagenomic sequencing of gut microbiome and antibiotic resistance genes after antibiotics therapy for Helicobacter pylori

Abstract

The gut microbiome plays a pivotal role in maintaining homeostasis in the human body. This study investigated the impacts of different Helicobacter pylori (H. pylori) eradication therapies on the gut microbial composition, the gut resistome profile, the longitudinal dynamics of gut virome biodiversity and the virus-bacteria interactions after antibiotic treatment, as well as revealing the dynamic changes in the gut fungal community and the cross-kingdom correlations between fungi and bacteria in H. pylori-infected patients. Using bioinformatics and whole-genome shotgun sequencing approaches, I conducted a comprehensive study of the gut microbiome and resistome in H. pylori-positive subjects who had received eradication treatments. The gut microbiota and resistome were extensively investigated at different time points, including baseline, 4-8 weeks (average 6 weeks after the eradication therapy), and 6 months. Metagenomic analysis of the microbiota communities showed a transient decreased in alpha diversity and taxonomy abundance at 6 weeks, which was partially restored at 6 months. Treatment-specific alteration of the bacteria structures was observed at 6 weeks. Besides the alterations in the gut microbiota, the gut resistome also displayed antibiotic-specific adaptation, which was characterized by increased macrolide resistance after clarithromycin-containing therapy and enriched Escherichia coli-associated multidrug resistance after levofloxacin treatment. The biosynthesis-associated functional pathways were also significantly altered after the therapy. Further evaluation of the gut virome suggested the presence of a set of core viruses in the human gut, which is mainly composed of bacteriophages. There was significantly decreased virome alpha diversity and distinct virome structures at 6 weeks and at 6 months, suggesting the virome community is less resilient than the microbiota community that showed a transient decrease at 6 weeks and restoration at 6 months. Inter-kingdom correlation analysis indicated there was sophisticated virus-bacteria dynamics after the antibiotic-based eradication therapy, including predator-prey dynamics and co-evolution dynamics. Moreover, the results of host prediction revealed the bacterial host bacteriophage is highly individual-specific and mainly belongs to Proteobacteria and Firmicutes phyla. Lastly, one ongoing project included in my thesis involved the metagenomic study of gut fungi and bacteria profiles after H. pylori eradication therapy. The findings suggest that antibiotic therapy decreases the biodiversity of fungi and bacteria, triggering a stronger intra-kingdom integration of fungi at 6 months. Cross-kingdom correlation analysis showed there were strong and positive correlations in the diversity between fungi and bacteria. Moreover, antibiotic therapies induced constantly changing fungi-bacteria interactions.

Overall, this thesis presents the large-scale metagenomic profiling of the gut resistome, microbiota, viruses, fungi, and inter- and intra-kingdom interactions after H. pylori eradication therapy, which can facilitate future evaluation of the broader impacts of antibiotic-based eradication therapy. (An abstract of 426 words)