Development and application of bioinformatic tools for analyzing phage replication cycles and host interactions in health and disease

Peng, Xue (2025): Development and application of bioinformatic tools for analyzing phage replication cycles and host interactions in health and disease. Dissertation, LMU München: Fakultät für Biologie

Abstract

The phage-host interaction (PHI) is a dynamic and complex process influenced by multiple factors, such as extensive genetic and morphological diversity among bacteriophages. Prophages, as the direct interaction between phages and their bacterial hosts, can replicate alongside bacteria and facilitate their adaptation to the environment by providing additional functions. This study investigated the phage replication cycles—lytic, lysogenic, and chronic—to uncover their roles in phage therapy and patients with gut disorders. To enhance accuracy in identifying phage replication cycles, particularly the chronic cycle, I developed RepliDec, a computational tool capable of predicting lytic, lysogenic, and chronic lifecycles. RepliDec addresses existing limitations of available computational tools that often misclassify chronic phages within complete phage genomes and the fragmented sequences obtained from sequencing technology. I first assessed RepliDec's performance on complete phage genomes, and it outperformed all other tools, achieving the highest scores across all four metrics: sensitivity (86.76%), accuracy (85.57%), F1 score (87.31%), and Matthews correlation coefficient (MCC) (74.00%). Additionally, RepliDec demonstrated the best performance in all metrics for simulated phage contigs, achieving an accuracy of 77.04% and an F1 score of 70.69%. Furthermore, I developed an integrated pipeline, RepliDec+, designed for use in complex microbial communities, such as the human gut. Subsequently, by employing RepliDec+, I re-evaluated the prevalence of temperate phages in patients diagnosed with inflammatory bowel disease (IBD). I discovered that temperate phages are significantly more prevalent among IBD patients experiencing severe symptoms compared to healthy controls. Furthermore, I investigated the presence of temperate phages in four commercially available phage cocktails. It is crucial to note that temperate phages should be excluded from these cocktails due to their propensity for harboring virulent genes, which may be transmitted to bacteria, potentially leading to adverse outcomes. My analysis indicated the detection of several temperate sequences containing integrases within the PYO cocktails. Moreover, a minimal level of bacterial contamination was noted in this study. The insights gained through RepliDec and Replidec+ advance our understanding of prophages and contribute to microbiome studies as well as the development of bacteriophage-based therapeutic strategies. Identifying phage-host pairs is essential in PHI studies, with experimental methods, such as plaque assays, remaining the gold standard for this recognition. Investigating PHI in the gut environment is challenging due to its complex network, which involves mammalian hosts, bacteria, viruses, and fungi. To address this complexity, I utilized a modified version of viral tagging (VT) and whole genomic sequencing to establish potential phage-bacteria associations from cross-infection samples. I identified 607 viral clusters (VCs) and 208 bacterial taxa, contributing to the determination of the phage-bacteria association network across three disease conditions: ulcerative colitis (UC), early-stage colorectal cancer (CRCE), and advanced-stage colorectal cancer (CRCA). Thousands of phage-bacteria associations were detected within each disease condition. This approach enhances our understanding of gut microbiome dynamics and phage-host interactions in both health and disease. This work advances our understanding of phage-host interactions, particularly in the context of the human gut microbiome. The findings demonstrated the key role of temperate phages with IBD and phage therapy. Furthermore, the use of the modified viral tagging (VT) method to establish phage-bacteria associations paves the way for future studies to explore microbial interaction pairs on a larger scale. Investigating the bacteria and their associated viral communities may provide new insights into the application of phage therapy as a viable treatment option.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Keywords: Bacteriophage, phage replication cycle, temperate phage, phage-host interaction
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
• Fakultäten: Fakultät für Biologie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 7. März 2025
• 1. Bericht­erstatter:in: Lassak, Jürgen