Addressing the impact of phages on gut microbial ecology and functions using a synthetic bacterial community

Strempel, Alexandra von (2024): Addressing the impact of phages on gut microbial ecology and functions using a synthetic bacterial community. Dissertation, LMU München: Medizinische Fakultät

Abstract

The human gut is a complex ecosystem, harboring eukaryotic cells, bacteria and viruses. Alterations of the intestinal microbial communities are associated with an increasing number of human diseases. On the other hand, the gut microbiota protects the host against a variety of major human gastrointestinal pathogens. Bacteriophages (phages), viruses that infect bacteria, are important effectors and indicators of human health and disease by managing specific bacterial population structures and by interacting with the mucosal immune system. They are ubiquitous in nature and frequently ingested via food and drinking water. Moreover, bacteriophages are an attractive tool for microbiome engineering due to their specificity and the lack of known serious adverse effects on the host. However, most of our knowledge on phages is based on metagenomic studies and the functional role of virulent phages within the gastrointestinal microbiome remain poorly understood. To obtain functional insights on the effect of phages in the gastrointestinal microbiome and its function in health and disease, I established a model to investigate the interaction of bacteriophages and cognate host bacteria in the mammalian gut. Therefore, I isolated specific phages targeting members of a synthetic bacterial consortium, the Oligo-MM14, which consists of 14 well-characterized bacterial strains that form a stable community in gnotobiotic mice and provide colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm). First, I characterized the isolated phages in vitro with respect to plaque morphologies, genomic features, lysis behaviors and host ranges. Further, I developed methods for specific absolute quantification via qPCR for the single phages, which allowed me to track the abundance of phages and host bacteria in the OMM community in vitro and in vivo, revealing that the phages amplify at varying degrees while not disturbing the overall community composition. Furthermore, I showed, that phages lead to initial depletion of the target population in the mouse gut and thereafter coexist with the bacteria for up to a week after phage challenge. Moreover, the addition of phages targeting Escherichia coli and Enterococcus faecalis, two bacteria previously identified to mediate colonization resistance, led to a significant decrease of colonization resistance against S. Tm. This demonstrates that phages can affect microbial community functions. Infection susceptibility to S. Tm was markedly increased at an early time point after challenge with both phage cocktails but surprisingly, OMM14 mice were also susceptible to S. Tm infection 7 days after a single phage inoculation, when the targeted bacterial populations were back to pre-phage administration density. Since the abundance of the other bacteria in the gut is not affected by administration of the phage cocktails, this effect is specifically attributed to the impact of the phages on their bacterial hosts. This suggests, that phages targeting protective members of the microbiota may in general increase the risk for S. Tm infection. In summary, this work yields insights into phage-bacterial interactions in the gut and the effect of phages on fundamental microbiome functions, which will be important for evaluating the future use of phages for targeted microbiome manipulation.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Keywords: Phages, Microbiome, OMM12, Gut, Bacteria, E.coli, Salmonella
• Themengebiete: 600 Technik, Medizin, angewandte Wissenschaften ; 600 Technik, Medizin, angewandte Wissenschaften > 610 Medizin und Gesundheit
• Fakultäten: Medizinische Fakultät
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 6. August 2024
• 1. Bericht­erstatter:in: Stecher-Letsch, Barbara