Author: Bhavya Papudeshi
Papudeshi, Bhavya, 2025 Decoding microbe host interactions , Flinders University, College of Science and Engineering
Terms of Use: This electronic version is (or will be) made publicly available by Flinders University in accordance with its open access policy for student theses. Copyright in this thesis remains with the author. You may use this material for uses permitted under the Copyright Act 1968. If you are the owner of any included third party copyright material and/or you believe that any material has been made available without permission of the copyright owner please contact copyright@flinders.edu.au with the details.
Microbial ecosystems are intricate networks of bacteria, viruses, fungi, and archaea that influence ecosystem health. However, uncovering these interactions remains challenging due to the limited genomic frameworks and the complexity of community interactions within microbial ecosystems. In this thesis, I focus on deciphering phage-bacteria and bacteria-host interactions. I identify the genetic factors using genome-resolved bioinformatic approaches.
While bacterial genomics has made significant strides, phage biology remains relatively underexplored, especially regarding host interactions. As interest in phage therapy to combat antimicrobial-resistant infections grows, the need for standardised frameworks to name, classify, and annotate phage genomes becomes critical. To address this, I begin with a review of phage biology and bioinformatic methods used to sequence and characterise phage genomes. Building on this review, I introduce Sphae, an automated, reproducible bioinformatics toolkit that can seamlessly assemble, annotate, and classify phages. Sphae incorporates advanced tools to rapidly detect genomic features, such as integrases, toxins, and antimicrobial resistance genes —elements that may disqualify phage candidates from therapeutic applications. While Sphae’s primary use case lies in the clinical evaluation of phages, it can also broadly characterise phages in other contexts and inform the current gaps in phage biology.
Building on this foundation, I characterised novel phages and explored their interactions with bacterial hosts, illustrating the kinds of questions Sphae is designed to facilitate. I focused on Crassvirales phages that infect Bacteroides, both key players in the human gut microbiome. In this work, I characterise 14 novel Crassvirales isolates, which were assigned to three genera across two families, despite infecting the same host, Bacteroides cellulosilyticus. Comparative genomics revealed a conserved tail spike protein across these phages, suggesting a role in host recognition. Using structural modelling and protein-protein interaction predictions, we demonstrate that this protein may interact with TonB-dependent receptors, suggesting convergent host attachment. These findings advance our understanding of phage-mediated modulation of gut microbiomes and highlight the potential of such phages in microbiome-based interventions.
Recognising that microbial ecosystems extend beyond simple phage-bacteria dynamics, I explored more complex interactions by investigating the tripartite relationship between the symbiont bacterium Xenorhabdus bovienii with its nematode host, Steinernema, and their joint parasitism of insect hosts. Analyses of 42 X. bovienii genomes revealed clustering not only by host species but also geography, underscoring the influence of ecological niches on bacterial population structure. Further, signatures of selective sweeps in genes associated with colonisation and interbacterial competition highlight host-specific and spatial drivers of microbial evolution in multipartite systems.
Together, this work elucidates how selective pressures shape microbial interactions across diverse contexts—from phage-bacteria dynamics in the gut to bacterial-eukaryote mutualisms. Through genome-resolved pipelines and structural modelling, this thesis provides both conceptual frameworks and tools to decode microbial interactions. These approaches advance our understanding of microbial community assembly and stability, while also informing future efforts to manipulate microbes or entire communities for therapeutic benefit.
Keywords: Phage-bacteria interactions; Phage genomics; Bioinformatics workflows; Host specificity; Gut microbiome; Crassvirales; Comparative genomics; Structural modelling; Microbial evolution; symbiosis
Subject: Biotechnology thesis
Thesis type: Doctor of Philosophy
Completed: 2025
School: College of Science and Engineering
Supervisor: Prof Robert Edwards