Biology subjects

Wiles, T. J.

Publications and source records attributed to Wiles, T. J..

8 recordsLinked to original sources

bioRxiv2026

Capsular Polysaccharide Safeguards a Prophage-Bacterium Symbiosis by Preventing Collateral Attack and Promoting Viral Transmission

Many symbioses exist along a continuum from cooperation to conflict. Latent bacterial viruses known as prophages embody this duality. Acting as both partner and predator, they can enhance bacterial fitness while retaining the capacity to kill their hosts through lytic replication. Yet what determines the balance between cooperation and conflict in prophage-bacterium symbioses, and how these associations avoid collapse, remains poorly characterized. To identify mechanisms that stabilize prophag-bacterium partnerships, we used experimental evolution to perturb a natural association through repeated cycles of transmission and reinfection. This perturbation consistently selected mutant hosts lacking capsular polysaccharide production and exposed a hidden conflict that proved detrimental to both partners. During lytic outbreaks, host cells suffered lethal collateral prophage attack while dispersing virions became entrapped on neighboring cells and lysis debris, severely restricting transmission. Genetic and imaging-based studies revealed that capsular polysaccharides suppress these maladaptive interactions by limiting phage readsorption at the cell surface. We term this host-mediated safeguard the Hyperion effect, after the Greek Titan of light. Hyperion interactions enable phages to radiate outward from host populations, thereby averting collateral attack and promoting viral transmission. Our findings demonstrate that conflicts between prophages and their hosts can extend beyond individual cells to whole populations, with consequences that scale to shape patterns of prophage spread and microbial community assembly. More broadly, our work illustrates how mutually beneficial prophage-bacterium interactions can arise not only through cooperation, but also through the suppression of mutually detrimental conflicts.

microbiology↗

bioRxiv2026

Imaging the impact of rotifer consumption on bacterial behaviors in the zebrafish gut

The gut microbiota influence many aspects of their hosts health and physiology including the digestion of food, and food intake in turn influences the composition of the gut microbiome. However, the ways in which food can alter the behavior of intestinal bacteria remain largely unknown, due in large part to the difficulty of assessing behavior in situ. Larval zebrafish provide a model for addressing this gap because of their optical transparency and their ability to be prepared germ-free and then associated with specific microbial species. Using light sheet fluorescence microscopy to visualize bacteria inside the intestines of live zebrafish larvae, we examine the properties of two commensal strains with markedly different physical characteristics. One is a zebrafish-commensal Enterobacter species that forms large aggregates in unfed larvae, and the other is a pathobiont Vibrio species that is motile and planktonic. Following host consumption of rotifers, a common food, Enterobacter clusters disintegrate into motile individuals. Vibrio remains planktonic in fed larvae but decreases the activity of its Type VI Secretion System, leading to a strong decrease in damage to host tissue. Our results reveal that feeding can have major impacts on bacterial behavior that should be considered in models of normal gut microbiome dynamics as well as pathogenesis.

microbiology↗

bioRxiv2024

Phollow: Visualizing Gut Bacteriophage Transmission within Microbial Communities and Living Animals

Bacterial viruses (known as "phages") shape the ecology and evolution of microbial communities, making them promising targets for microbiome engineering. However, knowledge of phage biology is constrained because it remains difficult to study phage transmission dynamics within multi-member communities and living animal hosts. We therefore created "Phollow": a live imaging-based approach for tracking phage replication and spread in situ with single-virion resolution. Combining Phollow with optically transparent zebrafish enabled us to directly visualize phage outbreaks within the vertebrate gut. We observed that virions can be rapidly taken up by intestinal tissues, including by enteroendocrine cells, and quickly disseminate to extraintestinal sites, including the liver and brain. Moreover, antibiotics trigger waves of interbacterial transmission leading to sudden shifts in spatial organization and composition of defined gut communities. Phollow ultimately empowers multiscale investigations connecting phage transmission to transkingdom interactions that have the potential to open new avenues for viral-based microbiome therapies.

microbiology↗

bioRxiv2024

Bacterial Modulation of Intestinal Motility through Macrophage Redistribution

Intestinal microbes, whether resident or transient, influence the physiology of their hosts, altering both the chemical and the physical characteristics of the gut. An example of the latter is the human pathogen Vibrio choleraes ability to induce strong mechanical contractions, discovered in zebrafish. The underlying mechanism has remained unknown, but the phenomenon requires the actin crosslinking domain (ACD) of Vibrios Type VI Secretion System (T6SS), a multicomponent protein syringe that pierces adjacent cells and delivers toxins. By using a zebrafish-native Vibrio and imaging-based assays of host intestinal mechanics and immune responses, we find that macrophages mediate the connection between the T6SS ACD and intestinal activity: ACD-dependent tissue damage activates macrophages and recruits them from their unperturbed positions near enteric neurons lining the midgut, spurring strong gut contractions resembling those resulting from genetic depletion of macrophages. In addition to illuminating host-directed actions of the widespread T6SS protein apparatus, our findings highlight how localized bacteria-induced injury can reshape neuro-immune cellular dynamics to impact whole-organ physiology.

microbiology↗

bioRxiv2019

Swimming motility and chemotaxis control the spatial organization, persistence, and inflammatory activity of a model intestinal pathobiont

Understanding the processes that spatially restrict resident gut bacteria and the mechanisms by which disease-causing pathobionts escape this control will open new avenues for microbiome-based therapies. Using live imaging and genetically engineered bacteria, we discovered that flagella-based swimming motility and chemotaxis enable a model Vibrio pathobiont to govern its own spatial organization within the larval zebrafish gut and to persist in the face of the disruptive forces of intestinal flow. Bacterial mutants lacking motility traits became aggregated and lumenally confined, making them susceptible to periodic expulsion from the host. Consequently, non-motile and non-chemotactic mutants experienced large fluctuations in absolute abundance and impaired interbacterial competition. Further, we found that motile bacterial cells induce expression of the proinflammatory cytokine TNF in gut-associated macrophages and the liver. Using inducible genetic switches, we demonstrate that swimming motility can be manipulated in situ to modulate the spatial organization, persistence, and inflammatory activity of gut bacteria.

microbiology↗

bioRxiv2019

Low-dose antibiotics can collapse gut bacterial populations via a gelation transition

Antibiotics can profoundly alter the intestinal microbiome even at the sublethal concentrations often encountered through environmental contamination. The mechanisms by which low-dose antibiotics induce large yet highly variable changes in gut communities have remained elusive. We therefore investigated the impact of antibiotics on intestinal bacteria using larval zebrafish, whose experimental tractability enables high-resolution in vivo examination of response dynamics. Live imaging revealed that sublethal doses of the common antibiotic ciprofloxacin lead to severe drops in bacterial abundance, coincident with changes in spatial organization that increase susceptibility to intestinal expulsion. Strikingly, our data can be mapped onto a physical model of living gels that links bacterial aggregation and expulsion to nonequilibrium abundance dynamics, providing a framework for predicting the impact of antibiotics on the intestinal microbiome.

microbiology↗

bioRxiv2018

Bacterial cohesion predicts spatial distribution in the larval zebrafish intestine

Are there general biophysical relationships governing the spatial organization of the gut microbiome? Despite growing realization that spatial structure is important for population stability, inter-bacterial competition, and host functions, it is unclear in any animal gut whether such structure is subject to predictive, unifying rules, or if it results from contextual, species-specific behaviors. To explore this, we used light sheet fluorescence microscopy to conduct a high-resolution comparative study of bacterial distribution patterns throughout the entire intestinal volume of live, larval zebrafish. Fluorescently tagged strains of seven bacterial symbionts, representing six different species native to zebrafish, were each separately mono-associated with animals that had been raised initially germ-free. The strains showed large differences in both cohesion--the degree to which they auto-aggregate--and spatial distribution. We uncovered a striking correlation between each strains mean position and its cohesion, whether quantified as the fraction of cells existing as planktonic individuals, the average aggregate size, or the total number of aggregates. Moreover, these correlations held within species as well; aggregates of different sizes localized as predicted from the pan-species observations. Together, our findings indicate that bacteria within the zebrafish intestine are subject to generic processes that organize populations by their cohesive properties. The likely drivers of this relationship, peristaltic fluid flow, tubular anatomy, and bacterial growth and aggregation kinetics, are common throughout animals. We therefore suggest that the framework introduced here, of biophysical links between bacterial cohesion and spatial organization, should be useful for directing explorations in other host-microbe systems, formulating detailed models that can quantitatively map onto experimental data, and developing new tools that manipulate cohesion to engineer microbiome function.

microbiology↗

bioRxiv2017

Modernized tools for streamlined genetic manipulation of wild and diverse symbiotic bacteria

The capacity to associate symbiotic bacteria with vital aspects of plant and animal biology is outpacing our understanding of the mechanisms shaping these interactions. A major barrier to mechanistic studies is the paucity of tools for genetically manipulating wild and diverse bacterial isolates. Solving this problem is crucial to elucidating the cellular and molecular rules that govern symbiotic relationships and ultimately harnessing them for agricultural and biomedical applications. Therefore, we constructed a series of vectors that expedite genetic knock-in and knock-out procedures across a range of bacterial lineages. This was accomplished by developing strategies for domestication-free bacterial conjugation, designing plasmids with customizable features, and streamlining allelic exchange using visual markers of homologous recombination. These tools enabled a comparative study based on live imaging of diverse bacterial symbionts native to the zebrafish intestine, with which we discovered heterogeneous colonization patterns and a striking correlation between bacterial population biogeography and cellular behavior.

genetics↗