Biology subjects

Schlomann, B. H.

Publications and source records attributed to Schlomann, B. H..

8 recordsLinked to original sources

bioRxiv2024

Spatial microenvironments tune immune response dynamics in the Drosophila larval fat body

Immune responses in tissues display complex spatial patterns of gene expression that are linked to disease outcomes. However, the mechanisms that generate these patterns--including the relative roles of noisy gene expression dynamics, microbial transport, and tissue anatomy-- are poorly understood. As a tractable model of spatial immune responses, we investigated heterogeneous expression of antimicrobial peptides in the larval fly fat body, an organ functionally analogous to the liver. Using live light sheet fluorescence microscopy, we discovered that individual fat body cells express antimicrobial peptides at approximately constant rates following infection, but that the average rate varies along the anterior-posterior axis of the fat body, with rapid expression in the anterior and posterior lobes. Overexpression of immune signaling components and analysis of spatial transcriptomes revealed that these tissue microenvironments are predefined independently of infection, with the rate-limiting step of antimicrobial peptide induction downstream of peptidoglycan sensing. The locations of these microevironments correlate with heartbeat-dependent fluid flow in a manner resembling the strategic positioning of immune cells in the liver, gut, and lymph nodes of mammals. We speculate that this spatial compartmentalization helps the fat body efficiently perform its diverse metabolic, enzymatic, and immunological functions. Author SummaryRecent sequencing and imaging technologies have revealed that immune responses in our organs are not spatially uniform, but occur in complex patterns in which clusters of nearby cells are strongly active. There is increasing evidence that these spatial interactions are important for controlling disease outcomes. However, little is known about the dynamics of how these spatial patterns form: are they created through randomness, are they shaped by external signals, such as pathogen localization, or are they predetermined, representing a fine-grained tissue anatomy? While it is practically infeasible to directly observe these types of cellular dynamics in humans or even mice, small, transparent organisms like fruit fly larvae offer a literal window into the inner workings of immune responses. We used a combined imaging and genetics approach to study heterogeneous spatial patterns of antimicrobial peptide production in the fruit fly equivalent of the liver. We discovered that these spatial patterns were in fact predetermined and represent previously unknown immune microenvironments within this important tissue that correlate with areas of fast blood flow. Since innate immune signaling in highly conserved, this spatial logic may be a general feature of immunological tissues that is relevant to other animals, including humans.

immunology↗

bioRxiv2024

Single-cell transcriptional dynamics in a living vertebrate

The ability to quantify transcriptional dynamics in individual cells via live imaging has revolutionized our understanding of gene regulation. However, such measurements are lacking in the context of vertebrate embryos. We addressed this deficit by applying MS2-MCP mRNA labeling to the quantification of transcription in zebrafish, a model vertebrate. We developed a platform of transgenic organisms, light sheet fluorescence microscopy, and optimized image analysis that enables visualization and quantification of MS2 reporters. With these tools, we obtained single-cell, real-time measurements of transcriptional dynamics of the segmentation clock. Our measurements challenge the traditional view of smooth clock oscillations and instead suggest a model of discrete transcriptional bursts that are organized in space and time. Together, these results highlight how measuring single-cell transcriptional activity in the context of vertebrate organisms can reveal unexpected features of gene regulation and how this data can fuel the dialogue between theory and experiment.

developmental biology↗

bioRxiv2021

Gut bacterial aggregates as living gels

The spatial organization of gut microbiota influences both microbial abundances and host-microbe interactions, but the underlying rules relating bacterial dynamics to large-scale structure remain unclear. To this end we studied experimentally and theoretically the formation of three-dimensional bacterial clusters, a key parameter controlling susceptibility to intestinal transport and access to the epithelium. Inspired by models of structure formation in soft materials, we sought to understand how the distribution of gut bacterial cluster sizes emerges from bacterial-scale kinetics. Analyzing imaging-derived data on cluster sizes for eight different bacterial strains in the larval zebrafish gut, we find a common family of size distributions that decay approximately as power laws with exponents close to -2, becoming shallower for large clusters in a strain-dependent manner. We show that this type of distribution arises naturally from a Yule-Simons-type process in which bacteria grow within clusters and can escape from them, coupled to an aggregation process that tends to condense the system toward a single massive cluster, reminiscent of gel formation. Together, these results point to the existence of general, biophysical principles governing the spatial organization of the gut microbiome that may be useful for inferring fast-timescale dynamics that are experimentally inaccessible.

microbiology↗

bioRxiv2020

Phenotypic parallelism during experimental adaptation of a free-living bacterium to the zebrafish gut

Despite the fact that animals encounter a plethora of bacterial species throughout their lives, only a subset are capable of colonizing vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. However, it is still unknown how bacteria evolve symbioses with animal hosts, and this process is central to both the assembly and function of gut bacterial communities. Therefore, we used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host. We serially passaged replicate populations of Shewanella oneidensis, through the digestive tracts of larval zebrafish (Danio rerio). After only 20 passages, representing approximately 200 bacterial generations, isolates from replicate evolved populations displayed an improved ability to colonize larval zebrafish digestive tracts during competition against their unpassaged ancestor. Upon sequencing the genomes of these evolved isolates, we discovered that the two isolates with the highest mean competitive fitness accumulated unique sets of mutations. We characterized the swimming motility and aggregation behavior of these isolates, as these phenotypes have previously been shown to alter host-microbe interactions. Despite exhibiting different biofilm characteristics, both isolates evolved augmented swimming motility. These enhancements are consistent with expectations based on the behavior of a closely related Shewanella strain previously isolated from the zebrafish digestive tract and suggest that our evolved isolates are pursuing a convergent adaptive trajectory with this zebrafish isolate. In addition, parallel enhancements in swimming motility among isolates from independently adapted populations implicates increased dispersal as an important factor in facilitating the onset of host association. Our results demonstrate that free-living bacteria can rapidly improve their associations with vertebrate hosts.

evolutionary biology↗

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↗