Biology subjects

Ludington, W. B.

Publications and source records attributed to Ludington, W. B..

14 recordsLinked to original sources

bioRxiv2026

Role of Early-Life Microbiome Colonization in Physiological Development of Drosophila melanogaster

The influences of the gut microbiome on animal physiology are well-documented, yet the developmental timing of microbial colonization and its long-term consequences remain poorly understood. In this study, we investigated how the timing of bacterial colonization during development affects transcriptional programming and phenotypic outcomes in adult Drosophila melanogaster reared on a common, rich diet. Using RNA-seq analysis on whole flies colonized either as newly hatched larvae or as newly eclosed adults, we observed minor but distinct transcriptional responses dependent on when flies were colonized. Both embryonic and adult colonization were associated with ~ 25 to ~ 200 differentially expressed genes compared to axenic controls, with the majority upregulated and enriched for immune-response genes, suggesting that colonization establishes a broader immune competence. However, only 10 genes showed persistent differential expression that was not normalized by introducing bacteria to adult axenic flies, including mitochondrial genes, the adipokinetic hormone (Adh), and a putative secreted neuropeptide. Overall, these findings suggest that Drosophila development on a rich diet is largely robust to the timing of bacterial colonization but that certain metabolic effects may occur.

developmental biology↗

bioRxiv2025

Gut microbe-derived lactic acid optimizes host energy metabolism during starvation

Gut microbes convert dietary compounds into an array of metabolites that can directly provide energy to their host and indirectly impact host metabolism as systemic endocrine signals. Here, we show that gut microbe-derived metabolites can extend Drosophila melanogaster survival during starvation, despite minimal alteration of dietary energy intake. Combining survival assays with mathematical modeling and untargeted metabolomics, we identify a single, dominant mediator of starvation resilience: lactic acid produced by the commensal bacterium Lactiplantibacillus plantarum. We discover that the basis of starvation resilience is not catabolism of lactic acid using lactate dehydrogenase, but rather increased dietary energy yield through lactic acid-driven promotion of oxidative phosphorylation. Our findings emphasize the role of the microbiome as a source of endocrine cues coordinating host metabolism and underscore the potential of microbiome-derived metabolites as therapeutic molecules for manipulating metabolic health and preventing disease.

physiology↗

bioRxiv2025

Commensal acidification of specific gut regions produces a protective priority effect against enteropathogenic bacterial infection

The commensal microbiome has been shown to protect against newly introduced enteric pathogens in multiple host species, a phenomenon known as a priority effect. Multiple mechanisms can contribute to this protective priority effect, including antimicrobial compounds, nutrient competition, and pH changes. In Drosophila melanogaster, Lactiplantibacillus plantarum has been shown to protect against enteric pathogens. However, the strains of L. plantarum studied were derived from laboratory flies or non-fly environments and have been found to be unstable colonizers of the fly gut that mainly reside on the food. To study the priority effect using a naturally occurring microbial relationship, we isolated a wild-fly derived strain of L. plantarum that stably colonizes the fly gut in conjunction with a common enteric pathogen, Serratia marcescens. Flies stably associated with the L. plantarum strain were more resilient to oral Serratia marcescens infection as seen by longer lifespan and lower S. marcescens load in the gut. Through in vitro experiments, we found that L. plantarum inhibits S. marcescens growth due to acidification. We used gut imaging with pH-indicator dyes to show that L. plantarum reduces the gut pH to levels that restrict S. marcescens growth in vivo. In flies colonized with L. plantarum prior to S. marcescens infection, L. plantarum and S. marcescens are spatially segregated in the gut and S. marcescens is less abundant where L. plantarum heavily colonizes, indicating that acidification of specific gut regions is a mechanism of a protective priority effect.

microbiology↗

bioRxiv2024

PeakClimber: A software tool for analyzing biological HPLC data using the exponential Gaussian function

High-performance liquid chromatography (HPLC) is a common medium-throughput technique to quantify the components of often complex mixtures like those typically obtained from biological tissue extracts. However, analysis of HPLC data from complex multianalyte samples is hampered by a lack of tools to accurately determine the precise analyte quantities on a level of precision equivalent to mass-spectrometry approaches. To address this problem, we developed a tool we call PeakClimber, that uses a sum of exponential Gaussian functions to accurately deconvolve overlapping, multianalyte peaks in HPLC traces. Here we analytically show that HPLC peaks are well-fit by an exponential Gaussian function, that PeakClimber more accurately quantifies known peak areas than standard industry software for both HPLC and mass spectrometry applications, and that PeakClimber accurately quantifies differences in triglyceride abundances between colonized and germ-free fruit flies.

bioengineering↗

bioRxiv2024

A conserved genetic basis for commensal-host specificity through live imaging of colonization dynamics

Animals throughout the metazoa selectively acquire specific symbiotic gut bacteria from their environment that aid host fitness. Current models of colonization suggest these bacteria use weakly specific receptors to stick to host tissues and that colonization results when they stick in a region of the host gut that overlaps with their nutritional niche. An alternative model is that unique receptor-ligand binding interactions provide specificity for target niches. Here we use live imaging of individual symbiotic bacterial cells colonizing the gut of living Drosophila melanogaster to show that Lactiplantibacillus plantarum specifically recognizes a distinct physical niche in the host gut. We find that recognition is controlled by a colonization island that is widely conserved in commensals and pathogens from the Lactobacillales to the Clostridia. Our findings indicate a genetic mechanism of host specificity that is broadly conserved. One-Sentence SummaryHost-symbiont specificity is encoded by a conserved colonization island that provides molecular precision to host niche access.

microbiology↗

bioRxiv2022

Why resource dynamics matter in the optimization of microbial communities

The impact of resource supply on microbial community dynamics is rarely treated explicitly in research into the control and optimization of natural and synthetic microbial communities. Using simulations, we show that compositional overlap between microbial communities decays rapidly with a change in the frequency of resource pulsing, particularly in the presence of a metabolic trade-off in resource affinity and maximum growth rate. We conclude that resource supply dynamics should be considered both a constraint and a tuning mechanism in microbial community optimization.

ecology↗

bioRxiv2021

A gut commensal niche regulates stable association of a multispecies microbiota

The intestines of animals are typically colonized by a complex, relatively stable microbiota that influences health and fitness, but the underlying mechanisms of colonization remain poorly understood. As a typical animal, the fruit fly, Drosophila melanogaster, is associated with a consistent set of commensal bacterial species, yet the reason for this consistency is unknown. Here, we use gnotobiotic flies, microscopy, and microbial pulse-chase protocols to show that a commensal niche exists within the proventriculus region of the Drosophila foregut that selectively binds bacteria with exquisite strain-level specificity. Primary colonizers saturate the niche and exclude secondary colonizers of the same strain, but initial colonization by Lactobacillus physically remodels the niche to favor secondary colonization by Acetobacter. Our results provide a mechanistic framework for understanding the establishment and stability of an intestinal microbiome. One-Sentence SummaryA strain-specific set of bacteria inhabits a defined spatial region of the Drosophila gut that forms a commensal niche.

microbiology↗

bioRxiv2021

High dimensional geometry of fitness landscapes identifies master regulators of evolution and the microbiome

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Yet biological interactions between genes (1, 2), species (3-6), and different environmental contexts (7-9) change the individual effects due to non-additive interactions, known as epistasis. In the fitness landscape concept, each gene/organism/environment is modeled as a separate biological dimension (10), yielding a high dimensional landscape, with epistasis adding local peaks and valleys to the landscape. Massive efforts have defined dense epistasis networks on a genome-wide scale (2), but these have mostly been limited to pairwise, or two-dimensional, interactions (11). Here we develop a new mathematical formalism that allows us to quantify interactions at high dimensionality in genetics and the microbiome. We then generate and also reanalyze combinatorically complete datasets (two genetic, two microbiome). In higher dimensions, we find that key genes (e.g. pykF) and species (e.g. Lactobacillus plantarum) distort the fitness landscape, changing the interactions for many other genes/species. These distortions can fracture a "smooth" landscape with one optimal fitness peak into a landscape with many local optima, regulating evolutionary or ecological diversification (12), which may explain how a probiotic bacterium can stabilize the gut microbiome.

systems biology↗

bioRxiv2021

Stochastic microbiome assembly depends on context

Observational studies reveal substantial variability in microbiome composition across individuals. While some of this variability can be explained by external factors like environmental, dietary, and genetic differences between individuals, in this paper we show that for the model organism Drosophila melanogaster the process of microbiome assembly is inherently stochastic and contributes a baseline level of microbiome variability even among organisms that are identically reared, housed, and fed. In germ-free flies fed known combinations of bacterial species, we find that some species colonize more frequently than others even when fed at the same high concentration. We develop a new ecological technique that infers the presence of interactions between bacterial species based on their colonization odds in different contexts, requiring only presence/absence data from two-species experiments. We use a progressive sequence of probabilistic models, in which the colonization of each bacterial species is treated as an independent stochastic process, to reproduce the empirical distributions of colonization outcomes across experiments. We find that incorporating context-dependent interactions substantially improves the performance of the models. Stochastic, context-dependent microbiome assembly underlies clinical therapies like fecal microbiota transplantation and probiotic administration, and should inform the design of synthetic fecal transplants and dosing regimes. Significance StatementIndividuals are constantly exposed to microbial organisms that may or may not colonize their gut microbiome, and newborn individuals assemble their microbiomes through a number of these acquisition events. Since microbiome composition has been shown to influence host physiology, a mechanistic understanding of community assembly has potentially therapeutic applications. In this paper we study microbiome acquisition in a highly-controlled setting using germ-free fruit flies inoculated with specific bacterial species at known abundances. Our approach revealed that acquisition events are stochastic, and the colonization odds of different species in different contexts encode ecological information about interactions. These findings have consequences for microbiome-based therapies like fecal microbiota transplantation that attempt to modify a persons gut microbiome by deliberately introducing foreign microbes.

microbiology↗

bioRxiv2021

A chemically-defined growth medium to support Lactobacillus-Acetobacter community analysis

Lactobacilli and acetobacters are commercially important bacteria that often form communities in natural fermentations, including food preparations, spoilage, and in the digestive tract of Drosophila melanogaster fruit flies. Communities of these bacteria are widespread and prolific, despite numerous strain-specific auxotrophies, suggesting they have evolved nutrient interdependencies that regulate their growths. The use of a chemically-defined medium (CDM) supporting the growth of both groups of bacteria would greatly facilitate identification of the precise metabolic interactions between these two groups of bacteria. While numerous such media have been developed that support specific strains of lactobacilli and acetobacters, there has not been a medium formulated to support both genera. We developed such a medium, based on a previous Lactobacillus CDM, by modifying the nutrient abundances to improve growth of both groups of bacteria. We further simplified the medium by substituting casamino acids for individual amino acids and the standard Wolfes vitamins and mineral stocks for individual vitamins and minerals, resulting in a reduction from 40 to 8 stock solutions. The new CDM and variations of it support robust growth of lactobacilli and acetobacters. We provide the composition and an example of its use to measure nutritional interactions.

microbiology↗

bioRxiv2019

Bellymount enables longitudinal, intravital imaging of abdominal organs and the gut microbiota in adult Drosophila

Cell- and tissue-level processes often occur across days or weeks, but few imaging methods can capture such long timescales. Here we describe Bellymount, a simple, non-invasive method for longitudinal imaging of the Drosophila abdomen at sub-cellular resolution. Bellymounted flies remain live and intact, so the same individual can be imaged serially to yield vivid time series of multi-day processes. This feature opens the door to longitudinal studies of Drosophila internal organs in their native context. Exploiting Bellymounts capabilities, we track intestinal stem cell lineages and gut microbial colonization in single flies, revealing spatiotemporal dynamics undetectable by previously available methods.

developmental biology↗

bioRxiv2019

Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota

Despite decades of investigation into how antibiotics affect isolated bacteria, it remains highly challenging to predict consequences for communities in complex environments such as the human intestine. Interspecies interactions can impact antibiotic activity through alterations to the extracellular environment that change bacterial physiology. By measuring key metabolites and environmental pH, we determined that metabolic cross-feeding among members of the fruit fly gut microbiota drives changes in antibiotic sensitivity in vitro. Co-culturing of Lactobacillus plantarum with Acetobacter species induced tolerance to rifampin. Mechanistically, we found that acetobacters counter the acidification driven by L. plantarum production of lactate, and that pH shifts during stationary phase were sufficient to drive rifampin tolerance in L. plantarum monocultures. The key Lactobacillus physiological parameter related to tolerance was a reduction in lag time exiting stationary phase, opposite to a previously identified mode of tolerance to ampicillin in E. coli. Lactobacillus tolerance to erythromycin also depended on growth status and pH, suggesting that our findings generalize to other antibiotics. Finally, tolerance of L. plantarum to rifampin varied spatially across the fruit fly gut. This mechanistic understanding of the coupling among interspecies interactions, environmental pH, and antibiotic tolerance enables future predictions of growth and the effects of antibiotics in more complex communities and within hosts.

microbiology↗

bioRxiv2017

High-dimensional microbiome interactions shape host fitness

Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host in turn shapes the gut microbiome. Microbiomes co-evolve with their hosts and have been implicated in host speciation. However, it is unclear to what extent individual species versus community interactions within the microbiome are linked to host fitness. Here we combinatorially dissect the natural microbiome of Drosophila melanogaster and reveal that interactions between bacteria shape host fitness through life history tradeoffs. We find that the same microbial interactions that shape host fitness also shape microbiome abundances, suggesting a potential evolutionary mechanism by which microbiome communities (rather than just individual species) may be intertwined in co-selection with their hosts. Empirically, we made germ-free flies colonized with each possible combination of the five core species of fly gut bacteria. We measured the resulting bacterial community abundances and fly fitness traits including development, reproduction, and lifespan. The fly gut promoted bacterial diversity, which in turn accelerated development, reproduction, and aging: flies that reproduced more died sooner. From these measurements we calculated the impact of bacterial interactions on fly fitness by adapting the mathematics of genetic epistasis to the microbiome. Host physiology phenotypes were highly dependent on interactions between bacterial species. Higher-order interactions (involving 3, 4, and 5 species) were widely prevalent and impacted both host physiology and the maintenance of gut diversity. The parallel impacts of bacterial interactions on the microbiome and on host fitness suggest that microbiome interactions may be key drivers of evolution.\n\nSignificanceAll animals have associated microbial communities called microbiomes that can influence the physiology and fitness of their host. It is unclear to what extent individual microbial species versus ecology of the microbiome influences fitness of the host. Here we mapped all the possible interactions between individual species of bacteria with each other and with the hosts physiology. Our approach revealed that the same bacterial interactions that shape microbiome abundances also shape host fitness traits. This relationship provides a feedback that may favor the emergence of co-evolving microbiome-host units.

microbiology↗

bioRxiv2017

Microbiome-by-ethanol interactions impact Drosophila melanogaster fitness and physiology

Ethanol is one of the worlds most abused drugs yet the impacts of chronic ethanol consumption are debated. Ethanol is a prevalent component in the diets of diverse animals and can act as a nutritional source, behavior modulator, and a toxin. The source of ethanol is microbes, which can both produce and degrade ethanol, and the gut microbiome has been associated with differential health outcomes in chronic alcoholism. To disentangle the various and potentially interacting roles of bacteria and ethanol on host health, we developed a model for chronic ethanol ingestion in the adult fruit fly, Drosophila melanogaster, which naturally consumes a diet between 0 and 5% ethanol. We took advantage of the tractability of the fly microbiome, which can be experimentally removed to separate the direct and indirect effects of commensal microbes. We found that moderate to heavy ethanol ingestion decreased lifespan and reproduction, without causing inebriation. These effects were more pronounced in flies lacking a microbiome, but could not be explained by simple bacterial degradation of ethanol. However, moderate ethanol ingestion increased reproduction in bacterially-colonized flies, relative to bacteria-free flies. Ethanol decreased intestinal stem cell turnover in bacterially-colonized flies and decreased intestinal barrier failure and increased fat content in all flies, regardless of microbiome status. Analysis of host gene expression finds that ethanol triggers the innate immune response, but only in flies colonized with bacteria. Taken together we show that, chronic ethanol ingestion negatively impacts fly health in a microbiome-dependent manner.

microbiology↗