Biology subjects

Stacy, A.

Publications and source records attributed to Stacy, A..

6 recordsLinked to original sources

bioRxiv2026

CFTR dysfunction in the intestinal epithelium is sufficient to promote pathogenic expansion of E. coli and enhanced barrier permeability in cystic fibrosis

Changes in the gut microbiome in cystic fibrosis (CF) are well characterized, yet their causes and downstream effects remain largely unknown. Well-documented alterations include reduced overall complexity (i.e. alpha diversity) of the gut microbiota and increased relative abundance of E. coli, which are associated with greater inflammation and shorter stature in infants. Previous results from our laboratory using a germ-free cystic fibrosis transmembrane conductance regulator (Cftr) mutant mouse model (CF mouse) demonstrated that the observed fecal microbiome dysbiosis is driven by mutated Cftr independent of factors such as diet or antibiotic treatment. We expand on these results in this report by using the defined 8-member community Altered Schaedler Flora (ASF) with and without E. coli, to show that E. coli is pathogenic in the context of the CF gut microbiome, resulting in increased intestinal permeability. We also show that Cftr deletion in intestinal epithelial cells alone, using a Villin-Cre targeted model, is sufficient to raise E. coli abundance in the fecal microbiome, increase intestinal permeability, and amplify the number of TH17 cells in the mesenteric lymph nodes. Together, our results demonstrate that the intestinal epithelium plays a dominant role in fecal microbiome alterations in CF and that the resultant dysbiosis contributes to CF pathogenesis.

microbiology↗

bioRxiv2025

Metabolic Strategies That Enable Oral Commensal Persistence in a Lower Airway Environment

Oral microbiota are increasingly implicated in chronic inflammatory diseases beyond the mouth, including bronchiectasis, a condition marked by persistent airway inflammation, mucus accumulation, and limited therapeutic options. Among these microbes, commensal Neisseria, typically considered health-associated in the upper airway, are emerging as opportunistic colonists of the inflamed lower airway. However, mechanisms supporting their persistence in this hostile environment, characterized by antibiotic pressure, nutrient limitation, and interspecies competition, remain poorly defined. Here, we show that the prevalent oral commensal Neisseria mucosa exhibits markedly enhanced antibiotic resistance and anoxic growth in a synthetic medium (SCFM2) that mimics sputum from individuals with bronchiectasis. Using genome-wide transposon sequencing (Tn-seq), we identified key genetic determinants of N. mucosa fitness, including pathways for L-lactate catabolism and pyrimidine biosynthesis. Notably, nitrate respiration was also essential for growth, linking use of this inflammation-associated electron acceptor to fitness under oxygen-limited, sputum-like conditions. Loss of nitrate reductase impaired anoxic L-lactate catabolism, reduced competitive fitness against Pseudomonas aeruginosa, and abrogated growth in SCFM2, as well as human saliva--a relevant, nitrate-rich nutrient source in the oral cavity. Furthermore, chemical inhibition of nitrate reductase using tungstate suppressed growth of both N. mucosa and P. aeruginosa in SCFM2, but not in standard media, revealing a context-specific metabolic vulnerability of nitrate-respiring airway pathogens. These findings suggest that inflammation-compatible traits like nitrate respiration, while supporting oral commensalism, may also drive opportunistic expansion in the inflamed airway. Targeting such pathways could offer a non-antibiotic approach to limit oral bacterial persistence in bronchiectasis and other chronic diseases. ImportanceChronic respiratory diseases such as bronchiectasis and cystic fibrosis are marked by persistent infection and inflammation, with oral bacteria increasingly recognized as active contributors. Among these, Neisseria species, typically considered health-associated commensals, are frequently detected in the lower airway, yet little is known about how they persist in this hostile environment. Here, we identify key metabolic pathways that support the survival of Neisseria mucosa in sputum-like media, including nitrate respiration, a pathway closely linked to inflammation. We also show that N. mucosa exhibits enhanced antibiotic resistance under these conditions, underscoring the need to study microbial physiology in host-relevant contexts. Finally, we demonstrate that a selective inhibitor of nitrate respiration suppresses N. mucosa growth in sputum-like but not standard media, revealing a context-specific vulnerability. These findings suggest that targeting inflammation-compatible metabolic pathways may inform new, non-antibiotic approaches for managing chronic respiratory diseases.

microbiology↗

bioRxiv2025

Sulfide is a keystone metabolite for gut homeostasis and immunity

Hydrogen sulfide is a gaseous, reactive molecule specifically enriched in the gastrointestinal tract. Here, we uncover a non-redundant role for sulfide in the control of both microbial and immune homeostasis of the gut. Notably, depletion of sulfide via both pharmaceutical and dietary interventions led to a profound collapse of CD4 T cells in the ileum of the small intestine lamina propria and significant impact on microbial ecology. As a result, mice with reduced sulfide within the gut were deficient in their ability to mount T cell dependent antibody responses to oral vaccine. Mechanistically, our results support the idea that sulfide could act directly on CD4 T cells via enhanced AP-1 activation, leading to heightened proliferation and cytokine production. This study uncovers sulfides as keystone components in gut ecology and provides mechanistic insight between diet, gut sulfide production and mucosal immunity.

immunology↗

bioRxiv2024

Inverted topologies in sequential fitness landscapes enable evolutionary control

Adaptive populations rarely evolve in a static environment. Therefore, understanding and ultimately controlling the evolution of a population requires consideration of fluctuating selective pressures. The fitness landscape metaphor has long been used as a tool for representing the selective pressures a given environment imposes on a population. Much work has already been done to understand the dynamics of evolution on a single fitness landscape. More recently, evolution on fluctuating or sequentially applied landscapes has come to the fore of evolutionary biology. As more empirical landscapes are described, metrics for describing salient features of paired landscapes will have uses for understanding likely evolutionary dynamics. Currently, Pearson correlation coefficient and collateral sensitivity likelihoods are used to quantify topographical relatedness or dissimilarity of a pair of landscapes. Here, we introduce the edge flip fraction, a new metric for comparing landscapes, which quantifies changes in the directionality of evolution between pairs of fitness landscapes. We demonstrate that the edge flip fraction captures topographical differences in landscapes that traditional metrics may overlook which have important consequences for the trajectories of populations evolving on them. By applying this metric to both empirical and synthetic fitness landscapes, we show that it partially predicts the collateral sensitivity likelihoods and can inform the optimality of drug sequences. We show that optimal drug sequences that keep populations within lower fitness regions require shifts in evolutionary directions, which are quantified by the edge flip fraction. Edge flip fraction complements existing measures and may help researchers understand how populations evolve under changing environmental conditions, and could yield clues in the pursuit of evolutionary control.

evolutionary biology↗

bioRxiv2021

A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae

BackgroundThe human intestinal microbiome is a complex community that contributes to host health and disease. In addition to normal microbiota, pathogens like carbapenem-resistant Enterobacteriaceae may be asymptomatically present. When these bacteria are present at very low levels, they are often undetectable in hospital surveillance cultures, known as occult or subclinical colonization. Through the use of antibiotics, these subclinical pathogens can increase to sufficiently high levels to become detectable, in a process called outgrowth. However, little is known about the interaction between gut microbiota and Enterobacteriaceae during occult colonization and outgrowth. ResultsWe developed a clinically relevant mouse model for studying occult colonization. Conventional wild-type mice without antibiotic pre-treatment were exposed to K. pneumoniae but rapidly tested negative for colonization. This occult colonization was found to perturb the microbiome as detected by both 16S rRNA amplicon and shotgun metagenomic sequencing. Outgrowth of occult K. pneumoniae was induced either by a four-antibiotic cocktail or by individual receipt of ampicillin, vancomycin or azithromycin, which all reduced overall microbial diversity. Notably, vancomycin was shown to trigger K. pneumoniae outgrowth in only a subset of exposed animals (outgrowth-susceptible). To identify factors that underlie outgrowth susceptibility, we analyzed microbiome-encoded gene functions and were able to classify outgrowth-susceptible microbiomes using pathways associated with mRNA stability. Lastly, an evolutionary approach illuminated the importance of xylose metabolism in K. pneumoniae colonization, supporting xylose abundance as a second susceptibility indicator. We showed that our model is generalizable to other pathogens, including carbapenem-resistant Escherichia coli and Enterobacter cloacae. ConclusionsThis study suggests that microbiota mRNA and small-molecule metabolites may be used to predict outgrowth-susceptibility. Our modeling of occult colonization and outgrowth could help the development of strategies to mitigate the risk of subsequent infection and transmission in medical facilities and the wider community.

microbiology↗

bioRxiv2021

Maternal infection promotes offspring tissue-specific immune fitness

The mammalian immune system has evolved in the face of microbial exposure. How maternal infection experienced at distinct developmental stages shapes the offspring immune system remains poorly understood. Here we show that during pregnancy, maternally restricted infection can have permanent and tissue-specific impacts on offspring immunity. Mechanistically, maternal IL-6 produced in response to infection can specifically and directly impose epigenetic changes on fetal intestinal epithelial cells. Such imprinting is associated with long-lasting impacts on intestinal immune homeostasis, characterized by enhanced tonic immunity to the microbiota and heightened Th17 responses within the gut, but not at other barrier sites. Furthermore, the offspring from IL-6-exposed dams developed enhanced protective immunity to gastrointestinal infection. Together, this work demonstrates that maternal infection experienced during pregnancy can be coopted by the fetus to promote long-term tissue-specific fitness. Summary sentenceInfection-induced maternal IL-6 impacts offspring epithelial cells, resulting in heightened immunity to the microbiota and pathogens.

immunology↗