Biology subjects

Green, L. N.

Publications and source records attributed to Green, L. N..

6 recordsLinked to original sources

bioRxiv2025

Identifying a Vaginal Microbiome-Derived Selective Antibiotic Metabolite via Microbiome Pharmacology Analysis

The vaginal microbiome plays a critical role in maintaining immune and epithelial homeostasis in the female reproductive tract. Bacterial Vaginosis (BV) is deleterious to female health, causing the loss of beneficial Lactobacillus species, overgrowth of anaerobic taxa, changes in vaginal pH, breakdown of protective mucins and epithelial barriers, and activation of the immune system. Treatment with gel-based antibiotics (Metronidazole or Clindamycin) resolves BV for 85% of patients, but 50% of those cases recur, indicating a need to identify strategies for overcoming antibiotic resistance and achieving a more durable response. Here, we developed a systems biology approach termed Microbiome Pharmacology Analysis to characterize the antibiotic potential of vaginal microbes, their metabolites and functions, via computational fusion of human cohort multi-omics and post-drug perturbation transcriptomic profiles. We focused on Clindamycin and Metronidazole as candidate drugs and screened 780 vaginal microbiome-drug mimicry candidates to identify candidate taxa and metabolites with antibiotic potential. We demonstrate experimentally that Lactobacillus crispatus-derived Hydroxyisocaproate (HICA) selectively kills Gardnerella vaginalis and that HICA enhances epithelial barrier integrity in a human vagina-on-a-chip system. Our work demonstrates the first use of Pharmacobiome Analysis, for discovering novel, selective antibiotic metabolites for BV with implications for charting the full pharmacologic potential of the vaginal microbiome.

microbiology↗

bioRxiv2025

Comparative Metabolomic Analysis of Vaginal Microbiota in Planktonic and Biofilm States Unveils Species-Specific Metabolic Signatures

Bacterial vaginosis (BV) affects approximately 29% of women in the U.S., with higher rates among certain demographics and up to 50% recurrence within a year. Besides complications like increased risk of sexually transmitted infections (STIs), pregnancy-related issues, it can negatively impact psychological well-being, leading to discomfort and reduced quality of life. While previous studies have provided insights into the overall metabolomic profile of healthy and diseased vaginal environments, the elucidation of individual microbial metabolite signatures remains limited. Furthermore, given that biofilms exhibit distinct metabolic requirements compared to planktonic cultures, a differential analysis of metabolites in both growth conditions could reveal potential therapeutic targets. This study presents a comprehensive metabolomic analysis and comparison of significant vaginal microbes including Lactobacillus crispatus, Gardenerella vaginalis, and Lactobacillus iners in both planktonic and biofilm growth conditions. Our analysis revealed distinct metabolite production and consumption patterns among different microbes and growth modes. In biofilm cultures, metabolite consumption is influenced by nutrient availability, which in turn regulates the profile of produced metabolites. G. vaginalis demonstrated the ability to form biofilms in various media types. Limited shared metabolic pathways in both biofilm types of G. vaginalis, highlights the unique metabolic processes involved in their formation. Despite L. crispatus suspension and biofilm cultures sharing 142 consumed and 104 produced metabolites, the biofilm culture demonstrated a remarkable metabolic shift. While comparing suspension and biofilm cultures of L. crispatus, L. iners, and G. vaginalis, we found convergence in nutrient utilization, but divergence in metabolic outputs reflecting growth-specific adaptations and underscore the importance of considering the state of existence when studying the vaginal microbiome. This study provides valuable insights into the growth mode-specific metabolic requirements of key vaginal microbes. The findings underscore the potential for leveraging metabolite-mediated microbial cross-talk as a novel therapeutic approach against BV. This avenue of research warrants further investigation, as it could lead to the development of targeted interventions that modulate the vaginal microbiome through metabolic manipulation, potentially offering more effective and personalized treatments for BV.

microbiology↗

bioRxiv2024

Computational Microbiome Pharmacology Analysis Elucidates the Anti-Cancer Potential of Vaginal Microbes and Metabolites

The vaginal microbiomes role in risk, progression, and treatment of female cancers has been widely explored. Yet, there remains a need to develop methods to understand the interaction of microbiome factors with host cells and to characterize their potential therapeutic functions. To address this challenge, we developed a systems biology framework we term the Pharmacobiome for microbiome pharmacology analysis. The Pharmacobiome framework evaluates similarities between microbes and microbial byproducts and known drugs based on their impact on host transcriptomic cellular signatures. Here, we apply our framework to characterization of the Anti-Gynecologic Cancer Vaginal Pharmacobiome. Using published vaginal microbiome multi-omics data from the Partners PrEP clinical trial, we constructed vaginal epithelial gene signatures associated with each profiled vaginal microbe and metabolite. We compared these microbiome-associated host gene signatures to post-drug perturbation host gene signatures associated with 35 FDA-approved anti-cancer drugs from the Library of Integrated Network-based Cellular Signatures database to identify vaginal microbes and metabolites with high statistical and functional similarity to these drugs. We found that Lactobacilli and their metabolites can regulate host gene expression in ways similar to many anti-cancer drugs. Additionally, we experimentally tested our model prediction that taurine, a metabolite produced by L. crispatus, kills cancerous breast and endometrial cancer cells. Our study shows that the Pharmacobiome is a powerful framework for characterizing the anti-cancer therapeutic potential of vaginal microbiome factors with generalizability to other cancers, microbiomes, and diseases.

systems biology↗

bioRxiv2020

Engineering Logical Inflammation Sensing Circuit for Modulating Gut Conditions

Bacteria genetically engineered to execute defined therapeutic and diagnostic functions in physiological settings can be applied to colonize the human microbiome, providing in situ surveillance and conditional disease modulation. However, many engineered microbes can only respond to single-input environmental factors, limiting their tunability, precision, and effectiveness as living diagnostic and therapeutic systems. For engineering microbes to improve complex chronic disorders such as inflammatory bowel disease, the bacteria must respond to combinations of stimuli in the proper context and time. This work implements a previously characterized split activator AND logic gate in the probiotic Escherichia coli strain Nissle 1917. Our system can respond to two input signals: the inflammatory biomarker tetrathionate and a second input signal, anhydrotetracycline (aTc), for manual control. We report 4-6 fold induction with a minimal leak when the two chemical signals are present. We model the AND gate dynamics using chemical reaction networks and tune parameters in silico to identify critical perturbations that affect our circuits selectivity. Finally, we engineer the optimized AND gate to secrete a therapeutic anti-inflammatory cytokine IL-22 using the hemolysin secretion pathway in the probiotic E. coli strain. We used a germ-free transwell model of the human gut epithelium to show that our engineering bacteria produce similar host cytokine responses compared to pure cytokine. Our study presents a scalable workflow to engineer cytokine-secreting microbes. It demonstrates the feasibility of IL-22 derived from probiotic E. coli Nissle with minimal off-target effects in a gut epithelial context.

synthetic biology↗

bioRxiv2019

Bacterial Controller Aided Wound Healing: A Case Study in Dynamical Population Controller Design

Wound healing is a complicated biological process consisting of many types of cellular dynamics and functions regulated by chemical and molecular signals. Recent advances in synthetic biology have made it possible to predictably design and build closed-loop controllers that can function appropriately alongside biological species. In this paper we develop a simple dynamical population model mimicking the sequential relay-like dynamics of cellular populations involved in the wound healing process. Our model consists of four nodes and five signals whose parameters we can tune to simulate various chronic healing conditions. We also develop a set of regulator functions based on type-1 incoherent feed forward loops (IFFL) that can sense the change from acute healing to incomplete chronic wounds, improving the system in a timely manner. Both the wound healing and type-1 IFFL controller architectures are compatible with available synthetic biology experimental tools for potential applications.Competing Interest StatementThe authors have declared no competing interest.View Full Text

synthetic biology↗

bioRxiv2017

Control of bacterial population density with population feedback and molecular sequestration

Genetic engineering technology has become sophisticated enough to allow precise manipulation of bacterial genetic material. Engineering efforts with these technologies have created modified bacteria for various medical, industrial, and environmental purposes, but organisms designed for specific functions require improvements in stability, longevity, or efficiency of function. Most bacteria live in multispecies communities, whose composition may be closely linked to the effect the community has on the environment. Bacterial engineering efforts will benefit from building communities with regulated compositions, which will enable more stable and powerful community functions.\n\nWe present a design of a synthetic two member bacterial community capable of maintaining its composition at a defined ratio of [cell type 1]: [cell type 2]. We have constructed the genetic motif that will act in each cell in the two member community, containing an AHL-based negative feedback loop that activates ccdB toxin, which caps population density with increasing feedback strength. It also contains one of two ccdB sequestration modules, either the ccdA protein antitoxin, or an RNA device which prevents transcription and translation of ccdB mRNA, that rescues capped population density with induction. We compare absorbance and colony counting methods of estimating bacterial population density, finding that absorbance-based methods overestimate viable population density when ccdB toxin is used to control population density.\n\nPrior modeling results show that two cell types containing this genetic circuit motif that reciprocally activate the others ccdB sequestration device will establish a steady state ratio of cell types. Experimental testing and tuning the full two member community will help us improve our modeling of multi-member bacterial communities, learn more about the strengths and weaknesses of our design for community composition control, and identify general principles of design of compositionally-regulated microbial communities.

synthetic biology↗