Biology subjects

Forney, L. J.

Publications and source records attributed to Forney, L. J..

5 recordsLinked to original sources

bioRxiv2024

Inferring stability and persistence in the vaginal microbiome: A stochastic model of ecological dynamics

The vaginal microbiome is dynamic, yet the ecological and stochastic forces shaping its stability and persistence remain poorly understood. We developed a multi-species stochastic population model to analyze time-series data from 135 individuals sampled daily over 70 days, integrating ecological theory with microbial dynamics. Our framework explicitly incorporates stochasticity, ecological feedback, and sampling error to quantify community stability. We show that intra- and inter-species interactions and environmental fluctuations critically shape microbial population trajectories. This approach enabled the estimation of species competition coefficients and the identification of distinct stability regimes across individuals. We also introduce a Risk Prediction Monitoring (RPM) tool to track persistence probabilities of key taxa, particularly Lactobacillus spp., mirroring extinction risk models in conservation biology. Our findings challenge static "healthy" vs. "dysbiotic" categorizations and offer a quantitative framework for assessing microbiome resilience. This has direct implications for microbiome-targeted therapies aimed at promoting ecological stability in vaginal bacterial communities.

ecology↗

bioRxiv2023

The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated by L. iners regardless of HPV status

IntroductionThe cervicovaginal microbiota is influenced by host physiology, immunology, lifestyle, and ethnicity. We hypothesized that there would be differences in the cervicovaginal microbiota among pregnant, non-pregnant and menopausal women living in Puerto Rico with and without Human Papillomavirus (HPV) infection and cervical cancer. We specifically wanted to determine if the microbiota associated with variation in cervical cytology. A total of 294 women comprised of reproductive-age non-pregnant (N=196), pregnant (N=37), and menopausal (N=61) women were enrolled. The cervicovaginal bacteria was characterized by 16S rRNA amplicon sequencing, the HPV were genotyped with SPF10-LiPA, and cervical cytology was quantified. High-risk HPV (HR-HPV, 67.3%) was prevalent, including genotypes not covered by the 9vt HPV vaccine. Cervical lesions (34%) were also common. The cervical microbiota was dominated by Lactobacillus iners. Pregnant women in the 2nd and 3rd trimesters had decreased diversity and a decreased abundance of microbes associated with bacterial vaginosis. Women in menopause had greater alpha diversity, a greater proportion of facultative and strictly anaerobic bacteria, and higher cervicovaginal pH than pre-menopausal women. Cervical lesions were associated with greater alpha diversity. However, no significant associations between the microbiota and HPV infection (HR or LR-HPV types) were found. The cervicovaginal microbiota women living in Puerto Rican were either dominated by L. iners or diverse microbial communities regardless of a womans physiological stage. We postulate that the microbiota and the high prevalence of HR-HPV, increase the risk of cervical lesions of women living in Puerto Rico.

microbiology↗

bioRxiv2021

Three-dimensional models of the cervicovaginal epithelia to study host-microbiome interactions and sexually transmitted infections

Two-dimensional (2D) cell culture systems have provided controlled, reproducible means to analyze host-pathogen interactions. Although inexpensive, straightforward, and requiring very short time commitment, these models recapitulate neither the functionality of multi-layered cell types nor the microbial diversity of an infected human. Animal models have commonly been used to recreate the complexity of human infections. However, extensive modifications are commonly required to recreate interactions that resemble those in the human reproductive tract microbiologically and physiologically. Three-dimensional (3D) cell culture models have emerged as alternative means of reproducing key elements of human infections at a fraction of the cost of animal models and on a scale that allows for replicative experiments to be readily performed. Here we describe a new 3D model that utilizes transwells with epithelial cells seeded apically and a basolateral extra cellular matrix (ECM)-like layer containing collagen and fibroblasts. In this system, basal feeding creates a liquid/air interface on the apical side. The model produced tissues with close morphologic and physiological resemblance to human cervical and vaginal epithelia, including observable levels of mucus produced by cervical cells. Infection by both Chlamydia trachomatis and Neisseria gonorrhoeae was demonstrated as well as the growth of bacterial species observed in the human vaginal microbiota, enabling controlled mechanistic analyses of the interactions between host cells, vaginal microbiota and STI pathogens. Future experiments may include immune cells to mimic more closely the genital environment. Finally, the modular set up of the model makes it fully applicable to the analysis of non-genital host-microbiome-pathogen interactions. IMPORTANCEInfected sites in humans are a complex mix of host and microbial cell types interacting with each other to perform specific and necessary functions. The ability to understand the mechanism(s) that facilitate these interactions, and interactions with external factors is paramount to being able to develop preventative therapies. Models that attempt to faithfully replicate the complexity of these interactions are time intensive, costly, and not conducive to high throughput analysis. Two-dimensional (2D) models that have been used as a platform to understand these interactions, while cost effective, are generally limiting in experimental flexibility and structural/physiological relevance. Our three-dimensional (3D) models of the cervicovaginal epithelium can facilitate analysis of interactions between the host epithelium, sexually transmitted pathogens and bacteria present in the vaginal microbiota. Due to the modular design, additional cell types and environmental modulators can be introduced to the system to provide added complexity, approaching conditions in the infected human host.

cell biology↗

bioRxiv2021

Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data

Vaginal bacterial communities dominated by Lactobacillus species are associated with a reduced risk to various adverse health outcomes. However, somewhat unexpectedly many healthy women have microbiota that are not dominated by lactobacilli. To determine the factors that drive vaginal community composition we characterized the genetic composition and transcriptional activities of vaginal microbiota in healthy women. We demonstrated that the abundance of a species is not always indicative of its transcriptional activity and that impending changes in community composition can be predicted from metatranscriptomic data. Functional comparisons highlight differences in the metabolic activities of these communities, notably in their degradation of host-produced mucin but not glycogen. Degradation of mucin by communities not dominated by Lactobacillus may play a role in their association with adverse health outcomes. Finally, we show that the transcriptional activities of L. crispatus, L. iners, and G. vaginalis vary with the taxonomic composition of the communities in which they reside. Notably, L. iners and G. vaginalis both demonstrated lower expression of their cholesterol-dependent cytolysins when co-resident with Lactobacillus spp. and higher expression when co-resident with other facultative and obligate anaerobes. The pathogenic potential of these species may depend on the communities in which they reside and thus could be modulated by interventional strategies. Our results provide insight to the functional ecology of vaginal microbiota and reveal strategies for management of these ecosystems.

microbiology↗

bioRxiv2020

Contagious Antibiotic Resistance: Plasmid Transfer Among Bacterial Residents of the Zebrafish Gut

By characterizing the trajectories of antibiotic resistance gene transfer in bacterial communities such as the gut microbiome, we will better understand the factors that influence this spread of resistance. Our aim was to investigate the host network of a multi-drug resistance broad-host-range plasmid in the culturable gut microbiome of zebrafish. This was done through in vitro and in vivo conjugation experiments with Escherichia coli as donor of the plasmid pB10::gfp. When this donor was mixed with the extracted gut microbiome, only transconjugants of Aeromonas veronii were detected. In separate matings between the same donor and four prominent isolates from the gut microbiome, the plasmid transferred to two of these four isolates, A. veronii and Plesiomonas shigelloides, but not to Shewanella putrefaciens and Vibrio mimicus. When these A. veronii and P. shigelloides transconjugants were the donors in matings with the same four isolates, the plasmid now also transferred from A. veronii to S. putrefaciens. P. shigelloides was unable to donate the plasmid and V. mimicus was unable to acquire it. Finally, when the E. coli donor was added in vivo to zebrafish through their food, plasmid transfer was observed in the gut but only to Achromobacter sp., a rare member of the gut microbiome. This work shows that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome depends on the donor-recipient species combinations and therefore their spatial arrangement. It also suggests that rare gut microbiome members should not be ignored as potential reservoirs of multi-drug resistance plasmids from food. ImportanceTo understand how antibiotic resistance plasmids end up in human pathogens it is crucial to learn how, where and when they are transferred and maintained in members of bacterial communities such as the gut microbiome. To gain insight into the network of plasmid-mediated antibiotic resistance sharing in the gut microbiome, we investigated the transferability and maintenance of a multi-drug resistance plasmid among the culturable bacteria of the zebrafish gut. We show that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome can depend on which species are involved, as some are important nodes in the plasmid-host network and others dead-ends. Our findings also suggest that rare gut microbiome members should not be ignored as potential reservoirs of multi-drug resistance plasmids from food.

microbiology↗