A systems biology approach to evaluate potential probiotic candidates for women’s vaginal health
Probiotic supplements are marketed for diverse health benefits, yet species inclusion often lacks functional rationale. We surveyed 352 U.S. probiotic products and found 36 unique microbial species, with most supplements containing only one species and no clear link between species and intended health benefit. To evaluate probiotic function, we developed CoPaPro, a collection of 1,012 […]
Read MoreTen simple rules for developing a training program
PMID:40644437 | DOI:10.1371/journal.pcbi.1013200
Read MoreReframing the role of the objective function in its proper context for metabolic network modeling
The “objective function” is a core concept in metabolic network modeling. Its use has enabled the analysis of large data to drive deeper understanding of cellular metabolism. This commentary reframes how the objective function is discussed to enhance its value and clarify misunderstandings in metabolic network modeling. PMID:40541323 | DOI:10.1016/j.cels.2025.101298
Read MoreGenome-scale metabolic network reconstruction analysis identifies bacterial vaginosis-associated metabolic interactions
Bacterial vaginosis (BV) is the most prevalent vaginal condition among reproductive-age women presenting with vaginal complaints. Despite its significant impact on women’s health, limited knowledge exists regarding the microbial community composition and metabolic interactions associated with BV. In this study, we analyze metagenomic data obtained from human vaginal swabs to generate in silico predictions of […]
Read MoreApplying a polysaccharide lyase from Stenotrophomonas maltophilia to disrupt alginate exopolysaccharide produced by Pseudomonas aeruginosa clinical isolates
Pseudomonas aeruginosa is considered one of the most challenging, drug-resistant, opportunistic pathogens partly due to its ability to synthesize robust biofilms. Biofilm is a mixture of extracellular polymeric substances (EPS) that encapsulates microbial cells, leading to immune evasion, antibiotic resistance, and thus higher risk of infection. In the cystic fibrosis lung environment, P. aeruginosa undergoes […]
Read MoreNiche-specific metabolic phenotypes can be used to identify antimicrobial targets in pathogens
Bacterial pathogens pose a major risk to human health, leading to tens of millions of deaths annually and significant global economic losses. While bacterial infections are typically treated with antibiotic regimens, there has been a rapid emergence of antimicrobial resistant (AMR) bacterial strains due to antibiotic overuse. Because of this, treatment of infections with traditional […]
Read MoreSpatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment
With the generation of spatially resolved transcriptomics of microbial biofilms, computational tools can be used to integrate this data to elucidate the multi-scale mechanisms controlling heterogeneous biofilm metabolism. This work presents a Multi-scale model of Metabolism In Cellular Systems (MiMICS) which is a computational framework that couples a genome-scale metabolic network reconstruction (GENRE) with Hybrid […]
Read MoreIdentifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism
Improvements in the diagnosis and treatment of cancer have revealed long-term side effects of chemotherapeutics, particularly cardiotoxicity. Here, we present paired transcriptomics and metabolomics data characterizing in vitro cardiotoxicity to three compounds: 5-fluorouracil, acetaminophen, and doxorubicin. Standard gene enrichment and metabolomics approaches identify some commonly affected pathways and metabolites but are not able to readily […]
Read MoreA computational model of Pseudomonas syringae metabolism unveils a role for branched-chain amino acids in Arabidopsis leaf colonization
Bacterial pathogens adapt their metabolism to the plant environment to successfully colonize their hosts. In our efforts to uncover the metabolic pathways that contribute to the colonization of Arabidopsis thaliana leaves by Pseudomonas syringae pv tomato DC3000 (Pst DC3000), we created iPst19, an ensemble of 100 genome-scale network reconstructions of Pst DC3000 metabolism. We developed […]
Read More