Biology subjects

Ghali, J.

Publications and source records attributed to Ghali, J..

4 recordsLinked to original sources

bioRxiv2026

Mining Microbial Transcriptomes to Engineer Cell-Based Bacterial Biosensors in Gut-Resident Bacteroidaceae

The gastrointestinal tract is rich in metabolic, immune, and microbiome-derived signals that can inform the design of live biotherapeutics and diagnosis of intestinal disorders. Engineered cell-based biosensors can tap into this molecular information and report on their environment, yet their development in gut-resident symbionts has been limited by a lack of validated sensor systems. Here, we present a generalizable pipeline that leverages bacterial transcriptional profiling to identify environment-responsive systems for biosensor engineering. Candidate Sensors Systems (CSSs) mined from healthy, disease, and in vitro transcriptomes were assembled into a barcoded library in Bacteroidaceae chassis and screened in high-throughput in vivo to identify responsive promoters. A unique Bacteroidales ECF-type sigma factor operon with ties to sphingolipid metabolism and flux was highly responsive in chemically-induced colitis models. The biosensor responded robustly to disease and returned to baseline upon recovery, establishing an in vivo-driven strategy for discovering functional biosensors in non-model gut-resident bacteria.

synthetic biology↗

bioRxiv2026

Microbiome histidine competition mediates dietary control of systemic imidazole propionate

The gut microbiome produces numerous metabolites that influence mammalian health. While microbiome composition and diet influence metabolite concentrations, how these factors interact remains incompletely defined. Here we find production of imidazole propionate (ImP), a microbial metabolite associated with cardiometabolic and neurodegenerative diseases, is determined by the balance of competing metabolic pathways that catabolize histidine to ImP or short-chain fatty acids (SCFAs). We show glutamate serves as a preferred substrate that selectively inhibits histidine conversion to SCFAs, redirecting flux to increased ImP production across mouse- and human-derived microbial communities. We find dietary monosodium glutamate (MSG) acting via this mechanism boosts ImP production in the mouse gut, transiently impairing glucose tolerance and increasing systemic ImP. These findings show that predictable interactions between dietary substrate and microbial competition control systemic ImP levels, providing a mechanistic framework for understanding microbiome metabolite production more broadly.

microbiology↗

bioRxiv2026

Engineered gut symbionts mediate cross-phylum antagonism to suppress uropathogenic Escherichia coli colonization

Urinary tract infections (UTIs) are among the most common bacterial infections globally and create a large burden on the healthcare system. Uropathogenic Escherichia coli (UPEC) account for the majority of UTIs and increase the risk of recurrence. The standard treatment is antibiotics and, with the rise of multi-drug resistant UPEC lineages, there is a need for alternative treatments and prevention. Colicins, bacteriocins targeting and produced by E. coli, have previously been shown to inhibit the growth of pathogenic E. coli and are a promising alternative. Here, we engineer commensal Bacteroidaceae to secrete colicins via outer membrane vesicle (OMV) targeting signal peptides to suppress E. coli in the mouse gut. Secreted colicins were assessed for their ability to kill primary clinical isolate UPEC strains, including epidemic multi-drug resistant ST131 strains, along with other pathogenic and type strains. Specifically, secreted colicin E7, from Phocaeicola vulgatus fully eliminated of several UPEC strains in culture. In mice, P. vulgatus secreting colicin E7 prevented the extended colonization of two clinical UPEC strains and restored microbiome diversity. Together, this work shows the viability of secreted, heterologous antimicrobials from P. vulgatus as prophylactic treatment against the colonization of pathogenic E. coli utilizing cross-phylum antagonism in the gut. Significance StatementRecurrent urinary tract infections can be driven by intestinal reservoirs of uropathogenic Escherichia coli that are difficult to eliminate and increasingly recalcitrant to conventional antibiotic therapy. Here, we show that engineered gut symbionts from the Bacteroidaceae family can secrete targeted protein antibiotics to selectively kill these uropathogenic E. coli. Leveraging outer membrane vesicle-based secretion, we demonstrate that bacteriocin secretion can prevent gut colonization by clinically relevant pathogens, while preserving overall microbiome diversity. This work establishes a strategy for programmable, cross-phylum antimicrobial delivery within the gut microbiome, providing a potential alternative to conventional antibiotics for preventing recurrent infections and other enteric diseases.

synthetic biology↗

bioRxiv2021

Glucose uptake in mammalian cells measured by ICP-MS

We developed a sensitive, ratiometric method to measure simultaneously 13C-labeled glucose and rubidium in biological samples using ICP-MS. The method uses probe-assisted ultra-sonication with water to extract 13C-[6C]-labeled-D-glucose and other polar analytes from mammalian tissues. It extracts >80% of the reference value for Rb and >95 % of 13C in a CRM spiked with 13C-[6C]-labeled-D-glucose in the micro-molar range. Using optimized instrument conditions, the method achieves a stable 13C/12C signal without spectral interferences. The 13C/12C signal is independent of sample composition and depends linearly on the concentration of 13C-[6C]-labeled-D-glucose in spiked samples. Overall, the method achieves a limit of detection of 10 {micro}M for 6-C-labeled 13C glucose in biological tissues. This detection capability for carbon in biological matrices by ICP-MS opens a wider range of applications for ICP-MS in biomedical research. As proof-of-principle, we combined 13C detection with the multi-channel capability of ICP-MS to measure glucose and rubidium uptake in the same contracting skeletal muscles. Multi-isotope detection is needed to study many biological processes, including coupled membrane transport. These results demonstrate a capability for carbon detection by ICP-MS that can significantly advance studies of complex biological processes that require multi-isotope detection.

systems biology↗