Biology subjects

Udekwu, K.

Publications and source records attributed to Udekwu, K..

5 recordsLinked to original sources

bioRxiv2025

Spatial and Temporal Patterns of Public Transit Aerobiomes

BackgroundAerobiome diversity is extensive, however community structure at the species level remains elusive. Likewise, microbiomes of public transit systems are of public interest due to their importance for health, though few studies have focused on these ecosystems whilst utilising shotgun metagenomics. Aerosol studies have focused predominantly on individual cities, with limited between-city comparisons suggesting specific community structures. Longitudinal studies show aerobiome diversity as dynamic, fluctuating during seasonal and daily cycles, though an annual cycle remains to be considered. Further, a bacterial bias has limited fungal aerobiome studies, with few considering both fractions collectively. As such, the objective of this study was to examine spatial and temporal patterns in the species diversity of public transit aerobiomes, with an emphasis on bacteria and fungi. ResultsAir samples taken over a three-year period (2017-2019) from six global cities were subjected to shotgun metagenomic sequencing. Improved classification databases, notably for fungi, applying stringent parameters for trimming, exogenous contamination removal and classification yielded high species-level resolution. Microbial diversity varied substantially among cities, while human and environmental factors, recorded in parallel, were of secondary significance. Bacteria dominated the public transit aerobiome with increased presence in cities with higher population densities. All aerobiomes had complex compositions, consisting of hundreds to thousands of species. Annual variation had limited significance on the public transit aerobiome diversity and community structure. ConclusionsCities were the most important factor contributing to diversity and community structure, demonstrating specific bacterial and fungal signatures. Further, a correlation between geographical distance and the genetic signatures of aerobiomes is suggested. Bacteria are the most abundant constituent of public transit aerobiomes, though no single species is globally dominant, conversely indicating a large inter-city variation in community structure. The presence of a ubiquitous global species core is rejected, though an aerobiome sub-core is confirmed. For the first time, local public transit aerobiome cores are presented for each city and related to ecological niches. Further, the importance of a robust bioinformatics analysis pipeline to identify and remove exogenous contaminants for studying low biomass samples is highlighted. Lastly, a core and sub-core definition of contaminant aerobiome species with taxon tables, to facilitate future environmental studies, is presented.

microbiology↗

bioRxiv2025

Computational Platform for streamlining the success of sequential antibiotic therapy

The scarcity of antibiotics and the need for swift decision-making present significant challenges for healthcare practitioners. When confronted with such circumstances, practitioners must prioritize their approach based on several key factors. By leveraging the recent biological discovery of collateral sensitivity, we have devised an open-source computational platform. This platform utilizes the drug resistance profile of an evolved strain and initial population conditions to potentially predict the failure of cycling therapy in eradicating or restraining a multi-drug resistant bacterial population. We demonstrate how this framework can anticipate potential failures for a range of antibiotics in chronic pseudomonas aeruginosa infections. This innovative methodology lays the foundation for evolutionary therapies that can facilitate the selection of appropriate treatments, thereby reducing antibiotic resistance.

evolutionary biology↗

bioRxiv2024

Invariant sets for switched systems to tackle bacterial resistance

The limited availability of antibiotics and the need for prompt decision-making present significant challenges for healthcare practitioners. When faced with this situation, practitioners must prioritize their approach based on several key factors. By leveraging the emergent understanding of collateral sensitivity among antibiotic-exposed pathogens, we demonstrate the utility of control invariant sets to predict treatment failure when antibiotic cycling is applied as a therapeutic strategy aiming to eradicate or prevent emergence of multi-drug resistant pathogens. Our results here pave the way for point-of-care diagnostic technologies to identify infections and select appropriate treatments quickly, reducing unnecessary antibiotic use.

bioinformatics↗

bioRxiv2019

Disparate effects of antibiotic-induced microbiome change and enhanced fitness in Daphnia magna

It is a common view that an organisms microbiota has a profound influence on host fitness; however, supporting evidence is lacking in many organisms. We manipulated the gut microbiome of Daphnia magna by chronic exposure to different concentrations of the antibiotic Ciprofloxacin (0.01 - 1 mg L-1), and evaluated whether this affected the animals fitness and antioxidant capacity. In line with our expectations, antibiotic exposure altered the microbiome in a concentration-dependent manner. However, contrary to these expectations, the reduced diversity of gut bacteria was not associated with any fitness detriment. Moreover, the growth-related parameters correlated negatively with diversity indices; and, in the daphnids exposed to the lowest ciprofloxacin concentrations, the antioxidant capacity, growth, and fecundity were even higher than in control animals. These findings suggest that ciprofloxacin exerts direct stimulatory effects on growth and reproduction in Daphnia, while microbiome-mediated effects are of lesser importance. Thus, although microbiome profiling of Daphnia may be a sensitive tool to identify early effects of antibiotic exposure, disentangling direct and microbiome-mediated effects on host fitness is not straightforward.

pharmacology and toxicology↗

bioRxiv2018

Mitochondrial proline catabolism activates Ras1/cAMP/PKA-induced filamentation in Candida albicans

Amino acids are among the earliest identified inducers of yeast-to-hyphal transitions in Candida albicans, an opportunistic fungal pathogen of humans. Here, we show that the morphogenic amino acids arginine, ornithine and proline are internalized and metabolized in mitochondria via a PUT1- and PUT2-dependent pathway that results in enhanced ATP production. Elevated ATP levels correlate with Ras1/cAMP/PKA pathway activation and Efg1-induced gene expression. The magnitude of amino acid-induced filamentation is linked to glucose availability; high levels of glucose repress mitochondrial function thereby dampening filamentation. Furthermore, arginine-induced morphogenesis occurs more rapidly and independently of Dur1,2-catalyzed urea degradation, indicating that mitochondrial-generated ATP, not CO2, is the primary morphogenic signal derived from arginine metabolism. The important role of the SPS-sensor of extracellular amino acids in morphogenesis is the consequence of induced amino acid permease gene expression, i.e., SPS-sensor activation enhances the capacity of cells to take up morphogenic amino acids, a requisite for their catabolism. C. albicans cells engulfed by murine macrophages filament, resulting in macrophage lysis. Phagocytosed put1-/- and put2-/- cells do not filament and do not lyse macrophages, consistent with a critical role of mitochondrial proline metabolism in virulence.

microbiology↗