Events

Metatranscriptomics identifies pathogens and host responses associated with acute sinusitis in children

Abstract: Acute sinusitis (AS) is a frequent cause of antibiotic prescriptions in children. Distinguishing bacterial AS from common viral upper respiratory infections is crucial to prevent unnecessary antibiotic use. We performed RNA-seq of nasopharyngeal samples from 221 children with AS to better understand the etiology of AS and the impact of bacterial and viral infections on host immune responses. Metatranscriptomics detected three AS-associated bacterial pathogens with 87%/81% sensitivity/specificity (sens/spec) compared to culture, and 12 respiratory viruses with 86%/92% sens/spec compared to qRT-PCR. Metatranscriptomics also detected 22 additional pathogens not tested for in the clinical panel, and facilitated assembly of 205 viral genomes including new strains of coronaviruses, respiratory syncytial virus, and enterovirus D68. Lastly, metatranscriptomic analysis identified distinct host immune responses in individuals with bacterial versus viral infections. Our study demonstrates the power of metatranscriptomics for comprehensive analysis of AS etiology, and reveals host responses that could enable new diagnostic approaches.

Shirley Wong, Postdoctoral Fellow presents:

Towards valorization of food waste to bioplastic in Pseudomonas alloputida 

Abstract:

Annually, over a billion tonnes of food is wasted, where it largely ends up in landfills and massively contributes to the emission of greenhouse gases. To improve global sustainability, this low-value carbon resource can instead be converted into high-value bio-based products. Microbial valorization of food waste has been validated for many applications, from biofuels to bioplastic polymers like polyhydroxyalkanoates (PHAs). Much effort has gone into processing heterogenous food waste towards such applications, such as anaerobic digestion to produce short-chain fatty acids (scFAs), a group of industrially-relevant fatty acids that can be used as building blocks for other bioproducts. Pseudomonas alloputida is a highly promising PHA producer but its ability to metabolize scFAs is limited.

To improve the capacity of PH production on scFAs and, therefore, enable its upcycling of food waste into high-value bioplastic, we are using functional metagenomics to mine exogenous carbon utilization pathways from the environment. Environmental microbial communities represent rich, untapped reservoirs of novel genes and metabolic pathways. Here, we present community analyses of compost and soil microbiomes enriched for utilization of short (C2-C5) versus medium chain fatty acids (C8 and C9) under conditions conducive to PHA accumulation. We are furthermore constructing metagenomic libraries from the enriched cultures using the broad-host-range cosmid pJC8, with an average insert size of 33 kb. The metagenomic libraries will enable us to functionally screen for, identify, and isolate exogenous metabolic pathways that could support scFA-PHA conversion by P. alloputida. Additionally, we further characterize the ability of engineered P. alloputida to use VFAs in bioplastic production, demonstrating its use in food waste valorization.