Enterococci enhance Clostridioides difficile pathogenesis
Nature. 2022 Nov 16. doi: 10.1038/s41586-022-05438-x. Online ahead of print. ABSTRACT Enteric pathogens are exposed to a dynamic polymicrobial environment in the gastrointestinal tract1. This microbial community has been shown to be important during infection, but there are few examples illustrating how microbial interactions can influence the virulence of invading pathogens2. Here we show that […]
Read MoreGenome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae
NPJ Syst Biol Appl. 2022 Oct 28;8(1):41. doi: 10.1038/s41540-022-00252-7. ABSTRACT Infections due to carbapenem-resistant Enterobacteriaceae have recently emerged as one of the most urgent threats to hospitalized patients within the United States and Europe. By far the most common etiological agent of these infections is Klebsiella pneumoniae, frequently manifesting in hospital-acquired pneumonia with a mortality […]
Read MoreNew perspectives into the vaginal microbiome with systems biology
Trends Microbiol. 2022 Oct 19:S0966-842X(22)00257-8. doi: 10.1016/j.tim.2022.09.011. Online ahead of print. ABSTRACT The vaginal microbiome (VMB) is critical to female reproductive health; however, the mechanisms associated with optimal and non-optimal states remain poorly understood due to the complex community structure and dynamic nature. Quantitative systems biology techniques applied to the VMB have improved understanding of […]
Read MoreHistone deacetylase inhibition by gut microbe-generated short chain fatty acids entrains intestinal epithelial circadian rhythms
Gastroenterology. 2022 Aug 4:S0016-5085(22)00827-7. doi: 10.1053/j.gastro.2022.07.051. Online ahead of print. ABSTRACT BACKGROUND & AIMS: The circadian clock orchestrates ∼24-hour oscillations of gastrointestinal epithelial structure and function that drive diurnal rhythms in gut microbiota. Here, we use experimental and computational approaches in intestinal organoids to reveal reciprocal effects of gut microbial metabolites on epithelial timekeeping by […]
Read MoreLeveraging metabolic modeling to identify functional metabolic alterations associated with COVID-19 disease severity
Metabolomics. 2022 Jul 11;18(7):51. doi: 10.1007/s11306-022-01904-9. ABSTRACT OBJECTIVE: Since the COVID-19 pandemic began in early 2020, SARS-CoV2 has claimed more than six million lives world-wide, with over 510 million cases to date. To reduce healthcare burden, we must investigate how to prevent non-acute disease from progressing to severe infection requiring hospitalization. METHODS: To achieve this […]
Read MoreFecal sphingolipids predict parenteral nutrition associated cholestasis in the neonatal intensive care unit
JPEN J Parenter Enteral Nutr. 2022 Mar 13. doi: 10.1002/jpen.2374. Online ahead of print. ABSTRACT BACKGROUND: Parenteral nutrition associated cholestasis (PNAC) in the neonatal intensive care unit (NICU) causes significant morbidity and associated healthcare costs. Laboratory detection of PNAC currently relies on elevated serum conjugated bilirubin levels in the aftermath of impaired bile flow. Here, […]
Read MoreComparative analyses of parasites with a comprehensive database of genome-scale metabolic models
PLoS Comput Biol. 2022 Feb 23;18(2):e1009870. doi: 10.1371/journal.pcbi.1009870. eCollection 2022 Feb. ABSTRACT Protozoan parasites cause diverse diseases with large global impacts. Research on the pathogenesis and biology of these organisms is limited by economic and experimental constraints. Accordingly, studies of one parasite are frequently extrapolated to infer knowledge about another parasite, across and within genera. […]
Read MoreComparative analyses of parasites with a comprehensive database of geno-scale metabolic models
PLoS Comput Biol. 2022 Feb 23;18(2):e1009870. doi: 10.1371/journal.pcbi.1009870. Online ahead of print. ABSTRACT Protozoan parasites cause diverse diseases with large global impacts. Research on the pathogenesis and biology of these organisms is limited by economic and experimental constraints. Accordingly, studies of one parasite are frequently extrapolated to infer knowledge about another parasite, across and within […]
Read MoreQuantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions
PLoS Comput Biol. 2022 Feb 7;18(2):e1009341. doi: 10.1371/journal.pcbi.1009341. Online ahead of print. ABSTRACT Genome-scale metabolic network reconstructions (GENREs) are valuable tools for understanding microbial metabolism. The process of automatically generating GENREs includes identifying metabolic reactions supported by sufficient genomic evidence to generate a draft metabolic network. The draft GENRE is then gapfilled with additional reactions […]
Read MoreComputational approaches to understanding Clostridioides difficile metabolism and virulence
Curr Opin Microbiol. 2022 Feb;65:108-115. doi: 10.1016/j.mib.2021.11.002. Epub 2021 Nov 25. ABSTRACT The progress of infection by Clostridioides difficile is strongly influenced by metabolic cues it encounters as it colonizes the gastrointestinal tract. Both colonization and regulation of virulence have a multi-factorial interaction between host, microbiome, and gene expression cascades. While these connections with metabolism […]
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