Comparative 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 […]
Read MoreAn updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism
NPJ Syst Biol Appl. 2021 Oct 8;7(1):37. doi: 10.1038/s41540-021-00198-2. ABSTRACT Mucins are present in mucosal membranes throughout the body and play a key role in the microbe clearance and infection prevention. Understanding the metabolic responses of pathogens to mucins will further enable the development of protective approaches against infections. We update the genome-scale metabolic network […]
Read MoreNovel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis
mSystems. 2021 Oct 26;6(5):e0091921. doi: 10.1128/mSystems.00919-21. Epub 2021 Oct 5. ABSTRACT The pathogen Clostridioides difficile causes toxin-mediated diarrhea and is the leading cause of hospital-acquired infection in the United States. Due to growing antibiotic resistance and recurrent infection, targeting C. difficile metabolism presents a new approach to combat this infection. Genome-scale metabolic network reconstructions (GENREs) […]
Read MorePerinatal Outcomes of Asynchronous Influenza Vaccination, Ceará, Brazil, 2013-2018
Emerg Infect Dis. 2021;27(9):2409-2420. doi: 10.3201/eid2709.203791. ABSTRACT In Ceará, Brazil, seasonal influenza transmission begins before national annual vaccination campaigns commence. To assess the perinatal consequences of this misalignment, we tracked severe acute respiratory infection (SARI), influenza, and influenza immunizations during 2013-2018. Among 3,297 SARI cases, 145 (4.4%) occurred in pregnant women. Statewide vaccination coverage was […]
Read MoreMultidimensional Clinical Surveillance of Pseudomonas aeruginosa Reveals Complex Relationships between Isolate Source, Morphology, and Antimicrobial Resistance
mSphere. 2021 Aug 25;6(4):e0039321. doi: 10.1128/mSphere.00393-21. Epub 2021 Jul 14. ABSTRACT Antimicrobial susceptibility in Pseudomonas aeruginosa is dependent on a complex combination of host and pathogen-specific factors. Through the profiling of 971 clinical P. aeruginosa isolates from 590 patients and collection of paired patient metadata, we show that antimicrobial resistance is associated with not only […]
Read MoreUntargeted Metabolomics Reveals Species-Specific Metabolite Production and Shared Nutrient Consumption by Pseudomonas aeruginosa and Staphylococcus aureus
mSystems. 2021 Jun 29;6(3):e0048021. doi: 10.1128/mSystems.00480-21. Epub 2021 Jun 22. ABSTRACT While bacterial metabolism is known to impact antibiotic efficacy and virulence, the metabolic capacities of individual microbes in cystic fibrosis lung infections are difficult to disentangle from sputum samples. Here, we show that untargeted metabolomic profiling of supernatants of multiple strains of Pseudomonas aeruginosa […]
Read MoreMechanistic models of microbial community metabolism
Mol Omics. 2021 Jun 14;17(3):365-375. doi: 10.1039/d0mo00154f. ABSTRACT Microbial communities affect many facets of human health and well-being. Naturally occurring bacteria, whether in nature or the human body, rarely exist in isolation. A deeper understanding of the metabolic functions of these communities is now possible with emerging computational models. In this review, we summarize frameworks […]
Read MoreCollaborating with our community to increase code sharing
PLoS Comput Biol. 2021 Mar 30;17(3):e1008867. doi: 10.1371/journal.pcbi.1008867. eCollection 2021 Mar. NO ABSTRACT PMID:33784294 | PMC:PMC8009435 | DOI:10.1371/journal.pcbi.1008867
Read More