History of antibiotic adaptation influences microbial evolutionary dynamics during subsequent treatment
PLoS Biol. 2017 Aug 8;15(8):e2001586. doi: 10.1371/journal.pbio.2001586. eCollection 2017 Aug. ABSTRACT Antibiotic regimens often include the sequential changing of drugs to limit the development and evolution of resistance of bacterial pathogens. It remains unclear how history of adaptation to one antibiotic can influence the resistance profiles when bacteria subsequently adapt to a different antibiotic. Here, […]
Read MoreNovel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions
PLoS One. 2017 Aug 2;12(8):e0182163. doi: 10.1371/journal.pone.0182163. eCollection 2017. ABSTRACT Interactions between microbes are central to the dynamics of microbial communities. Understanding these interactions is essential for the characterization of communities, yet challenging to accomplish in practice. There are limited available tools for characterizing diffusion-mediated, contact-independent microbial interactions. A practical and widely implemented technique in […]
Read MoreNovel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance
BMC Genomics. 2017 Jul 19;18(1):543. doi: 10.1186/s12864-017-3905-1. ABSTRACT BACKGROUND: Malaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug, artemisinin. Our limited understanding of Plasmodium biology hinders the elucidation of resistance mechanisms. In this regard, systems biology approaches can facilitate the integration of existing […]
Read MoreAn engineering design approach to systems biology
Integr Biol (Camb). 2017 Jul 17;9(7):574-583. doi: 10.1039/c7ib00014f. ABSTRACT Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which […]
Read MoreIncreased Urinary Trimethylamine N-Oxide Following Cryptosporidium Infection and Protein Malnutrition Independent of Microbiome Effects
J Infect Dis. 2017 Jul 1;216(1):64-71. doi: 10.1093/infdis/jix234. ABSTRACT Cryptosporidium infections have been associated with growth stunting, even in the absence of diarrhea. Having previously detailed the effects of protein deficiency on both microbiome and metabolome in this model, we now describe the specific gut microbial and biochemical effects of Cryptosporidium infection. Protein-deficient mice were […]
Read MoreGrowth-altering microbial interactions are responsive to chemical context
PLoS One. 2017 Mar 20;12(3):e0164919. doi: 10.1371/journal.pone.0164919. eCollection 2017. ABSTRACT Microbial interactions are ubiquitous in nature, and are equally as relevant to human wellbeing as the identities of the interacting microbes. However, microbial interactions are difficult to measure and characterize. Furthermore, there is growing evidence that they are not fixed, but dependent on environmental context. […]
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