[HTML][HTML] Distribution of antibiotic resistance genes in the environment
The prevalence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs)
in the microbiome is a major public health concern globally. Many habitats in the …
in the microbiome is a major public health concern globally. Many habitats in the …
[HTML][HTML] Reconstructing organisms in silico: genome-scale models and their emerging applications
X Fang, CJ Lloyd, BO Palsson - Nature Reviews Microbiology, 2020 - nature.com
Escherichia coli is considered to be the best-known microorganism given the large number
of published studies detailing its genes, its genome and the biochemical functions of its …
of published studies detailing its genes, its genome and the biochemical functions of its …
Metabolic interaction models recapitulate leaf microbiota ecology
Resource allocation affects the structure of microbiomes, including those associated with
living hosts. Understanding the degree to which this dependency determines interspecies …
living hosts. Understanding the degree to which this dependency determines interspecies …
Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics
Synthetic biology is a design-driven discipline centered on engineering novel biological
functions through the discovery, characterization, and repurposing of molecular parts …
functions through the discovery, characterization, and repurposing of molecular parts …
Genome-scale metabolic modeling enables in-depth understanding of big data
Genome-scale metabolic models (GEMs) enable the mathematical simulation of the
metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a …
metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a …
Gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
Genome-scale metabolic models of microorganisms are powerful frameworks to predict
phenotypes from an organism's genotype. While manual reconstructions are laborious …
phenotypes from an organism's genotype. While manual reconstructions are laborious …
Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model
Soil microbiomes are highly diverse, and to improve their representation in biogeochemical
models, microbial genome data can be leveraged to infer key functional traits. By integrating …
models, microbial genome data can be leveraged to infer key functional traits. By integrating …
Ecological dynamics of the gut microbiome in response to dietary fiber
H Liu, C Liao, L Wu, J Tang, J Chen, C Lei… - The ISME …, 2022 - academic.oup.com
Dietary fibers are generally thought to benefit intestinal health. Their impacts on the
composition and metabolic function of the gut microbiome, however, vary greatly across …
composition and metabolic function of the gut microbiome, however, vary greatly across …
Quantitative principles of microbial metabolism shared across scales
Metabolism is the complex network of chemical reactions occurring within every cell and
organism, maintaining life, mediating ecosystem processes and affecting Earth's climate …
organism, maintaining life, mediating ecosystem processes and affecting Earth's climate …
Nitrogen recovery by a halophilic ammonium-assimilating microbiome: a new strategy for saline wastewater treatment
Wastewater with high salinity is one of the major challenges for conventional wastewater
treatment. Although nitrogen management is vital for wastewater treatment, efficient …
treatment. Although nitrogen management is vital for wastewater treatment, efficient …