Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

By Roie Levy, Elhanan Borenstein. Proceedings of the National Academy of Sciences of the United States of America, 2013

398 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/6eb9958944847be9b1dad93da422bc4f37bdeed3

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In Molecular Biology

Citations in the corpus

Using Genome-Scale Models to Predict Biological Capabilities (2015, neutral): “Recapitulation Quantitative phenotype predictions initially focused on simple physiological predictions and are still expanding to more complex phenotypes, biological systems (Levy and Borenstein, 2013), and environments.”
Metabolic dependencies drive species co-occurrence in diverse microbial communities (2015, background): “These communities exhibit a great compositional variety, ranging from hot-spring assemblies with low species diversity (6) to the human gut microbiota harboring hundreds of species (7, 8).”
Constraint-based models predict metabolic and associated cellular functions (2014, background): “There has also been a steady increase in the amount of omic data of the human microbiome, and CBMs will have an important role in analysing these complex data sets 98,99 .”
Co-occurrence is not evidence of ecological interactions. (2020, background): “This is not unique to ecology, environmental microbiology (Rocca et al., 2019) and microbiome research (e.g. Levy & Borenstein, 2013) suffer from the same problem.”
Diet dominates host genotype in shaping the murine gut microbiota (2014, background): “…adynamic lagbetween the dietary input and the change in bacterial abundance (i.e., rate-dependent hysteresis) or to another as-of-yet unknown mechanism that allows the gut microbiota to remember its past dietary exposures (e.g., through bacterial interaction networks) (Levy and Borenstein, 2013).”
Microbial diversity and ecological networks as indicators of environmental quality (2017, background): “pathways (Levy and Borenstein 2013; Zelezniak et al. 2015), or the effect of engineering species (Jones et al.”
Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development (2015, background): “…have been studied, including host species, genotype, diet and health (Rawls et al., 2006; Turnbaugh et al., 2006; Benson et al., 2010; Goodrich et al., 2014), as well as microbe-specific factors, including mutualistic and competitive interactions (de Muinck et al., 2013; Levy and Borenstein, 2013).”