The community-function landscape of microbial consortia
Quantitatively linking the composition and function of microbial communities is a major
aspiration of microbial ecology. Microbial community functions emerge from a complex web …
aspiration of microbial ecology. Microbial community functions emerge from a complex web …
Robustness of microbiome function
Microbial communities perform metabolic processes that sustain life on Earth and promote
human health. Microbial consortia sustain these functions in the face of constant structural …
human health. Microbial consortia sustain these functions in the face of constant structural …
Carbohydrate complexity limits microbial growth and reduces the sensitivity of human gut communities to perturbations
E Ostrem Loss, J Thompson, PLK Cheung… - Nature ecology & …, 2023 - nature.com
Dietary fibre impacts the growth dynamics of human gut microbiota, yet we lack a detailed
and quantitative understanding of how these nutrients shape microbial interaction networks …
and quantitative understanding of how these nutrients shape microbial interaction networks …
Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes
S Arya, AB George, JP O'Dwyer - Proceedings of the …, 2023 - National Acad Sciences
Microbiome engineering offers the potential to leverage microbial communities to improve
outcomes in human health, agriculture, and climate. To translate this potential into reality, it …
outcomes in human health, agriculture, and climate. To translate this potential into reality, it …
Predicting metabolomic profiles from microbial composition through neural ordinary differential equations
Characterizing the metabolic profile of a microbial community is crucial for understanding its
biological function and its impact on the host or environment. Metabolomics experiments …
biological function and its impact on the host or environment. Metabolomics experiments …
Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions
JC Thompson, VM Zavala… - PLOS Computational …, 2023 - journals.plos.org
Microbiomes interact dynamically with their environment to perform exploitable functions
such as production of valuable metabolites and degradation of toxic metabolites for a wide …
such as production of valuable metabolites and degradation of toxic metabolites for a wide …
Control points for design of taxonomic composition in synthetic human gut communities
BM Connors, J Thompson, S Ertmer, RL Clark… - Cell Systems, 2023 - cell.com
Microbial communities offer vast potential across numerous sectors but remain challenging
to systematically control. We develop a two-stage approach to guide the taxonomic …
to systematically control. We develop a two-stage approach to guide the taxonomic …
Interactions between culturable bacteria are predicted by individual species' growth
E Nestor, G Toledano, J Friedman - Msystems, 2023 - Am Soc Microbiol
Predicting interspecies interactions is a key challenge in microbial ecology given that
interactions shape the composition and functioning of microbial communities. However …
interactions shape the composition and functioning of microbial communities. However …
Deep Neural Networks for Predicting Single-Cell Responses and Probability Landscapes
Engineering biology relies on the accurate prediction of cell responses. However, making
these predictions is challenging for a variety of reasons, including the stochasticity of …
these predictions is challenging for a variety of reasons, including the stochasticity of …
Predicting and Prioritising Community Assembly: Learning Outcomes via Experiments
Community assembly provides the foundation for applications in biodiversity conservation,
climate change, invasion, restoration and synthetic ecology. However, predicting and …
climate change, invasion, restoration and synthetic ecology. However, predicting and …