The community-function landscape of microbial consortia

A Sanchez, D Bajic, J Diaz-Colunga, A Skwara… - Cell Systems, 2023 - cell.com
Quantitatively linking the composition and function of microbial communities is a major
aspiration of microbial ecology. Microbial community functions emerge from a complex web …

Robustness of microbiome function

KK Lee, Y Park, S Kuehn - Current Opinion in Systems Biology, 2023 - Elsevier
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 …

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 …

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 …

Predicting metabolomic profiles from microbial composition through neural ordinary differential equations

T Wang, XW Wang, KA Lee-Sarwar… - Nature machine …, 2023 - nature.com
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 …

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 …

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 …

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 …

Deep Neural Networks for Predicting Single-Cell Responses and Probability Landscapes

HE Klumpe, JB Lugagne, AS Khalil… - ACS Synthetic …, 2023 - ACS Publications
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 …

Predicting and Prioritising Community Assembly: Learning Outcomes via Experiments

BW Blonder, MH Lim, O Godoy - Ecology Letters, 2024 - Wiley Online Library
Community assembly provides the foundation for applications in biodiversity conservation,
climate change, invasion, restoration and synthetic ecology. However, predicting and …