Statistically learning the functional landscape of microbial communities

A Skwara, K Gowda, M Yousef… - Nature Ecology & …, 2023 - nature.com
Microbial consortia exhibit complex functional properties in contexts ranging from soils to
bioreactors to human hosts. Understanding how community composition determines …

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 …

High-order interactions distort the functional landscape of microbial consortia

A Sanchez-Gorostiaga, D Bajić, ML Osborne… - PLoS …, 2019 - journals.plos.org
Understanding the link between community composition and function is a major challenge in
microbial population biology, with implications for the management of natural microbiomes …

Steering ecological-evolutionary dynamics to improve artificial selection of microbial communities

L Xie, W Shou - Nature Communications, 2021 - nature.com
Microbial communities often perform important functions that depend on inter-species
interactions. To improve community function via artificial selection, one can repeatedly grow …

Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities

S Estrela, SP Brown - PLoS Computational Biology, 2013 - journals.plos.org
Microbes are predominantly found in surface-attached and spatially structured polymicrobial
communities. Within these communities, microbial cells excrete a wide range of metabolites …

Metabolic rules of microbial community assembly

S Estrela, JCC Vila, N Lu, D Bajic, M Rebolleda-Gomez… - BioRxiv, 2020 - biorxiv.org
To develop a quantitative theory that can predict how microbiomes assemble, and how they
respond to perturbations, we must identify which descriptive features of microbial …

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 …

Modeling microbial community structure and functional diversity across time and space

PE Larsen, SM Gibbons, JA Gilbert - FEMS Microbiology Letters, 2012 - academic.oup.com
Microbial communities exhibit exquisitely complex structure. Many aspects of this
complexity, from the number of species to the total number of interactions, are currently very …

Phylogenetic diversity theory sheds light on the structure of microbial communities

JP O'Dwyer, SW Kembel, JL Green - PLoS computational biology, 2012 - journals.plos.org
Microbial communities are typically large, diverse, and complex, and identifying and
understanding the processes driving their structure has implications ranging from ecosystem …

Competitive and cooperative metabolic interactions in bacterial communities

S Freilich, R Zarecki, O Eilam, ES Segal… - Nature …, 2011 - nature.com
Revealing the ecological principles that shape communities is a major challenge of the post-
genomic era. To date, a systematic approach for describing inter-species interactions has …