Metabolic-network-driven analysis of bacterial ecological strategies
By Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Nir Yosef, Roded Sharan, U. Gophna, Eytan Ruppin. 2009
102 citations recorded by the source corpus.
BackgroundThe growth-rate of an organism is an important phenotypic trait, directly affecting its ability to survive in a given environment. Here we present the first large scale computational study of the association between ecological strategies and growth rate across 113 bacterial species, occupying a variety of metabolic habitats. Genomic data are used to reconstruct the species' metabolic networks and habitable metabolic environments. These reconstructions are then used to investigate the typical ecological strategies taken by organisms in terms of two basic species-specific measures: metabolic variability - the ability of a species to survive in a variety of different environments; and co-habitation score vector - the distribution of other species that co-inhabit each environment.ResultsWe find that growth rate is significantly correlated with metabolic variability and the level of co-habitation (that is, competition) encountered by an organism. Most bacterial organisms adopt one of two main ecological strategies: a specialized niche with little co-habitation, associated with a typically slow rate of growth; or ecological diversity with intense co-habitation, associated with a typically fast rate of growth.ConclusionsThe pattern observed suggests a universal principle where metabolic flexibility is associated with a need to grow fast, possibly in the face of competition. This new ability to produce a quantitative description of the growth rate-metabolism-community relationship lays a computational foundation for the study of a variety of aspects of the communal metabolic life.
Subfields: Ecology, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Ecology
In Molecular Biology
- Marinka Zitnik
- Jure Leskovec
- Rok Sosic
- Elhanan Borenstein
- Michal Feldman
- Peter J. Turnbaugh
- Sharon I. Greenblum
- Roie Levy
Citations in the corpus
- Evolution of resilience in protein interactomes across the tree of life (2018, methodology): “Furthermore, using a categorization of bacteria into five groups based on their natural environments [NCBI classification for bacterial lifestyle (terrestrial, multiple, host cell, aquatic, specialized) ordered by the complexity of each category (32)], we find that terrestrial bacteria living in the”
- Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease (2011, background): “The seed sets of metabolite-based networks of a large array of microbial species were shown to be a successful proxy for the biochemical environments of these species and to provide insights into their ecology (31, 32, 35).”
- Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules (2013, background): “Specifically, the reverse-ecology framework (18) has successfully used such models to predict important ecological attributes, including an organism’s biochemical environment (16), its interaction with its host or with other species (21–23), and ecological strategies for coping with cohabiting speci”