Open challenges for microbial network construction and analysis

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(11), P. 3111 - 3118

Published: June 9, 2021

Microbial network construction is a popular explorative data analysis technique in microbiome research. Although large number of microbial tools has been developed to date, there are several issues concerning the and interpretation networks that have received less attention. The purpose this perspective draw attention these underexplored challenges analysis.

Language: Английский

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Virus–host interactions and their roles in coral reef health and disease

Nature Reviews Microbiology, Journal Year: 2017, Volume and Issue: 15(4), P. 205 - 216

Published: Jan. 16, 2017

Language: Английский

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SteadyCom: Predicting microbial abundances while ensuring community stability

PLoS Computational Biology, Journal Year: 2017, Volume and Issue: 13(5), P. e1005539 - e1005539

Published: May 15, 2017

Genome-scale metabolic modeling has become widespread for analyzing microbial metabolism. Extending this established paradigm to more complex communities is emerging as a promising way unravel the interactions and biochemical repertoire of these omnipresent systems. While several techniques have been developed communities, little emphasis placed on need impose time-averaged constant growth rate across all members community ensure co-existence stability. In absence constraint, faster growing organism will ultimately displace other microbes in community. This particularly important predicting steady-state microbiota composition it imposes significant restrictions allowable membership, phenotypes. study, we introduce SteadyCom optimization framework flux distributions consistent with requirement. can be rapidly converged by iteratively solving linear programming (LP) problem number iterations independent organisms. A advantage compatibility variability analysis. first demonstrated four E. coli double auxotrophic mutants then applied gut model consisting nine species, representatives from phyla Bacteroidetes, Firmicutes, Actinobacteria Proteobacteria. contrast direct use FBA, able predict change species abundance response changes diets minimal additional imposed constraints model. By randomizing uptake rates microbes, an profile good agreement experimental inferred. provides step towards cross-cutting task given environment.

Language: Английский

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Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters

The ISME Journal, Journal Year: 2017, Volume and Issue: 11(7), P. 1614 - 1629

Published: April 11, 2017

Language: Английский

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Dominant role of abundant rather than rare bacterial taxa in maintaining agro-soil microbiomes under environmental disturbances

Chemosphere, Journal Year: 2019, Volume and Issue: 235, P. 248 - 259

Published: June 24, 2019

Language: Английский

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