Constraint-based Modeling of Marine Microbial Community Metabolism and Physiology

John Casey (CBIOMES Postdoctoral Fellow)
Massachusetts Institute of Techology

Marine microbial communities mediate the transformation of Earth’s major bioelements through an intricate web of inorganic and organic ‘conduits,’ connecting microbes to microbes, and connecting microbes to global biogeochemical cycles. Within the CBIOMES project, my objective is to identify and quantify the fluxes through each conduit within and between the numerically dominant microbial taxa of the oligotrophic ocean gyres: Prochlorococcus, Synechococcus, Crocosphaera, SAR11 and Roseobacter.

We will be reconstructing genome-scale metabolic networks — detailed and stoichiometrically balanced networks of the many biochemical transformations within a cell — from the ‘pangenomes’ of each taxonomic group. From each pangenome, hundreds of randomized in silico and sequenced strains will be reconstructed in an effort to capture the phylogenetic, physiological and metabolic microdiversity within each group. By leveraging laboratory and field data, including environmental ‘omics datasets, we plan to build realistic simulations designed to predict the winners and losers within the broad environmental niches they occupy.

Using a convex optimization approach (dynamic flux balance analysis and its family of variants) to predict fluxes and growth rates within and between each network, the costs and benefits associated with metabolic interactions of in silico representatives of microbial consortia will be quantified. Ultimately, reduced-complexity metabolic models will be designed to complement ecosystem-scale modeling approaches developed by other CBIOMES project investigators.

News from John Casey


Jann Paul Mattern, Kristof Glauninger, Gregory L. Britten, John R. Casey, Sangwon Hyun, Zhen Wu, E. Virginia Armbrust, Zaid Harchaoui, Francois Ribalet (2022), A Bayesian approach to modeling phytoplankton population...

Towards a systems perspective of trace metals co-limitation – John Casey (MIT)


A Systems Level Approach to Biogeography

Microbial simulations bridge the gap between the molecular and ecosystem scales. A new CBIOMES paper presents, for the first time, an interpretation of observed, strain-level, basin-scale biogeography using genome-scale modeling...

Recordings and microtalks from the Follows Group. Please note access to this page is restricted to CBIOMES associates. (more…)

2021 Annual Meeting microtalk: Advances in using flow cytometry to quantify picophytoplankton physical properties – Tim Smyth (PML)


2021 Annual Meeting microtalk: Simulating microbial growth, metabolism and physiology – John Casey (MIT)


Surface Area Limitation – a special case of nutrient limitation – John Casey (MIT)


November 2020 CBIOMES e-meeting – John Casey (MIT)

“Simulating Prochlorococcus growth, metabolism and physiology across a meridional transect of the North and South Atlantic Oceans” Please note access to this page is restricted to CBIOMES associates. (more…)

Towards a Better Model for the Microbe Membrane (Revisited)

Postdoc John Casey continues to work closely with MIT-CBIOMES Group PI Mick Follows on research combining quantitative proteomics, flux balance analysis, and molecular modeling of membrane transports to develop a...


John Casey and Michael J. Follows (2020), A steady-state model of microbial acclimation to substrate limitation, PLoS Computational Biology, doi: 10.1371/journal.pcbi.1008140 Get the PDF [Requires login]

2020 Annual Meeting e-poster: Pangenome-scale simulation of growth, metabolism and physiological acclimation of Prochlorococcus strains across a meridional transect – John Casey (MIT)


2020 Annual Meeting e-poster: A Bayesian Approach to Size-structured Matrix Population Model – Francois Ribalet (UW)


CBIOMES Goes to Ocean Sciences 2020

Look out for members of the CBIOMES team, sharing their work at this year’s Ocean Sciences conference taking place February 16-21 in San Diego, California. (more…)

Relating Marine Picoplankton Cell Size and Metabolism

CBIOMES postdoctoral fellow John Casey is a Microbial Oceanographer who combines observations, experimental approaches, and computational methods to better understand the diversity of metabolic and physiological designs that influence biogeochemical...

Towards a Better Model for the Microbe Membrane

by John Casey for CBIOMES CBIOMES Postdoctoral Fellow John Casey, has been working closely with MIT Group PI Mick Follows to combine quantitative proteomics, flux balance analysis of genome-scale metabolic...


Past Annual Reporting

2019 | 2018 [login required]