Synthetic microbial communities (SynComs) of the human gut: design, assembly, and applications

PT van Leeuwen, S Brul, J Zhang… - FEMS Microbiology …, 2023‏ - academic.oup.com
The human gut harbors native microbial communities, forming a highly complex ecosystem.
Synthetic microbial communities (SynComs) of the human gut are an assembly of …

Reconstructing organisms in silico: genome-scale models and their emerging applications

X Fang, CJ Lloyd, BO Palsson - Nature Reviews Microbiology, 2020‏ - nature.com
Escherichia coli is considered to be the best-known microorganism given the large number
of published studies detailing its genes, its genome and the biochemical functions of its …

Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future

SA Huws, CJ Creevey, LB Oyama, I Mizrahi… - Frontiers in …, 2018‏ - frontiersin.org
The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi,
methanogenic archaea and phages. These microbes interact closely to breakdown plant …

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

I Dukovski, D Bajić, JM Chacón, M Quintin, JCC Vila… - Nature protocols, 2021‏ - nature.com
Genome-scale stoichiometric modeling of metabolism has become a standard systems
biology tool for modeling cellular physiology and growth. Extensions of this approach are …

Challenges in microbial ecology: building predictive understanding of community function and dynamics

S Widder, RJ Allen, T Pfeiffer, TP Curtis, C Wiuf… - The ISME …, 2016‏ - academic.oup.com
The importance of microbial communities (MCs) cannot be overstated. MCs underpin the
biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform …

Genome-scale metabolic modeling enables in-depth understanding of big data

A Passi, JD Tibocha-Bonilla, M Kumar, D Tec-Campos… - Metabolites, 2022‏ - mdpi.com
Genome-scale metabolic models (GEMs) enable the mathematical simulation of the
metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a …

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

A Heinken, DA Ravcheev, F Baldini, L Heirendt… - Microbiome, 2019‏ - Springer
Background The human gut microbiome performs important functions in human health and
disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of …

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

AR Pacheco, M Moel, D Segrè - Nature communications, 2019‏ - nature.com
Metabolic exchange mediates interactions among microbes, hel** explain diversity in
microbial communities. As these interactions often involve a fitness cost, it is unclear how …

Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics

WR Harcombe, WJ Riehl, I Dukovski, BR Granger… - Cell reports, 2014‏ - cell.com
The interspecies exchange of metabolites plays a key role in the spatiotemporal dynamics of
microbial communities. This raises the question of whether ecosystem-level behavior of …

[كتاب][B] Nonlinear programming: concepts, algorithms, and applications to chemical processes

LT Biegler - 2010‏ - SIAM
Chemical engineering applications have been a source of challenging optimization
problems for over 50 years. For many chemical process systems, detailed steady state and …