Automated adjustment of metabolic niches enables the control of natural and engineered microbial co-cultures DOI Creative Commons

Juan Andres Martinez,

Romain Bouchat,

Tiphaine Gallet de Saint Aurin

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 14, 2024

Abstract A lot of attention has been given to the understanding microbial interactions leading stable co-cultures, but resulting technologies have rarely challenged in dynamic cultivation conditions. In this work, substrate pulsing was performed promote better control metabolic niches corresponding each species, continuous co-cultivation diverse organisms. For purpose, we used a cell-machine interface relying on automated flow cytometry, allowing adjust temporal profile two according rhythm ensuring successive growth species i.e., our case yeast and bacterium. The approach, called Automated Adjustment Metabolic Niches (AAMN), successfully employed for stabilizing both cooperative competitive co-cultures. Additionally, AAMN can be considered as an enabling technology deployment co-cultures bioprocesses, demonstrated here based bioproduction p-coumaric acid. Taken altogether, data accumulated suggest that could wider range biological systems, also gain fundamental insights about interaction mechanisms.

Language: Английский

Metabolic exchanges are ubiquitous in natural microbial communities DOI
Christian Kost, Kiran Raosaheb Patil, Jonathan Friedman

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(12), P. 2244 - 2252

Published: Nov. 23, 2023

Language: Английский

Citations

93
A molecular toolkit of cross-feeding strains for engineering synthetic yeast communities DOI Creative Commons
Huadong Peng, Alexander P. S. Darlington, Eric J. South

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(3), P. 848 - 863

Published: Feb. 7, 2024

Engineered microbial consortia often have enhanced system performance and robustness compared with single-strain biomanufacturing production platforms. However, few tools are available for generating co-cultures of the model key industrial host Saccharomyces cerevisiae. Here we engineer auxotrophic overexpression yeast strains that can be used to create through exchange essential metabolites. Using these as modules, engineered two- three-member using different cross-feeding architectures. Through a combination ensemble modelling experimentation, explored how cellular (for example, metabolite strength) environmental initial population ratio, density extracellular supplementation) factors govern dynamics in systems. We tested use toolkit division labour case study show it enables tuneable antioxidant resveratrol production. expect this become useful resource variety applications synthetic ecology biomanufacturing.

Language: Английский

Citations

25
De novo biosynthesis of plant lignans by synthetic yeast consortia DOI
Ruibing Chen, Xianghui Chen, Yu Chen

et al.

Nature Chemical Biology, Journal Year: 2025, Volume and Issue: unknown

Published: March 17, 2025

Language: Английский

Citations

3
Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast DOI Creative Commons
Charlotte Cautereels, Jolien Smets, Peter W. Bircham

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 7, 2024

Abstract Microbes are increasingly employed as cell factories to produce biomolecules. This often involves the expression of complex heterologous biosynthesis pathways in host strains. Achieving maximal product yields and avoiding build-up (toxic) intermediates requires balanced every pathway gene. However, despite progress metabolic modeling, optimization gene still heavily relies on trial-and-error. Here, we report an approach for vivo, multiplexed G ene E xpression M odification b y L oxPsym-Cr e R ecombination (GEMbLeR). GEMbLeR exploits orthogonal LoxPsym sites independently shuffle promoter terminator modules at distinct genomic loci. facilitates creation large strain libraries, which ranges over 120-fold each harbors a unique profile. When applied biosynthetic astaxanthin, industrially relevant antioxidant, single round improved flux doubled production titers. Together, this shows that allows rapid efficient pathways, offering possibilities enhancing performance microbial factories.

Language: Английский

Citations

13
A new flavor of synthetic yeast communities sees the light DOI Creative Commons

Vicente Rojas,

Daniela S. Rivera, Carlos Alberto Ruiz

et al.

mBio, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

ABSTRACT No organism is an island: organisms of varying taxonomic complexity, including genetic variants a single species, can coexist in particular niches, cooperating for survival while simultaneously competing environmental resources. In recent years, synthetic biology strategies have witnessed surge efforts focused on creating artificial microbial communities to tackle pressing questions about the complexity natural systems and interactions that underpin them. These engineered ecosystems depend number nature their members, allowing complex cell communication designs recreate create diverse interest. Due its experimental simplicity, budding yeast Saccharomyces cerevisiae has been harnessed establish mixture varied populations with potential explore ecology, metabolic bioprocessing, biosensing, pattern formation. Indeed, enable advanced molecule detection dynamics logic operations. Here, we present concise overview state-of-the-art, highlighting examples exploit optogenetics manipulate, through light stimulation, key phenotypes at community level, unprecedented spatial temporal regulation. Hence, envision bright future where application optogenetic approaches (optoecology) illuminates intricate drives innovations engineering strategies.

Language: Английский

Citations

2
Engineering is evolution: a perspective on design processes to engineer biology DOI Creative Commons
Simeon D. Castle, Michiel Stock, Thomas E. Gorochowski

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: April 29, 2024

Abstract Careful consideration of how we approach design is crucial to all areas biotechnology. However, choosing or developing an effective methodology not always easy as biology, unlike most engineering, able adapt and evolve. Here, put forward that evolution follow a similar cyclic process therefore methods, including traditional design, directed evolution, even random trial error, exist within evolutionary spectrum. This contrasts with conventional views often place these methods at odds provides valuable framework for unifying engineering approaches challenging biological problems.

Language: Английский

Citations

7
Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology DOI Creative Commons

Óscar Adrián Gallardo-Navarro,

Bernardo Aguilar-Salinas,

Jorge Gustavo Rocha

et al.

Heliyon, Journal Year: 2024, Volume and Issue: 10(14), P. e33896 - e33896

Published: July 1, 2024

Humans have long relied on microbial communities to create products, produce energy, and treat waste. The microbiota residing within our bodies directly impacts health, while the soil rhizosphere microbiomes influence productivity of crops. However, complexity diversity make them challenging study difficult develop into applications, as they often exhibit emergence unpredictable higher-order phenomena. Synthetic ecology aims at simplifying by constituting synthetic or semi-natural with reduced that become easier analyze. This strategy combines methodologies simplify existing complex systems (top-down approach) build system from its constituent components (bottom-up approach). Simplified are studied understand how interactions among populations shape behavior community model predict their response external stimuli. By harnessing potential through a multidisciplinary approach, we can advance knowledge ecological concepts address critical public agricultural, environmental issues more effectively.

Language: Английский

Citations

7
Automated adjustment of metabolic niches enables the control of natural and engineered microbial co-cultures DOI
Juan A. Martínez, Romain Bouchat,

Tiphaine Gallet de Saint Aurin

et al.

Trends in biotechnology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

1
Metabolic division engineering of Escherichia coli consortia for de novo biosynthesis of flavonoids and flavonoid glycosides DOI
Zetian Qiu, Yumei Han, Jia Li

et al.

Metabolic Engineering, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

Citations

1
Harnessing microbial co-culture to increase the production of known secondary metabolites DOI
Yuzhen Li, Wanqi Zhang, Pengfei Hu

et al.

Natural Product Reports, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Co-culturing may provoke the biosynthesis of novel natural products. However, various microbial co-culture techniques also boost fermentation titer, yield and rate known products – we review current progress towards such a goal.

Language: Английский

Citations

1