Majority sensing in synthetic microbial consortia DOI Creative Commons
Razan N. Alnahhas, Mehdi Sadeghpour, Ye Chen

et al.

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: July 21, 2020

Abstract As synthetic biocircuits become more complex, distributing computations within multi-strain microbial consortia becomes increasingly beneficial. However, designing distributed circuits that respond predictably to variation in consortium composition remains a challenge. Here we develop two-strain gene circuit senses and responds which strain is the majority. This involves co-repressive system each produces signaling molecule signals other down-regulate production of its own, orthogonal molecule. links expression ratio strains rather than population size. Further, control cross-over point for majority via external induction. We elucidate mechanisms driving these dynamics by developing mathematical model captures response as fractions induction are varied. These results show simple can be used multicellular systems sense state population.

Language: Английский

Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology DOI Creative Commons
Nicholas S. McCarty, Rodrigo Ledesma‐Amaro

Trends in biotechnology, Journal Year: 2018, Volume and Issue: 37(2), P. 181 - 197

Published: Nov. 26, 2018

Microbial consortia have been used in biotechnology processes, including fermentation, waste treatment, and agriculture, for millennia. Today, synthetic biologists are increasingly engineering microbial diverse applications, the bioproduction of medicines, biofuels, biomaterials from inexpensive carbon sources. An improved understanding natural ecosystems, development new tools to construct program their behaviors, will vastly expand functions that can be performed by communities interacting microorganisms. Here, we review recent advancements biology approaches engineer consortia, discuss ongoing emerging efforts apply various biotechnological suggest future applications.

Language: Английский

Citations

437
Pathways to cellular supremacy in biocomputing DOI Creative Commons
Lewis Grozinger, Martyn Amos, Thomas E. Gorochowski

et al.

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Nov. 20, 2019

Abstract Synthetic biology uses living cells as the substrate for performing human-defined computations. Many current implementations of cellular computing are based on “genetic circuit” metaphor, an approximation operation silicon-based computers. Although this conceptual mapping has been relatively successful, we argue that it fundamentally limits types computation may be engineered inside cell, and fails to exploit rich diverse functionality available in natural systems. We propose notion “cellular supremacy” focus attention domains which biocomputing might offer superior performance over traditional consider potential pathways toward supremacy, suggest application areas found.

Language: Английский

Citations

151
Design and regulation of engineered bacteria for environmental release DOI
Yonatan Chemla, Connor J. Sweeney,

Christopher A. Wozniak

et al.

Nature Microbiology, Journal Year: 2025, Volume and Issue: 10(2), P. 281 - 300

Published: Feb. 4, 2025

Language: Английский

Citations

4
Design of a new model yeast consortium for ecological studies of enological fermentation DOI Creative Commons
Eléonore Pourcelot,

Audrey Vigna,

Thérèse Marlin

et al.

Peer Community Journal, Journal Year: 2025, Volume and Issue: 5

Published: Jan. 7, 2025

Wine fermentation involves complex microbial communities of non-Saccharomyces yeast species besides the well-known Saccharomyces cerevisiae. While extensive research has enhanced our understanding S. cerevisiae, development multi-species starters led to increased interest in interactions and role diversity winemaking. Consequently, molecular methods have emerged identify different at stages winemaking process. Model or consortia, which provide simplified systems resembling natural diversity, offer opportunities investigate population dynamics understand community ecosystem performance. Here, this work aims design a consortium reflecting wine yeasts develop method for accurately tracking their during fermentation. We developed characterized six-species consortium, with Hanseniaspora uvarum, Starmerella bacillaris, Metschnikowia pulcherrima, Lachancea thermotolerans Torulaspora delbrueckii. By tagging each distinct fluorescent markers, study enables real-time monitoring individual within using flow cytometry. carried out complete analysis studying evolution populations over time examining factors such as metabolite production kinetics. In addition, was used test diversity-function relationship proof concept. sought determine impact initial evenness on communities' performances subjected osmotic stress. To end, ten randomly designed consortia varying proportions were followed enological 200 280 g/L sugars. The proportion certain affected however no demonstrable effect response stress shown. These results demonstrated usefulness presented is now available scientific can contribute future trying decipher multispecies

Language: Английский

Citations

2
Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges DOI Open Access
Shun Che, Yujie Men

Journal of Industrial Microbiology & Biotechnology, Journal Year: 2019, Volume and Issue: 46(9-10), P. 1343 - 1358

Published: July 5, 2019

Language: Английский

Citations

125
Bacterial co-culture with cell signaling translator and growth controller modules for autonomously regulated culture composition DOI Creative Commons
Kristina Stephens, Maria Pozo,

Chen‐Yu Tsao

et al.

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Sept. 11, 2019

Synthetic biology and metabolic engineering have expanded the possibilities for engineered cell-based systems. The addition of non-native biosynthetic regulatory components can, however, overburden reprogrammed cells. In order to avoid overload, an emerging area focus is on consortia, wherein cell subpopulations work together carry out a desired function. This strategy requires regulation populations. Here, we design synthetic co-culture controller consisting signal translator growth-controller modules that, when implemented, provide autonomous consortia composition. system co-opts orthogonal autoinducer AI-1 AI-2 cell-cell signaling mechanisms bacterial quorum sensing (QS) enable cross-talk between strains QS signal-controlled growth rate modulate relative population densities. We further develop simple mathematical model that enables closed-loop control trajectories.

Language: Английский

Citations

106
Automated design of synthetic microbial communities DOI Creative Commons
Behzad D Karkaria, Alex J. H. Fedorec, C. Barnes

et al.

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Jan. 28, 2021

Abstract Microbial species rarely exist in isolation. In naturally occurring microbial systems there is strong evidence for a positive relationship between diversity and productivity of communities. The pervasiveness these communities nature highlights possible advantages genetically engineered strains to cocultures as well. Building synthetic allows us create distributed that mitigate issues often found engineering monoculture, especially functional complexity increases. Here, we demonstrate methodology designing robust include competition nutrients, use quorum sensing control amensal bacteriocin interactions chemostat environment. We computationally explore all two- three- strain systems, using Bayesian methods perform model selection, identify the most candidates producing stable steady state Our findings highlight important interaction motifs provide stability, requirements selecting genetic parts further tuning community composition.

Language: Английский

Citations

103
Quorum Sensing Signal Selectivity and the Potential for Interspecies Cross Talk DOI Creative Commons

Samantha Wellington,

E. Peter Greenberg

mBio, Journal Year: 2019, Volume and Issue: 10(2)

Published: March 4, 2019

Many species of proteobacteria communicate with kin and coordinate group behaviors through a form cell-cell signaling called acyl-homoserine lactone (AHL) quorum sensing (QS). Most AHL receptors are thought to be specific for their cognate signal, ensuring that bacteria cooperate share resources only closely related cells. Although specificity is considered fundamental QS, there reports "promiscuous" respond broadly nonself signals. These promiscuous responses expand the function QS systems include interspecies interactions have been implicated in both competition cooperation. Because frequently members polymicrobial communities, cross talk between could profound impacts. To better understand prevalence promiscuity, we measured activity seven native host organisms. facilitate comparison our results previous studies, also receptor using heterologous expression

Language: Английский

Citations

101
Synthetic Biology for Manipulating Quorum Sensing in Microbial Consortia DOI Creative Commons
Kristina Stephens, William E. Bentley

Trends in Microbiology, Journal Year: 2020, Volume and Issue: 28(8), P. 633 - 643

Published: April 24, 2020

Language: Английский

Citations

101
Soil Microbiomes—a Promising Strategy for Contaminated Soil Remediation: A Review DOI
Ying Teng, Wei Chen

Pedosphere, Journal Year: 2019, Volume and Issue: 29(3), P. 283 - 297

Published: May 16, 2019

Language: Английский

Citations

90