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

и другие.

Nature Communications, Год журнала: 2020, Номер 11(1)

Опубликована: Июль 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.

Язык: Английский

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

Trends in biotechnology, Год журнала: 2018, Номер 37(2), С. 181 - 197

Опубликована: Ноя. 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.

Язык: Английский

Процитировано

439
Pathways to cellular supremacy in biocomputing DOI Creative Commons
Lewis Grozinger, Martyn Amos, Thomas E. Gorochowski

и другие.

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Ноя. 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.

Язык: Английский

Процитировано

153
Design and regulation of engineered bacteria for environmental release DOI
Yonatan Chemla, Connor J. Sweeney,

Christopher A. Wozniak

и другие.

Nature Microbiology, Год журнала: 2025, Номер 10(2), С. 281 - 300

Опубликована: Фев. 4, 2025

Язык: Английский

Процитировано

5
Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges DOI Open Access
Shun Che, Yujie Men

Journal of Industrial Microbiology & Biotechnology, Год журнала: 2019, Номер 46(9-10), С. 1343 - 1358

Опубликована: Июль 5, 2019

Язык: Английский

Процитировано

126
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

и другие.

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Сен. 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.

Язык: Английский

Процитировано

106
Quorum Sensing Signal Selectivity and the Potential for Interspecies Cross Talk DOI Creative Commons

Samantha Wellington,

E. Peter Greenberg

mBio, Год журнала: 2019, Номер 10(2)

Опубликована: Март 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

Язык: Английский

Процитировано

104
Automated design of synthetic microbial communities DOI Creative Commons
Behzad D Karkaria, Alex J. H. Fedorec, C. Barnes

и другие.

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Янв. 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.

Язык: Английский

Процитировано

104
Synthetic Biology for Manipulating Quorum Sensing in Microbial Consortia DOI Creative Commons
Kristina Stephens, William E. Bentley

Trends in Microbiology, Год журнала: 2020, Номер 28(8), С. 633 - 643

Опубликована: Апрель 24, 2020

Язык: Английский

Процитировано

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

Pedosphere, Год журнала: 2019, Номер 29(3), С. 283 - 297

Опубликована: Май 16, 2019

Язык: Английский

Процитировано

90
Potential use of fungal-bacterial co-cultures for the removal of organic pollutants DOI
Erika J. Espinosa-Ortiz, Eldon R. Rene, Robin Gerlach

и другие.

Critical Reviews in Biotechnology, Год журнала: 2021, Номер 42(3), С. 361 - 383

Опубликована: Июль 29, 2021

Fungi and bacteria coexist in a wide variety of natural artificial environments which can lead to their association interaction - ranging from antagonism cooperation that affect the survival, colonization, spatial distribution stress resistance interacting partners. The use polymicrobial cultivation approaches has facilitated more thorough understanding microbial dynamics mixed communities, such as those composed fungi bacteria, influence on ecosystem functions. Mixed (multi-domain) communities exhibit unique associations interactions could result efficient systems for degradation removal organic pollutants. Several previous studies have reported enhanced biodegradation certain pollutants when using combined fungal-bacterial treatments compared pure cultures or either (single domain systems). This article reviews: (i) mechanisms pollutant occur (e.g.: co-degradation, production secondary metabolites, enhancement degradative enzyme production, transport by fungal mycelia); (ii) case co-cultures various (synthetic dyes, polycyclic aromatic hydrocarbons, pesticides, other trace volatile compounds) different environmental matrices (e.g. water, gas/vapors, soil); (iii) key aspects engineering co-cultures, (iv) current challenges future perspectives remediation.

Язык: Английский

Процитировано

89