The architecture of theory and data in microbiome design: towards an S-matrix for microbiomes

Current Opinion in Microbiology, Год журнала: 2025, Номер 83, С. 102580 - 102580

Опубликована: Янв. 22, 2025

Язык: Английский

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Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms

Metabolic Engineering, Год журнала: 2025, Номер 90, С. 67 - 77

Опубликована: Март 11, 2025

Язык: Английский

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Advances in synthetic microbial ecosystems approach for studying ecological interactions and their influencing factors

Engineering Microbiology, Год журнала: 2025, Номер unknown, С. 100205 - 100205

Опубликована: Март 1, 2025

Язык: Английский

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Microbial electrotaxis: rewiring environmental microbiomes

Trends in Microbiology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

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Design and analysis of quorum sensing language “Interpreter” ecosystem for microbial community

Chemical Engineering Journal, Год журнала: 2024, Номер 496, С. 153148 - 153148

Опубликована: Июнь 26, 2024

Язык: Английский

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The Architecture of Theory and Data in Microbiome Design: towards an S-matrix for microbiomes

Опубликована: Авг. 9, 2024

Designing microbiomes for applications in health, bioengineering, and sustainability is intrinsically linked to a fundamental theoretical understanding of the rules governing microbial community assembly. Microbial ecologists have used range mathematical models understand, predict, control microbiomes, ranging from mechanistic models, putting populations their interactions as focus, purely statistical approaches, searching patterns empirical experimental data. We review success limitations these modeling approaches when designing novel especially guided by (inevitably) incomplete Although successful at predicting generic assembly, phenomenological tend fall short precision needed design implement specific functionality microbiome. argue that effectively with optimal functions diverse environments, should combine data-driven techniques models---a middle, third way using theory inform design.

Язык: Английский

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Quorum sensing regulating the productivity and stability of cross-feeding cocultivation

Chemical Engineering Journal, Год журнала: 2024, Номер unknown, С. 158167 - 158167

Опубликована: Ноя. 1, 2024

Язык: Английский

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Guided assembly of multispecies positive biofilms targeting undesirable bacteria

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 17, 2024

Abstract The use of synthetic microbial communities (SynComs) engineered to form positive biofilms that prevent the settlement harmful bacteria is emerging as a promising strategy in biotechnology, particularly reducing reliance on chemical antimicrobials. Despite this potential, rationale for selecting specific strains SynComs and mechanisms underlying their antagonistic effects remains insufficiently understood. In study, we present bottom-up approach integrating live-cell imaging with high-throughput analysis multi-strain across diverse scenarios. Through method, identified beneficial based superior ability exclude undesirable mixed biofilms. Notably, our findings revealed competitive against could also other strains, emphasising need compatibility control design. composed B. velezensis Pediococcus spp. demonstrated enhanced pathogen exclusion compared single strains. Temporal biofilm interactions, supported by mathematical models, showed was primarily driven nutritional competition (Jameson effect) additional interference (prey-predator Lotka-Volterra model). Furthermore, pre-establishing surfaces significantly increased inhibition, indicating distinct biofilm-associated effect. These insights offer framework rational SynCom design deepen understanding underpinning applications. Figure

Язык: Английский

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Metabolic cross-feeding interactions modulate the dynamic community structure in microbial fuel cell under variable organic loading wastewaters

PLoS Computational Biology, Год журнала: 2024, Номер 20(10), С. e1012533 - e1012533

Опубликована: Окт. 17, 2024

The efficiency of microbial fuel cells (MFCs) in industrial wastewater treatment is profoundly influenced by the community, which can be disrupted variable operations. Although guilds linked to MFC performance under specific conditions have been identified, comprehensive knowledge convergent community structure and pathways adaptation lacking. Here, we developed a microbe-microbe interaction genome-scale metabolic model (mmGEM) based on cross-feeding study communities MFCs treating sulfide-containing from canned-pineapple factory. encompassed three major guilds: sulfate-reducing bacteria (SRB), methanogens (MET), sulfide-oxidizing (SOB). Our findings revealed shift an SOB-dominant MET-dominant as organic loading rates (OLRs) increased, along with decline performance. mmGEM accurately predicted relative abundance at low OLRs (L-OLRs) high (H-OLRs). simulations constraints SOB growth H-OLRs due reduced sulfate-sulfide (S) cycling acetate SRB. More cross-fed metabolites SRB were diverted MET, facilitating their competitive dominance. Assessing dynamics varying enabled execution practical scenario-based explore potential impact elevated acidity levels This work highlights role shaping response OLRs. insights gained will inform development effective strategies for implementing technology real-world environments.

Язык: Английский

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Analysis of the baijiu pit mud microorganisms and sub-communities that biosynthesize specific metabolites, using genomic and metabolic models

Food Bioscience, Год журнала: 2024, Номер 63, С. 105648 - 105648

Опубликована: Дек. 11, 2024

Язык: Английский

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