Disentangling microbial interaction networks

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

Published: March 1, 2025

The structure and function of microbial communities is shaped by intricate ecological interactions amongst the constituent microorganisms. Thus, a mechanistic understanding emergent community-level functions requires knowledge on how architecture underlying interaction networks affects these properties. To address this, researchers employ different sequencing-based experimental approaches to infer topology given network. However, it remains generally unclear which method best suited for quantifying critical network parameters. Here we provide comparative overview serving this purpose, with particular emphasis their strengths weaknesses. In way, our work can help guide design studies that aim at unraveling structure-function relationships in communities.

Language: Английский

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Editorial: Microbial co-cultures: a new era of synthetic biology and metabolic engineering, volume II

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: March 20, 2025

Microbial co-cultures-the controlled cultivation of two or more microbial species in a shared environment-have emerged as transformative paradigm synthetic biology and metabolic engineering, addressing limitations inherent monoculture systems. By harnessing synergistic interactions, co-cultures enable modular division labor, spatial organization, crossfeeding dynamics that optimize pathways, enhance substrate conversion efficiency, expand bioproduction capabilities (Brenner et al., 2008;Wang 2024). This second volume the special issue underscores rapid advancements this field, highlighting empirical successes biomanufacturing, environmental remediation, therapeutic development. It also emphasizes critical role computational modelling systems designing robust consortia, providing reassurance about scientific rigor field (De Lorenzo 2018).A key advantage lies their ability to compartmentalize complex biochemical tasks. For instance, Saccharomyces cerevisiae Clostridium autoethanogenum achieved 40% increase bioethanol yield compared monocultures by segregating sugar fermentation carbon fixation mitigating redox imbalances (Chen Co-cultures' application extends pharmaceutical production, where incompatible biosynthetic pathways are partitioned between species. A notable example is synthesis antimalarial precursor artemisinin-11,10-epoxide. co-culturing S. (engineered for amorpha-4,11-diene production) with Pichia pastoris (expressing cytochrome P450 enzymes), titers reached 2.8 g/L-a 15-fold improvement over attempts (Ro 2006). Similarly, Streptomyces coelicolor Bacillus subtilis produced novel polyketide antibiotics via horizontal gene transfer, illustrating potential "synthetic ecology" drug discovery (Traxler 2013).From an perspective, consortia pivotal sustainable bioprocessing. Lignocellulosic biomass degradation, challenge biofuel has been enhanced through fungal-bacterial synergy. In study Xia Machine learning greatly improved our predict interactions. example, researchers used models forecast how bacteria interact based on growth metabolism. helps engineer beneficial communities understanding interact, crucial predicting community structure function (Nestor 2023).This highlights agricultural, industrial scalability considerations. The features several noteworthy papers contribute significantly field:Microbial interactions play defense mechanisms plants against various pathogens. Recent studies have highlighted significance these particularly context enhancing agricultural resilience sustainability. coli strains presence β-lactam antibiotic cefotaxime (CTX). findings revealed cross-protection window sensitive strain, extending up approximately 100 times its minimal inhibitory concentration (MIC). Microscopic observations enzyme activity assays indicated antibiotic-induced bacterial filamentation contributes protective effect.Moreover, demonstrated extent influenced disparity β-lactamase co-cultured strains; larger differences shifted toward higher CTX concentrations. These insights underscore complexity under stress highlight survival bacteria. Understanding developing effective therapies challenges posed resistance.Sustainable practices management pressing pollution, resource depletion, climate change. research innovative strategies leverage biotechnological foster sustainability.Kherdekar provides comprehensive overview integrated approaches plastic waste management" discusses pollution evaluates mitigate impact. authors emphasize importance multifaceted approach, combining mechanical recycling, chemical biological degradation address waste. They recycling currently most widely method, accounting 20% global processing. However, effectiveness limited properties after multiple cycles. contrast, offers breaking down plastics into monomers, allowing production virgin-quality polymers. Despite potential, energy-intensive accounts less than 1% treatment. article explores noting certain microorganisms identified capability decompose specific types plastics, such polyethylene terephthalate (PET).While promising, approach still experimental stage faces related efficiency. advocate system leverages strengths each coupled policy interventions public awareness campaigns, effectively tackle growing crisis. As we advance new era integration will likely food security, sustainability, health care. presented interdisciplinary collaboration among microbiologists, engineers, biotechnologists. conclusion, "Microbial Co-cultures: New Era Synthetic Biology Metabolic Engineering, Volume II" serves not only current but paves way future innovations biotechnology. collective from essential aiming harness power drive solutions across industries.

Language: Английский

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Distributing Chemical Reactions between Cell Populations: Exemplar Studies

Computers & Chemical Engineering, Journal Year: 2025, Volume and Issue: unknown, P. 109110 - 109110

Published: April 1, 2025

Language: Английский

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Phage-mediated intercellular CRISPRi for biocomputation in bacterial consortia

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 27, 2024

Abstract Coordinated actions of cells in microbial communities and multicellular organisms enable them to perform complex tasks otherwise difficult for single cells. This has inspired biological engineers build cellular consortia larger circuits with improved functionalities while implementing communication systems coordination among Here, we investigate the signalling dynamics a phage-mediated synthetic DNA messaging system couple it CRISPR interference distributed that logic gate operations bacterial consortia. We find growth phases both sender receiver cells, as well resource competition between them, shape outcomes. Leveraging easy programmability messages, eight orthogonal signals demonstrate intercellular CRISPRi (i-CRISPRi) regulates gene expression across Finally, multiplex i-CRISPRi implement several gates involve up seven take three inputs simultaneously, single- dual-rail encoding: NOT, YES, AND AND-AND-NOT. The developed here lays groundwork engineered communities, using phage communication.

Language: Английский

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