Unravelling metabolic cross‐feeding in a yeast–bacteria community using ¹³C‐based proteomics

Molecular Systems Biology, Journal Year: 2023, Volume and Issue: 19(4)

Published: Feb. 13, 2023

Abstract Cross‐feeding is fundamental to the diversity and function of microbial communities. However, identification cross‐fed metabolites often challenging due universality metabolic biosynthetic intermediates. Here, we use 13 C isotope tracing in peptides elucidate co‐cultures Saccharomyces cerevisiae Lactococcus lactis . The community was grown on lactose as main carbon source with either glucose or galactose fraction molecule labelled C. Data analysis allowing for possible mass‐shifts yielded hundreds which could assign both species identity labelling degree. pattern showed that yeast utilized and, a lesser extent, lactic acid shared by L. sources. While provided essential amino acids bacterium expected, data also uncovered complex exchange. further supported metabolite co‐culture supernatant, diminished fitness galactose‐negative mutant community. Together, our results demonstrate utility C‐based proteomics uncovering interactions.

Language: Английский

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Modeling Microbial Communities: Perspective and Challenges

ACS Synthetic Biology, Journal Year: 2024, Volume and Issue: 13(8), P. 2260 - 2270

Published: Aug. 16, 2024

Microbial communities are immensely important due to their widespread presence and profound impact on various facets of life. Understanding these complex systems necessitates mathematical modeling, a powerful tool for simulating predicting microbial community behavior. This review offers critical analysis metabolic modeling highlights key areas that would greatly benefit from broader discussion collaboration. Moreover, we explore the challenges opportunities linked intricate nature communities, spanning data generation, validation. We confident ongoing advancements in techniques, such as machine learning, coupled with interdisciplinary collaborations, will unlock full potential across diverse applications.

Language: Английский

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Can a microbial community become an evolutionary individual?

Current Opinion in Microbiology, Journal Year: 2025, Volume and Issue: 84, P. 102596 - 102596

Published: Feb. 20, 2025

Microbial communities provide crucial services for human well-being, driving an interest in designing and controlling them towards optimised or novel functions. Unfortunately, promising strategies such as community breeding - sometimes referred to 'directed evolution' 'artificial selection' have shown limited success. A key issue is that microbial do not reliably exhibit heritable variation, limiting their capacity adaptive evolution. In other words, are evolutionary individuals. Here, we overview of the literature on transitions individuality and, with insights from paradigmatic organisms, build a multidimensional space which multispecies characterised by three ecological traits: positive interactions, functional integration, entrenchment. We then place within this space, explore how they can be directed toward increased individuality, discuss perspective help improve our approach breeding.

Language: Английский

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Industrial Microbial Technologies for Feed Protein Production from Non-Protein Nitrogen

Microorganisms, Journal Year: 2025, Volume and Issue: 13(4), P. 742 - 742

Published: March 25, 2025

Due to the increasing global demand for feed protein, microbial protein has great potential of being able sustainably. However, application in animal cultivation industry is still limited by its high cost and availability on scale. From viewpoint industrial production, it vital specify crucial processes components further technical exploration process optimization. This article presents state-of-the-art technologies non-protein nitrogen (NPN) assimilation production. Nitrogen sources are one main factors media used large-scale fermentation. Therefore, available NPN synthesis, utilization mechanisms, fermentation corresponding strain reviewed this paper. Especially, random mutagenesis adaptive laboratory evolution (ALE) approach combined with (ultra-) throughput screening provided impetus increase yield. Despite underlying technological advances production extensive research development efforts required before commercial feed.

Language: Английский

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Intelligent biomanufacturing of water-soluble vitamins

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

Published: May 1, 2025

Language: Английский

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Discovery of novel amino acid production traits by evolution of synthetic co-cultures

Microbial Cell Factories, Journal Year: 2023, Volume and Issue: 22(1)

Published: April 15, 2023

Amino acid production features of Corynebacterium glutamicum were extensively studied in the last two decades. Many metabolic pathways, regulatory and transport principles are known, but purely rational approaches often provide only limited progress optimization. We recently generated stable synthetic co-cultures, termed Communities Niche-optimized Strains (CoNoS), that rely on cross-feeding amino acids for growth. This setup has potential to evolve strains with improved by selection faster growing communities.Here we performed adaptive laboratory evolution (ALE) a CoNoS identify mutations relevant both mono- co-cultures. During ALE composed auxotrophic either L-leucine or L-arginine, obtained 23% growth rate increase. Via whole-genome sequencing reverse engineering, identified several involved beneficial The strain carried an expression-promoting mutation promoter region brnQ (cg2537), encoding branched-chain transporter combination genes Na+/H+-antiporter Mrp1 (cg0326-cg0321). suggested unexpected link transport. L-arginine partner evolved near transcriptional start site yet uncharacterized operon argTUV (cg1504-02). By studies ITC, characterized ArgTUV as uptake system C. affinity KD = 30 nM. Finally, deletion producer resulted 24% higher comparison parental strain.Our work demonstrates power CoNoS-approach evolution-guided identification non-obvious traits, which can also advance monocultures. Further rounds import-optimized potentially reveal pathway enzymes. approach easily be extended all kinds metabolite pairings different organisms same organism, thereby enabling systems other favorable mutations.

Language: Английский

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In vivo, in vitro and in silico: an open space for the development of microbe‐based applications of synthetic biology

Microbial Biotechnology, Journal Year: 2021, Volume and Issue: 15(1), P. 42 - 64

Published: Sept. 27, 2021

Summary Living systems are studied using three complementary approaches: living cells, cell‐free and computer‐mediated modelling. Progresses in understanding, allowing researchers to create novel chassis industrial processes rest on a cycle that combines vivo , vitro silico studies. This design–build–test–learn iteration loop between experiments analyses together physiology, genetics, biochemistry bioinformatics way keeps going forward. Because computer‐aided approaches not directly constrained by the material nature of entities interest, we illustrate here how this virtuous allows explore chemistry which is foreign present extant life, from whole metabolic cycles. Particular emphasis placed importance evolution.

Language: Английский

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Prevalent emergence of reciprocity among cross-feeding bacteria

ISME Communications, Journal Year: 2022, Volume and Issue: 2(1)

Published: Aug. 15, 2022

Explaining the de novo evolution of obligate cooperative cross-feeding interactions among bacteria is a fundamental problem. A critical step during this process emergence reciprocity two interaction partners, because mutually beneficial exchange metabolic byproducts can subsequently favour cross-feeding. However, so far, propensity with which unidirectional transition into bidirectional remains unknown. To address issue, we systematically cocultured four amino acid auxotrophic genotypes bacterial species potential donors belonging to 25 different species. Surprisingly, results experiment revealed that in around 40% all cases analysed, both recipient and metabolically autonomous donor gained significant growth advantage coculture. Subsequent experiments clarified auxotrophy-causing mutation did not induce growth-enhancing effect recipients, but it was rather due generally high engage synergistic interactions. Together, these findings show commonly emerges spontaneously interactions, thus paving way for even tighter

Language: Английский

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Moving beyond descriptive studies: harnessing metabolomics to elucidate the molecular mechanisms underpinning host-microbiome phenotypes

Mucosal Immunology, Journal Year: 2022, Volume and Issue: 15(6), P. 1071 - 1084

Published: Aug. 15, 2022

Language: Английский

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A constraint-based framework to reconstruct interaction networks in microbial communities

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

Published: Jan. 31, 2024

Abstract Microbial communities live in diverse habitats and significantly impact our health the environment. However, principles that govern their formation evolution remain poorly understood. A crucial step studying microbial is to identify potential metabolic interactions between community members, such as competition for nutrients or cross-feeding. Due size complexity of network each organism, there may be a variety connections pair organisms, which poses challenge unraveling interactions. Here, we present ReMIND, computational framework reconstruct interaction networks based on capabilities individual organisms. We applied ReMIND well-studied uranium-reducing honeybee gut microbiome. Our results provide new perspectives evolutionary forces shape these ecosystems trade-off metabolite exchange biomass yield. By enumerating alternative networks, systematically identified most likely metabolites exchanged highlighted could mediate competitive envision will help characterize capacity members elucidate communities, thus holds guide many applications precision medicine synthetic ecology.

Language: Английский

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