Global epistasis and the emergence of function in microbial consortia

Cell, Journal Year: 2024, Volume and Issue: 187(12), P. 3108 - 3119.e30

Published: May 21, 2024

The many functions of microbial communities emerge from a complex web interactions between organisms and their environment. This poses significant obstacle to engineering consortia, hindering our ability harness the potential microorganisms for biotechnological applications. In this study, we demonstrate that collective effect ecological microbes in community can be captured by simple statistical models predict how adding new species will affect its function. These predictive mirror patterns global epistasis reported genetics, they quantitatively interpreted terms pairwise members. Our results illuminate an unexplored path predicting function consortia composition, paving way optimizing desirable properties bringing tasks biological at genetic, organismal, scales under same quantitative formalism.

Language: Английский

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Design of a new model yeast consortium for ecological studies of enological fermentation

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

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Ecology and Evolutionary Biology as Frameworks to Study Wine Fermentations

Microbial Biotechnology, Journal Year: 2025, Volume and Issue: 18(3)

Published: March 1, 2025

Winemaking has leveraged microbiology to enhance wine quality, typically by engineering and inoculating individual yeast strains with desirable traits. However, do not grow alone during fermentation, rather they are embedded in diverse evolving microbial communities exhibiting complex ecological dynamics. Understanding predicting the interplay between community over course of species succession chemical matrix can benefit from recognising that wine, like all ecosystems, is subject general evolutionary rules. In this piece, we outline how conceptual methodological frameworks ecology biology assist researchers improving fermentation processes understanding mechanisms governing population dynamics, these important microcosms, unlocking genetic potential for strain development.

Language: Английский

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The optimization of microbial functions through rational environmental manipulations

Molecular Microbiology, Journal Year: 2024, Volume and Issue: 122(3), P. 294 - 303

Published: Feb. 19, 2024

Abstract Microorganisms play a central role in biotechnology and it is key that we develop strategies to engineer optimize their functionality. To this end, most efforts have focused on introducing genetic manipulations microorganisms which are then grown either monoculture or mixed‐species consortia. An alternative strategy microbial processes rationally the environment microbes grow. The multidimensional, including factors such as temperature, pH, salinity, nutrient composition, etc. These environmental all influence growth phenotypes of they generally “interact” with one another, combining effects complex, non‐additive ways. In piece, overview origins consequences these “interactions” between discuss how been built into statistical, bottom‐up predictive models function identify optimal conditions for monocultures We also “top‐down” approaches, algorithms, finding combinations factors. By providing brief summary state field, hope stimulate further work rational manipulation optimization environment.

Language: Английский

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Whole‐Genome Sequencing and Phenotyping Reveal Specific Adaptations of Lachancea thermotolerans to the Winemaking Environment

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

ABSTRACT Adaptation to the environment plays an essential role in yeast evolution as a consequence of selective pressures. Lachancea thermotolerans , related fermentation and one current trends wine technology research, has undergone anthropisation process, leading notable genomic phenomic differentiation. Using whole‐genome sequencing, 145 L. strains, we identified six well‐defined groups primarily delineated by their ecological origin exhibiting high levels genetic diversity. Anthropised strains showed lower diversity due pressure imposed winemaking environment. Strong evidence adaptation through modification gene content was also found. Differences genes involved assimilation alternative carbon nitrogen sources, such MAL31 DAL5 genes, which confer greater fitness environment, were observed. Additionally, found that phenotypic traits considered domestication hallmarks are present anthropised strains. Among these, increased presence ethanol sulphites, non‐fermentable residual fructose under fermentative conditions highlight. We hypothesise lactic acid production Saccharomyces‐Lachancea lineage is signature linked winemaking, resulting from loss respiratory chain complex I evolutionary preference for over respiration, even oxygen. Overall, results this work provide valuable insight into process demonstrate how environments give rise similar adaptations different species.

Language: Английский

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A Rapid Growth Rate Underpins the Dominance of Hanseniaspora uvarum in Spontaneous Grape Juice Fermentations

Yeast, Journal Year: 2025, Volume and Issue: unknown

Published: March 21, 2025

Hanseniaspora uvarum is consistently observed as the dominant non-Saccharomyces species in spontaneous grape juice fermentations. However, physiological mechanisms and physicochemical variables influencing prevalence of H. over other remain unclear. We tested factors contributing to dominance by inoculating a chemically diverse set juices with mock community whose composition was based on previously published comprehensive microbial survey commercial The these appeared have minimal impact overall dynamics fermentation, emerging nearly all conditions tested. Flow cytometry analysis confirmed that has faster growth rate than Saccharomyces cerevisiae several species. Moreover, its not affected presence S. cerevisiae. negatively cerevisiae, significant implications for fermentation performance sugar consumption. Our study suggests fast enables it dominate environment quickly during early stages. This advantage may be critical outcome fermentations, evidenced direct performance.

Language: Английский

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Wine Fermentation as a Model System for Microbial Ecology and Evolution

Environmental Microbiology, Journal Year: 2025, Volume and Issue: 27(4)

Published: April 1, 2025

In vitro microbial communities have proven to be invaluable model systems for studying ecological and evolutionary processes experimentally. However, it remains unclear whether quantitative insights obtained from these laboratory can applied complex assembling evolving in their natural context. To bridge the gap between lab 'real-world', there is a need that better approximate semi-natural ecosystems. Wine fermentation presents an ideal system this purpose, balancing experimental tractability with rich dynamics. perspective piece we outline key features make wine fruitful ecologists biologists. We highlight diversity of environmentally mediated interactions shape community dynamics during fermentation, history populations, opportunity study impact ecologies on By integrating knowledge both research ecology evolution aim enhance understanding foster collaboration fields.

Language: Английский

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Design of a new model yeast consortium for ecological studies of enological fermentation

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

Published: May 6, 2024

Abstract Wine fermentation involves complex microbial communities of non- Saccharomyces yeast species besides the well-known cerevisiae . While extensive research has enhanced our understanding S. , 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

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Multi-omics framework to reveal the molecular determinants of fermentation performance in wine yeast populations

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: Oct. 15, 2024

Connecting the composition and function of industrial microbiomes is a major aspiration in microbial biotechnology. Here, we address this question wine fermentation, model system where diversity functioning fermenting yeast species are determinant flavor quality resulting wines.

Language: Английский

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Gradient boosted regression as a tool to reveal key drivers of temporal dynamics in a synthetic yeast community

FEMS Microbiology Ecology, Journal Year: 2024, Volume and Issue: 100(7)

Published: May 22, 2024

Microbial communities are vital to our lives, yet their ecological functioning and dynamics remain poorly understood. This understanding is crucial for assessing threats these systems leveraging biotechnological applications. Given that temporal linked community functioning, this study investigated the drivers of succession in wine yeast community. We experimentally generated population data used it create an interpretable model with a gradient boosted regression tree approach. The was trained on viable species populations various combinations, including pairs, triplets, quadruplets, evaluated predictive accuracy input feature importance. Key findings revealed inoculation dosage non-Saccharomyces significantly influences performance mixed cultures, while Saccharomyces cerevisiae consistently dominates regardless initial abundance. Additionally, we observed multispecies interactions where Wickerhamomyces anomalus were influenced by Torulaspora delbrueckii pairwise but interaction altered inclusion S. cerevisiae. provides insights into offers valuable machine learning-based analysis techniques applicable other microbial communities, opening new avenues harnessing communities.

Language: Английский

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