Mixed culture engineering for steering starter functionality

Spus, M.

doi:10.18174/383695

Cited by 4 publications

(9 citation statements)

References 144 publications

(251 reference statements)

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“…Lowly abundant species may be still important for ecosystem functionality but may be missed when assembling the synthetic community. In an experiment using a microbial community from cheese, an initially very rare species became predominant upon long-term propagation in a novel environment [ 34 ]. Further experiments showed the influence of bacteriophages on culture diversity.…”

Section: Microbial Model Systemsmentioning

confidence: 99%

“…Researchers found that the simple bacterial blends used in their experiments did not represent the diversity of the original complex starter culture enough to evaluate the role of phage predation [ 35 ]. Later, Spus repeated the experiment with more complex blends of bacterial strains and highlighted the impact of phage predation on community diversity [ 34 ].…”

Section: Microbial Model Systemsmentioning

confidence: 99%

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Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

Alekseeva

Groenenboom

Smid

et al. 2021

IJERPH

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Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body of theory, which has partially been experimentally tested by mimicking evolutionary processes in the laboratory. In the first part of this perspective, we outline what model systems are used for experimental testing of eco-evolutionary processes, ranging from simple microbial combinations and, more recently, to complex natural communities. Microbial communities of spontaneous fermented foods are a promising model system to study eco-evolutionary dynamics. They combine the complexity of a natural community with extensive knowledge about community members and the ease of manipulating the system in a laboratory setup. Due to rapidly developing sequencing techniques and meta-omics approaches incorporating data in building ecosystem models, the diversity in these communities can be analysed with relative ease while hypotheses developed in simple systems can be tested. Here, we highlight several eco-evolutionary questions that are addressed using microbial communities from fermented foods. These questions relate to analysing species frequencies in space and time, the diversity-stability relationship, niche space and community coalescence. We provide several hypotheses of the influence of these factors on community evolution specifying the experimental setup of studies where microbial communities of spontaneous fermented food are used.

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Section: Microbial Model Systemsmentioning

confidence: 99%

Section: Microbial Model Systemsmentioning

confidence: 99%

Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

Alekseeva

Groenenboom

Smid

et al. 2021

IJERPH

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“…Species (initially) present at low abundance may be important for eco-system functionality but may be missed when assembling the synthetic community. In an experiment using a microbial community from cheese, an initially very rare species became predominant upon longterm propagation in a novel environment (3). A further illustration is an experiment on the influence of bacteriophages on culture diversity of Spus and his colleagues (2015).…”

Section: Synthetic Communitiesmentioning

confidence: 99%

“…These non-co-operators can stabilise a diverse community when growth rates of different members greatly differ. The member with the highest growth rate is the preferred victim of a predator according to the kill the winner principle (3,101). The fastest grower in a community could potentially provide most nutrients for a predator and will therefore be the preferred pray, keeping the community stable.…”

Section: Diversity Stability Hypothesismentioning

confidence: 99%

“…The maintained diversity can be explained by negative frequency dependence, where a species with the highest abundance is also most likely to have enemies such as bacteriophages. This is also referred to as the 'kill the winner' principle (3,101). Stability in a certain diversity can also be a necessity of a system because the addition of species as well as the removal of species can destabilize the system due to the (evolved) bacterial interactions (210).…”

Section: A B Cmentioning

confidence: 99%

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Microbial community dynamics in traditionally fermented milk

Groenenboom

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Table of contents Chapter 1 Introduction Chapter 2 Microbial communities from spontaneously fermented foods as model system to study eco-evolutionary dynamics. Chapter 3 Robust sampling and preservation of DNA for microbial community profiling in field experiments. Chapter 4 Microbial population dynamics during traditional production of Mabisi, a spontaneously fermented milk product from Zambia. A field trial. Chapter 5 Does change in bacterial species composition of natural communities reflect adaptation to a new environment? Chapter 6 Bacterial community dynamics in Lait caillé, a traditional product of spontaneous fermentation from Senegal.

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Influence of metabolic guilds on a temporal scale in an experimental fermented food derived microbial community

Leale,

Auxier,

Smid

et al. 2023

FEMS Microbiology Ecology

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The influence of community diversity, which can be measured at the level of metabolic guilds, on community function is a central question in ecology. Particularly, the long-term temporal dynamic between a community's function and its diversity remains unclear. We investigated the influence of metabolic guild diversity on associated community function by propagating natural microbial communities from a traditionally fermented milk beverage diluted to various levels. Specifically, we assessed the influence of less abundant microbial types, such as yeast, on community functionality and bacterial community compositions over repeated propagation cycles amounting to ∼100 generations. The starting richness of metabolic guilds had a repeatable effect on bacterial community compositions, metabolic profiles, and acidity. The influence of a single metabolic guild, yeast in our study, played a dramatic role on function, but interestingly not on long-term species sorting trajectories of the remaining bacterial community. Our results together suggest an unexpected niche division between yeast and bacterial communities and evidence ecological selection on the microbial communities in our system.

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Mixed culture engineering for steering starter functionality

Cited by 4 publications

References 144 publications

Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

Microbial community dynamics in traditionally fermented milk

Influence of metabolic guilds on a temporal scale in an experimental fermented food derived microbial community

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