Exciting strain‐level resolution studies of the food microbiome

Ercolini, Danilo

doi:10.1111/1751-7915.12593

Cited by 15 publications

(6 citation statements)

References 11 publications

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“…Through variations in abiotic (salinity, pH, resource availability) and biotic (presence of bacterial and fungal neighbors) selection pressures applied during cheese production and aging (25), cheese microbiomes have the potential to evolve new genotypes and phenotypes with divergent functions. Some studies have characterized the strain diversity of individual cheese rind microbes for technological applications (26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36), but whether this strain diversity impacts ecological interactions and community development of cheese rind microbial communities has not been examined.…”

Section: Abstract Cheese Genomics Microbial Communities Microbiome Assembly Strain Diversitymentioning

confidence: 99%

Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function

et al. 2020

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Diversification can generate genomic and phenotypic strain-level diversity within microbial species. This microdiversity is widely recognized in populations, but the community-level consequences of microbial strain-level diversity are poorly characterized. Using the cheese rind model system, we tested whether strain diversity across microbiomes from distinct geographic regions impacts assembly dynamics and functional outputs. We first isolated the same three bacterial species (Staphylococcus equorum, Brevibacterium auranticum, and Brachybacterium alimentarium) from nine cheeses produced in different regions of the United States and Europe to construct nine synthetic microbial communities consisting of distinct strains of the same three bacterial species. Comparative genomics identified distinct phylogenetic clusters and significant variation in genome content across the nine synthetic communities. When we assembled each synthetic community with initially identical compositions, community structure diverged over time, resulting in communities with different dominant taxa. The taxonomically identical communities showed differing responses to abiotic (high salt) and biotic (the fungus Penicillium) perturbations, with some communities showing no response and others substantially shifting in composition. Functional differences were also observed across the nine communities, with significant variation in pigment production (light yellow to orange) and in composition of volatile organic compound profiles emitted from the rinds (nutty to sulfury). IMPORTANCE Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities also suggest that strain-level diversity has the potential to drive variability in the aesthetics and quality of surface-ripened cheeses.

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Section: Abstract Cheese Genomics Microbial Communities Microbiome Assembly Strain Diversitymentioning

confidence: 99%

Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function

et al. 2020

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“…Микроорганизмы, которые используются при производстве (сквашивании) йогуртов, наряду с теми микробами, которые добавляются в йогурты в качестве пробиотических штаммов, оказывают существенное влияние на формирование микропейзажа человека, получающего этот продукт [37,38]. Для идентификации микробов, внесенных с ферментированным продуктом, в последние годы применяются молекулярно-генетические методы [39,40]. Установлено, что многие из этих микроорганизмов выживают при пассаже через желудочно-кишечный тракт.…”

Section: йогурты и становление кишечной микробиотыunclassified

Yoghurts in Infants’ Nutrition: Opportunities of Infectious and Non-Communicable Diseases’ Prevention

Belyaeva,

Bombardirova,

Turti

2023

Vopr. sovr. pediatr.

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This review provides data on the use of yogurts in infants’ nutrition. The properties of these fermented milk products and associated urgent and delayed sanogenetic effects are described. The experience of yogurts (enriched with pre- and probiotics) implementation in the nutrition therapy of children who have undergone infectious diseases is shown. The yogurt usage for intestinal microbiota disorders correction in children with functional digestive disorders and chronic somatic pathology is discussed.

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“…Deeply understanding changes in genomic features between strains belonging to the same species in foods will give the ability to easily modulate specific strains in processing conditions. By this new knowledge we can have the possibility for example to control the dynamics and conditions necessary to modulate proteolytic or lipolytic activity and obtain a desired cheese aroma (Ercolini, 2016). The importance of this technique should be highlighted not only in the study of the microbial dynamics for organoleptic or technological purposes, but also in the light of risk assessment in the dairy food chain.…”

Section: Deeply Understanding Changes In Genomic Featuresmentioning

confidence: 99%

Microbiota of Milk and Dairy Foods: Structure and Function by -omics Approaches

Ferrocino

Rantsiou

Cocolin

2022

Encyclopedia of Dairy Sciences

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In the era of big data we are able to generate billions of individual sequences in order to better identify strains, enzymes or genes in complex food systems, including milk and dairy products. In the last 20 years the number of studies, projects and researchers has increased, trying to discover the microbial complexity in food systems. The -omics technologies that can also be called food-omics techniques (including the study of microbes, genes, proteins and metabolites in food systems) are already widely used to track and map shifts in microbial communities, discover new molecules, new metabolic pathways and also new strains.

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Exciting strain‐level resolution studies of the food microbiome

Cited by 15 publications

References 11 publications

Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function

Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function

Yoghurts in Infants’ Nutrition: Opportunities of Infectious and Non-Communicable Diseases’ Prevention

Microbiota of Milk and Dairy Foods: Structure and Function by -omics Approaches

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