Fermented food products in the era of globalization: tradition meets biotechnology innovations

Galimberti, Andrea; Bruno, Antonia; Agostinetto, Giulia; Galimberti, Andrea; Guzzetti, Lorenzo; Labra, Massimo

doi:10.1016/j.copbio.2020.10.006

Cited by 60 publications

(29 citation statements)

References 56 publications

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“…Since its "formalization" in 2012, the DNA metabarcoding approach has revolutionized the field of biodiversity investigation, and it has even provided insights for studying biological interactions. Its application has rapidly spread and has contributed to research contexts such as microbiome [78,79], food [80][81][82], trophic ecology [83,84], and environmental DNA-based analyses [85]. In spite of its usefulness, methodological choices during the whole DNA metabarcoding pipeline and specifically the bioinformatics processing could deeply influence the obtained results and their interpretation [86][87][88].…”

Section: Discussionmentioning

confidence: 99%

Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches

et al. 2021

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Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological results. Here, we reviewed how this choice has been addressed in 43 studies featuring pollen DNA metabarcoding, which highlighted a very high heterogeneity of filtering methods. We assessed how these strategies shaped pollen assemblage composition, species richness, and interaction networks. To do so, we compared four processing methods: unfiltering, filtering with a proportional 1% of sample reads, a fixed threshold of 100 reads, and the ROC approach (Receiver Operator Characteristic). The results indicated that filtering impacted species composition and reduced species richness, with ROC emerging as a conservative approach. Moreover, in contrast to unfiltered networks, filtering decreased network Connectance and Entropy, and it increased Modularity and Connectivity, indicating that using cut-off thresholds better describes interactions. Overall, unfiltering might compromise reliable ecological interpretations, unless a study targets rare species. We discuss the suitability of each filtering type,plead for justifying filtering strategies on biological or methodological bases and for developing shared approaches to make future studies more comparable.

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Section: Discussionmentioning

confidence: 99%

Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches

et al. 2021

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“…Since its ‘formalization’ in 2012, the DNA metabarcoding approach has revolutionized the field of biodiversity investigation and provided many insights into the study of biological interactions. Its application has rapidly spread and has contributed to support several research contexts such as microbiome (Bruno et al, 2018; Frigerio et al, 2020), food, (Galimberti et al, 2015; 2019; 2021), trophic ecology (Casey et al, 2019; Arrizabalaga-Escudero et al, 2018), and environmental DNA-based analyses (Ruppert et al, 2019). In spite of its usefulness, the whole DNA metabarcoding pipeline and specifically the bioinformatic processing could deeply influence the obtained results and their interpretation (Andriollo et al, 2019; Zinger et al, 2019 Elbrecht et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Harnessing the power of metabarcoding in the ecological interpretation of plant-pollinator DNA data: strategies and consequences of reads filtering

Tommasi

Ferrari

Galimberti

et al. 2021

Preprint

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DNA metabarcoding approaches to analyse complex mixtures of pollen has become the standard in pollination biology, especially in the light of recent threats affecting pollination. In spite of the increasing adoption of High Throughput Sequencing (HTS) approaches, these studies generate huge numbers of raw reads, some of which might be associated to false positives or infrequently recorded species with potentially little biological information. If these reads are not discarded (i.e. pruned), they can lead to changes in the ecological findings and lead to biased conclusions. In this study we reviewed 42 papers in the recent pollen DNA metabarcoding literature and focused on the type of pruning applied. We also tested whether the different types of those cut off threshold may leave a mark on the DNA metabarcoding data. To do so, we compared for the first time community composition, species richness and networks of species interactions (i.e. Connectace, Modularity, Connectivity and Shannon entropy) associated with the most relevant ways of treating HTS outputs: no cut (no reads filtering), or cutting levels obtained as proportional 1% of sample total reads, or as fixed amount of 100 reads, or from ROC (Receiver operator characteristic). Results clearly indicated that pruning type shapes species composition and that to apply or not a threshold dramatically impacts ecological indices, potentially increasing the risk of misinterpreting DNA metabarcoding data under an ecological point of view. Given the high methodological heterogeneity from the revised literature, we discuss in what conditions filtering types may be more appropriate, and also recommend to biologically justify the pruning threshold when analysing DNA metabarcoding raw reads, and to develop shared approaches to make future studies more comparable.

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“…It is estimated that the deliberate fermentation of foods and beverages as a means to extend their shelf-life has been practised for almost 13,000 years [1] . Early food fermentations were introduced at this time on every continent and fermentation substrates encompassed regionally and seasonally available raw materials, including animal milk, meats, fish, cereals, vegetables, legumes, seeds, roots, and fruits [2,3] . While the earliest fermentations were spontaneous and prone to quality variation and failure, modern industry has adapted these fermentations to facilitate large scale productions with highly reproducible outcomes.…”

Section: Introductionmentioning

confidence: 99%

Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods

White¹,

Yu²,

Eraclio³

et al. 2022

MRR

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Food fermentation relies on the activity of robust starter cultures, which are commonly comprised of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus. While bacteriophage infection represents a persistent threat that may cause slowed or failed fermentations, their beneficial role in fermentations is also being appreciated. In order to develop robust starter cultures, it is important to understand how phages interact with and modulate the compositional landscape of these complex microbial communities. Both culture-dependent and -independent methods have been instrumental in defining individual phage-host interactions of many lactic acid bacteria (LAB). This knowledge needs to be integrated and expanded to obtain a full understanding of the overall complexity of such interactions pertinent to fermented foods through a combination of culturomics, metagenomics, and phageomics. With such knowledge, it is believed that factory-specific detection and monitoring systems may be developed to ensure robust and reliable fermentation practices. In this review, we explore/discuss phage-host interactions of LAB, the role of both virulent and temperate phages on the microbial composition, and the current knowledge of phageomes of fermented foods.

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Fermented food products in the era of globalization: tradition meets biotechnology innovations

Cited by 60 publications

References 56 publications

Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches

Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches

Harnessing the power of metabarcoding in the ecological interpretation of plant-pollinator DNA data: strategies and consequences of reads filtering

Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods

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