Tasting the differences: Microbiota analysis of different insect-based novel food

Frigerio, Jessica; Agostinetto, Giulia; Galimberti, Andrea; Mattia, Fabrizio De; Labra, Massimo; Bruno, Antonia

doi:10.1016/j.foodres.2020.109426

Cited by 19 publications

(10 citation statements)

References 56 publications

(36 reference statements)

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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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“…22 Besides having an average protein content that varies from 30% to 65% on a dry basis, insects are sources of lipids, carbohydrates, vitamins, and minerals, such as iron, zinc, and calcium. 23,24 The digestibility of insect proteins can vary from 76 to 96%, being lower than the digestibility of eggs (95%) and beef (98%), however, superior to the digestibility of vegetable proteins (13-60%). 24,25 Regarding the amino acids present in the protein fraction, 35 to 50% of these are essential.…”

Section: Edible Insectsmentioning

confidence: 99%

Insects as a sustainable source of emerging proteins and their processing to obtain bioactive compounds: an updated review

de Matos,

Rasera,

de Castro

2024

Sustainable Food Technol.

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Tasting the differences: Microbiota analysis of different insect-based novel food

Cited by 19 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

Insects as a sustainable source of emerging proteins and their processing to obtain bioactive compounds: an updated review

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