Comparison of diet and prey selectivity of the Pyrenean desman and the Eurasian water shrew using next-generation sequencing methods

Biffi, M.; Laffaille, Pascal; Jabiol, Jérémy; André, Adrien; Gillet, François; Lamothe, Sylvain; Michaux, Johan; Buisson, Laëtitia

doi:10.1016/j.mambio.2017.09.001

Cited by 18 publications

(30 citation statements)

References 56 publications

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“…Overall, our results are similar to those of previous studies on the diet of the Pyrenean desman [ 31 – 33 , 36 – 38 ]. All studies found high amounts of Ephemeroptera, Plecoptera, and Trichoptera.…”

Section: Discussionsupporting

confidence: 92%

“…A substantial proportion of excrements with terrestrial species such as Orthoptera, Hemiptera and Lepidoptera, among others, was reported in the genetic study of Biffi et al [ 37 ]. However, since Biffi et al [ 37 ] only used frequencies of occurrence and did not associate read numbers to each species, these molecular data do not allow a quantitative assessment of the prey consumed, as already suggested [ 38 ]. Notably, studies based on morphological examination of gut contents also found terrestrial organisms, but only at much lower proportions [ 31 – 33 ].…”

Section: Discussionmentioning

confidence: 99%

“…Metabarcoding of fecal samples presents a potential solution to these problems because sampling is non-invasive, requires significantly less effort, and prey items may be reliably identified to species level provided a comprehensive reference library is available [ 34 , 35 ]. Recent genetic studies on the diet of the Pyrenean desman [ 36 – 38 ] already employed a metabarcoding approach. These works were based on BLAST database searches alone, which allow an accurate identification at the species level but have more difficulties with the identification at higher taxonomic ranks due to inherent limitations of this method derived from heterogeneity of evolutionary rates [ 39 – 41 ].…”

Section: Introductionmentioning

confidence: 99%

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A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal

et al. 2018

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Metabarcoding allows the genetic analysis of pooled samples of various sources. It is becoming popular in the study of animal diet, especially because it allows the analysis of the composition of feces without the need of handling animals. In this work, we studied the diet of the Pyrenean desman (Galemys pyrenaicus), a small semi-aquatic mammal endemic to the Iberian Peninsula and the Pyrenees, by sequencing COI minibarcodes from feces using next-generation sequencing techniques. For the identification of assembled sequences, we employed a tree-based identification method that used a reference tree of sequences of freshwater organisms. The comparison of freshly collected fecal samples and older samples showed that fresh samples produced significantly more sequencing reads. They also rendered more operational taxonomical units (OTUs), but not significantly. Our analyses of 41 samples identified 224 OTUs corresponding to species of the reference tree. Ephemeroptera, Diptera excl. Chironomidae, and Chironomidae were the most highly represented groups in terms of reads as well as samples. Other groups of freshwater organisms detected were Plecoptera, Trichoptera, Neuropteroida, Coleoptera, Crustacea, and Annelida. Our results are largely in line with previous morphological and genetic studies on the diet of the Pyrenean desman, but allowed the identification of a higher diversity of OTUs in each sample. Additionally, the bioinformatic pipeline we developed for deep sequencing of fecal samples will enable the quantitative analysis of the diet of this and other species, which can be highly useful to determine their ecological requirements.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal

et al. 2018

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“…We used the 133-bp minibarcode of COI described in Gillet et al (2015). Its efficiency to identify a wide taxonomic range of arthropods from France has been proven recently: 20 arthropod orders were detected in the diet of Galemys pyrenaicus and 24 in the diet of Neomys fodiens (Biffi, Gillet, et al, 2017;Biffi, Laffaille, et al, 2017). We have verified the discriminatory power of this minibarcode for resolving bat species identification using an in silico analysis based on 444 BOLD (Barcode of Life DataBase) reference sequences corresponding to the 33 bat species found in France (see the phylogenetic tree provided in Figure S1 and the Table S2).…”

Section: Coi Minibarcode Pcr and Library Constructionmentioning

confidence: 99%

Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis

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et al. 2018

Molecular Ecology Resources

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Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the "all at once" taxonomic identification of bats and their arthropod prey for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods, and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity and amplification biases. Our parallel identification strategy of predators and prey reduces the risk of mis-assigning prey to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing "chirosurveillance" and conservation strategies.

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“…Such sequencing techniques and related automated species identification allow the characterization of multiple assemblages of prey species through a single sequencing process, and has typically been applied to identify food resources recovered in feces, stomach contents or regurgitates [4]. So far, metabarcoding approaches has been used to unravel the diet of a diversity of invertebrates [5–7], fishes [8–10], reptiles [11], birds [12] or mammals [13–16]. It has been widely used in descriptive studies of diet composition, foraging strategies, and to resolve more complex questions about trophic ecology (e.g., resource partitioning, food web studies).…”

Section: Introductionmentioning

confidence: 99%

The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus

et al. 2019

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Metabarcoding of feces has revolutionized the knowledge of animal diets by providing unprecedented resolution of consumed resources. However, it is still unclear how different methodological approaches influence the ecological conclusions that can be drawn from such data. Here, we propose a critical evaluation of several data treatments on the inferred diet of the bat Plecotus auritus using guano regularly collected from various colonies throughout the entire active season. First and unlike previous claims, our data indicates that DNA extracted from large amounts of fecal material issued from guano accumulates yield broader taxonomic diversity of prey than smaller numbers of pellets would do, provided that extraction buffer volumes are adapted to such increased amounts of material. Second, trophic niche analyses based on prey occurrence data uncover strong seasonality in the bat’s diet and major differences among neighboring maternity colonies. Third, while the removal of rare prey items is not always warranted as it introduces biases affecting particularly samples with greater prey species richness. Fourth, examination of distinct taxonomic depths in diet analyses highlights different aspects of food consumption providing a better understanding of the consumer’s diet. Finally, the biologically meaningful patterns recovered with presence-absence approaches are virtually lost when attempting to quantify prey consumed using relative read abundances. Even in an ideal situation where reference barcodes are available for most potential prey species, inferring realistic patterns of prey consumption remains relatively challenging. Although best practice in metabarcoding analyses will depend on the aims of the study, several previous methodological recommendations seem unwarranted for studying such diverse diets as that of brown long-eared bats.

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Comparison of diet and prey selectivity of the Pyrenean desman and the Eurasian water shrew using next-generation sequencing methods

Cited by 18 publications

References 56 publications

A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal

A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal

Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis

The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus

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