Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?

By B. Deagle, A. Chiaradia, Julie C. McInnes, Simon N. Jarman. Conservation Genetics, 2010

269 citations recorded by the source corpus.

DNA barcoding of faeces or stomach contents is an emerging approach for dietary analysis. We pyrosequenced mtDNA 16S markers amplified from faeces of captive little penguins (Eudyptula minor) to examine if recovered sequences reflect the proportions of species consumed. We also analysed wild little penguin faeces collected from 100 nests in southeast Australia. In the captive study, pilchards were the primary fish fed to the penguins and DNA sequences from pilchard were the most common sequences recovered. Sequences of three other fish fed in constant mass proportions (45:35:20) were all detected, but proportions of sequences (60:6:34) were considerably different than mass proportions in the diet. Correction factors based on relative mtDNA density in the fish did not improve diet estimates. Consistency between replicate samples suggests that the observed bias resulted from differences in prey digestibility. Detection of DNA from fish consumed before the penguins were brought into captivity indicates that a DNA signal in faeces can persist for at least 4 days after ingestion. In the wild-collected faeces, 24 distinct fish and 1 squid were identified; anchovy, barracouta and pilchard accounted for over 80% of these sequences. Our results highlight that DNA sequences recovered in dietary barcoding studies can provide semi-quantitative information on diet composition, but these data should be given wide confidence intervals.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e86cc0c5c7a0cf3945abce08b5b25401497308dc

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Citations in the corpus

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data? (2018, background): “Similarly, in faecal samples from captive penguins fed pilchards as the majority of their diet, sequence reads from pilchards were most common in the data; however, the three other fish species fed in mass ratios 45:35:20 produced sequences counts of 60:6:34 (Deagle et al. 2010).”
Ocean's eleven: a critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries (2015, background): “2010) and the little penguin (Spheniscidae; Deagle et al. 2010).”
A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents (2013, unknown): “It has also been found to be an effective tool for assessing the diversity of insects collected from traps [7] and characterize the diet of predators [8-11] and herbivores [12,13] through analysis of their feces or gut content.”
Harbour seals target juvenile salmon of conservation concern (2017, methodology): “…diet analysis, DNA metabarcoding is applied to scat samples or the stomach contents of individual animals, and DNA sequence percentages are used as a semiquantitative measure of the relative mass of species consumed (Deagle et al. 2010; Ford et al. 2016; Jarman et al. 2013; Pompanon et al. 2012).”
Resolving Food-Web Structure (2020, background): “This assumption is strong and loaded with caveats (see Section 4.3); it performs reasonably well in some contexts (Willerslev et al. 2014, Craine et al. 2015, Kartzinel et al. 2015) and worse in others (Deagle et al. 2010).”
Current progress in DNA barcoding and future implications for entomology (2011, background): “Although there have been no studies on insects using this method, several attempts have been made on diets of vertebrates (Soininen et al. 2009; Valentini et al. 2009; Deagle et al. 2010) and these showed that pyrosequencing is an effective method for DNA barcoding.”
Who is eating what: diet assessment using next generation sequencing (2012, background): “One study has investigated the accuracy of quantitative diet data from highthroughput amplicon sequencing (Deagle et al. 2010).”
Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates (2017, background): “To ensure fresh scats are collected in the field, some studies have captured or contained animals (Kartzinel & Pringle 2015; Lopes et al. 2015), or placed sheets to collect fresh faeces (Deagle et al. 2010; Vesterinen et al. 2016).”
From lavage to lipids: Estimating diets of seabirds (2012, unknown): “PLoS ONE 2: e831 doi: 10.1371/journal.pone.0000831 Deagle BE, Chiaradia A, McInnes J, Jarman SN (2010) Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?”
Methods of estimating marine mammal diets: A review of validation experiments and sources of bias and uncertainty (2012, background): “Recently, Deagle et al. (2010) pyrosequenced mtDNA markers amplified from feces of captive little penguins (Eudyptula minor) fed known diets.”
How will the ‘molecular revolution’ contribute to biological recording? (2015, background): “…bison, Bison bonasus, Kowalczyk et al., 2011; Asian musk shrew, Suncus murinus, Brown DS et al., 2014), birds (little penguins, Eudyptula minor, Deagle et al., 2010; Cory’s shearwaters, Calonectris diomedea, Alonso et al., 2014), reptiles (slow worms, Anguis fragilis, Brown, Jarman, &…”
Use of DNA metabarcoding for stomach content analysis in the invasive lionfish Pterois volitans in Puerto Rico (2016, background): “There are known constraints on metabarcoding, including the inability to quantify the species information obtained (Deagle et al. 2010, 2013, Bowles et al. 2011, Murray et al. 2011).”