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The prospective of using DNA as a dietary biomarker was first highlighted 20 years ago[1]. Nowadays, DNA barcoding is broadly used to analyse the diet of both invertebrate and vertebrate organisms[2][3] and further detect and characterize their trophic interactions[4][5]. This approach is based on the identification of consumed species by characterization of DNA present in dietary samples[6], such as individual food remains, regurgitates, gut and fecal samples, or the homogenized body of the host organism, as it can occur for example with insects[7].


Method

Describe method for diet assessment and highlight main approaches depending on previous knowledge on diet: use of specific or generic markers. Also metabarcoding.

DNA barcoding with species-/group-specific primers has been used to identify the diet composition for species with known diets (Casper et al., 2007; Deagle et al., 2007; reviewed in King et al., 2008; King et al., 2010). This approach is feasible and cost effective when a small number of food types is diagnosed. When studying generalist species or predators with unknown diets, DNA metabarcoding with generic primers is mostly used (Clare et al., 2009; Deagle et al., 2009; Valentini et al., 2009; De Barba et al., 2014). When using generic primers that amplify ‘barcode’ regions from a broad range of food species, the amplifiable host DNA may largely outnumber the presence of prey DNA, complicating prey detection. However, a strategy to prevent the host DNA amplification has been developed, by the addition of a predator-specific blocking primer[8][9] [10]. Indeed, blocking primers for suppressing amplification of predator DNA produce amplicon mixes that are predominately food DNA[11][12].

Case studies

Mammals

bear (De Barba et al., 2014)

leopard cat (Shehzad et al., 2012)

macaroni penguin (Deagle et al., 2007)

seal (Casper et al., 2007; Meheust et al., 2015)

red bat (Clare et al., 2009)

Birds

Arthropods


Potentials and pitfalls compared with traditional diet assessment approaches

Casper et al., 2007a-b; Mumma et al., 2015; Shores et al., 2015; Nielsen et al., 2018 review

A major benefit is the ability to provide high taxonomic resolution of prey species and the sensitivity to rare, soft or highly degraded items and those that leave no visual trace, such as liquid feeding[13].



  1. ^ Höss, Matthias; Kohn, Michael; Pääbo, Svante; Knauer, Felix; Schröder, Wolfgang (1992-09). "Excrement analysis by PCR". Nature. 359 (6392): 199–199. doi:10.1038/359199a0. ISSN 0028-0836. {{cite journal}}: Check date values in: |date= (help)
  2. ^ King, R. A.; Read, D. S.; Traugott, M.; Symondson, W. O. C. (2008-01-14). "INVITED REVIEW: Molecular analysis of predation: a review of best practice for DNA-based approaches: OPTIMIZING MOLECULAR ANALYSIS OF PREDATION". Molecular Ecology. 17 (4): 947–963. doi:10.1111/j.1365-294X.2007.03613.x.
  3. ^ Pompanon, Francois; Deagle, Bruce E.; Symondson, William O. C.; Brown, David S.; Jarman, Simon N.; Taberlet, Pierre (2012). "Who is eating what: diet assessment using next generation sequencing". Molecular Ecology. 21 (8): 1931–1950. doi:10.1111/j.1365-294X.2011.05403.x. ISSN 1365-294X.
  4. ^ Sheppard, S. K.; Harwood, J. D. (2005-10). "Advances in molecular ecology: tracking trophic links through predator-prey food-webs". Functional Ecology. 19 (5): 751–762. doi:10.1111/j.1365-2435.2005.01041.x. ISSN 0269-8463. {{cite journal}}: Check date values in: |date= (help)
  5. ^ Erickson, David L.; Uriarte, Maria; García-Robledo, Carlos; Kress, W. John (2015-01-01). "DNA barcodes for ecology, evolution, and conservation". Trends in Ecology & Evolution. 30 (1): 25–35. doi:10.1016/j.tree.2014.10.008. ISSN 0169-5347. PMID 25468359.
  6. ^ POMPANON, FRANCOIS; DEAGLE, BRUCE E.; SYMONDSON, WILLIAM O. C.; BROWN, DAVID S.; JARMAN, SIMON N.; TABERLET, PIERRE (2011-12-15). "Who is eating what: diet assessment using next generation sequencing". Molecular Ecology. 21 (8): 1931–1950. doi:10.1111/j.1365-294x.2011.05403.x. ISSN 0962-1083.
  7. ^ HARWOOD, JAMES D.; DESNEUX, NICOLAS; YOO, HO JUNG S.; ROWLEY, DANIEL L.; GREENSTONE, MATTHEW H.; OBRYCKI, JOHN J.; O′NEIL, ROBERT J. (2007-10). "Tracking the role of alternative prey in soybean aphid predation byOrius insidiosus: a molecular approach". Molecular Ecology. 16 (20): 4390–4400. doi:10.1111/j.1365-294x.2007.03482.x. ISSN 0962-1083. {{cite journal}}: Check date values in: |date= (help)
  8. ^ Vestheim, Hege; Jarman, Simon N (2008). "Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs". Frontiers in Zoology. 5 (1): 12. doi:10.1186/1742-9994-5-12. ISSN 1742-9994.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  9. ^ SHEHZAD, WASIM; RIAZ, TIAYYBA; NAWAZ, MUHAMMAD A.; MIQUEL, CHRISTIAN; POILLOT, CAROLE; SHAH, SAFDAR A.; POMPANON, FRANÇOIS; COISSAC, ERIC; TABERLET, PIERRE (2012-01-17). "Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan". Molecular Ecology. 21 (8): 1951–1965. doi:10.1111/j.1365-294x.2011.05424.x. ISSN 0962-1083.
  10. ^ Jarman, Simon N.; McInnes, Julie C.; Faux, Cassandra; Polanowski, Andrea M.; Marthick, James; Deagle, Bruce E.; Southwell, Colin; Emmerson, Louise (2013-12-16). "Adélie Penguin Population Diet Monitoring by Analysis of Food DNA in Scats". PLoS ONE. 8 (12): e82227. doi:10.1371/journal.pone.0082227. ISSN 1932-6203.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  11. ^ Vestheim, Hege; Jarman, Simon N (2008). "Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs". Frontiers in Zoology. 5 (1): 12. doi:10.1186/1742-9994-5-12. ISSN 1742-9994. PMC 2517594. PMID 18638418.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  12. ^ Vestheim, Hege; Deagle, Bruce E.; Jarman, Simon N. (2010-09-29), "Application of Blocking Oligonucleotides to Improve Signal-to-Noise Ratio in a PCR", Methods in Molecular Biology, Humana Press, pp. 265–274, ISBN 9781607619437, retrieved 2019-03-29
  13. ^ Piñol, J.; San Andrés, V.; Clare, E. L.; Mir, G.; Symondson, W. O. C. (2013-08-20). "A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes". Molecular Ecology Resources. 14 (1): 18–26. doi:10.1111/1755-0998.12156. ISSN 1755-098X.
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