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DNA barcoding is broadly used to analyse the diet of both invertebrate and vertebrate organisms[1][2] to detect and describe their trophic interactions[3][4]. This approach is based on the identification of consumed species by characterization of DNA present in dietary samples[5], e.g. individual food remains, regurgitates, gut and fecal samples, homogenized body of the host organism (for example with insects[6]).

The barcode markers utilized for amplification will differ depending on the diet of the organism. For herbivore diets, the standard DNA barcode loci will differ significantly depending on the plant taxonomic level[7]. Therefore, for identifying plant tissue at the taxonomic family or genus level, the markers rbcL and trn-L-intron are used, which differ from the loci ITS2, matK, trnH-psbA (noncoding intergenic spacer) used to identify diet items to genus and species level[8]. For animal prey, the most broadly used DNA barcode markers to identify diets are the mitochondrial Cytocrome C oxydase (COI) and Cytochrome b (cytb)[9]. However, DNA metabarcoding is used to identify most of the prey items when the diet is broad and diverse[10].


Applications

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)

Fish

Birds

Arthropods


Potentials and challanges

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[11][12] [13]. Indeed, blocking primers for suppressing amplification of predator DNA produce amplicon mixes that are predominately food DNA[14][15].


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[16].

Diet quantification issue



  1. ^ 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.
  2. ^ 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.
  3. ^ 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)
  4. ^ 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.
  5. ^ 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.
  6. ^ 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)
  7. ^ Kress, W. John; García-Robledo, Carlos; Uriarte, Maria; Erickson, David L. (2015-01). "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. {{cite journal}}: Check date values in: |date= (help)
  8. ^ Kress, W. John; García-Robledo, Carlos; Uriarte, Maria; Erickson, David L. (2015-01). "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. {{cite journal}}: Check date values in: |date= (help)
  9. ^ Tobe, Shanan S.; Kitchener, Andrew; Linacre, Adrian (2009-12). "Cytochrome b or cytochrome c oxidase subunit I for mammalian species identification—An answer to the debate". Forensic Science International: Genetics Supplement Series. 2 (1): 306–307. doi:10.1016/j.fsigss.2009.08.053. ISSN 1875-1768. {{cite journal}}: Check date values in: |date= (help)
  10. ^ Jakubavičiūtė, Eglė; Bergström, Ulf; Eklöf, Johan S.; Haenel, Quiterie; Bourlat, Sarah J. (2017-10-23). "DNA metabarcoding reveals diverse diet of the three-spined stickleback in a coastal ecosystem". PLOS ONE. 12 (10): e0186929. doi:10.1371/journal.pone.0186929. 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  12. ^ 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.
  13. ^ 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)
  14. ^ 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)
  15. ^ 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
  16. ^ 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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