Methodological trends and perspectives of animal dietary studies by noninvasive fecal DNA metabarcoding

Abstract

Molecular scatology is a genetic technique used to analyze feces in studies of animal ecology (Kohn & Wayne, 1997), and it encompasses the field of environmental DNA studies (Taberlet, Coissac, Hajibabaei, & Rieseberg, 2012). Since 1990, fecal samples have been commonly used as noninvasive genetic sources for animal populations to estimate phylogeny, home range, and population sizes (Kohn & Wayne, 1997). Simultaneously, molecular techniques to detect food items from fecal DNA have been developed to overcome the difficulties of detecting food through conventional methods. Fecal DNA analyses are able to detect prey items that are difficult to identify by direct observations of feeding behavior, and these analyses also help where a robust diagnostic tool for identifying morphological features from visual observation of gut contents and feces is lacking. The first DNA-based diet studies detected specific food by taxon-specific PCR amplification (Deagle et al., 2005; Höss, Kohn, Pääbo, Knauer, & Schröder, 1992). Then, cloning and Sanger sequencing were used to isolate food DNA sequences from a multispecies mixture of fecal DNA (Deagle et al., 2007; Jarman, Deagle, & Gales, 2004). The taxa of the obtained sequences were identified by

Diet diversity and environment determine the intestinal microbiome and bacterial pathogen load of fire salamanders

“…Amounts of DNA in the fecal matter need to be exactly proportionate to ingested prey biomass, which is not always the case, due to biological and technical biases, such as different speeds of digestion, size of ingested prey, possible presence of multicopy genes, DNA degradation in fecal samples and availability of DNA reference sequences of potential prey in public databases [59][60][61] . Nonetheless, DNA sequencing of fecal matter is a more viable technique to identify soft-tissued, easily digestible prey 59 , and able to provide higher resolution than conventional stomach content analysis 62,63 . This technique has been applied successfully in unravelling diets for many species, including birds 44,56 , mammals 59,64,65 , fish 66,67 and reptiles 68 , but so far has not been used for amphibians.…”

Research priorities to fill knowledge gaps in wild boar management measures that could improve the control of African swine fever in wild boar populations

“…This study should be carried out together with a cross‐sectional study of the wild boar diet, using barcoding techniques of non‐invasive faecal samples over different seasons (Monterroso et al., 2019 ; Ando et al., 2020 ).…”

eDNA metabarcoding reveals dietary niche overlap among herbivores in an Indian wildlife sanctuary

“…More recently, advances in eDNA metabarcoding have enabled broad application of this method in biodiversity monitoring (for reviews see, e.g., Bohmann et al., 2014; Cristescu & Hebert, 2018), and the application to fecal samples provides a valuable alternative approach for dietary reconstruction. This value is evidenced both by direct comparison of different approaches (e.g., Newmaster et al., 2013) and by the rapidly increasing number of studies using this method (for recent reviews see, e.g., Ando et al., 2020; de Sousa, Silva, & Xavier et al., 2019). So far, fecal DNA metabarcoding has been successfully applied to reconstruct the diets of a range of different herbivores, including birds, insects, molluscs (e.g., Valentini et al., 2009) and a wide range of mammalian herbivores such as small rodents (e.g., Lopes et al., 2015; Sato et al., 2018; Soininen et al., 2014, 2015), a number of deer species (e.g., Bison et al., 2015; Czernik et al., 2013; Fløjgaard, De Barba, Taberlet, & Ejrnæs, 2017; Rayé et al., 2011), tapirs (e.g., Hibert et al., 2013), several primate species (e.g., Bradley et al., 2007), the European bison (e.g., Kowalczyk et al., 2011, 2019), and large herbivore assemblages in Kenya (Kartzinel et al., 2015; Kartzinel & Pringle, 2020) and Mozambique (Pansu et al., 2019).…”