DNA metabarcoding of faecal samples at AIM


In many metabarcoding applications, in particular those applied to tracking large mammals, bats, or birds, the animal is difficult to observe directly, but it may be possible to find residual material, such as faeces. An exact determination of the species can be of crucial importance, e.g. for implementing protective measures. Furthermore, in times of changing and ever diminishing biodiversity, it is important to know what kind of food is available to the animal throughout the year, and how changes in the food web might affect the individual species.



Ideally, faecal samples will contain information about the host, as well as the prey of the host. Whether the species can be identified depends heavily on the quality and the degree of degradation of the genetic material in the faeces. That said, molecular methods such as DNA metabarcoding make it possible to monitor animals without having to observe them directly, supplementing the data recorded using camera traps. Standard prey detection methods are mostly restricted to visual detection of remains in faecal samples. Their effectiveness is limited by the host's digestive system and the resulting quality of the remains of the prey parts. Consequently, very small or well-digested prey may no longer be identifiable and can no longer be recognized using visual methods.


Fortunately, even though small and well-digested prey might not be identifiable visually, faecal samples usually still contain both the animal's own DNA, as well as that of the eaten animals, fungi and plants. By analyzing the DNA found in the faeces after the digestive process, DNA metabarcoding can be used to determine both the animal species and that of the eaten species. The latter enables efficient monitoring of domestic diversity without disturbing the animals.



DNA metabarcoding offers a non-inasive and quick way to gain insight into the distribution and occurrence of individual species, as well as local biodiversity via the food web. This enables species to be protected and promoted in a more targeted manner and for specific issues to be examined.

There are many applications for DNA metabarcoding of faecal samples, for instance:

  • support in species monitoring, e.g. observation of protected species or urban mammals;
  • prey analysis, creation of lists of species of consumed prey taxa;
  • indirect identification of food left behind by humans that reappears in the food web (e.g., raccoon);
  • detection of invasive species and pest species such as plant pest species;
  • evidence of disease-transmitting species, e.g. via the detection of mosquito species in bat droppings;
  • statements about the health status of individuals, e.g. via the detection of parasites in faeces;
  • investigation of changes in the food spectrum due to changes in the landscape.


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