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Metagenomics and Histology Gave Complementary Views of Parasites in Red Deer and European Roe Deer

Two European roe deer standing in a field
Research · Disease, parasites & microbiology

A study of 106 wild cervids in Mecklenburg-Western Pomerania, Germany, found that shotgun metagenomics and histology provided different but complementary views of gastrointestinal parasites. Shotgun metagenomics sequences many DNA fragments in a sample without targeting one parasite in advance, while histology examines thin tissue sections directly under the microscope. The researchers examined 78 red deer (Cervus elaphus) and 28 European roe deer (Capreolus capreolus), analysing parasite DNA in faeces and parasites and tissue changes directly in the gastrointestinal tract.

The sampling was not identical for the two species. Red deer were collected across roughly a year at Gut Klepelshagen, whereas roe deer were sampled during spring at two areas south of Greifswald. The authors therefore stress that infection levels in the two species should not be compared directly. Statistical analyses of season, age and sex were restricted to the larger red-deer dataset.

Red deer showed clear seasonal changes

In the red-deer metagenomic data, parasite richness—the number of parasite genera detected—was higher in summer than in autumn and winter. Shannon diversity, which combines how many genera are present with how evenly they are represented, and community evenness were higher in autumn than in summer. Community composition also differed clearly between summer and autumn.

The metagenomic parasite profiles differed between the two species. In red deer, Entamoeba, Blastocystis and Onchocerca produced the highest genus-level read abundances. In roe deer, Haemonchus, Chabertia and Ostertagia stood out. These read abundances are the proportions of DNA sequence fragments assigned to each parasite group; they describe the sequencing data rather than numbers of parasites. The authors caution against treating them as direct estimates of parasite prevalence or burden in the populations.

Histology found worms that sequencing sometimes missed

Histological examination found helminths in 21 of 78 red deer and 21 of 28 roe deer. Most were nematodes consistent with trichostrongyloid worms, often in the abomasum. In roe deer, 19 animals had nematodes in the abomasum. The tissue sections also showed inflammatory changes associated with parasitic infestation in almost all of the affected samples examined in detail.

The two methods did not consistently agree within individual animals. Some deer had parasites visible in tissue despite little or no corresponding metagenomic signal, while others produced many parasite reads without parasites being detected histologically.

The methods answer different parts of the same question

The authors explain that neither negative result necessarily proves that a parasite was absent. Parasites do not continuously shed DNA or reproductive stages into faeces, so a small faecal sample may miss them. Histology, meanwhile, examines only small sections of tissue and can also miss an infection. Metagenomic assignments additionally depend on the quality and completeness of reference databases and can be affected by contamination.

Shotgun metagenomics offers broad information from easily collected faecal material, whereas histology can demonstrate a parasite directly in tissue and reveal its life stage and pathological context. The study therefore presents the approaches as complementary rather than interchangeable. Its strongest conclusions concern parasite composition, seasonal dynamics and method performance—not a direct comparison of parasite prevalence between red deer and roe deer.

Sources and image credit

  1. Lechleiter, N., Wedemeyer, J., Junker, J., Sehl-Ewert, J., & Homeier-Bachmann, T. (2026). Gastrointestinal parasites of red and roe deer investigated via metagenomics and histology. Parasites & Vectors, 19, 277.Open-access primary research article. The study examined 106 hunt-harvested wild cervids in Mecklenburg-Western Pomerania using shotgun metagenomics of feces and histopathology of gastrointestinal tissue, with seasonal analyses in red deer and an explicit warning against direct prevalence comparisons between the two host species.

Image: Kristian Pikner / Wikimedia Commons — two wild European roe deer in Lääneranna Parish, Estonia, 30 September 2017; Wikimedia Commons Quality Image. Representative image for this story; not presented as an animal or scene from the reported study or event. · CC BY-SA 4.0 · Source

About this content: This story was produced with AI assistance within an editorial workflow developed by Wildlife Vagabond. Editorial responsibility remains with Wildlife Vagabond.How AI is used

Disease, parasites & microbiology

SPECIES IN THIS STORY

Species in this story

Red Deer Cervus elaphus Explore species European Roe Deer Capreolus capreolus Explore species

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