Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)

Michael S. Robeson, Kamil Khanipov, George Golovko, Samantha M. Wisely, Michael D. White, Michael Bodenchuck, Timothy J. Smyser, Yuriy Fofanov, Noah Fierer, Antoinette J. Piaggio

Research output: Contribution to journalArticlepeer-review

55 Scopus citations


Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free-ranging exotic ungulate in the United States. Large and ever-increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing-based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations.

Original languageEnglish (US)
Pages (from-to)185-196
Number of pages12
JournalEcology and Evolution
Issue number1
StatePublished - Jan 2018


  • CO1
  • blocking primer
  • diet
  • feral swine
  • metabarcoding
  • trnL

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecology
  • Nature and Landscape Conservation


Dive into the research topics of 'Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)'. Together they form a unique fingerprint.

Cite this