Establishing Molecular Methods to Quantitatively Profile Gastric Diet Items of Fish—Application to the Invasive Blue Catfish (Ictalurus furcatus)

Open-File Report 2019-1021
By: , and 



Understanding the diet of invasive species helps researchers to more accurately assess the health, survivorship, growth, and stability of an invasive fish species, as well as their effects on native populations. Techniques capable of identifying multiple prey species from fish stomach contents have been developed. In this study, a multi-locus metabarcoding approach was used to identify fish and invertebrate prey in stomach samples of Ictalurus furcatus (blue catfish), which were collected from two sites on the Mattawomen Creek and Nanjemoy Creek in Maryland.

The mitochondrial 12S (mt12S) and mitochondrial 16S (mt16S) gene regions were sequenced and compared. First, a mock sample for each gene region was created with the pooled polymerase chain reaction product of known fish species, and quantities of the sample were used to determine efficacy of the amplicon. Results varied between gene regions analyzed. Then, when using the mt12S primers, next-generation sequencing determined that nine fish species were found at levels greater than 1 percent of the diet of blue catfish. The most common species were Perca flavescens (yellow perch) and Cyprinus carpio (common carp). The mt16S gene region analyses found 10 fish species at greater than 1 percent of the diet, which primarily included Orconectes limosus (spinycheek crayfish), Alosa pseudoharengus (alewife), and yellow perch. Partially digested eggs were identified using next-generation sequencing of yellow perch in two of the stomach samples, and a TaqMan® quantitative polymerase chain reaction (qPCR) assay was developed to more economically identify egg species in the future.

The yellow-perch-specific TaqMan® qPCR assay was tested using primers that were developed to detect a 154-base-pair amplicon in the mitochondrial control region. Consumption of yellow perch eggs indicates that blue catfish could potentially negatively affect young-of-year recruitment of this native sportfish. Analyses of two gene regions helped confirm the major prey of the fish sampled and allowed identification of fish species as prey that were not included in a database for the two gene regions. We concluded that the mitochondrial ribosomal-marker-based next-generation sequencing method is useful in determining the prey of fish species.

Suggested Citation

Iwanowicz, D.D., Schill, W.B., Sanders, L.R., Groves, T., and Groves, M.C., 2019, Establishing molecular methods to quantitatively profile gastric diet items of fish—Application to the invasive blue catfish (Ictalurus furcatus): U.S. Geological Survey Open-File Report 2019–1021, 15 p.,

ISSN: 2331-1258 (online)

Study Area

Table of Contents

  • Abstract
  • Introduction
  • Methods
  • Results
  • Discussion
  • References Cited
  • Appendix 1. Species with Accession Number and Sequence
Publication type Report
Publication Subtype USGS Numbered Series
Title Establishing molecular methods to quantitatively profile gastric diet items of fish—Application to the invasive blue catfish (ictalurus furcatus)
Series title Open-File Report
Series number 2019-1021
DOI 10.3133/ofr20191021
Year Published 2019
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) Leetown Science Center
Description Report: vii, 15 p.; Appendix
Country United States
Other Geospatial Potomac River
Online Only (Y/N) Y
Additional Online Files (Y/N) Y
Google Analytic Metrics Metrics page
Additional publication details