Comparison of high-throughput sequencing analysis of gut contents between silver carp Hypophthalmichthys molitrix and bighead carp Hypophthalmichthys nobilis in mesotrophic and eutrophic lakes

High-throughput sequencing analysis of gut contents was used to study the feeding habits of two filter-feeding fish, namely silver carp Hypophthalmichthys molitrix and bighead carp Hypophthalmichthys nobilis, in mesotrophic Lake Qiandao and eutrophic Lake Taihu. Silver carp feed primarily on phytoplankton, with a feeding preference for Chlorophyta, in Lake Qiandao and rely on phytoplankton in Lake Taihu. Bighead carp feed more on zooplankton in Lake Qiandao and on phytoplankton in Lake Taihu. With increasing levels of algae, bighead carp feed more on phytoplankton. The dietary shifts suggest that bighead carp would be useful in controlling nuisance algae in lakes.