Estimating the prevalence of game meat utilization in Nairobi using cytochrome b sequences

Abstract

Consumption of meat from wildlife, so called bushmeat is gaining popularity because it offers cheaper alternative sources of protein to the food-poor families. Such illegal utilization also increases revenue for retailers who sell it to unsuspecting customers. However, bushmeat consumption compromises wildlife conservation efforts and may result in common species becoming rare and endangered species get threatened with extinction. In Kenya such utilization is outlawed by The Wildlife Conservation and Management Act (Cap 376). The objective of this study was to estimate the prevalence of bushmeat consumption in Nairobi. 556 unknown raw meat samples were obtained from butcheries in and around Nairobi, 12 known samples were obtained, six from the Kenya wildlife service and six from the international livestock research institute. DNA was extracted from the samples using the Qiagen® kit and cytochrome b was amplified from each sample using PCR. Homologous cytochrome b nucleotide sequences were generated from purified PCR amplicons. The species of origin of each meat sample was determined by aligning its cytochrome b sequence to sequences in GenBank® genetic database using BLAST. All the meat samples were from domestic animals with 0% prevalence in game meat utilization. However, there were high levels of substitution between chevon and mutton especially in regions in the outskirts of Nairobi. The sequence polymorphism of the cytochrome b was assessed using DNAsp to determine its suitability in animal species identification. The average genetic distances within the same species were 0.01 and the genetic distances between different species was approximately 0.6. This shows that the gene is suitable for species identification because its highly conserved within the same species yet its highly polymorphic between different species. In analyzing mixtures of different animal, 12 pairs of species-specific primers were designed using Amplicon® software. These primers were specific for seven wild and five domestic animals and were used to identify component species in a multiplex PCR. At optimal conditions, all the primer pairs were specific to the species they had been designed for and could detect presence of specific species in mixtures using multiplex PCR. All the samples tested using this method were composed of single species, however, the technique requires validation to establish the minimum concentration of DNA that can be detected by the primers in the multiplex PCR.