Metagenome analysis reveals presence of Antibiotic Resistant Genes in Ethiopian chicken

Poultry farming in Ethiopia is of significant importance, both economically and nutritionally. Chicken cecum microbiomes play a significant role in host digestion, absorption of nutrients, defense against pathogens, and performance. Here, we analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above mean sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Whole metagenome sequencing approach has been used to decipher species biodiversity, functions, pathways and antibiotic resistant genes present in cecum microbes. We found that microbial populations were mainly dominated by Bacteroidetes, Firmicutes, and Proteobacteri. We identified 2210 common genes between the two groups of chickens and observed that geographical locations had a significant impact on microbial compositions. Linear discriminant analysis effect size (LEfSe) showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were biomarkers that were significantly more abundant in AF than AM. To gain insights into the physiological function of the microbial community, we decoded the genomes of the microbiomes. Analyses using KEGG, eggNOG, and CAZy databases indicated that pathways of metabolism, genetic information processing, environmental information processing, and cellular process are significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of the indigenous chickens. We have also investigated the distribution of antibiotic resistant genes in the microbiomes and found that some of the antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM. In conclusion the whole genome of cecum microbiomes generated in this study is a valuable resource to understand their potential functions to facilitate the adaptation of indigenous chickens to different environmental and climatic conditions.