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Background  Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels.    Results  The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes ( tet A and  tet W) and inhibited multidrug resistance genes ( mdt A,  mdt C,  mdt K,  omp R, and  Tol C). The therapeutic dose of chlortetracycline led to loss of  Proteobacteria  mainly due to the decrease of  Escherichia / Shigella  (from 72 to 58%). Inhibition of  Escherichia  by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host  Bifidobacterium  were enriched due to  tet W harbored by  Bifidobacterium  under chlortetracycline treatment.  Escherichia  was always the major host for multidrug resistance genes, whereas the primary host was changed from  Escherichia  to  Klebsiella  for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline.    Conclusions  We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms.    Graphical abstract  Resistome variations in faecal microbiome of chickens exposed to chlortetracyclineElectronic supplementary material  The online version of this article (10.1186/s40168-018-0419-2) contains supplementary material, which is available to authorized users.

Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes