Antibiotics are widely used at sub-lethal concentrations as a feed supplement to enhance poultry productivity. To understand antibiotic-induced temporal changes in the structure and function of gut microbiota of chicken, two flocks were maintained for six weeks on a carbohydrate- and protein-rich diet. The feed in the conventional diet (CD) group was supplemented with sub-lethal doses of chlorotetracycline, virginiamycin and amoxicillin, while the organic diet (OD) had no such addition. Antibiotic-fed birds were more productive, with a lower feed conversion ratio (FCR). Their faecal samples also had higher total heterotrophic bacterial load and antibiotic resistance capability. Deep sequencing of 16S rDNA V1-V2 amplicons revealed Firmicutes as the most dominant phylum at all time points, with the predominant presence of Lactobacillales members in the OD group. The productivity indicator, i.e. higher Firmicutes:Bacteroidetes ratio, particularly in the late growth phase, was more marked in CD amplicon sequences, which was supported by culture-based enumerations on selective media. CD datasets also showed the prevalence of known butyrate-producing genera such as Faecalibacterium, Ruminococcus, Blautia, Coprococcus and Bacteroides, which correlates closely with their higher PICRUSt-based in silico predicted 'glycan biosynthesis and metabolism'-related Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues. Semi-quantitative end-point PCR targeting of the butyryl-CoA: acetate CoA-transferase gene also confirmed butyrate producers as being late colonizers, particularly in antibiotic-fed birds in both the CD flocks and commercial rearing farms. Thus, antibiotics preferentially enrich bacterial populations, particularly short-chain fatty acid producers that can efficiently metabolize hitherto undigestable feed material such as glycans, thereby increasing the energy budget of the host and its productivity.
Keywords: 16S rDNA amplicon sequencing; butyrate; gut microbiota; short chain fatty acid; sub-lethal dose of antibiotics.