Different antibiotic growth promoters induce specific changes in the cecal microbiota membership of broiler chicken

<div><p>Antimicrobials are sometimes given to food animals at low doses in order to promote faster growth. However, the mechanisms by which those drugs improve performance are not fully understood. This study aimed to investigate the impact of zinc bacitracin (55g/ton), enramycin (10g/ton); halquinol^® (30g/ton); virginiamycin (16,5g/ton) and avilamycin (10g/ton) on the cecal microbiota of broiler chicken, compared to a control group. Six hundred and twenty four chicks (Cobb 500) arriving to an experimental unit were randomly assigned into each treatment with four repetitions per treatment. The cecal content of 16 animals per treatment (n = 96) was used for DNA extraction and sequencing of the V4 region of the 16S rRNA gene using Illumina technology. The use of antimicrobials induced significant changes in membership but not in structure of the cecal microbiota compared to the control group, suggesting a greater impact on the less abundant species of bacteria present in that environment. Halquinol was the only drug that did not affect microbial membership. Firmicutes comprised the major bacterial phylum present in the cecum of all groups. There was no statistical difference in relative abundances of the main phyla between treated animals and the control group (all P>0.05). Treatment with enramycin was associated with decreased richness and with lower relative abundance of unclassified Firmicutes, <i>Clostridium XI</i>, unclassified Peptostreptococcaceae (all P<0.001) and greater abundance of <i>Clostridium XIVb</i> (P = 0.004) and <i>Anaerosporobacter</i> spp. (P = 0.015), and treatment with bacitracin with greater relative abundance of <i>Bilophila</i> spp. (P = 0.004). Several bacterial genera were identified as representative of usage of each drug. This study used high throughput sequencing to characterize the impact of several antimicrobials in broiler chicken under controlled conditions and add new insights to the current knowledge on how AGPs affect the cecal microbiota of chicken.</p></div

Weight gain (in grams), feed conversion and viability (in percentage) observed in chickens treated with different antibiotic growth promoters.

<p>Weight gain (in grams), feed conversion and viability (in percentage) observed in chickens treated with different antibiotic growth promoters.</p

Bacterial taxa found to be significantly associated with as representative of each treatment as per the indicator analysis.

<p>Bacterial taxa found to be significantly associated with as representative of each treatment as per the indicator analysis.</p

P values obtained from the comparison of microbial membership (gray background) and structure (white background) using the Parsimony and AMOVA tests.

<p>P values obtained from the comparison of microbial membership (gray background) and structure (white background) using the Parsimony and AMOVA tests.</p

Average and standard deviation (in brackets) of the number of different genera and results of Chao, Simpson and Shannon indexes present in the cecum of broiler chicken after treatment with different antibiotic growth promoters.

<p>Average and standard deviation (in brackets) of the number of different genera and results of Chao, Simpson and Shannon indexes present in the cecum of broiler chicken after treatment with different antibiotic growth promoters.</p

Principal Coordinate Analysis (PCoA) representing the similarity between membership (A) and structure (B) of bacterial communities found in cecum of broiler chicken treated with several antibiotic growth promoters.

<p>Principal Coordinate Analysis (PCoA) representing the similarity between membership (A) and structure (B) of bacterial communities found in cecum of broiler chicken treated with several antibiotic growth promoters.</p

Firmicutes to Bacteroidetes (F:B) and Firmicutes to Proteobacteria (F:P) ratios present in the cecum of broiler chicken treated with different antibiotic growth promoters.

<p>Firmicutes to Bacteroidetes (F:B) and Firmicutes to Proteobacteria (F:P) ratios present in the cecum of broiler chicken treated with different antibiotic growth promoters.</p

Dendrograms representing the similarity between membership (A) and structure (B) of bacterial communities found in cecum of broiler chicken treated with zinc bacitracin (orange), enramycin (red); halquinol (green); virginiamycin (blue), avilamycin (purple) and in a control group (black).

<p>CQH: Halquinol.</p

Relative abundances at the phylum (A) and genus (B) level of the main bacteria found in the cecum of broiler chicken treated with zinc bacitracin, enramycin; halquinol; virginamycin, avilamycin and in a control group.

<p>Relative abundances at the phylum (A) and genus (B) level of the main bacteria found in the cecum of broiler chicken treated with zinc bacitracin, enramycin; halquinol; virginamycin, avilamycin and in a control group.</p

Pyrosequencing metrics of the cleaned data and its distribution at the Kingdom level.

<p>Total number of reads after data cleaning (pyrosequencing noise and chimera removal), after filtering (e-value of 30, minimum identity of 97% and minimum alignment of 75bp on MG-RAST), and percentage of reads classified by MG-RAST using the SSU databank as Bacteria, Eukaryota, Archaea, unclassified bacteria and sequences unassigned to any Kingdom. Means and standard deviations (±SD) among healthy horses and horses with colitis are also presented.</p