Characterization of the Young Turkey Cecal Microbiome and Its Role in the Prevention of Irritable Crabby Syndrome (ICS)

Introduction: Turkey production is vital to the US poultry industry. However, young turkeys are susceptible to a specific syndrome, designated Irritable Crabby Syndrome (ICS), which leads to gastrointestinal distress, weight loss, and failure to thrive. ICS is currently treated with a combination of penicillin and gentamicin; but, with increasing public concern about antibiotic use in animal production, interest in promoting a healthy gut microbiota, as a preventative treatment, has increased. Impacts of ICS and accompanying antimicrobial treatment on the gut microbiome remain uncharacterized.

Purpose: The purpose of the study was to characterize impacts of ICS and accompanying antibiotic treatment on the gut microbiome of young turkeys.

Methods: Cecal samples were taken from four flocks over five weeks. Bacterial community DNA was extracted and purified. The 16S rRNA genes were amplified and sequenced using an Illumina MiSeq. The data were processed in QIIME and statistical analysis performed in R.

Results: The turkey cecal microbiome tended to increase in diversity with age and primarily included members of the phyla Firmicutes, Bacteroidetes, and Proteobacteria. Samples fell into two distinct paths, one more diverse than the other. Samples tended to cluster by age instead of flock. Flocks that developed ICS exhibited an overabundance of Lactobacillus spp. and Campylobacter spp., while other microbiome were more diverse with higher levels of Clostridiales. Antibiotics had no significant impact on the microbiome.

Significance:  Patterns of diversity and variability among turkey cecal microbiomes are not well understood at either the individual or the flock scale. This study provided detailed information for individual birds from four flocks. A large number of birds with less diverse microbiomes or low relative prevalence of Clostridiales could serve as indicators for flock susceptibility to ICS, potentially leading to novel strategies to decrease ICS in young flocks.