Exploring the effects of
management strategies on the gut
microbiome and metabolome of
growing broiler chickens:
an integrated metagenomic and
metabolomic approach
Advances in genetic selection and intensification of management systems has led to
the production of highly efficient broiler chickens. Attention is being turned to the role
of gut microbes to further growth efficiency and improve animal health, particularly with
the rise of antimicrobial resistance and the need to consider animal welfare and food
safety. The microbiome is sensitive to management strategies, which may affect the
growth and metabolism of the bird. Here, four studies are presented which explore the
effects of antibiotic treatment with Linco-spectin and the subsequent use of Aviguard®,
a mixed probiotic, diet in terms of protein source and the use of wheat or maize as a
cereal base, and the supplementation of bedding with excreta from mature birds on
the caecal microbiome and hepatic metabolome of broilers through population profiling
metabolomic approaches. A final analysis of all datasets highlights consistent trends
that appeared irrespective of treatment.
Alpha diversity increased between days 4 and 9 (P<0.001) and 15 and 22 (P=0.001)
and was affected by all treatments but differences dissipated with age. Beta diversity
also changed with age, but again differences were reduced by around two weeks of
age, suggesting that diversity naturally reaches a plateau, irrespective of perturbations
in early life. Age-related shifts in bacterial populations were observed in all studies with
a reciprocal relationship between phyla Firmicutes and Tenericutes (P<0.001). The
microbiome was consistently affected by management strategy, with evidence that
different taxa are affected by diet, bedding and antibiotic/probiotic treatment. Energyrelated metabolites were affected by treatment, but birds appeared to grow equally as
well suggesting isofunctionality of the hepatic metabolome. Concentrations of short
chain fatty acids (SCFA) increased between days 4 and 15 (P<0.001) and were
affected by diet alone. Concentrations of all SCFA exhibited both positive and negative
relationships with bacterial taxa.
Despite the plethora of treatment-associated differences in the microbiome, no single
group of birds performed worse than another with a lack of a significant relationships between differences in the caecal bacterial populations and differences in feed
conversion ratio (r=0.386; P=0.270). It is hypothesised that the ability of a bird to thrive
and grow is independent of the profile of its microbiome, so long as key metabolic
activities are performed. This thesis is an overview that will provide a base to be utilised
in exploring more specific relationships in depth in future work with methods and
understanding of metagenomic-metabolomic relationships improved by the findings
herein
