Quantitative molecular assays for evaluating changes in broiler gut microbiota linked with diet and performance

Changes in the levels of specific gut bacteria have been linked to improved broiler feed efficiency. Quantitative polymerase chain reaction (qPCR) assays were developed to five potential performance-related bacteria (Lactobacillus salivarius, L. crispatus, L. aviarius, Gallibacterium anatis and Escherichia coli) and generic eubacteria. These were used to screen broiler gut samples from four geographically diverse Australian feeding trials showing significant treatment-related differences in feed efficiency. It was our aim to validate the association of particular bacteria with broiler feed efficiency across a broad range of environmental and dietary conditions, and hence to evaluate their predictive potential for monitoring broiler performance. Across trials L. salivarius, L. crispatus, L. aviarius, E. coli and total eubacterial numbers were significantly altered by diet, environment (litter), and/or sex of birds. Furthermore, changes in the numbers of these gut bacteria were significantly linked to broiler performance. Lactobacilli and total eubacteria were significantly decreased in birds that were more feed efficient. E. coli was not consistently linked with either improved or decreased performance and these discrepancies may be due to differences at the strain level which were not detectable using our assays. G. anatis was detected only in two of the four trials and found not to be significantly linked with broiler performance. These qPCR assays have been useful in either validating or disproving previous reported findings for the association of specific gut bacteria with broiler feed efficiency. This qPCR format can be easily expanded to include other organisms and used as a quantitative screening tool in evaluating dietary additives for improved broiler production.