The turkey microbiome – a fitting Thanksgiving tribute

Since turkeys are on the mind this time of year, I thought it would be fitting to write a little more about our work on the turkey bacterial microbiome. The link describing this project is here, and the direct link to a manuscript in revision at PeerJ is here. The project data is available here through MG-RAST. The entire point of this project from the beginning was to 1) identify the bacteria in the gastrointestinal tract of the commercial turkeys over time, 2) identify differences in the microbiomes of high-performing versus poor-performing birds, and 3) develop diagnostic tools to predict performance outcome in a bird based upon ileum microbiome. The long-term goal of this project is to identify antibiotic-free alternatives to modulate the gut and improve turkey health and performance.

I’m writing this post, in part, because we are nearly finished with the descriptive portion of the project and moving on to the animal experiments aimed at modulating the turkey microbiome. First, what have we learned? Much of what we have learned is not so surprising, but some of what we have learned is quite interesting. We looked at the bacterial populations in the turkey ileum via 16S rRNA profiling using MiSeq on the V3 hypervariable region. First, the not-so-surprising. The ileum microbiome diversifies with age. It also stabilizes with age. And age is more of a driver of the ileum microbiome than are environment or treatment effects.

Now, the interesting. There were a number of specific markers (note I say markers and not drivers) of gut development in the bacterial microbiome, including several notable Lactobacillus species (L. aviarius, L. johnsonii, etc.). More prominent of a marker was a segmented filamentous bacteria (SFB) known as Candidatus division Arthromitus. These SFB bacteria were positively associated with high-performing flocks. What was interesting was that SFBs were of very short duration in the ileum, less than two weeks on average. After SFBs appeared, and disappeared, along came the other notable Lactobacillus species. This same pattern was observed in all birds in multiple flocks studied. However, the timing of this succession differed from bird-to-bird and flock-to-flock. The pattern that stood out was that the shift in microbiome occurred earlier in flocks performing better than their counterparts, suggesting a correlation between bacterial community succession and flock performance.

Now we are faced with a lot of lingering questions. There might be a cause-effect relationship between the ileum microbiome and immune system development, nutrient utilization, and ultimately growth of the bird. If there is a causative effect of modulating the microbiome, then it should be relatively straightforward to test such a hypothesis through animal inoculation experiments with cultured bacteria. But, animal experiments are costly and time consuming. We don’t know the best timing of inoculations, best combinations of bacteria, best dosage of bacteria, etc. Not to mention that we need to culture these bacteria and find representative isolates to use for the challenges. And some bacteria such as SFBs are non-culturable and will require other approaches to collect and inoculate them. We are currently looking for some in vitro screens that can be used to better refine the list of microbes to study in the animal. This too can be challenging, as there are limited cell lines and immunological tools available for turkeys. This is an exciting project with huge potential, but a great deal of challenges lie ahead….

Comments and suggestions welcomed!!


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