Function, not form, key to understanding poultry microbiome

The functions performed by the poultry gut microbiome are more important than the specific bacteria living in the gastrointestinal tract.

Too much attention is currently given to gastrointestinal microbiome form and not its function. Reversing this would help us to understand this complex environment more clearly. i_photos |
Too much attention is currently given to gastrointestinal microbiome form and not its function. Reversing this would help us to understand this complex environment more clearly. i_photos |

I was speaking with a colleague recently and he mentioned that in his poultry flocks he was seeing that gut microbiomes were “established” and unchanging after approximately 28 days. His point was that any subsequent interventions were not effective because the gut microbiome would not change.

It occurred to me that this is true from a certain point of view, but that point of view limits us in understanding what is going on and to what extent we can influence the chicken’s gastrointestinal microbiome. A different point of view is that form - the species makeup of the microbiome - does not necessarily follow function or the metabolic action of these various species. 

To truly understand the chicken gut microbiome, we need to understand how it is functioning, to understand the metabolic changes and outcomes, not simply which bacteria are present. 


It is easy to get lost in the form of the poultry gut microbiome. The form is made up of the specific types of bacteria present, the ratios of those bacteria to one another, their variability and their change over time. When looking at the poultry microbiome’s form we see that it can be very different from bird to bird and flock to flock. 

We find it difficult to define any consistent microbiome and we question what a “healthy” gut microbiome looks like. This is the view that most people take today, but the ongoing study of the gut microbiome of various animals points us to look at the more stable function of the gut microbiome, rather than its more variable from.


The function of the microbiome tells us what the microbiome is doing rather than which bacteria are there. The key insight is to understand that many different bacteria types tend to do similar jobs, they have similar functions. 

Those functions include, for example, processing carbohydrates, or production of vitamins and amino acids, or DNA synthesis. Published research over the last 10 years all points to the same thing, you can have tremendous variability in the microbiome form, or which bacteria are doing the job, but you have a much more consistent microbiome function, or the jobs being done.

When we start looking at the function of the gut microbiome, we get a new perspective that grounds us more solidly in nutrition, metabolism, and immunity. 

Functionally, the microbiome is producing metabolites, proteins, and molecules that has an impact on the bird. We may have metabolites that are directly absorbed by, and benefit, the chicken, for example, vitamins. There may also be metabolites produced by the microbiome that isn't directly absorbed but beneficially impact the local environment. A good example of this is butyrate and speculation that butyrate produced by certain bacteria in the microbiome may be more effective than butyrate added to feed. 

We have molecules such as proteins and enzymes that are functionally important for the microbiome but that also have an impact on a bird’s health. An example of this is the enzymes responsible for breaking down bile salts into short-chain fatty acids. 

Finally, several functions may be dangerous for the chicken, for example when microbiome bacteria produce biogenic amines, oxidative byproducts or toxins.

The microbes that make up the poultry gut microbiome can be very flexible and multifunctional. Many different species can fulfill the same roles within the gut, creating a very confusing picture. The future of poultry microbiome study - and poultry gut health - will be to look at the function of the gut microbiome. When we change how we look at the gut microbiome, when we take a functional view, we will begin to understand this complex system much more clearly. 







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