Guts of Growth : The “-omics” revolution

The study of poultry production has progressed significantly over the past several years, including the introduction of more complex research approaches to understand changes in the bird.

Traditionally, in research, scientists ask a question and then answer it – at least partly – through a study or a series of studies. While this approach is still extremely useful, modern science allows researchers to use “-omics” technologies to consider a subject more holistically and better understand different combined pieces.  

This holistic view can help better define an original research question and act as a problem-solving tool. Research like this is happening in many labs across Canada and beyond, but translating it to and implementing it on the farm will help us better understand the mode of action of certain technologies or their impact on the animal – and to understand the “why”.

What are “-omics” technologies?
These “-omics” technologies look at the totality of a biological subject – i.e., broad-spectrum data – to characterize and quantify this information for interpretation by the researcher. Essentially, this type of work allows the researcher to profile a large pool of biological data in a single snapshot, and this information can help us understand the dynamics of, or changes to the subject. Often, “-omics” work is paired with current or previous animal data to better understand how this new information can be applied.  

There are many kinds of “-omics” technologies, including proteomics, which measures protein levels, and transcriptomics, which measures the messenger molecules, mRNA. These “-omics” technologies have been around for a while, but thanks to the ease of conducting the work and recent reductions in costs, more academics are making use of this field of research. Often, researchers can use the data generated to understand what is happening in the bird and help inform field decisions – or it can be used the other way around, with an observation in the field that provokes a question to be answered.  

Different “-omics” technologies
Functional transcriptomics is used to measure the level of expression of either all the genes or a selected group, to determine whether these genes are turned on or off and at what intensity they are activated or inactivated. These genes, which are the code for the body, can have a direct function or be part of a bigger system of a direct function. A genotype (the sequence of genes an organism carries) helps make up a phenotype (observable characteristics – that is, what we see on the outside) that can be impacted by genes and the environment.  

Epigenomics is the study of epigenetic modifications – for example, changes in gene expression that do not alter the actual DNA sequence in a cell at a given time. These epigenetic changes can be produced by many different outside factors, such as age, diet, environment, microbes and so on. When applied in poultry production research, epigenomics can help determine if certain experimental conditions can have an impact on the genes being expressed and, if paired with watching the birds, can change certain aspects of poultry performance.  

Additionally, epigenomics can study whether changes in a parent bird have an impact on offspring development, a phenomenon known as maternal programming or fetal programming. This type of research is not limited to just looking at genes, as you can also look at proteins being expressed, changes in metabolites (substances formed during chemical processes to maintain life) and so on. This helps us understand how genes are turned on and off, and helps us understand the ways these genes are affected or, conversely, affect other genes.  

In the body, signaling pathways function similarly to “the domino effect” – if you line up dominos and knock the first one over, it will subsequently knock the second domino over, which will knock the third one over, and so on, until all the dominos have fallen. In the same way, activation or deactivation of genes impacts more than one individual gene – it can also change the activity of other downstream targets, just like dominos.

The use of microbiomics, the study of the totality of microbes in an environment, has been on the rise as more countries announce antibiotic reduction strategies or regulations. Information provided by microbiomics can help us understand what microbes are present in a certain environment (like the intestine) at a given time or what has changed there, as microbes can change depending on such factors as age, diet and environment.  

Using the information microbiomics provides, communities of microbes and their total present population in an environment can be better understood, but this analysis does not necessarily tell us the microbes’ function or how they work in an animal. Part of the key to making this work practical is understanding the function of microbes and what they release into the gut, their impact on the gut and, ultimately, their impact on the whole bird. More researchers are interested in looking not only at the microbiome but also at the changes in metabolites produced by microbes and the animal in response to the changes in the microbiome – a separate area of research called metabolomics.

In terms of understanding the intestine, these different “-omics” technologies can help us learn how the gut grows under normal conditions and what has a positive or negative impact on it. They can also reveal what affects the gut in different challenge situations.  

To better understand how everything works together, there is an analogy equating these concepts of “-omics” to a movie. In this example, the life of the bird is the movie, the cells are the main actors, the microbes are the actors’ managers and DNA is the script (genotype), with the DNA sequence being the words on the page. The script tells the actors what to do, the managers work around the actors and the director has the power to change scenes or dialogue. The director, like epigenetics, can be influenced by many outside factors to make changes to the movie, but the resulting movie is all that the audience can observe (phenotype). The same movie may turn out differently depending on the director or the director’s mood during filming.  

The future of “-omics” technologies
In the world of nutrition, nutrigenomics can be used to study the effect of nutrients or different “bioactive” feeds on gene expression, how they impact the bird on a genetic level and what can be observed. Nutrigenomics also allows us to better understand the impact of different nutrients on a genetic level and how that impact might affect different poultry breeds and production states. This, in turn, can lead to a better understanding of precision nutrition and what is turned on and off in different production states. From this information, researchers can then determine what is needed in terms of specific nutrition to combat these changes.  

However, it is important to note that this information is generated in the lab and using it directly on the farm could be different when utilized in the future. Different bioactive technologies – like alternatives to antibiotics or mineral sources – can influence not only the genes of the animal but also how the animal responds during times of good health or health challenges.

At the end of the day, these techniques provide a better understanding of what is happening inside the animal during different conditions. When paired with good barn management and husbandry, these techniques could help further innovation within the poultry industry, especially as we move into a new era of oversight of antibiotic use.  

Dr. Kayla Price is poultry technical manager for Alltech Canada and is an expert in poultry intestinal health.