Getting a better understanding of the pig microbiome
Using porcine microbiota-associate porcine models as research tools
By Nirosh Aluthge
Through research conducted over the past couple of decades, we have come to understand that the microbial communities that reside in and on humans and other animals play an important role in host health and well-being.
The community of microorganisms associated with pigs, known as the porcine microbiome, isn’t an exception to this and is believed to contribute significantly to porcine health and performance.
For example, the porcine gut microbiome (which is the most widely-studied microbial community in pigs) has been shown to contribute to feed digestion as well as offering colonization resistance against pathogenic bacteria.
While the importance of the microbiome to the porcine animal is well established, there are still many factors related to colonization dynamics and how the microbiome interacts with the host which are not well understood.
For example, what are the origins of the microbes that colonize pigs (are they coming from the sow, environment, feed, etc.)? How do different diets alter microbiome composition and how may these changes, in turn, relate to differences in feed efficiency? Why do piglets from the same litter sharing the same pen/environment have different intestinal microbiome profiles?
What are the mechanisms through which the microbiome interacts with the porcine host to influence host physiology and growth? How might probiotics/direct-fed microbials promote improved health and/or performance in pigs?
The answers to these questions have the potential to not only expand our knowledge on host-microbiome interactions but to also lead to more informed strategies to manipulate the porcine microbiome to derive pigs that are healthier and have more desirable economic characteristics.
One of the major hurdles which makes the study of the porcine gut microbiome at a mechanistic level challenging is its complexity. The presence of hundreds of different prokaryotic species (bacteria and archaea), eukaryotic microbes such as fungi and protozoa, not to mention the myriad viruses that inhabit the gut of just a single animal, makes the study of the microbiome as a whole a very complicated undertaking.
Added to this complexity are the ever-increasing number of factors that seem to affect the microbiome. These can be factors related directly to the animal (such as the age of the animal, breed, genetics, etc.) or external factors (such as diet, housing, animal husbandry practices, antibiotic usage, etc.).
One of the consequences of this complexity is the difficulty of identifying factors/interventions that can predictably cause similar microbiome changes broadly across the pork industry.
For example, a dietary change which results in the increase of a desirable microbe in a particular production environment might not provide similar results if the same diet was provided to other animals in a different production setting. The complexities of the microbiome also render identifying mechanisms related to host-microbiome interactions quite challenging.
Establishment of PMA porcine models Animals that are derived without any bacteria colonizing them (known as ‘germ-free’ animals) provide a powerful tool for researchers to study the impact of one or more specific microbes or a whole microbial community on a given host animal.
These models are particularly useful in demonstrating the causality of a particular microbe or microbial community in producing a given outcome in a host animal.
For example, in the human microbiome field, human microbiota-associated (HMA) mice have been used to demonstrate the ability of microbial communities to contribute to disease conditions such as obesity (Turnbaugh et al., 2006) and the development of asthma (Arrieta et al., 2015).
Pigs that are derived germ-free and subsequently colonized with microbes of interest, which can be referred to as porcine microbiota-associated (PMA) porcine models, have the potential to provide us with a much deeper understanding about the porcine microbiome and how its functions affect the host animal.
Germ-free piglets are typically obtained via Cesarean section surgeries on sows within a pre-sterilized environment (a surgery ‘bubble’) followed by rearing these piglets in sterile isolators which have sterile milk and sterile solid food required for their nourishment.
Microbes or microbial communities of interest can subsequently be introduced to these animals so that they are colonized with target microbes. Once established, this microbial community can be manipulated experimentally (e. g., through prebiotic supplementation, antibiotic treatment, etc.) to observe the effects of such manipulations on the microbiome and the porcine host.
In order to provide useful insights, a PMA porcine model will have to be capable of replicating the microbiome composition and characteristics of a ‘real world’ porcine microbiome in a commercial setting. In a study conducted by us (manuscript currently under preparation) we observed that the colonization pattern of PMA porcine animals closely mirrors that of conventional pigs, and that > 90% of the amplicon sequence variants (ASVs) – which are equivalent to bacterial/archaeal species – observed in conventional pigs can be detected in these animals.
These observations are encouraging as they indicate that PMA porcine models can be established that are representative of conventional pigs in terms of their microbiome composition.
Opportunities and challenges with PMA porcine modelsThe ability to establish PMA porcine models which can recapitulate a realistic porcine microbiome opens up a number of opportunities to gain a deeper and more mechanistic understanding of the structure and function of the porcine microbiome.
For instance, they may provide the possibility to study ‘microbiomes of interest’ – such as those of piglets resistant to weaning-associated diarrhea or of pigs that are higher in feed efficiency- in a very detailed manner in order to identify the microbes and mechanisms that contribute to a desired phenotype.
The development and study of novel probiotics and prebiotics also stand to benefit through the use of these animal models. Germ-free pigs can be inoculated with a probiotic of interest to observe what effect(s) the probiotic has on markers of host health (such as anti-inflammatory immune markers).
We can also investigate the effects of a perturbed microbiome (such as a microbiome exposed to antibiotics) on the host animal and then try to identify interventions which can remedy these perturbations.
The expenses and labor associated with the derivation and maintenance of PMA porcine animals may be a hurdle to the widespread use of these animal models for studying the porcine microbiome.
The large size of pigs also makes it difficult to maintain PMA pigs in their isolators for a long period of time – which is especially important to study the influence of the microbiome on economically important characteristics such as market weight.
Another drawback of the larger size of pigs is that this limits the number of animals that can be housed in an isolator at any given time which may reduce the statistical power of studies conducted using PMA porcine models.
ConclusionsThe power of PMA porcine models as a research tool is the ability to carefully control the microbiome in vivo and clearly identify the effects of microbiome modulation on the porcine host while controlling for the many confounding factors that are encountered in microbiome studies performed using conventional pigs.
Despite some of the challenges related to the use of PMA porcine models, the many advantages associated with them has the potential to provide unprecedented insights into the structure and functioning of the porcine microbiome which can better inform the development of strategies to modulate the porcine microbiome to improve animal health and performance.
Aluthge is a postdoctoral research associate in the Department of Animal Science at the University of Nebraska-Lincoln.
