Why is the microbiome such a popular area of study these days?
“There’s hope that by controlling the microbiome, we’ll be able to make some of the gains that need to be made in production and environmental impact,” says Tim Johnson, associate professor in the College of Agriculture’s Department of Animal Sciences at Purdue University.
An analysis combining the results of 14 studies from around the globe has uncovered some common patterns in how the piglet microbiome, specifically the gut bacteria, changes over time, Purdue University reports in a release. The study comes as the $54 billion pig industry works under pressure to create a high-quality, economically important, nutritious product while also lowering its environmental impact and using fewer antibiotics to keep the animals healthy, researchers explain.
“There are exceptions, but overall, we found general trends between all those animals,” Johnson says. “We think these patterns are widely applicable because our dataset came from multiple studies around the world, and when we tested the predictions in unrelated datasets, the patterns held.”
Although studies like this are fairly common in the human microbiome field, relatively few have focused on animal microbiomes. Johnson, along with three co-authors, published their recent analysis in the journal Microbiology Spectrum.
“We’re trying to bring the animal side up to speed with the human side,” Johnson says. “This field is just beginning. A study like this one lays a lot of foundation work, which was missing up to this point.”
A Global Opportunity for Growth
The study brought together data from studies published between 2019 and 2021 conducted in Australia, Canada, China, the Netherlands, Norway and the U.S. The data spanned more than 3,300 fecal microbial communities sampled from about 350 pigs over 60 time points ranging from birth to market age, the release says.
Nicole Ricker, co-author and assistant professor in the Department of Pathobiology in the Ontario Veterinary College at the University of Guelph in Canada, highlighted two key findings in the work that provide a foundation for future studies. Her work first appeared in 2020 in Frontiers in Veterinary Science.
“First, the overall trajectory of the microbiome development through piglet development is predictable and can be modeled effectively, despite methodological differences in the studies examined,” Ricker says in a release.
The animals from the studies included various breeds that not only differed in genetics, but also in their nutritional diets. The research also revealed important details of the piglet microbiome at a fine time scale, the article says.
“This opens a diversity of research avenues for understanding how piglet microbiome development is impacted by different management strategies including feed additives, weaning time and antibiotic use,” she said.
Combined Dataset Allows for Greater Comparisons
Researchers wanted to predict the age of the animals based on their microbiomes in the study. Results showed they could with an accuracy of about 70%. Evidence has suggested that a more mature microbial community becomes stable more quickly, the researchers explain. This might translate into more consistent growth conditions for the animal.
“That’s important because the microbial community plays a major role in influencing the animals’ immune system, health, how well they digest their feed and how quickly they grow,” Johnson says.
Although research showed the bacterial community in the piglets did change over time, the rate of change slowed.
“The most surprising part for me is we were able to find that specific bacteria that are important to the succession or the maturity of the community were similar between all the different study locations,” Johnson adds.
The project also showcased the need for more frequent microbiome sampling. Some studies took samples once a week, while others gave a treatment for several weeks, then took a sample at the end to see what had happened.
The assembled dataset now opens the door for researchers to compare how treatments affect normal animals. Although previous studies have also done this, they relied on single datasets that compared treated to untreated animals, the researchers point out. The combined dataset allows researchers to compare the global average to local studies.
“In an individual study, control animals may not actually represent a global average of a normal microbiota. The controls may deviate from a more global average,” Johnson says.
Researchers explain that the global average size and variety of the gut bacteria populations varied in an “oscillating pattern that showed a general increase in diversity over time.” What does this mean? Sampling a treatment group during a big swing in the microbiota population could provide misleading results, the researchers say.
“It is possible that the difference that you see between treatment group microbiomes is during one of these temporary changes rather than the general trend,” Johnson adds. “We want to encourage people to sample multiple time points so that you make sure you’re on a general trend and not in some temporary swing.”
The lead author, Wenxuan Dong, is a recent Master of Science graduate of Johnson’s lab. Devin Holman of Agriculture and Agri-Food Canada also contributed to this research.
