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Scientists pioneer methods for culturing swine gut microbiomes

University of Arkansas Zhaolab05.jpg
Researchers isolate three bacterial strains, develop into probiotics.

Arkansas Agricultural Experiment Station scientists have developed bacterial cultivation methods to isolate different bacteria from pigs. These methods could be used to culture beneficial bacteria in swine intestinal, or gut, microbiomes that can serve as probiotics to protect or improve the health of pigs.

Guided by these methods, the researchers isolated three bacterial strains that were positively correlated with swine growth performance, said Jiangchao Zhao, associate professor of animal science for the Agricultural Experiment Station, the research arm of the U of A System Division of Agriculture. These strains were developed into probiotics.

"Probiotics improve swine health and performance, benefit the animals and agriculture, and help feed the world," Zhao said

The bacterial cultivation methods were published in a scientific paper, "Comprehensive Cultivation of the Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs," which was published in July on mSystems, a journal of the American Society for Microbiology.

Probiotics can reduce reliance on antibiotics to protect animal health, Zhao said.

"The remarkable progress in swine gut microbiome and big data analysis have revealed many potential probiotics that are positively correlated with growth performance," he said. "However, we can't call them probiotics until we are able to culture them and prove their beneficial effects.”

Zhao continued, "We've developed a roadmap to culture a huge variety of bacteria, including these potential probiotics, from pigs. This is the first step to develop novel, next-generation probiotics that improve health and growth performance of pigs."

Kent Nutrition Group Inc., a member of the Kent Corporation family of businesses, will take the probiotics to market under an exclusive licensing agreement.

"This discovery by the university and Dr. Zhao's team is an innovative breakthrough in animal nutrition," said Mike Gauss, president of Kent Nutrition Group, headquartered in Muscatine, Iowa. "Today, more than ever, pork producers around the world need alternative nutrition solutions to improve efficiencies, profitability and sustainability. Kent Nutrition Group is extremely proud and eager to now roll up our sleeves and make this swine probiotic advancement commercially available worldwide."

Arkansas ranks 24th in the nation in hog and pig production, which contributed nearly $52 million to the state's agricultural economy in 2019, according to "Arkansas Agricultural Profile," the 2020 Pocket Facts published by the Division of Agriculture.

Getting here

Developing a useful probiotic for swine begins by identifying bacteria populations living in a pig's intestinal tract, called the gut microbiome, Zhao said. Swine gut microbiome studies have been the focus of many research projects because pigs serve as excellent biomedical models for human diseases and because they are an important source of dietary protein. But a thorough and inclusive survey of the microbial environment in the swine gut had not been done.

Xiaofan Wang, a post-doctoral research associate in Zhao's lab, began a comprehensive investigation of the swine gut microbiome aimed at improving swine health. Zhao's research team collected fecal samples from pigs at the experiment station's Swine Research and Teaching Center and subjected them to next generation DNA sequencing. Also known as high-throughput sequencing, this is a scientific method that allows researchers to sequence DNA for massive numbers of organism samples quickly.

Their investigation resulted in a highly detailed description of the bacterial environment of swine guts, and they discovered that there are many more bacteria in there than previously known. "We identified previously undetected bacteria," Zhao said.

They also identified many core bacteria species that are essential for swine health from birth and throughout the animals' lives.

"Some of these are likely transmitted from the sow to the pigs," Zhao said. "Some come from the environment and some probably from diet." He said research was ongoing to discover the sources of hundreds of these bacteria.

"The swine gut microbiome is very complicated," Zhao said. "There are countless bacteria interactions with the host animal, each other, and with their environment."

The next step was to figure out which bacteria provided health benefits and which were potentially disease-causing. The individual species of microbiota had to be separated and multiplied, then fed back to the pigs to see which had benefits and which might make them sick. And there was no roadmap for that.

"Little was known about how to culture swine gut microbiota," Zhao said. His research team had to develop new methodologies for isolating individual bacteria and culturing them.

"Culturing bacteria outside a pig is hard," Zhao said. "We had to reproduce the environment of the swine gut."

To accomplish that, the researchers used 53 bacterial cultivation methods using different combinations of growth media and gases. Their subjects were three pigs from four different growth stages. The work resulted in successful culturing techniques that gave them sometimes surprising results.

"We've spent a lot of time, money and effort doing this for pigs," Zhao said. "We're one of the few labs doing this. We were able to culture a significant number of bacteria from the swine gut.

"Using extensive culturation, we've found even more previously undetected bacteria, even beyond the new species we found using next generation sequencing," he said.

Their goal was to correlate specific bacteria to feed efficiency — or how well pigs turn food into muscle. "We wanted to identify which were the good ones and which were the bad ones," Zhao said.

Next steps

Their published paper on culturing has become a guidebook that can help other researchers conduct swine microbiome culture research.

Numerous companies, research institutions and scientific organizations have invited Zhao to speak about this research and its results.

"People in this field are very excited to see this study," Zhao said. "They want this roadmap so that they don't have to recreate the research for their own investigations. They can culture bacterial species of their interests from pigs to test their functions using our methods."

When Zhao's group fed the three bacteria strains, they isolated with the new culturing methods were fed to the pigs, they significantly improved pig health and feed efficiency, Zhao said.

These were cultured to expand the amount of each bacterium to develop the three probiotics, live bacteria that are beneficial to their host animals. The Division of Agriculture patented Zhao's process for making them.

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