Scientists tested five different strains of bacteria called Pediococcus acidilactici that are used as probiotics in livestock to see if they’re truly safe. Using advanced genetic testing, they discovered that some strains carry genes that could make antibiotics less effective, while others appear completely safe. The study found that three of the five strains had no dangerous genes and no ability to spread resistance to other bacteria, making them better choices for use in animals. This research helps farmers and regulators decide which probiotics are safest to use.

The Quick Take

  • What they studied: Whether five different probiotic bacteria strains are safe to give to farm animals, specifically checking if they carry genes that could cause antibiotic resistance problems
  • Who participated: Five strains of Pediococcus acidilactici bacteria from Thailand that had already been tested for probiotic benefits in livestock
  • Key finding: Three of the five bacterial strains (IAF6519, IAF5919, and P72N) were found to be safe with no dangerous genes, while two strains (AF2519 and AF2019) carried genes that could reduce antibiotic effectiveness
  • What it means for you: If you work in agriculture or livestock farming, this research suggests choosing the safer probiotic strains for your animals. However, this is specialized information mainly for farmers, veterinarians, and regulatory agencies rather than the general public

The Research Details

Scientists used two different high-tech methods to read the complete genetic code of five bacterial strains. They used long-read sequencing (like reading a long book in one go) and short-read sequencing (like reading the same book in small chunks) to get a complete picture. They looked for three main things: genes that make bacteria resistant to antibiotics, genes that could make bacteria harmful, and genes that help bacteria work as probiotics. They also did lab tests to see how the bacteria actually behaved when exposed to different antibiotics.

This approach is like being a detective who not only reads a suspect’s diary (the genes) but also watches their actual behavior (the lab tests) to get the full story. The researchers were extra careful because probiotics are increasingly used in farm animals, and they wanted to make sure these bacteria wouldn’t accidentally make antibiotics stop working.

Using both genetic analysis and real-world testing is important because sometimes bacteria behave differently than their genes suggest. A bacteria might have a resistance gene but not actually use it, or it might show resistance without having the expected gene. This study shows why scientists need to check both the blueprint (genes) and the actual behavior (lab tests) before saying a probiotic is safe. This is especially important for farm animals because if probiotics spread antibiotic resistance, it could make treating sick animals much harder.

This study used advanced, well-established technology from respected companies (Oxford Nanopore and Illumina) to read bacterial genes. The researchers were thorough, checking for multiple types of potential problems. However, the study only looked at five bacterial strains, which is a small number. The study also found some puzzling results where the genes didn’t match the behavior, which the researchers honestly reported. The fact that they published in a peer-reviewed journal (PLoS ONE) means other scientists reviewed their work before publication.

What the Results Show

The research revealed a clear split among the five bacterial strains. Three strains (IAF6519, IAF5919, and P72N) came out clean—they had no genes for antibiotic resistance and no genes that could make them harmful to animals. These appear to be the safest choice for use as probiotics.

The other two strains (AF2519 and AF2019) carried concerning genes. Specifically, they had genes called tet(M) and erm(B) that live on plasmids (small circles of DNA separate from the main genetic code). These genes can make bacteria resistant to tetracycline and clindamycin antibiotics. The tet(M) gene was arranged in an unusual way with mobile elements around it, suggesting it could potentially move between bacteria more easily.

Interestingly, the lab tests didn’t always match the genetic findings. AF2019 showed resistance to clindamycin in tests even though scientists couldn’t find the expected resistance gene. Meanwhile, it was susceptible to tetracycline despite having the tet(M) gene. This mismatch highlights why checking both genes and actual behavior is crucial.

The study found that even though two strains had antibiotic resistance genes, they lacked the complete machinery needed to transfer these genes to other bacteria. This is good news because it suggests the resistance genes are less likely to spread to other bacteria in the animal’s gut. The researchers also found that none of the strains had virulence genes—genes that would make them actively harmful or disease-causing. This means even the strains with resistance genes aren’t inherently dangerous pathogens.

This research builds on growing concerns in the scientific community about probiotics potentially contributing to antibiotic resistance problems. Previous studies have raised alarms about some probiotics carrying resistance genes, but this study is more thorough because it combines genetic analysis with actual behavior testing. The findings support the idea that not all probiotic strains are equally safe, and that careful screening is necessary before use in animals.

The study only examined five bacterial strains, all from Thailand, so the results may not apply to all Pediococcus acidilactici strains worldwide. The researchers didn’t test what happens when these bacteria are actually used in living animals—only in lab conditions. The puzzling results where genes didn’t match behavior suggest there’s still more to learn about how these bacteria work. Additionally, the study didn’t examine whether the safe strains actually work as well as probiotics compared to the strains with resistance genes.

The Bottom Line

For livestock producers and veterinarians: The three safe strains (IAF6519, IAF5919, and P72N) appear to be better choices for probiotic use based on this research. The two strains with antibiotic resistance genes (AF2519 and AF2019) should be used with caution or avoided until more research confirms they’re safe in real-world conditions. For regulatory agencies: This research supports the need for genetic screening of all probiotic strains before approval for livestock use. Confidence level: Moderate—this is solid research but involves only five strains.

This research is most relevant to livestock farmers, veterinarians, animal health companies developing probiotics, and government agencies that regulate animal feed and probiotics. It’s less directly relevant to people who consume animal products, though indirectly it affects food safety. People taking human probiotics should note that this study is about animal probiotics and different strains, so the results don’t necessarily apply to human probiotic supplements.

If farmers switch to safer probiotic strains, they wouldn’t see immediate changes in their animals. Probiotics work gradually over weeks to months. The real benefit would be long-term: reduced risk of antibiotic resistance developing in their herds over years of use.

Want to Apply This Research?

  • For livestock producers using the app: Track which probiotic strains you’re using and monitor antibiotic effectiveness in your herd over time. Record any instances where antibiotics seem less effective than expected, which could indicate resistance development.
  • If you manage livestock: Request documentation from your probiotic supplier showing genetic safety testing results. Ask specifically whether your probiotic strains have been screened for antibiotic resistance genes. Consider switching to strains that have passed safety screening if you’re currently using untested products.
  • Establish a baseline of antibiotic effectiveness in your herd now, then monitor it annually. Keep records of which probiotics you use and any changes in how well antibiotics work. Share this information with your veterinarian to help identify any emerging resistance problems early.

This research is specialized scientific information about probiotic bacteria used in livestock. It is not medical advice for humans. If you are a livestock producer or veterinarian considering probiotic use, consult with a veterinary professional about which products are appropriate for your animals. This study examined only five bacterial strains in laboratory conditions, not in living animals, so results may not directly predict real-world performance. Always follow local regulations regarding probiotic use in livestock and consult with regulatory agencies about approved products in your region.