Advancements in Probiotic Therapies through Bacterial Genome Analysis

In a groundbreaking study published on July 16, 2025, in *Nature Microbiology*, researchers from Sanford Burnham Prebys, along with collaborators from Washington University School of Medicine, Sabanci University, and the University of California San Diego, have made significant strides in personalized probiotic therapies. Their research focuses on the genomic analysis of *Bifidobacterium* strains, which are utilized in neonatal intensive care units (NICUs) to improve health outcomes in preterm infants and to prevent conditions such as necrotizing enterocolitis.

Approximately 10% of preterm infants in the United States receive probiotic treatment, which has been shown to reduce mortality rates associated with intestinal diseases (Sanford Burnham Prebys, 2025). The study, led by Dr. Aleksandr Arzamasov, a postdoctoral associate at Sanford Burnham Prebys, highlights the importance of understanding the metabolic capabilities of these bacterial strains to tailor therapies to specific populations.

The research team's innovative approach involved analyzing 263 *Bifidobacterium* genomes to identify metabolic genes that enable these bacteria to utilize various carbohydrates as energy sources. The researchers constructed a comprehensive model that predicts the carbohydrate utilization pathways in over 2,800 strains of *Bifidobacterium*, achieving an accuracy rate of over 94% in their validations (Arzamasov et al., 2025).

"When we consume food, a significant amount of dietary carbohydrates are not digested by our bodies, especially complex fibers. Instead, they reach the large intestine, where gut bacteria metabolize them," explained Dr. Arzamasov. This understanding is crucial as it allows for the development of probiotics that are not only effective but also tailored to the dietary habits of specific populations.

Dr. Andrei Osterman, a professor at Sanford Burnham Prebys and co-author of the study, remarked on the unique adaptations of *Bifidobacterium* strains from Bangladeshi infants. The research uncovered that these strains possess distinct genetic clusters and metabolic characteristics that enhance their ability to digest both human milk and plant fibers. This suggests that probiotics must be adapted to the local diets to maximize their health benefits.

The study demonstrates the potential for utilizing genomic data to inform the development of personalized probiotic therapies. By understanding how carbohydrate metabolism varies among *Bifidobacterium* species, researchers can predict which strains are best suited for different dietary and ecological contexts, thereby improving the efficacy of probiotic treatments worldwide.

This research not only contributes to the field of microbiome studies but also holds profound implications for public health, particularly in regions where malnutrition is prevalent. The findings underline the necessity of studying gut microbiomes in diverse populations to appreciate the biological diversity that can enhance health outcomes.

As the landscape of probiotic therapy evolves, the integration of genomic analysis into the development of tailored treatments could transform neonatal care and contribute to healthier outcomes for vulnerable populations. Future research will focus on expanding these genomic insights to other bacterial strains and health conditions, ensuring that probiotic therapies can be effectively personalized for various demographic groups.

In conclusion, the integration of advanced genomic analysis in probiotic development represents a promising frontier in medical research, paving the way for innovative solutions to health challenges faced by infants and other populations at risk of intestinal diseases.