Seed Health unveils AI-powered platform to unlock “microbiome clock” secrets

16 Apr 2024 --- Seed Health launched CODA, a new computational biology platform that uses AI and machine learning to discover and develop next-generation precision probiotics and microbiome-directed interventions. The platform translates insights from the multi-omic Human Phenotype Project featuring 200 terabytes of human data to advance metabolic health, brain health, menopause and longevity.

“CODA enables the development of next-generation precision probiotics in a powerful way. Rather than relying on a few biomarkers in isolation, CODA empowers us to examine them within a network of hundreds of other biological data points,” says Dr. Dirk Gevers, chief scientific officer at Seed Health.

“This comprehensive approach allows us to unravel the complex interactions between diet, supplementation, the microbiome and multi-system human health more effectively than before,” says Dr. Dirk Gevers, chief scientific officer at Seed Health.”

The platform’s dataset integrates over three million phenotypic data points from more than 13,000 people across 40,000 cumulative subject years. It combines microbiome analysis with genetic, immune, metabolomic and proteomic data. 

Independent research from the University of Oxford, UK, shows that diverse communities of resident bacteria can protect the human gut from harmful pathogens by consuming nutrients that these disease-causing microorganisms need. The researchers note their findings could help develop new strategies to optimize gut health.

Microbiome clock
CODA’s combinatorial dataset unlocks new insights into the complex interactions of the microbiome with key biological systems like the gut-brain, gut-heart, gut-liver, gut-skin and gut-eye axes. This facilitates the development of organ-specific clocks by revealing the diverse aging rates of different organs in an individual. 

The microbiome clock emerged as a key predictor of biological health across multiple organ systems and is seen as a critical interventional target to enhance human health. CODA helps explain “unknown” connections between the microbiome and health and the development of outcome-specific interventions.

“Our CODA platform is tracking the health data of tens of thousands of individuals over decades, offering a comprehensive, multi-omics perspective. This allows us to uncover and address critical connections between the microbiome and health, enabling the creation of targeted interventions to improve outcomes across diverse populations,” says Raja Dhir, co-founder of Seed Health.CODA's initial programs prioritize cardiometabolic and brain health and menopause and longevity.

CODA improves the company’s full-stack platform and boosts its computational capabilities across various microbiomes. One of the main insights reveals a distinction between biological and chronological age that offers a better understanding of health and disease patterns.  

“Our development of organ-specific clocks has revealed the microbiome’s extraordinary capacity not just to predict but to actively shape health outcomes across key biological systems. CODA empowers the transition from insight to action, enabling the creation of interventions that target health outcomes across these different organ systems to support lifelong health,” says Dr. Eran Segal, computational biologist and professor at the Weizmann Institute of Science, Israel.

The multidimensional approach encompasses biological, environmental and dietary influences, lifestyles and medical histories and shows the interactions between the host and microbiome. These interactions reveal the underlying causes of health or disease.

Microbe ecosystems
The platform uses microbial genomics to identify bacterial genes and then employs a network effect analysis to understand how the microbes operate in their ecosystems. Many of the microbes have yet to be discovered or named in existing microbiome databases.

CODA’s first programs include cardiometabolic health, brain health, menopause and longevity. The platform will translate the information for the creation of consumer health products. One study by Seed Health researchers showed a causal relationship in how diet modifies metabolic parameters through microbiome modulation to improve metabolic health.

Early findings underscore the significant role of microbial metabolites in brain development and function, opening the door for microbiome-targeted interventions to enhance neurocognitive health. The menopause program develops solutions to mitigate menopause-induced symptoms and age acceleration.

“CODA significantly expands our platform’s capacity to realize the full promise of the microbiome. With a deeper and more nuanced understanding of the microbiome’s role in human health, we are better positioned to translate these breakthrough research findings into interventions that have a meaningful impact on human health globally,” says Ara Katz, co-CEO and co-founder of Seed Health. 

Meanwhile, researchers at the University of Massachusetts Lowell’s Zuckerberg College of Health Sciences are exploring the effect of gut microorganisms on the onset of disease, which they believe will facilitate early detection and improved treatments, especially for cognitive disorders such as Alzheimer’s and Parkinson’s.

By Inga de Jong