Karolinska’s Microbiome Revolution

Introduction

Microbiome research at Karolinska Institutet is reshaping our understanding of human health by examining the diverse microbial communities inhabiting the body. Professor Lars Engstrand, Director of the Center for Translational Microbiome Research, has spearheaded large-scale studies that integrate sophisticated next-generation sequencing platforms with comprehensive metadata analysis. This approach offers unparalleled insights into how the microbiome evolves over time, across different body sites, and among various populations—primarily in Scandinavia, but increasingly worldwide.

“It’s obvious that the microbiome is a dynamic organ… We’re expanding beyond the gut to the oral, vaginal, and skin microbiomes.”
— Professor Lars Engstrand

Dynamic and Varied Microbiomes

Karolinska’s research underscores the dynamic nature of the human microbiome:

• Within Individuals: Microbial composition can change dramatically over weeks or months, influenced by diet, medications, and lifestyle.

• Across Populations: Large-scale studies reveal significant variations tied to regional or cultural practices.

• Metadata Integration: Researchers meticulously document living conditions, dietary factors, and drug intake to interpret microbiome shifts more accurately.

Large-Scale Sampling and Sequencing Technological Advancements

In pursuit of a broad understanding of these microbial ecosystems, the center has gathered roughly 500,000 samples from both European and Chinese populations since 2019. Key to this process:

1. High-Throughput Sequencing: Shotgun metagenomics enables the identification of microbial species and functional genes at scale.

2. Robotic Automation: Streamlined sample prep and processing address the growing demands of population-level studies.

3. Multi-Site Focus: Beyond the gut, researchers collect samples from oral, vaginal, and skin sites to map interrelated microbial communities throughout the body.

“We’ve sequenced over 50,000 shotgun metagenomes… the bottleneck is moving to sample processing.”
— Professor Lars Engstrand

Short-Read and Long-Read Sequencing Synergy to study the human microbiome

While short-read platforms excel at high-throughput sequencing, the addition of long-read sequencing opens new possibilities:

• Completing the Picture: Long-read data resolves complex regions that short reads miss—vital for understanding specific bacterial strains.

• Single-Cell and Spatial Applications: Coupled with single-cell approaches or spatial transcriptomics, long-read technology offers deeper functional insights into host–microbe interactions.

• MGI Technology: Karolinska’s team values MGI for its reliability and capacity, praising the T7 platform for large-scale shotgun metagenomics while looking forward to future expansions.

Future Directions

Karolinska Institutet aims to push boundaries by investigating:

• Early Detection and Intervention: Identifying bacterial signatures that may predict disease onset.

• Personalized Medicine: Leveraging metadata to tailor interventions or probiotics.

• Single-Cell & Spatial Insights: Examining localized gene expression in individual microbes, advancing precision health strategies.

“Certain parts of our microbiome research will benefit greatly from combining short-read and long-read sequencing.”
— Professor Lars Engstrand

Conclusion

By blending large-scale sampling, advanced sequencing technologies, and comprehensive metadata, Karolinska Institutet’s microbiome program stands at the forefront of biomedical research. Professor Lars Engstrand’s emphasis on capturing multiple body sites and integrating new platforms paves the way for personalized health solutions, early disease detection, and a holistic understanding of human–microbe relationships.

References

Karolinska Institutet Official Website

Center for Translational Microbiome Research

Nature: Microbiome Studies

PubMed: Microbiome and Metadata