The project progressed for all 4 Aims.
Aim 1: Developing Better Tools to Study Microbiome Transmission
We’ve made exciting progress in improving the methodologies enabling the study of microbiome transmission between people, animals, and environments:
- We expanded our dataset to include over 1 million metagenome-assembled genomes and cataloged over 20,000 human metagenomes. This database, called MetaRef-SGB, supports cutting-edge tools like MetaPhlAn and StrainPhlAn, now in their most advanced version (4.0).
- Using these tools, we created models to track how microbial strains (specific genetic variants within a microbial species) are shared. This tracking is effective also for the so-called "dark matter" of the microbiome—microbes that have no isolated representative but are key microbiome members.
- We have developed new computational metagenomic methods to study and model transmission for microbiome members we know less about, such as viruses, micro-eukaryotes (tiny organisms like fungi).
Aim 2: Exploring Microbiome Transmission in Real-Life Settings
We’re investigating how microbes spread between individuals and communities in in different settings:
- In a landmark study we already published we investigated nearly 10,000 samples from around the world revealing the basic patterns of microbiome sharing across ages, regions, and social connections.
- In daycare centers, we tracked hundreds of infants, their families, and educators over six months. Our preliminary and unpublished results show how social interactions at daycare shape the developing microbiome of infants.
- In a unique study on captive primates, we are exploring how social behavior and group changes influence microbiome sharing between chimpanzees and their human caretakers.
- In a school-based study we are following children for two years to learn how sharing a classroom environment affects their microbiomes.
Aim 3: Understanding How and Why Microbes Spread
We are uncovering how microbes are transmitted in different ways—between family members, across households, through shared environments, or even via food. We published rankings of the most transmissible microbes and started studying uncultured, harder-to-detect species. We also created a microbial biobank to preserve and study these microbes further. We are now focusing on understanding which microbes preferentially use which transmission modes.
Aim 4: Linking Microbiome Transmission to Health
We have started exploring how the movement of microbes between individuals is linked to diseases. Early findings suggest weak but likely meaningful links between microbiome transmission and conditions like autism and obesity. Ongoing studies are focusing on colorectal cancer and cardiometabolic diseases.
