Relating Bacterial Microbiome Structure to Specific Diseases: We’re One Step Closer

I wasn’t surprised to see this research out of Harvard University:  it was inevitable. Scientists at Harvard and the Joslin Diabetes Center have analyzed the genetic makeup of bacterial microbiomes and linked these DNA signatures directly to specific diseases.[i]   As more and more research has been done looking at the specifics of microbiome species in diseases like Parkinson’s, autism, depression, Alzheimer’s, ALS and so many more, there was going to come a time when we had enough information to start computing this kind of relational information:  microbiome pattern = X disease.

You know how I am always pointing out the insane complexity of the human biome?  Well, in previous work, these Harvard researchers have found that there may be more genes in the human biome than there are stars in the observable universe.  In a prior research study, for example, they found 46 million genes in just 3500 human microbiome samples. So instead of trying to settle on one type of bacteria that may be problematic, these scientists instead analyzed what they call “microbiome architecture,” meaning the structure and composition of groups of bacteria that might more easily be associated with disease.[ii]

The scientists collected microbiome data from 13 groups of patients – more than 2500 samples – and analyzed the links between these 7 illnesses and the bacterial genes found in the samples.  They computed 67 million different statistical samples and found distinct clusters and were able to relate specific microbial DNA patterns to coronary artery disease (CAD), cirrhosis of the liver, inflammatory bowel disease (IBD), colon cancer and type 2 diabetes.  Three of these (CAD, IBD and cirrhosis) share many of the same bacteria:  those who have this pattern have a measurably increased risk of having one of these diseases: “We find coronary artery disease, inflammatory bowel diseases, and liver cirrhosis to share gene-level signatures ascribed to the Streptococcus genus.”  Type 2 diabetes has a very different and distinct microbiome signature.  It is the cluster of bacteria, rather than a single member, that were linked to the specific disease:  “Type 2 diabetes, by comparison, has a distinct metagenomic signature not linked to any one specific species or genus”

The hope is that in the near-term future, a single stool sample will be able to predict the risk of developing one of these diseases.  But considering the unbelievable complexity of the bacterial microbiome, defining such tests may take quite some time!  However, as one of the researchers involved states, they’ve taken us one step closer to that dream: “We’ve identified genetic markers that we think could eventually lead to tests, or just one test, to identify associations with a number of medical conditions.”[iii]

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[i] Tierney, B.T., Tan, Y., Kostic, A.D. et al. Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators. Nat Commun 12, 2907 (2021). https://doi.org/10.1038/s41467-021-23029-8

[ii] https://newatlas.com/science/microbiome-architecture-gut-bacteria-genes-human-diseases/

[iii] https://news.harvard.edu/gazette/story/2021/05/study-links-genetic-makeup-of-bacteria-in-the-human-gut-to-several-diseases/