7.7 Lyme Disease

NOTE: THIS CHAPTER IS AN EARLY DRAFT

What can we learn about Lyme disease?

We know that Lyme disease has been linked to the pathogen Borrelia. The uBiome 16S pipeline doesn’t appear able to distinguish among the different species of that taxa, so let’s look at a higher level, the family Spirochaetaceae, which includes Borrelia. Several people with confirmed lyme disease sent me their samples, and indeed I do find some Spirochaetaceae in these samples, albeit at very low abundance.

I was unable to find any Spirochaetaceae in any of the other hundreds of samples I examined, including from a few people with confirmed lyme.

Let’s do an ordination. How do lyme patients resemble one another? 7.9

## Square root transformation
## Wisconsin double standardization
## Run 0 stress 0.1311851 
## Run 1 stress 0.1202691 
## ... New best solution
## ... Procrustes: rmse 0.1726209  max resid 0.407332 
## Run 2 stress 0.1202691 
## ... Procrustes: rmse 0.001003481  max resid 0.00173526 
## ... Similar to previous best
## Run 3 stress 0.1202687 
## ... New best solution
## ... Procrustes: rmse 0.0005346505  max resid 0.0009185695 
## ... Similar to previous best
## Run 4 stress 0.1202686 
## ... New best solution
## ... Procrustes: rmse 0.00004360464  max resid 0.0000872375 
## ... Similar to previous best
## Run 5 stress 0.1311851 
## Run 6 stress 0.1310013 
## Run 7 stress 0.1220377 
## Run 8 stress 0.1363568 
## Run 9 stress 0.1202689 
## ... Procrustes: rmse 0.00009739231  max resid 0.0001936635 
## ... Similar to previous best
## Run 10 stress 0.1202697 
## ... Procrustes: rmse 0.0007844823  max resid 0.001459528 
## ... Similar to previous best
## Run 11 stress 0.1322627 
## Run 12 stress 0.1202688 
## ... Procrustes: rmse 0.0001130062  max resid 0.0001978608 
## ... Similar to previous best
## Run 13 stress 0.1310022 
## Run 14 stress 0.1220378 
## Run 15 stress 0.1379099 
## Run 16 stress 0.1202687 
## ... Procrustes: rmse 0.0001070191  max resid 0.0001973935 
## ... Similar to previous best
## Run 17 stress 0.1311856 
## Run 18 stress 0.1322637 
## Run 19 stress 0.1684776 
## Run 20 stress 0.1425374 
## *** Solution reached
Clusters of lyme patients

Figure 7.9: Clusters of lyme patients

This person tried Kefir to see if they could increase Fusicatenibacter: