7.6 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? 7.7

## Square root transformation
## Wisconsin double standardization
## Run 0 stress 0.1311851 
## Run 1 stress 0.3153599 
## Run 2 stress 0.1310014 
## ... New best solution
## ... Procrustes: rmse 0.1344121  max resid 0.2514105 
## Run 3 stress 0.1202687 
## ... New best solution
## ... Procrustes: rmse 0.181741  max resid 0.3223 
## Run 4 stress 0.1220377 
## Run 5 stress 0.1310013 
## Run 6 stress 0.1202687 
## ... New best solution
## ... Procrustes: rmse 0.00002551973  max resid 0.00005530593 
## ... Similar to previous best
## Run 7 stress 0.1518418 
## Run 8 stress 0.242134 
## Run 9 stress 0.1606191 
## Run 10 stress 0.1202687 
## ... New best solution
## ... Procrustes: rmse 0.0001830635  max resid 0.0003433725 
## ... Similar to previous best
## Run 11 stress 0.132263 
## Run 12 stress 0.1220378 
## Run 13 stress 0.1220377 
## Run 14 stress 0.1202691 
## ... Procrustes: rmse 0.0004401232  max resid 0.0007878116 
## ... Similar to previous best
## Run 15 stress 0.1220378 
## Run 16 stress 0.1202694 
## ... Procrustes: rmse 0.000744479  max resid 0.001376227 
## ... Similar to previous best
## Run 17 stress 0.1202693 
## ... Procrustes: rmse 0.0006519559  max resid 0.001198076 
## ... Similar to previous best
## Run 18 stress 0.1310013 
## Run 19 stress 0.1310013 
## Run 20 stress 0.1202687 
## ... Procrustes: rmse 0.00008291044  max resid 0.0001602819 
## ... Similar to previous best
## *** Solution reached
Clusters of lyme patients

Figure 7.7: Clusters of lyme patients

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