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Nickel on NGS and the urobiome

Posted: Thu Oct 07, 2021 3:07 am
by webslave
The urinary tract has been called a "veritable microbial jungle". In 2020 Dr Curtis Nickel from Canada gave a key lecture on the urinary microbiome or urobiome.

He found that in >70,000 urine samples collected, >4,000 species of bacteria were identified, including E. coli being predominant in 28% of samples (which shows how ludicrous it is for men to panic when they see "E. coli" on their NGS/PCR results). As such, Dr. Nickel notes that the urinary tract is complicated, wherein the microbiota of different sites are often very different, depending on how/where the urine was collected. So your NGS results are going to differ based on how the sample is taken, and where the sample is taken. It makes a mockery of the Microgen Dx business model, where patients themselves collect samples and mail them in. 😖

Dr. Nickel noted that there are ways to manipulate our urinary microbiome, including through diet, exercise, avoiding environmental pollution, and avoiding antibiotics.

Then, at the AUA 2021 Meeting, he reported that the microbiome of IC/BPS patients is divergent from healthy controls and acute/chronic cystitis patients, but is taxonomically more similar to a healthy cohort than to those with a diagnosis of [bacterial] cystitis. So the UCPPS urobiome looks more like a normal urobiome than the biome of people with obvious infections. :idea:

And in another study paid for by MicroGenDx, he compared NGS urine specimens from men with chronic prostatitis, men with acute cystitis, and healthy men. Turns out, there is almost no difference in the microbiota:
Microbiome composition was also associated to diagnostic group, though the effect was small and diagnosis only explained approximately 1% of variation among diagnostic groups.
He comments that there may be an infection in a small subset of men with CP, which we have known all along (and that infection may not be the source of the pain, we should note).

He concludes that complex next generation sequencing (NGS) analysis reports from urine specimens from men diagnosed with chronic prostatitis (CP) are difficult to interpret. So if an expert like Nickel finds it difficult to interpret, how useful are these reports in the hands of surgeons (urologists are essentially surgeons), or even worse, your bumbling family doctor?

In another study looking at the urobiome of normal men and women, Nickel found that Staphylococcus is one of the most common bacteria found. So an astronomic number of men have taken long courses of antibiotics based on small numbers of Staph in their NGS/PCR test results ... for nothing.

Bottom line is this: here we have a researcher (Nickel) who for years has been a fan of the infection theory of UCPPS, working for funded by a company (Microgen Dx) with huge vested interests in finding that UCPPS has a microbial source, and what have they come up with? Essentially, nothing. 🙄

Re: Nickel on NGS and the urobiome

Posted: Thu Oct 07, 2021 7:24 am
by Ranzzar
Thank you, webslave. In a few short lines you have very succinctly delivered a lot of clarity on this topic with good evidence to back it up. Unfortunately people promoting these tests try to do the opposite to keep desperate people spending their money on dubious investigations.