I researched biome tests. Some of the companies that offer them have questionable credentials and/or poor Better Business Bureau ratings. The best test I found is from Life Extension, a company that markets pharmaceutical grade supplements and uses some of its profits to support anti-aging research. The comprehensive report goes directly to the patient, but it would obviously be preferable to interpret the results in conjunction with a physician. The standard opinion in the gastroenterology field, echoed by your gastroenterologist, is that the science of biome analysis is still in its infancy. I have a gastro appt in May (had to wait over half a year to get one), plan to print out the information from Life Extension about the test panel, which includes tests for pathogens (harmful microbes) and discuss it with him. The test is pricey, however, $499. Life Extension has a sale on tests in the spring, but I doubt that there would be much of a discount for this test, nor would insurance be likely to pay for it. Check it out though. At the very least you'll be better informed if you discuss testing with your naturopath.
https://www.lifeextension.com/lab-testing/itemlc100088/gi360-stool-analysis-fecal-test