The color of the stools indicates infection, or could be a lack of bile as the previous poster stated. Usually with low bile the stools turn clay colored http://www.mayoclinic.org/stool-color/expert-answers/FAQ-20058080. The link indicates that yellow stool may indicate malabsorption, gluten sensitivity or celiac which has infectious origins.
The GI tract is the most susceptible for contracting infection and medical testing is woefully inadequate in finding stealth infections.
There can a number of pathogens that can harbor the gut including viruses, yeast/fungal, parasites (worm and protozoa) and rogue bacteria. uBiome is a novel testing method that is relatively cheap, I do not think it is inclusive (meaning can test for every pathogen).
When there is infection, there will always be oxidative stress and oxidative stress makes people sick. I would support the body with nutrients to help my body cope better with an emphasis on antioxidants. For instance, vitamin C can support immunity and detoxification.
If it were me, I would start with colostrum. Colostrum is a miracle for many people, it contains many immune factors and can benefit the gut. Vitamins A & D support the mucous (GI)environments (immunity).
If that did not improve my situation then I would start with broad spectrum approaches that can potentially address several different types of infections. Items in this category would be raw garlic, caprylic acid, turmeric, cinnamon and black seed with honey.
If this does not help then I would opt for some other testing labs such as ParaWellness for parasites and a gut ecology test.
Disclaimer: I am not a doctor so I am unable to diagnose or treat. Information is considered educational to be shared with your healthcare provider.