I didn't say it was all nutrition yet it plays a role.
The study was conducted to investigate the effects of dietary n-3 highly unsaturated fatty acid (n-3 HUFA) on growth, nonspecific immunity, expression of some immune related genes and disease resistance of juvenile large yellow croaker (Larmichthys crocea) following natural infestation of...
pubmed.ncbi.nlm.nih.gov
Tldr Omega 3 helped survival of yellow croaker from crypt infection.
Now extrapolation of published research needs to be done carefully. It is without a doubt that fish have gut bacteria, and without a doubt some strains are beneficial while others not so much. Those effects are not just based around fish health, for example if you have a probiotic that increases feed conversion we would see that as a benefit. However this might not increase the actual health of the fish, and a lot of times can be detrimental. Also when we look at probiotic studies they use large amounts of a single bacterium for therapy. This is not the same as the soil biome at all.
And when we add a immune system to the discussion it gets really complicated. The reason our immune system is most active in the gut is because we have many billions of bacteria there. We need to keep them out or we die. And when we die they start eating us from the inside. These immune reactions however will not help against non gut associated pathogens. So you're not protected from many many pathogens. Even a slight change in some bacteria you're exposed to in the gut will lead to disease. You have plenty of E.coli in your gut but if you go to Mexico there is good odds that if you drink the water you'll get a different strain of E. coli which will lead to travelers diarrhea.
Which brings me to the aforementioned trout.
These were fed large amounts of a single bacterium and they saw resistance to ich and Aeromonas bestiarum. This isn't totally surprising because if you deliver enough unknown antigen(s) to the gut you can cause immune system upregulation. Thus they knew this and only looked at the innate response in relation to both. Not going to go far down a rabbit hole but the innate response does not have to be linked with B or T cell mediated response. (So not adaptive immunity like a vaccine produces). Now what's interesting is the Aeromonas sobria might have produced cross reactivity to protect against A. bestiarum but they didn't look at that. Also the probiotics in the paper have not been realized in the intervening 12 years as they likely turned out to be not very effective or not cost effective. Also A. sobria can cause disease in other fish and diarrheal diseases in humans so that could be the reason as well
The basic facts are that we lose much food to disease whether it be farmed, farm raised, wild, aquacultured, maricultured or wild caught. Just because we wish nature was nicer or harken to the good old days, it just isn't and without antibiotics, vaccinations and other scientific techniques (e.g. sanitation and water treatment) we would be absolutely surrounded by death. And the idea that you can eliminate all disease from an aquarium is groundless, that is until you show that your fish have never ever died. You can make it the most resistant possible though through the aforementioned nutrition and ecology, and proper QT techniques including the use of medicines when required.
And some may say I came into this thread hot... Wasnt sure I was going to address this because I had hoped others noticed but....
You may have missed the early implication by the OP that a person was ignorant because they saw their fish ingest soil and die a day in a half later and make the likely conclusion that there was cause and effect. (There are many pathogens within the soil biome as well as other interactions we can't possibly understand in this situation and to suggest knowing otherwise is irresponsible.). And then avoid that person within this very thread.
@ingchr1 there is a chance that your fish died from soil ingestion, whether it could have been chemical or pathogen mediated we obviously have no idea. Sorry that happened to you!