Another thing worth looking into is low-carb diets. I won't try to give specific details because it's outside my expertise, so I'll just say anyone interested should do their own research, but I will recommend the book
The Art and Science of Low Carbohydrate Living by Volek & Phinney as probably the best starting point. It mentions the topic but it's something I've only skimmed over: there is apparently a known connection between carbohydrates and inflammation. It's something I have personally noticed if I switch between a ketogenic and "normal" diet: I get a lot less knee pain while on low carb. I plan to do further research into this myself, but I haven't had the time to look into it thoroughly yet.
There are even specifically
anti-inflammatory diets, although I would caution against reading too much into the "evidence" given in articles like that one (which was the first I happened to stumble upon, as I said not an expert on this just pointing it out). I would instead recommend the aforementioned
Volek & Phinney, because it gives a good overview of the science to date, from which to draw conclusions about any dietary modifications. That, I think, is always better than these magic bullet diets, often based on very thin science such as individual studies with small sample sizes.
Personally I would not be surprised at all if the recent trend towards gluten-free dieting is actually just about cutting down on refined grain products like bread and pasta generally, which then reduces this carbohydrate inflammation response making people feel better, even though the vast majority probably aren't gluten intolerant in the slightest. I think there's a lot to be said for cutting or significantly reducing bread, pasta and probably rice, even without going full-on keto.
I would also agree that there's a lot of evidence that the gut biome is extremely important. However, to my knowledge there isn't a lot of concrete evidence about in what way it's important, or that anything like prebiotics/probiotics actually make any difference. The real, hard evidence is mainly to do with what is, almost euphemistically, known as a "faecal microbiota transplant" (basically, eating other people's poop - note: consult your doctor first!).
I recommended something similar to a friend who, while otherwise perfectly healthy, has been struggling with dangerously low bodyweight. The traditional weightlifter's energy drink is simply milk, eggs and honey thrown in a blender. It's actually very nice and you can vary it by changing the ingredients, for example I sometimes make it with malt extract instead of honey, but you could put strawberries or blueberries in it. Really anything that would work as an ice cream flavour should work well, as it's basically a milkshake. I personally find it has a much nicer texture than pre-packaged "protein drinks" which tend to be a bit gritty and artificial-tasting. It's fallen out of favour with weightlifters somewhat in recent years, because of the fact that if you cook eggs, it makes the protein twice as bioavailable as if you eat them raw. However, it's harder to eat 3 hard-boiled eggs than it is to drink 6 raw ones and either way, you get the same amount of protein.
As a starting point I would suggest 2 eggs (I usually have 3 or 4) and one tablespoon of honey topped up with milk to make a pint (measure just under because it will froth up a bit). But you can add more or fewer eggs to taste and for digestibility. You can easily increase the calorie-density by adding some double cream and/or more honey (but I'd recommend not going too mad with what is basically pure sugar, even if weight gain is the goal).
Another thing you can do is to add egg whites instead of or as well as whole egg(s), which gives you a higher protein:fat ratio and may taste "lighter". However, in that case it's a good idea to add a drop or two of biotin (vitamin B7), because egg whites contain an antinutrient called avidin that blocks biotin absorption. In the case of whole eggs, this is balanced by the extra biotin present in the yolk, but eating too much raw egg white for weeks on end can lead to something known as “egg white injury” (yes, that's the real name) which is basically biotin deficiency. It's called that because people started getting it before biotin was discovered. The cause was figured out later. As a guide, a yolk contains about 20mcg of biotin, so that's what you need to make up if you have raw whites (35g of whites is approximately one egg).