From my reading of the scientific literature in this area the worst you can expect is mild gastro - compared to a C. difficile infection this is not really a concern.

I was thinking more that the cultures in the donor poop are unknown. There are numerous horrible things that you don't want stuffed up your bum from more c.diff to worms to ulcerative bleeding carrying HIV for example.

Yes this is a risk, but in general pretty low if you know the person well. If you are taking the sample from your husband or wife you would hope you would know if they have HIV or not.

Actually the risk of getting worms is an interesting potential positive. There is a lot of data suggesting that the lack of intestinal worms in western countries is one of the reason for the rise of autoimmune diseases like Crohns. The theory is that the immune system in the gut is designed up to keep worms under control and in their absence starts attacking things like the gut tissue instead. There are a couple of stage three trial currently running that are giving people pig wipworms (they can infect but not reproduce in the human gut) to treat Crohns. The earlier trials were really encouraging so it will be interesting to see how they turn out.

This is why the doctors/scientists in the article recommended that donors be screened first.

But the more I discover about medicine and biology, the more I realize how much we still don't know. Hundreds of types of bacteria in a typical stool sample? This is amazing! Whole biomes await study... from internal gut bacteria (very small scale), to microbial colonies (regional or national scale) that we use for fermentation. Exciting!

We actually don't know how many bacteria live in the human gut, but may be as many as 100,000 different species although around 1000 dominate. One of the difficulties with estimating how many species are present is that it is hard to know if a particular species is a member of the "native" gut microflora or just passing through.

No one knows - that's the biggest issue. It is very complex. Based on studies it seems pretty low risk, as long as the donor is tested for disease.