Has this procedure been investigated to ensure proper gut colonization in new borns after labor that involves antibiotics? Either via a transplant to the mother or child?

Not that I know of.

An interesting aside - as you may have read, FMT is being investigated as a treatment for autism. The thinking here is as follows. Babies are born with a certain level of Clostridium species (not necessarily C. diff). Clostridium are very good at producing toxins (botulism and the toxins involved in C.diff). Normally the level of clostridium in babies drops on its own. It's believed that in some babies, this drop never happens. These babies are then therefore continually exposed to toxins from these clostridium bugs, some of which may have neurotoxic properties and can result in autism. The goal of FMT is to alter the gut flora enough to get rid of these Clostridium species and stop the toxin from reaching the brain. There has been success in young children. What we need to keep in mind though is that autism is a spectrum of not only symptoms, but also a spectrum of causes as well, so FMT won't necessarily work for everyone.

Fascinating. What are the symptoms or diagnostic tests that would lead a doctor to consider this?

It would mostly be a parent investigating it on their own I would say.

It's well known that children with autism have frequent GI issues (diarrhea etc). You'll find that many parents have their autistic children on special diets (gluten free, dairy free etc) all of which attempt to alleviate the GI symptoms. They may work, but it's likely because they are changing the gut flora, rather than removing the gluten protein for example.

>ensure proper gut colonization in new borns after labor that involves antibiotics

Babies get their intestinal bacteria during the birthing process from the vagina, their mother, the mother's feces, etc. That's why C-section infants have vastly different gut flora initially. They never made that trip down the vagina to be exposed to vaginal bacteria and are exposed to different types of bacteria during the first few weeks of life. I'm not sure the effect of antibiotics are the same or similar to that of a c-section baby. I'm not sure we know the long term effects of c-section babies and gut flora especially later in life. I would think c-section would be much more disturbing to gut flora than antibiotics.

http://en.wikipedia.org/wiki/Gut_flora#Acquisition_of_gut_fl...

As a potentially interesting correlation: difficult pregnancies/cesareans tend to produce more autism:

http://www.autismtoday.com/library-back/Autism_More_Likely_i...

I'm sure your right but my wife and I just had a kid through lengthy vaginal birth with antibiotics which is why I asked. (FWIW I'm a computational biologists working on medical studies and have the seen some of the research in this area before, not just one to randomly self medicate.)

I have some problems that I don't have any particular diagnosis for. Is there any way I can find out whether it's worth trying this? Is it a problem for someone to get a transplant when they don't actually need it? (The article writer seemed to think it was a bad thing, but if it really is "as dangerous as changing a baby's diaper", then it doesn't sound any worse than taking unnecessary vitamins.)

(Problems are food intolerances, some cause unusually painful gas, others affect my mind. My doctor has no idea what causes it, and some of them are to really common foods, so staying on my diet is difficult.)

I'd speak with your physician about the possibility of FMT. Your MD can get in touch with these guys http://www.openbiome.org/ that provide low cost samples for transplant ($250).