Microbiologist here - the name anaerobe is a pretty broad term. Within the gut there is going to be obligate anaerobes (killed by atmospheric O2) and facultative anaerobes (can survive in both oxygen rich and oxygen deplete environments).

In a blender, the obligates will likely die but the facultative will remain.

I am also a microbiologist (my Ph.D was in molecular microbiology). I didn't work on obligate anerobes, but the lab next door did. They had to go to a lot of trouble to keep oxygen out of all their experiments by using aneroboic chambers and the like (a total pain).

The problem is that most of the organisms in the gut are obligate (strict) anerobes. Sure the faculatative anaerobes will survive, but this is going to create an imbalance in the populations being transplanted. If the aim is to restore tha balance present in a healthy individual why introduce oxygen when it is easy to avoid.

Two things, you aren't necessarily trying to achieve the identical balance. Most of the research in this area is finding the particular bacteria that are important to repopulate the ill gut. The aim is to eventually transplant only the important bugs or just grow the important ones and skip the fecal donors all together.

The other issue is that it would be very hard to get a fecal sample that hasn't been exposed to O2.

I think I remember reading that the rough-and-ready procedure being used by doctors performing the study also involved the laboratory equivalent of a blender. Not sure if I'm misremembering, or if there are laboratory blenders that don't introduce oxygen, or if the researchers don't think it matters, or what.

I am a donor at a large center performing these procedures and work with the physician and lab staff. The purpose of the blender is to make the fecal material into a slurry, after that it is filter through paper to remove food particles. The filter paper allows the bacteria to pass through. The resultant liquid is given to the patient (enema, NG tube, pill).

Can you address danieltillett's question regarding anaerobes?

For sure.... quoted below.

Microbiologist here - the name anaerobe is a pretty broad term. Within the gut there is going to be obligate anaerobes (killed by atmospheric O2) and facultative anaerobes (can survive in both oxygen rich and oxygen deplete environments).

In a blender, the obligates will likely die but the facultative will remain.

You sir, have just ruined... everything.