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I am tasked with designing an in vivo experiment in humans that requires manipulating the gut flora in one sample group to gauge its effect. Please suggest ways of doing this besides administering antibiotics.

I am of the view that antibiotics may have unintended consequences and may be unethical; explain any opposing view.

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I think it would be helpful if you explained more about what you want to compare, and/or the rationale for experimentation. What do you want to gauge its effect on? Before/after antibiotics is probably the simplest and certainly statistically the most powerful approach. – kmm Feb 6 '13 at 13:33
i'm sure that changes of diet would also substantially change the gut flora mixture. this has been shown already, but i don't have the reference at hand... – shigeta Feb 6 '13 at 18:34
up vote 1 down vote accepted

I can't think of any way to start with an intestinal "blank slate", so to speak, except with antibiotics.

Perhaps it's possible to at least partially homogenize/standardize a sample group's biota with probiotics?

If it's ethics you're worried about, perhaps draw experimental subjects from a pool already being treated with antibiotics (although this, I suppose, introduces it's own biases?).

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Thank you Atticus29, this has re-assured me that antibiotics is the way to go.. – lizhys Feb 6 '13 at 18:24

I'm no expert, but I read this, and I found it very intresting:

In its study, Henry Ford treated patients between May 2010 and June 2012 with a therapy called intestinal microbiota transplantation (IMT), using donated stool from a healthy family member.

Here are the results:

“More than 90 percent of the patients in our study were cured of their C.diff infection,” says Dr. Ramesh. “This treatment is a viable option for patients who are not responding to conventional treatment and who want to avoid surgery."

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Thanks. I knew that was an option, but not viable for my study. Reason is: I want to gauge low level microbiome against normal. In essence, I need reduced gut flora and not different flora..+1 though. Just realised I cant't upVote..:) – lizhys Feb 6 '13 at 11:49

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