[mercurialshark]

Can someone speak to my theory (that's based on limited knowledge), that if we wanted to "reset" the gut, we could deliberately take antibiotics to wipe out good/bad colonies of microbes and tailor a hyper-specific diet for sought after results. The hypothesis being that if certain microbes flourish for years and that if it is impractical to genetically map the gut biome to identify which are thriving in every patient, this could help us get to a clean slate before therapy is attempted.

[beltranrm]

IMHO, that seems like a bad idea. Two thoughts (these are only very overly generalized opinions, biology is a little bit complicated):

1) You might not get them all, and the ones that survive might transfer the traits of antibiotic survival and pathogenic-ability (if present) to the new population.

2) You would need to ensure that your hyper-specific diet contains the right mixture of microbes, say, you would need to avoid irradiated food, and a bunch of other things. "Bad microbes" coming into an empty gut seems to me like a bad thing.

[mercurialshark]

Thanks, both are good points! I assumed there were downsides to if you weren't able to wipe out the robust bad microbes but that's even worse than I had expected. Perhaps I'll wait on self-experimentation. The possibility of nefarious and now genetically enhanced microbes reigning supreme in my body is not cool.

[acomjean]

Antibiotics don't wipe out all the bacteria, just some of them. Its a bit of a problem because if some are effected less by the antibiotic, you can change the balance when the bacteria populations bounce back. The bacteria that are there do set up shop and don't like others crowding in.

We don't really enough enough about what should be the optimal mix of bacteria to make someone healthy.

They do "fecal" transplants to help people get back bacteria that are missing.

There was a graduate student talk (an hour) about some of this stuff last spring. slide decked linked to the right.

http://sitn.hms.harvard.edu/seminars/2014/in-the-loop-with-p...

[mercurialshark]

I've read a bit about fecal transplants and they apparently have good results. I just wanted to oversimplify and remove as many variables as possible before introducing new ones. No longer liking the idea...

[beltranrm]

Another option is to skip the antibiotic and use a probiotic to nudge your microbiome toward healthier regions. I am aware of two modern probiotics that might help you:

repoopulate - http://www.microbiomejournal.com/content/1/1/3

equilibrium - http://www.generalbiotics.com

Both of them are designed thinking of ecosystems more than individual strains (repoopulate has 33 strains, equilibrium has 115). Of course, these aren’t an alternative to FMT if you’re treating a disease… but for general health/wellness I think they’re both quite good.

disclosure: I worked on equilibrium

[aroch]

As mentioned by acomjean, fecal transplant (FMT) is the typically how we restore "healthy" biota in the gut. Interestingly, only a handful of species play a large role in the regulation of gut microbiota and physiology/psychology of the host. Recolonizing the gut with these species alone is enough to restore a "healthier" mix.

[1] http://dx.doi.org/10.1016/j.cell.2013.11.024

[Mz]

There is a book called "Seeing like a state" http://www.amazon.com/Seeing-like-State-Certain-Condition/dp...

In it, the author tells a story of someone in a village in a less developed country who cannot afford pesticides. So he starts a war between two ant colonies in order to drive out the ants that are destroying a beloved fruit tree.

You can do the same thing for gut flora. You don't have to wipe things out first. Trying to wipe the gut clean is extremely hard on the body. It's much easier on the body to just feed the good flora and give them support so they start crowding out things you don't want. It's a gentler path. It just takes persistence.