A reader wrote:
“QUESTION: What are the best probiotics/doses to take post-Xifaxan to repopulate/maintain gut? “
What I am going to do in this post is use this question to work logically thru the process in a step by step manner.
- Know the alternative names and the family of antibiotics that it belongs to –
- Start with a general query of pubmed for “rifaximin microbiome” – why, you want to see if they have been any general studies done on it effects. In this case, I got 94 hits. See section below
- Follow up with queries for specific bacteria that are available as probiotics. I used this post as reference
- “Rifaximin e.coli ”
- “Synergic Interaction of Rifaximin and Mutaflor (Escherichia coli Nissle 1917) in the Treatment of Acetic Acid-Induced Colitis in Rats.
- Effecive against enteropathogenic Escherichia coli 
- Rifaximin Bacillus
- “rifaximin possessed best activity against…Bacillus cereus” 
- Rifaximin Freudenreichii – nothing
- Rifaximin Enterococcus
- “rifaximin possessed best activity against…Enterococcus spp. ” 
- Rifaximin Clostridium
- Some are resistant. Some are not.
- “Rifaximin e.coli ”
- If you do not find specific information, then repeat the search using the family that the antibiotics belong to. (Minocycline –> Tetracycline)
- Beware of assuming that only the bad is killed off — likely the good and the bad are diminished.
Microbiome Inpact of Rifaximin
A  study had a nice table of before and after. Because there is so little that we know, I will assume that any decrease seen was of bad strains and if you can supplement with good strains — then that is the direction
- “B. longum W11 could be used in combined therapy with rifaximin,”
- ” It is still not clear to what extent rifaximin can be able to modulate gut microbiota composition and diversity in different clinical settings. Studies based on culture-dependent techniques revealed that rifaximin treatment promotes the growth of beneficial bacteria, such as Bifidobacteria and Lactobacilli.”
- ” Rifaximin appeared to influence mainly potentially detrimental bacteria, such as Clostridium, but increasing the presence of some species, such as Faecalibacterium prausnitzii. A decrease in the Firmicutes/Bacteroidetes ratio after 14 days of treatment and bacterial profiles with higher biodiversity were observed during the follow-up compared to baseline… It was not possible to speculate on differences of fecal microbiota modification between responders vs nonresponders” 
- “Studies of changes of intestinal flora during therapy and the health implications of these changes are also needed.”
My suggestions are:
- Broad Spectrum non-Lactobacillus Probiotics
- General Biotic Equilibrium
- Prescript Assist
- E.Coli Probiotic (Mutaflor, Symbioflor-2)
- A Bacillus Probiotic (see this post — are you histamine sensitive?)
- A Enterococcus probiotics (Symbioflor-1 or Biofermin+S)
- Possibly Kyo Dophilus 9 (contains 2 different B. longums)
Both Mutaflor and Kyo Dphilus 9 can be taken while on Rifaximin and would appear to increase it’s effectiveness.
See this post as reference.
As always, consult with your knowledgeable medical professional over these suggestions and the literature supporting them.