The following are a list of probiotics effective (i.e. improve, not necessarily cure) Irritable Bowel Syndrome according to studies on PubMed.com. IBS is co-morbid with CFS and thus they become recommended probiotics for CFS. For this I raised the criteria to studies on humans and not on mice. In general mixtures were eliminated with the exception of “unique mixtures” – Prescript Assist and VSL#3
NOTE: Probiotics do produce natural antibiotics. It is strongly recommended that the probiotics below be rotated and not taken continuously. Two weeks on one and then move to the next. Why? We want to minimize the risk of antiibiotic resistance to the natural antibiotics produced by the probiotics.
“Overall, more than 50% of trials presented negative outcomes. The majority of the single-strain probiotictrials employing lactobacilli or Saccharomyces were negative, whereas trials employing bifidobacteria showed positive results.” Probiotic Therapy of the Irritable Bowel Syndrome: Why Is the Evidence Still Poor and What Can Be Done About It? 
“because bifidobacteria concentrations have been found to be reduced in IBS compared with healthy controls, it seems reasonable, logical and safe to use prebiotics to enhance the growth of bifidobacteria and other beneficial bacteria to improve symptoms in these patients. However, based on available evidence, general use cannot be recommended in patients with IBS .
Only Positive Effects
Prescript Assist – multiple species
- Bittner AC, Croffut RM, Stranahan MC. Prescript-Assist probiotic-prebiotic treatment for irritable bowel syndrome: a methodologically oriented, 2-week, randomized, placebo-controlled, double-blind clinical study. Clin Ther. 2005 Jun;27(6):755-61.
- Bittner AC, Croffut RM, Stranahan MC, Yokelson TN. Prescript-assist probiotic-prebiotic treatment for irritable bowel syndrome: an open-label, partially controlled, 1-year extension of a previously published controlled clinical trial. Clin Ther. 2007 Jun;29(6):1153-60.
- General Biotics Equilibrium is a probable – but lacks studies to date.
Symbioflor 2 – E.Coli Probiotic
- Probiotic treatment of irritable bowel syndrome in children.Martens U, Enck P, Zieseniss E. Ger Med Sci. 2010
Randomized controlled treatment trial of irritable bowel syndrome with a probiotic E.-coli preparation (DSM17252) compared to placebo. Enck P, Zimmermann K, Menke G, Klosterhalfen S Z Gastroenterol. 2009
Mutaflor — E.Coli Nissle 1917
Efficacy of Probiotic Escherichia coli Nissle 1917 in Patients with Irritable Bowel Syndrome: a Double Blind Placebo-controlled Randomized Trial.Faghihi AH, Agah S, Masoudi M, Ghafoori SM, Eshraghi A. Acta Med Indones. 2015 Jul;47(3):201-8.
“IBS patients were recategorized to subgroups according to their main symptoms, evaluation of the efficacy of the probiotic on some individual items in the symptom list reached the significance level.”
Clostridium butyricum probiotics
- ” In conclusion, CB improves overall symptoms, quality of life and stool frequency in IBS-D patients and is considered to be used as a probiotics in treating IBS-D clinically.” 
- Clostridium butyricum regulates visceral hypersensitivity of irritable bowel syndrome by inhibiting colonic mucous low grade inflammation through its action on NLRP6. 
- “The metabolic profile of IBS mice is significantly altered compared to control mice. Supplementation with C. butyricum to IBS mice may provide a considerable benefit by modulating host metabolism.” 
- Vitamin D associates with improved quality of life in participants with irritable bowel syndrome: outcomes from a pilot trial. Tazzyman S, Richards N, Trueman AR, Evans AL, Grant VA, Garaiova I, Plummer SF, Williams EA, Corfe BM. BMJ Open Gastroenterol. 2015
Inconclusive or negative effects
I am tough here — if there is disagreement between studies, the probiotic is dropped into the list below. One of the main reason is that only 1 in 10(100?) negative studies get published, but every positive one gets published.
- Clinical trial: Lactobacillus plantarum 299v (DSM 9843) improves symptoms of irritable bowel syndrome   Not repeated in   unfavorable in 
Yakult – Lactobacillus Shirota
- Efficacy of Lactobacillus casei Shirota for patients with irritable bowel syndrome.Thijssen AY, Clemens CH, Vankerckhoven V, Goossens H, Jonkers DM, Masclee AA. Eur J Gastroenterol Hepatol. 2016 “After probiotic treatment with LcS, no improvement of 30% in MSS was observed after 8 weeks.”
VSL#3 Multiple Lactobacillus, Bifidobacterium, Streptococcus
- Does VSL#3 really improve symptoms in children with IBS? 
- Gut microbiota is not modified by Randomized, Double-blind, Placebo-controlled Trial of VSL#3 in Diarrhea-predominant Irritable Bowel Syndrome. 
- VSL#3 improves symptoms in children with irritable bowel syndrome: a multicenter, randomized, placebo-controlled, double-blind, crossover study. 
- “Probiotic treatment in IBS patients was associated with a significant reduction of the genus Bacteroides (all taxonomy levels; P < 0.05) to levels similar to that of controls.”  None of the other species identified to be low were improved.
May be effective for children only.
- Probiotic for irritable bowel syndrome in pediatric patients: a randomized controlled clinical trial. Kianifar H, Jafari SA, Kiani M, Ahanchian H, Ghasemi SV, Grover Z, Mahmoodi LZ, Bagherian R, Khalesi M. Electron Physician. 2015 “Lactobacillus GG at a concentration of 1×10(10) cfu/ml for a period of four weeks can lessen the severity of the patients’ pain and improve the functional scale in patients with irritable bowel syndrome.” – 1 x 10(10) is 10 billion
The use of Lactobacillus GG in irritable bowel syndrome in children: a double-blind randomized control trial. Bauserman M, Michail S. J Pediatr. 2005 Aug;147(2):197-201. Erratum in: J Pediatr. 2014 Oct;165(4):878. Bausserman, Melissa “Lactobacillus GG was not superior to placebo”
Ehealth: low FODMAP diet vs Lactobacillus rhamnosus GG in irritable bowel syndrome. Pedersen N, Andersen NN, Végh Z, Jensen L, Ankersen DV, Felding M, Simonsen MH, Burisch J, Munkholm P. World J Gastroenterol. 2014 “Both LFD and LGG are efficatious in patients with IBS.”
[Irritable Bowel Syndrome; gut microbiota and probiotic therapy]. Tojo González R, Suarez Gonzalez A, Rúas Madiedo P, Mancebo Mata A, Pipa Muñiz M, Barreiro Alonso E, Roman Llorente FJ, Moro Villar MC, Arce González MM, Villegas Diaz MF, Mosquera Sierra E, Ruiz Ruiz M. Nutr Hosp. 2015 “Probiotic therapy has a modest effect on IBS symptomatic relief, but the actual evidence is not strong enough to support a general recommendation of use. The best results are achieved, in children, with Lactobacillus rhamnusus GG, which moderately improves abdominal pain, while in adults the benefit appears to be greatest employing Bifidobacterium species.”
Lactobaccilus probiotics all show little effect (and possibly negative effect). Prescript Assist, E.Coli Probiotics and Bifidobacterium probiotics show effects (but only one strain is well reported).