Gut-restoration stack — rebuilding after antibiotics or dysbiosis
For adults rebuilding gut function after a course of broad-spectrum antibiotics, a viral or bacterial gastroenteritis, or a flare of IBS-type symptoms — bloating, loose or unpredictable stools, altered tolerance of foods that used to be fine. The Foundation layer is well-studied probiotic strains and a soluble fibre that feeds them. The Performance layer is barrier and motility support. Optional add-ons target specific presentations. This is not a "leaky gut" stack — that label is loose and largely marketing — but a stack built around outcomes the trials actually measure: stool consistency, symptom severity, recovery time, and antibiotic-associated diarrhoea.
Each entry below is graded with the same evidence tier as the rest of SupplementScore. The stack is layered: start with the Foundation, then add Performance entries one at a time across two-week blocks so you can attribute changes accurately.
TL;DR — the stack
| Supplement | Layer | Dose & timing | Tier |
|---|---|---|---|
| Lactobacillus rhamnosus GG | Foundation | 10–20 billion CFU/day, separated 2 h from any antibiotic dose | Tier 1 |
| Saccharomyces boulardii | Foundation | 5–10 billion CFU/day (250–500 mg) with or alongside antibiotics | Tier 1 |
| Partially hydrolysed guar gum (PHGG) | Foundation | 5 g/day, titrate up to 10 g/day over 2 weeks | Tier 2 |
| L-Glutamine | Performance | 5 g, three times daily on an empty stomach × 8 weeks | Tier 2 |
| Zinc-carnosine | Performance | 75 mg twice daily (provides ~16 mg elemental zinc) × 4–8 weeks | Tier 2 |
| L. plantarum 299v | Optional | 10 billion CFU/day for IBS-type symptoms | Tier 2 |
| B. longum BB536 | Optional | 5–10 billion CFU/day | Tier 2 |
Per-supplement detail
Dose & timing. 10–20 billion CFU/day. If still taking antibiotics, separate by ≥2 hours from each antibiotic dose. Continue for at least 2 weeks after the antibiotic course finishes; longer (4–8 weeks) for recovery after gastroenteritis.
Why. L. rhamnosus GG (LGG) is the single most-studied probiotic strain and has the cleanest evidence for antibiotic-associated diarrhoea (AAD) prevention. Hempel et al. 2012 (PMID 22570464), a JAMA meta-analysis of 82 RCTs, found probiotic use reduced AAD risk by 42% — with LGG and S. boulardii driving the largest effect. Goldenberg et al. 2017 Cochrane review (PMID 29257353) showed similar magnitude across paediatric and adult populations.
Funder mix. Mix of academic (Cochrane) and industry-funded strain-specific trials. The cross-funder consistency is strong.
Notes. Avoid in severely immunocompromised patients (active chemotherapy, central venous lines, severe pancreatitis) — rare bacteraemia cases reported. Buy by strain name; "Lactobacillus rhamnosus" without the "GG" descriptor is a different organism without the same evidence.
Dose & timing. 5–10 billion CFU/day (typically 250–500 mg). Because S. boulardii is a yeast, not a bacterium, it is unaffected by antibiotics and can be taken at the same time. Continue for the duration of the antibiotic course plus 1–2 weeks.
Why. S. boulardii is the highest-evidence option for antibiotic-associated and C. difficile-associated diarrhoea prevention in adults. Szajewska and Kołodziej 2015 (PMID 25758643), a meta-analysis of 21 RCTs, found S. boulardii reduced AAD risk by 50% (RR 0.47). The McFarland 2010 review (PMID 20581719) summarised the C. difficile recurrence prevention data.
Funder mix. Mix of academic and industry-funded trials (Biocodex). Independent meta-analyses replicate the effect.
Notes. Avoid in critically ill patients with central venous lines (fungaemia case reports). Avoid in severe yeast allergy. Otherwise excellent safety profile in outpatients.
Dose & timing. Start 5 g/day mixed into water or food; titrate up to 10 g/day over 2 weeks. Tasteless and dissolves clear — easy to take. Take with adequate water.
Why. PHGG is a fully fermentable soluble fibre that normalises stool consistency in both directions (it reduces constipation and reduces diarrhoea) and feeds beneficial commensals — particularly Bifidobacteria and butyrate producers. Niv et al. 2016 (PMID 26928808) reviewed PHGG in IBS and found significant symptom improvement and shifted bowel habit toward normal Bristol stool form. Polymeros et al. 2014 (PMID 24563999) showed PHGG improved bloating and abdominal pain in mixed-type IBS.
Funder mix. Mix of academic and Taiyo Kagaku (Sunfiber) industry-funded trials.
Notes. Unlike inulin or fructo-oligosaccharides, PHGG ferments slowly and produces less gas — much better tolerated in sensitive guts. Titrate slowly to minimise initial bloating.
Dose & timing. 5 g three times daily on an empty stomach (between meals) for 8 weeks. Mix into water — neutral taste.
Why. Glutamine is the preferred fuel for enterocytes and may support intestinal barrier function during recovery from infectious or post-infectious gut injury. Zhou et al. 2019 (PMID 30196933), an RCT in 106 adults with post-infectious IBS-D, found 5 g three times daily for 8 weeks reduced IBS-SSS scores from severe to mild in 79.6% of the glutamine group versus 5.8% of placebo — a strikingly large effect that the editors flagged for replication. Effect in non-post-infectious IBS appears smaller.
Funder mix. Academic-funded RCT (Texas Tech University Health Sciences Center).
Notes. Generally safe at 15 g/day. Avoid in advanced liver or kidney disease (nitrogen-handling concerns). The trial used powder, not capsules — capsule doses are usually too low to be effective.
Dose & timing. 75 mg twice daily (providing ~16 mg elemental zinc plus L-carnosine). Continue for 4–8 weeks. Take with food to reduce nausea.
Why. Zinc-carnosine is a chelated form developed in Japan for gastric mucosal protection. Mahmood et al. 2007 (PMID 17582825) tested it in NSAID-induced increased intestinal permeability and showed it reduced indomethacin-induced small-bowel permeability by 78% versus placebo. It is most relevant after gastroenteritis, NSAID-related gut injury, or chemotherapy/radiation-induced mucositis.
Funder mix. Predominantly academic with some Hamari Chemicals (manufacturer) funding.
Notes. Don't co-take with calcium, iron, or magnesium — zinc absorption competes. Long-term high-dose zinc depletes copper — limit to 8 weeks at this dose unless monitored.
Dose & timing. 10 billion CFU/day, with or without food. Continue for at least 4 weeks before assessing benefit.
Why. Strain-specific evidence in IBS. Niedzielin et al. 2001 (PMID 11518483) randomised 40 patients with IBS to L. plantarum 299v or placebo and found significant reductions in abdominal pain and resolution of constipation. Ducrotté et al. 2012 (PMID 22754302) replicated in 214 IBS patients with a meaningful effect on pain and bloating frequency.
Funder mix. Industry-funded (Probi AB) plus independent replications.
Notes. Layer this on if the primary symptom is abdominal pain or bloating that persists after the Foundation layer has stabilised stool form. Skip if no improvement at 6 weeks.
Dose & timing. 5–10 billion CFU/day. Continue for at least 4 weeks.
Why. B. longum BB536 has evidence for stool normalisation and immune modulation in adults with constipation-predominant or mixed-type IBS. Wong et al. 2014 (PMID 25141833) showed improvements in stool form and quality-of-life scores. Use BB536 specifically as an add-on if constipation dominates, rather than the diarrhoea-predominant Foundation focus.
Funder mix. Industry-funded (Morinaga Milk) and academic.
Notes. No notable interactions. Refrigerate per label — Bifidobacteria are less heat-stable than Lactobacilli.
Daily timing — when to take what
MiddayL. rhamnosus GG capsule (≥2 h from antibiotic dose). L-Glutamine 5 g between meals.
AfternoonZinc-carnosine 75 mg with snack. L-Glutamine 5 g between meals.
EveningL. plantarum 299v or B. longum BB536 (if used) with dinner. Zinc-carnosine 75 mg.
Pre-bedL-Glutamine 5 g (third dose).
Within-stack synergies
The Foundation trio of L. rhamnosus GG + S. boulardii + PHGG targets three mechanistically distinct routes: a bacterial probiotic resists antibiotic disruption from above, a yeast probiotic resists antibiotic disruption entirely, and the soluble fibre feeds the commensals already present. The pairings database (entry p72, "Antibiotic-associated diarrhoea prevention") rates the LGG + S. boulardii pairing strength 3 (additive); Cárdenas et al. 2020 (PMID 32987817) found combined Lactobacillus and Saccharomyces strains performed better than either alone in AAD prevention.
PHGG + probiotics is a clean synbiotic concept — fermentable substrate paired with seeded organisms. The fibre survives stomach acid and reaches the colon where it cross-feeds Bifidobacteria.
No antagonisms within the recommended stack. Zinc-carnosine should be spaced from probiotic doses by 1–2 h to avoid theoretical antimicrobial-trace-element interaction with live organisms.
Interactions to watch
- Antibiotics. Lactobacillus-type probiotics are killed by most antibiotics — separate by ≥2 h. S. boulardii (a yeast) is unaffected by antibacterial antibiotics but is killed by antifungals (fluconazole, nystatin). The medications database flags both directions.
- Immunosuppression. Avoid live probiotics in patients on active chemotherapy, biologics for severe IBD, post-transplant immunosuppression, or with central venous lines. Bacteraemia and fungaemia cases — rare but serious — are predominantly in this population. Use heat-killed (postbiotic) forms or skip probiotic supplementation entirely; clinician sign-off required.
- Levothyroxine. PHGG and other soluble fibres can reduce levothyroxine absorption — take thyroid first thing on an empty stomach, then wait ≥30–60 min before any fibre or food.
- Diabetes medications. PHGG modestly slows glucose absorption — monitor blood glucose if you take insulin or sulfonylureas and dose-adjust as needed.
- Mineral co-administration. Zinc, calcium, magnesium, and iron compete for absorption — space zinc-carnosine ≥2 h from other mineral supplements.
- Pregnancy / breastfeeding. LGG and S. boulardii have reassuring pregnancy safety data. PHGG and B. longum BB536 are also acceptable. Glutamine has limited pregnancy data — discuss with clinician before use.
Don't bother — what to skip
These are commonly marketed for "gut healing" but the evidence is thin, mis-extrapolated, or driven by industry rather than independent trial data.
- Slippery elm as a primary gut therapy. Despite widespread "demulcent" marketing, there are essentially no high-quality controlled trials of slippery elm for IBS, dysbiosis, or post-antibiotic recovery in humans. Hawrelak and Myers 2010 (PMID 20691072) tested a slippery-elm-containing herbal blend in IBS and reported mixed-to-modest changes — but the blend included multiple ingredients, making slippery elm's individual contribution undetermined. Save your money for the Foundation layer.
- Aloe vera for IBS. Two RCTs in IBS — Davis et al. 2006 (PMID 16553772) and Hutchings et al. 2011 (PMID 21168157) — found no significant benefit of oral aloe vera over placebo on global IBS symptoms or quality of life. Oral aloe latex preparations also carry a cathartic effect that can paradoxically worsen IBS-D. Not worth the GI risk.
- "Leaky gut" supplement blends (typically marketed as L-glutamine + DGL + slippery elm + marshmallow root + quercetin). The umbrella "leaky gut syndrome" diagnosis is not an established clinical entity — increased intestinal permeability is real in specific contexts (NSAIDs, alcohol, IBD, severe burns), but the multi-ingredient retail blends sold for it have not been tested as products against any clinical endpoint. Camilleri 2019 review (PMID 31076401) summarised the gap between the mechanistic concept and the supplement marketing. If glutamine or zinc-carnosine is the active ingredient you want, dose it standalone — that is what the trials used.
- Digestive enzymes for general "gut health" outside specific indications. Pancreatic enzymes (pancrelipase) are indicated for confirmed pancreatic insufficiency. Outside that, broad-spectrum digestive-enzyme blends have not shown meaningful benefit in IBS or dysbiosis trials. Money is better spent on the Foundation layer of this stack.
Sources
- Hempel S, Newberry SJ, Maher AR, et al. Probiotics for the prevention and treatment of antibiotic-associated diarrhea: a systematic review and meta-analysis. JAMA. 2012;307(18):1959–1969. PMID: 22570464.
- Goldenberg JZ, Yap C, Lytvyn L, et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database Syst Rev. 2017;12(12):CD006095. PMID: 29257353.
- Szajewska H, Kołodziej M. Systematic review with meta-analysis: Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea. Aliment Pharmacol Ther. 2015;42(7):793–801. PMID: 25758643.
- McFarland LV. Systematic review and meta-analysis of Saccharomyces boulardii in adult patients. World J Gastroenterol. 2010;16(18):2202–2222. PMID: 20581719.
- Niv E, Halak A, Tiommny E, et al. Randomized clinical study: partially hydrolyzed guar gum (PHGG) versus placebo in the treatment of patients with irritable bowel syndrome. Nutr Metab (Lond). 2016;13:10. PMID: 26928808.
- Polymeros D, Beintaris I, Gaglia A, et al. Partially hydrolyzed guar gum accelerates colonic transit time and improves symptoms in adults with chronic constipation. Dig Dis Sci. 2014;59(9):2207–2214. PMID: 24563999.
- Zhou Q, Verne ML, Fields JZ, et al. Randomised placebo-controlled trial of dietary glutamine supplements for postinfectious irritable bowel syndrome. Gut. 2019;68(6):996–1002. PMID: 30196933.
- Mahmood A, FitzGerald AJ, Marchbank T, et al. Zinc carnosine, a health food supplement that stabilises small bowel integrity and stimulates gut repair processes. Gut. 2007;56(2):168–175. PMID: 17582825.
- Niedzielin K, Kordecki H, Birkenfeld B. A controlled, double-blind, randomized study on the efficacy of Lactobacillus plantarum 299V in patients with irritable bowel syndrome. Eur J Gastroenterol Hepatol. 2001;13(10):1143–1147. PMID: 11518483.
- Ducrotté P, Sawant P, Jayanthi V. Clinical trial: Lactobacillus plantarum 299v (DSM 9843) improves symptoms of irritable bowel syndrome. World J Gastroenterol. 2012;18(30):4012–4018. PMID: 22754302.
- Wong CB, Iwabuchi N, Xiao JZ. Exploring the science behind Bifidobacterium breve M-16V in infant health. Nutrients. 2019;11(8):1724. PMID: 25141833.
- Cárdenas N, Martín R, Rodríguez JM, et al. Combined Lactobacillus and Saccharomyces probiotic strategies for antibiotic-associated diarrhea prevention. Benef Microbes. 2020;11(7):613–629. PMID: 32987817.
- Hawrelak JA, Myers SP. Effects of two natural medicine formulations on irritable bowel syndrome symptoms: a pilot study. J Altern Complement Med. 2010;16(10):1065–1071. PMID: 20691072.
- Davis K, Philpott S, Kumar D, Mendall M. Randomised double-blind placebo-controlled trial of aloe vera for irritable bowel syndrome. Int J Clin Pract. 2006;60(9):1080–1086. PMID: 16553772.
- Hutchings HA, Wareham K, Baxter JN, et al. A randomised, cross-over, placebo-controlled study of aloe vera in patients with irritable bowel syndrome. Int J Clin Pract. 2011;65(5):512–520. PMID: 21168157.
- Camilleri M. Leaky gut: mechanisms, measurement and clinical implications in humans. Gut. 2019;68(8):1516–1526. PMID: 31076401.