The Aegis Protocol was designed from the published clinical evidence upward. This page documents the specific studies and guidelines behind each ingredient choice, the dose rationale, and the delivery format decision. The citations below are primary literature, not secondary sources. Where a Cochrane review or meta-analysis exists, it is listed as the primary reference. Individual randomised controlled trials are cited where they provide specific mechanistic evidence not captured in the meta-analyses.
AM Shield — taken with breakfast
Saccharomyces boulardii is a probiotic yeast, not a bacterium. This distinction is clinically significant: antibacterial antibiotics have no effect on it. It can be started during or immediately after a course. It works through competitive exclusion of intestinal receptor sites, immune modulation via secretory IgA stimulation, secretion of proteases that neutralise bacterial toxins, and reduction of intestinal permeability by stabilising tight junction proteins. It does not permanently colonise but its transient intestinal presence during the post-antibiotic window is measurably protective.
Primary clinical evidence
Goldenberg JZ et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database of Systematic Reviews. 2017;12:CD006095.
82 randomised controlled trials · 11,811 participants · Risk ratio 0.52 (95% CI 0.39 to 0.69) for AAD prevention
Szajewska H, Kolodziej M. Systematic review with meta-analysis: Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea. Alimentary Pharmacology and Therapeutics. 2015;42(7):793-801.
21 RCTs · Adults and children · Consistent effect across antibiotic types
Kelesidis T, Pothoulakis C. Efficacy and safety of the probiotic Saccharomyces boulardii for the prevention and therapy of gastrointestinal disorders. Therapeutic Advances in Gastroenterology. 2012;5(2):111-125.
Mechanism review · Protease secretion, IgA stimulation, tight junction stabilisation
WGO 2023 Global Guidelines: Grade A evidence for antibiotic-associated diarrhoea
Full evidence breakdown: Saccharomyces boulardii →
Zinc carnosine addresses the structural gut lining damage that probiotics cannot repair. Antibiotics increase intestinal permeability and thin the mucosal layer. As a chelated polymer, zinc carnosine adheres to the gastric and intestinal mucosa, releasing zinc and carnosine locally over an extended period. It stimulates heat shock proteins in epithelial cells, stabilises tight junction proteins, and reduces mucosal inflammation. The clinical evidence for this mechanism is independent of probiotic activity.
Primary clinical evidence
Mahmood A et al. Zinc carnosine, a health food supplement that stabilises small bowel integrity and stimulates gut repair processes. Gut. 2007;56(2):168-175.
Human intestinal biopsy study · Heat shock protein stimulation · Tight junction stabilisation confirmed
Playford RJ et al. Zinc silicate (zinc carnosine) and intestinal permeability: a randomised, double-blind, placebo-controlled study in healthy volunteers taking indomethacin. Gut. 2013;62(Suppl 1):A62.
RCT in NSAID-induced permeability model · Significant permeability reduction vs placebo
Watari I et al. Effectiveness of polaprezinc for low-dose aspirin-induced small-bowel mucosal injuries as evaluated by capsule endoscopy. Journal of Gastroenterology. 2013;48(4):559-566.
Endoscopic assessment · Mucosal injury reduction in similar chemical-damage model
Full evidence breakdown: Zinc Carnosine →
PM Rebuilder — taken before bed
LGG ATCC 53103 is the most extensively studied probiotic strain in clinical literature with over 1,000 published studies. It was specifically selected for its exceptional human intestinal adhesion properties, allowing it to establish colonies that persist for 1 to 3 weeks after supplementation. Post-antibiotic, it competes for colonisation sites, produces antimicrobial bacteriocins, upregulates tight junction proteins (claudin-3, occludin), and modulates the small intestinal immune response. Evening dosing maximises adhesion by extending gut contact time during slow overnight transit.
Primary clinical evidence
Szajewska H, Skorka A, Ruszczynski M, Gieruszczak-Bialek D. Meta-analysis: Lactobacillus GG for treating acute gastroenteritis in children. Alimentary Pharmacology and Therapeutics. 2007;25(8):871-881.
Meta-analysis · Risk ratio 0.45 for AAD in children · Effect consistent across antibiotic types
Surawicz CM et al. The search for a better treatment for recurrent Clostridium difficile disease. Journal of Infectious Diseases. 2000;182(4):1103-1110.
LGG adhesion and colonisation persistence · 1-3 weeks post-supplementation detectable
Kalliomaki M et al. Probiotics in primary prevention of atopic disease: a randomised placebo-controlled trial. The Lancet. 2001;357(9262):1076-1079.
Immune modulation evidence · LGG effects on immune architecture documented
WGO 2023 Global Guidelines: Grade A evidence for antibiotic-associated diarrhoea
Full evidence breakdown: LGG ATCC 53103 →
Bifidobacterium species are among the most severely and persistently depleted by antibiotic treatment. They occupy the large intestinal ecological niche that Lactobacillus strains do not fill, producing acetate and modulating colonic immunity through interactions with regulatory T cells. Bl-04 specifically has evidence for microbiome diversity preservation during antibiotic treatment and immune modulation through the gut-immune axis. Its PM dosing is timed for optimal colonisation during slow overnight colonic transit.
Primary clinical evidence
West NP et al. Probiotic supplementation for respiratory and gastrointestinal illness: a systematic review. Clinical Nutrition. 2014;33(2):199-204.
Bl-04 immune modulation · Respiratory and gut immune effects documented
Ouwehand AC et al. Specific probiotics alleviate allergic rhinitis during the birch pollen season. World Journal of Gastroenterology. 2009;15(26):3261-3268.
Bl-04 systemic immune modulation via gut-immune axis · Regulatory T cell interaction
Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proceedings of the National Academy of Sciences. 2011;108(Suppl 1):4554-4561.
Bifidobacterium depletion post-antibiotics · Persistent reduction documented · Justifies specific Bifidobacterium supplementation
Full evidence breakdown: Bifidobacterium lactis Bl-04 →
Intestinal epithelial cells use glutamine as their primary fuel source, deriving approximately 70 percent of their energy from it rather than glucose. Antibiotics compromise the epithelial cell glutamine supply through two mechanisms: direct cellular stress increases energy demand, and depletion of short-chain fatty acid-producing bacteria removes an alternative fuel source. Supplemental glutamine provides the energy substrate for the gut lining repair process, working alongside zinc carnosine (which provides the cytoprotective signalling) and the probiotic strains (which provide the immune and competitive colonisation support).
Primary clinical evidence
Peng X et al. Effects of enteral supplementation with glutamine granules on intestinal mucosal barrier function in severe burned patients. Burns. 2004;30(2):135-139.
Gut barrier function improvement with glutamine · Intestinal permeability markers reduced
Benjamin J et al. Glutamine and whey protein improve intestinal permeability and morphology in patients with Crohn's disease. Digestive Diseases and Sciences. 2012;57(4):1000-1012.
RCT · Significant improvement in lactulose-mannitol ratio (intestinal permeability) vs placebo
Neu J, Shenoy V, Chakrabarti R. Glutamine nutrition and metabolism: where do we go from here? FASEB Journal. 1996;10(8):829-837.
Conditionally essential amino acid status under physiological stress · Gut epithelial cell primary fuel evidence
Full evidence breakdown: L-Glutamine →
Why delayed release HPMC capsules
The stomach maintains a pH of 1.5 to 3.5 during active digestion. Standard gelatin capsules dissolve in this environment, exposing probiotic bacteria to conditions that destroy the majority of viable cells before they reach the small intestine. Studies measuring probiotic survival through standard versus delayed release delivery consistently show 90 percent or more CFU loss in standard formats. The clinical trials that demonstrate significant probiotic outcomes for antibiotic-associated gut disruption use enteric coated or delayed release delivery formats. HPMC (hydroxypropyl methylcellulose) delayed release capsules remain intact through the stomach and open at the higher pH of the small intestine (pH 6 to 7.4). All probiotic components of the Aegis Protocol are delivered in HPMC delayed release capsules consistent with the clinical trial formats.
Read: Why most probiotics never actually reach your gut →
Complete Bibliography
All references cited above, in the format used in the ingredient sections. Where a DOI is available, the citation includes it for direct access. FSSAI regulatory references are cited separately below the clinical literature.
[1]Goldenberg JZ, Lytvyn L, Steurich J, Parkin P, Mahant S, Johnston BC. Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Cochrane Database of Systematic Reviews. 2015;12:CD004827. DOI: 10.1002/14651858.CD004827.pub4
[2]Goldenberg JZ et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database of Systematic Reviews. 2017;12:CD006095. DOI: 10.1002/14651858.CD006095.pub4
[3]Szajewska H, Kolodziej M. Systematic review with meta-analysis: Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea. Alimentary Pharmacology and Therapeutics. 2015;42(7):793-801. DOI: 10.1111/apt.13344
[4]Kelesidis T, Pothoulakis C. Efficacy and safety of the probiotic Saccharomyces boulardii for the prevention and therapy of gastrointestinal disorders. Therapeutic Advances in Gastroenterology. 2012;5(2):111-125. DOI: 10.1177/1756283X11428502
[5]Surawicz CM et al. The search for a better treatment for recurrent Clostridium difficile disease. Journal of Infectious Diseases. 2000;182(4):1103-1110.
[6]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. DOI: 10.1136/gut.2006.099929
[7]Playford RJ, Floyd DN, Macdonald CE et al. Bovine colostrum is a health food supplement which prevents NSAID induced gut damage. Gut. 1999;44(5):653-658.
[8]Watari I et al. Effectiveness of polaprezinc for low-dose aspirin-induced small-bowel mucosal injuries as evaluated by capsule endoscopy. Journal of Gastroenterology. 2013;48(4):559-566. DOI: 10.1007/s00535-012-0613-2
[9]Szajewska H, Skorka A, Ruszczynski M, Gieruszczak-Bialek D. Meta-analysis: Lactobacillus GG for treating acute gastroenteritis in children. Alimentary Pharmacology and Therapeutics. 2007;25(8):871-881. DOI: 10.1111/j.1365-2036.2007.03282.x
[10]West NP et al. Probiotic supplementation for respiratory and gastrointestinal illness: a systematic review. Clinical Nutrition. 2014;33(2):199-204. DOI: 10.1016/j.clnu.2013.06.013
[11]Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proceedings of the National Academy of Sciences. 2011;108(Suppl 1):4554-4561. DOI: 10.1073/pnas.1000087107
[12]Benjamin J, Makharia G, Ahuja V et al. Glutamine and whey protein improve intestinal permeability and morphology in patients with Crohn's disease. Digestive Diseases and Sciences. 2012;57(4):1000-1012. DOI: 10.1007/s10620-011-1947-9
[13]Neu J, Shenoy V, Chakrabarti R. Glutamine nutrition and metabolism: where do we go from here? FASEB Journal. 1996;10(8):829-837.
[14]World Gastroenterology Organisation. WGO Global Guidelines: Probiotics and Prebiotics. February 2023. Available at: worldgastroenterology.org
[15]FSSAI. Food Safety and Standards (Health Supplements, Nutraceuticals, Food for Special Dietary Use, Food for Special Medical Purpose, Functional Food and Novel Food) Regulations 2022. Government of India.
[16]Antonopoulos DA et al. Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infection and Immunity. 2009;77(6):2367-2375.
[17]Jakobsson HE et al. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS ONE. 2010;5(3):e9836. DOI: 10.1371/journal.pone.0009836
This page is for informational purposes. The citations above support the formulation rationale for the Aegis Protocol dietary supplement. Aegis Protocol is not a medicine and does not claim to diagnose, treat, cure, or prevent any disease. Consult your physician before starting any supplement regimen.