One Hidden Immune Trigger Everyone Misses: A Complex Autoimmune Case Study

What happens when a patient with multiple autoimmune conditions has already addressed the obvious contributors—but continues to experience flares?In this Root Cause Medicine Podcast case study, Dr. Kate Kreske sits down with clinical nutritionist and IFM-certified practitioner Robyn Puglia to explore a complex case involving polyautoimmunity and persistent immune dysregulation. The patient had already worked with multiple practitioners and undergone extensive evaluation, including assessments related to gut health, food reactivity, mold, and stress. Yet something was still being missed.Robyn explains how additional testing shifted her attention away from the gut and toward an unexpected area: the respiratory tract. She walks through how those findings changed her clinical thinking, why complex cases sometimes require practitioners to reconsider their assumptions, and what happened when the care plan was adjusted based on this new information.The conversation offers an important reminder for practitioners: deeper testing can sometimes provide useful clues, but results need to be interpreted within the broader clinical picture rather than treated as a diagnosis on their own.Key TakeawaysHow Robyn approaches highly complex patients who have already addressed many common contributorsWhy gut health should not automatically be assumed to be the primary driver of every autoimmune presentationHow testing identified a respiratory microbial pattern that had not been clinically obviousWhy laboratory findings are most useful when interpreted alongside symptoms, history, prior testing, and the overall clinical pictureHow unexpected findings can change clinical decision-making in complex casesWhy an individual case can illustrate clinical reasoning without establishing that the same testing or intervention will produce similar outcomes in other patientsEpisode HighlightsWhen the obvious answers have already been exploredRobyn describes her practice as serving patients at the “zebra” or even “unicorn” stage—people who have often seen multiple experienced practitioners and already addressed common areas such as nutrition, metabolic health, circadian rhythms, stress, and gut health.Looking beyond the gut in autoimmunityThe featured patient had four autoimmune conditions and continued experiencing immune dysregulation and flares despite significant previous investigation and improvement. Rather than assuming the gastrointestinal tract remained the primary contributor, Robyn expanded the investigation.An unexpected respiratory findingTesting suggested a respiratory tract microbial pattern despite the absence of obvious respiratory symptoms. This finding shifted Robyn's clinical hypothesis and became an important part of how she approached the case.Practitioner TakeawayWhen a complex patient has already addressed the most plausible contributors but continues to experience symptoms, repeating the same investigation may not provide the missing answer. Consider stepping back and asking whether another system, exposure, infection, or contributor deserves evaluation.At the same time, avoid allowing a single specialized test result to become the new explanation for the entire case. Use testing to inform clinical reasoning alongside the patient's history, symptoms, conventional evaluation, and other relevant findings.Want to elevate your practice? This episode is sponsored by <a href="https://fullscript.com/?utm_source=fame&amp;utm_medium=podcast&amp;utm_campaign=fs_provider_2026-01_