The pandemic has supercharged growing awareness of the gut microbiome as a critical determinant of human health. “Long haulers” share microbiomes similar to those seen in myalgic encephalomyelitis/chronic fatigue syndrome and fibromyalgia, all frequently associated with Candida overgrowth (CO). Candida can synthesize its own IDO, altering tryptophan metabolism (ATM). Zonulin, a circulating protein that increases intestinal and endothelial permeability, has emerged as a central player. Candida hyphal walls express proteins analogous to gliadin/gluten, e.g., celiac disease (CeD), and mannans, e.g., Crohn’s disease (CrD), that may trigger antigliadin and anti-Gq coupled GPCR auto-antibodies linked to their lectin binding domain respectively. Hyphal mannan may induce auto-antibodies to AT1Rs, α1-ARs, mAChRs, and β2-ARs, prominent in LC, and regulate T cell receptors (TCRs) and regulatory B cell function, compromised in not only LC (vitiligo, psoriasis, alopecia) but also SLE, RA, and many other autoimmune diseases. All are Gq coupled GPCRs. The spike protein S on SARS CoV2 can attach to both the ACE2 receptor (required for tryptophan absorption) and Toll-like receptor4 (TLR4) bearing endothelial cells and enterocytes. Spike protein S is persistent in most with LC and, as a ligand for TLR4, can also activate zonulin. S can also activate the NLRP3 inflammasome, as can candidalysin. This inflammasome is directly connected to dementia, cancer, autoimmunity and obesity. Candidalysin causes hypercitrullination, instrumental in creating ACPAs (anti-citrullinated peptide antibodies) linked to LC, MCAS (mast cell activation syndrome), HSD (hypermobility spectrum disorder), and APS (antiphospholipid syndrome). A hypothetical pathophysiologic model is proposed implicating pre-existing CO, aggravated by Covid-19, in not only the genesis of LC but also that of autoimmune disease, dementia, cancer, many chronic diseases, and aging.