Tryptophan, an essential amino acid, from diet or synthesized by intestinal bacteria can follow one of three major metabolic pathways: 1) intestinal bacterial indole synthesis, 2) the kynurenine pathway in immune and epithelial cells (95% of tryptophan), or 3) the serotonin pathway (90% of total body serotonin) in enteroendocrine aka enterochromaffin cells and initiation of vagal afferent signals [
14]. During ATM tryptophan pivots away from the serotonin pathway and synthesis of serotonin and melatonin to the kynurenine pathway (see
Figure 2). Inhibitory parasympathetic signals are suppressed due to the increase in excitatory glutamate activity. This pivot down-regulates bacterial indole synthesis with loss of indole induced GLP-1. Benefits of GLP-1 include appetite suppression, stimulation of insulin [
15], decrease in fasting blood sugar [
16], suppression of obesity and T2DM [
17]. Many of the same bacteria that produce SCFAs, e.g., bifidobacteria and lactobacilli, also synthesize indoles from tryptophan [
18]. Although the end product NAD+ (see
Figure 2) assists dysfunctional mitochondria in ATP production, what drives the ATM pivot is not exactly clear. However, IFN-γ, upregulated in females, is a cofactor for many enzymes in the kynurenine pathway and may drive this pivot [
19] (see
Figure 2). Tryptophan depletion lowers HRV (and increases KTR) [
20]. Increased tryptophan intake (eggs) increases HRV, which appears to be due to the subsequent increase in serotonin [
21]. KTR, an indicator of rate-limiting IDO activity, is positively correlated with cardiovascular disease mortality [
22,
23], depression, bipolar disorder, schizoprenia, [
24] Alzheimer’s disease, fronto-temporal dementia, [
25] Parkinson’s disease [
26], and neurological disease in general [
27]. Increased KTR has also been reported in cancer [
28], autoimmune disease, including rheumatoid arthritis (RA) [
29], and systemic lupus erythematosis (SLE) [
30]. Infectious diseases are also linked to an elevated KTR [
31] with a ratio that directly reflects severity [
32,
33]. This includes SARS CoV2 [
34]. SARS CoV2 induced loss of ACE2 receptor bearing intestinal epithelial cells decreases absorption of the essential amino acid tryptophan [
35] with additional negative influence on KTR and prognosis. But there is another non enzymatic pathway from tryptophan that involves TGF-β.