Abstract: It has been about 2 years since the start of the SARS-CoV-2 outbreak worldwide. Despite this, there are no unique and certain protocols to treat COVID-19 and Long Covid patients in the global world. The clinical manifestations of COVID-19 are both pulmonary and extra-pulmonary. The extra-pulmonary ones include hyposmia, dysgeusia, and other neurological manifestations. In other autoimmune diseases, such as Parkinson's disease (PD) or Alzheimer's disease (AD), it is well known that the role of acetylcholine is crucial in olfactory dysfunction. We observed in plasma, urine, and fecal samples from COVID-19 patients, the presence of toxin-like peptides very similar to molecules known to alter acetylcholine signaling. After observing the production of these peptides in bacterial cultures, we performed proteomic analyses to better understand their behavior, reporting this new insight It appears that the gut microbiome continues to produce toxins such as peptides even after decreasing SARS-CoV-2 RNA viral load in molecular assays. These toxicological interactions between the bacteria of the gut/human microbiome and the virus suggest a new scenario in the study of clinical symptoms in long Covid and also in patients with acute Covid-19. It is acceptable that bacteria toxins produced continuously after viral aggression can be blocked using an appropriate combination of antibiotics.