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Intestinal dysbiosis can lead to the induction of systemic immune-mediated inflammatory diseases, such as Crohn’s disease Although archaea are part of the commensal microbiota, they are still one of the least studied microorganisms. The aim of our study was the standardization of the optimal conditions and primers for sequencing of the gut archaeome using Next Generation Sequencing, and evaluation of the differences between the composition of archaea in patients and healthy volunteers, as well as analysis of the changes that occur in the archaeome of patients depending on disease activity. Newly diagnosed patients were characterized by similar archeal profiles at every taxonomic level as in healthy individuals (the dominance of  Methanobacteria  at the class level, and  Methanobrevibacter  at the genus level). In turn, in patients previously diagnosed with Crohn’s disease (both in active and remission phase), an increased prevalence of  Thermoplasmata ,  Thermoprotei ,  Halobacteria  (at the class level), and  Halococcus ,  Methanospaera  or  Picrophilus  (at the genus level) were observed. Furthermore, we have found a significant correlation between the patient’s parameters and the individual class or species of Archaea. Our study confirms changes in archaeal composition in pediatric patients with Crohn’s disease, however, only in long-standing disease. At the beginning of the disease, the archeal profile is similar to that of healthy people. However, in the chronic form of the disease, significant differences in the composition of archaeome begin to appear. It seems that some archaea may be a good indicator of the chronicity and activity of Crohn’s disease.

Alterations in intestinal Archaea composition in pediatric patients with Crohn’s disease based on next-generation sequencing – a pilot study