ITS2 Sequencing and Targeted Meta-Proteomics of Infant Gut Mycobiome Reveal the Functional Role of Rhodotorula sp. during Atopic Dermatitis Manifestation

Abstract

Association between the gut mycobiome and atopic dermatitis was investigated in 9–12-month-old infants using metagenomics. Two groups of atopic dermatitis infants were classified according to their symptom development as outgrown (recovered) and persisted (still undergoing). The evenness and diversity of the mycobiome in the persisted group were higher than in the healthy and outgrown groups. Dysbiosis of the microbiome in the persisted group was observed by a reduction in the Ascomycota/Basidiomycota ratio. Five fungi were selected as markers from each sample group. In the persisted group, Rhodotorula sp. abundance increased significantly, while Wickerhamomyces sp. and Kodamaea sp. abundance increased in the healthy group, and Acremonium sp. and Rhizopus sp. abundance increased considerably in the outgrown group. Metaproteomic analysis revealed that the persisted group had a high abundance of fungal proteins, particularly those from Rhodotorula sp. Unique proteins such as RAN-binding protein 1 and glycerol kinase from Rhodotorula sp. were hypothesized to be related to atopic dermatitis manifestation in infants.

Bacterial, fungal, and interkingdom microbiome features of exclusively breastfeeding dyads are associated with infant age, antibiotic exposure, and birth mode

“…In addition, fungi are capable of substantial proliferation under certain conditions (e.g., antibiotic pressure). Recent studies have shown associations between gut fungi and healthy, as well as disordered, immune development ( Arrieta et al, 2015 ; Shao et al, 2019a ; Mok et al, 2021 ).…”

The Human Mycobiome: Colonization, Composition and the Role in Health and Disease

“…A modified gut mycobiome composition was shown in numerous conditions: inflammatory bowel disease [ 81 ], irritable bowel syndrome [ 82 ], colorectal cancer [ 57 ], obesity [ 31 , 33 ], alcoholic liver disease [ 83 ], diabetes type I and II [ 79 , 84 , 85 , 86 ], multiple sclerosis [ 78 , 87 ], chronic kidney disease [ 88 ], atopic dermatitis [ 89 ], Parkinson’s disease [ 90 ], schizophrenia [ 91 ], etc. Moreover, correlations of fungal taxa with innate and adaptive immunity, e.g., effector CD4+ T cells and CD8+ T cells, memory CD4+ T cells, NK cells, regulatory B cells and other proinflammatory cytokines, were observed [ 78 , 92 ].…”

“…Gut mycobiome enrichment and numerous correlations with bacterial taxa were reported in people with HIV [ 92 ]. The overgrowth of the genus Rhodotorula was related to atopic dermatitis manifestation in infants [ 89 ].…”

“…Besides the genus Malassezia , the perturbances of the skin mycobiome have been shown; for instance, in the study of nine 12-month-old infants with atopic dermatitis. Specifically, genera Rhodotorula , Wickerhamomyces , Kodamaea , Acremonium and Rhizopus showed the highest rates of perturbance [ 89 ].…”

Impact of diet and host genetics on the murine intestinal mycobiome

“…To date, whole metagenomic profiling and ITS1 and ITS2 sequencing have provided insights into the fungal kingdom within the gut ecosystem 14,15 . Recently, as a result of these advances, the important role of mycobiome, including the diversity and dynamics of fungi, in homeostasis as well as disease is being increasingly recognized [16][17][18][19] .…”