Atopic dermatitis (AD) is a chronic inflammatory skin disease clinically characterized by periodic flares of dry, red, itchy skin lesions that may extend involving all the skin surface in most severe forms. Its prevalence is remarkably increased in the last decades, becoming one of the major public health problems in Western countries. Adult patients with AD had significantly impaired health-related quality of life because of the impact of the disease on work, sleep, and social relations. The pathogenesis of AD is not well understood; complex interactions between defective skin barrier, recurrent infections, and immune system imbalance have been shown. Recently, loss of microbial diversity and over-abundance of certain microbial species on skin surfaces has been observed in patients affected by AD. It is known that skin commensal organisms play important role in promoting normal immune system functions and preventing the colonization of pathogens. Dysbiosis has been hypothesized to play a role in AD progression; however, variations of skin microbiota composition during the different phases of the disease is still mainly unknown.
The aim of this study is to understand if and how skin microbiota composition vary during the different phases of the disease (baseline, flare, post flare). In this research we propose, for the first time, an integrated metagenomic and culturomic approach, in order to achieve a better knowledge of variation in microbial composition at species and strains-level, to analyse the functional differences between strains within a single species and to isolate species and strains that will lets us to understand the functional consequences of strain-level variation within species
Atopic dermatitis (AD) is a chronic inflammatory skin disease whose prevalence is remarkably increased in the last decades, becoming one of the major public health problems in Western countries. Patients with AD generally need long treatment and their health-related quality of life is significantly impaired (1). The pathogenesis of AD is not well understood; complex interactions between defective skin barrier function, recurrent infections, and immune system imbalance have been shown. Recently, loss of microbial diversity and over-abundance of certain microbial species on skin surfaces has been observed in patients affected by AD (2). It is known that microbiome diversity decreased in the inflamed atopic skin with reductions in the genera Streptococcus, Corynebacterium, Propionibacterium and in Proteobacteria in favor of members of the genus Staphylococcus in general and S. aureus in particular (3, 4, 5). More than 80% of S. aureus isolated from patients with AD secrete superantigens, leading to significant inflammation in AD (6). In the context of barrier defects, S. aureus is able to traverse the epidermis reaching the dermis and triggers the expression of the inflammatory cytokines (7) and this ability can be strain-dependent (3). Our preliminary results of an ongoing research on nasal microbiota in pediatric patients with allergic rhinitis (AR) show that S. aureus strains associated with RA patients possess more virulence factors than those associated with healthy carriers. Moreover, different studies found that skin isolates of coagulase-negative Staphylococcus (CoNS) species can produce antimicrobial peptides AMPs that selectively killed S. aureus. A lack of this activity, on the skin of subjects with AD, is strongly associated with increased colonization by S. aureus and depletion of CoNS (8). Furthermore, with regard to skin fungal microbiota, it has been found difference between patients with AD and healthy individuals (9). The analysis of skin microbiota (SM) by 16S rRNA sequencing genes produced a major impact on understanding the changes in bacterial composition that occur during an eczema flare (10). However, such approaches provide limited information about the ecosystem's functionality. Metagenomic shotgun sequencing enables strain-level investigation of the broad microbial community composed by bacteria, fungi, and viruses, allowing characterization of the community's functional content and the characterization of genomes for which no targeted amplicon strategies exist. However, metagenomic shotgun sequencing cannot provide information about gene expression and point out if specific microbes are performing a specific function. Culturomics is an emerging field of study that has been applied to gut microbiota allowing the discovery of new bacterial species from human stools. In this research, we propose, as progress beyond the state of the art, to integrate metagenomics and culturomics to study microbial temporal dynamics in a cohort of AD patients sampled throughout the disease course. Such integrative approach will allow to capture the full genetic potential of SM in AD patients, to detect differences in SM composition at strain-level, to test the functional consequence of strain-level differences between patients and in the different stages of disease, to provide strains that allow extensive characterization of new species and to permit the study of interactions between different bacterial strains present in the skin microbiota. Moreover, species and strains obtained by culturomics will allow to develop in vitro and in vivo models to analyse the interactions between mutualistic bacteria, pathogens, and host in order to elucidate their role in the disease and healthy as an important step in the development of prebiotic and probiotic strategies and to obtained hints for the development of new drugs.
1. Kiebert et al.2002. Int J Dermatol.41, 151-8.
2.Powers et al. 2015.J Dermatol.42, 1137-42.
3.Byrd et al. 2017.Sci Transl Med. 9, 397.
4.Totté et al. 2016. Br J Dermatol. 175, 687-95.
5. Tauber et al. 2016.J. Allergy Clin. Immunol.137, 1272.
6. Travers et al. 2014. Invest Dermatol.;134,2069¿71.
7. Nakatsuji et al. 2016. J. Invest. Dermatol.136, 2192¿2200.
8.Nakatsuji et al. 2017. Sci Transl Med.9(378).
9.Zhang et al. 2011. Microbiol Immunol.9,625-32.
10. Kong et al. 2012. Genome Res. 22, 850¿859.