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\begin{document}

\title{The Skin Microbiome in Pediatric Atopic Dermatitis and Food Allergy}



\author[1]{Elizabeth Huiwen Tham}%
\author[2]{Minghao Chia}%
\author[3]{Carmen Riggioni}%
\author[2]{Niranjan Nagarajan}%
\author[4]{John E. Common}%
\author[5]{Heidi H Kong}%
\affil[1]{Khoo Teck Puat - National University Children's Medical Institute}%
\affil[2]{Genome Institute of Singapore}%
\affil[3]{National University of Singapore Yong Loo Lin School of Medicine}%
\affil[4]{Agency for Science Technology and Research}%
\affil[5]{National Institute of Arthritis and Musculoskeletal and Skin Diseases}%


\vspace{-1em}



  
  \date{June 14, 2024}


\begingroup
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\selectlanguage{english}
\begin{abstract}
The skin microbiome is an extensive community of bacteria, fungi, mites,
and viruses colonizing the skin. Fluctuations in the composition of the
skin microbiome have been observed in atopic dermatitis (AD) and food
allergy (FA), particularly in early life, established disease, and
associated with therapeutics. However, AD is a multifactorial disease
characterized by skin barrier aberrations modulated by genetics,
immunology, and environmental influences, thus the skin microbiome is
not the sole feature of this disease. Future research should focus on
mechanistic understanding of how early life skin microbial shifts may
influence AD and FA onset, to guide potential early intervention
strategies or as microbial biomarkers to identify high-risk infants who
may benefit from possible microbiome-based biotherapeutic strategies.
Harnessing skin microbes as AD biotherapeutics is an emerging field, but
more work is needed to investigate whether this approach can lead to
sustained clinical responses.%
\end{abstract}%



\sloppy


\textbf{Title: The Skin Microbiome in Pediatric Atopic Dermatitis and
Food Allergy}

\textbf{Short running title: Skin Microbiome in Atopic Dermatitis and
Food Allergy}

Elizabeth Huiwen Tham\textsuperscript{1,2\#}, Minghao
Chia\textsuperscript{3}, Carmen Riggioni\textsuperscript{2}, Niranjan
Nagarajan\textsuperscript{3}, John E.A. Common\textsuperscript{4}, Heidi
H. Kong\textsuperscript{5}

\textsuperscript{1}Khoo Teck Puat-National University Children's Medical
Institute, National University Health System (NUHS), Singapore

\textsuperscript{2}Department of Paediatrics, Yong Loo Lin School of
Medicine, National University of Singapore (NUS), Singapore

\textsuperscript{3}Genome Institute of Singapore (GIS), Agency for
Science, Technology and Research (A*STAR), Singapore

\textsuperscript{4}A*STAR Skin Research Labs (A*SRL), Agency for
Science, Technology and Research (A*STAR), Singapore

\textsuperscript{5}National Institute of Arthritis and Musculoskeletal
and Skin Diseases, National Institutes of Health, Bethesda, MD 20892,
USA

\textsuperscript{\textbf{\#}}\textbf{Corresponding Author}

Elizabeth Huiwen Tham

Address: Department of Paediatrics, Yong Loo Lin School of Medicine

National University of Singapore

1E Kent Ridge Road, Level 12, NUHS Tower Block

Singapore 119228

Email address: elizabeth\_tham@nus.edu.sg

Phone: (65) 6772-3394

Fax: (65) 6779-7486

\textbf{Authors Statement}

Elizabeth HW Tham contributed to conceptualisation, project
administration, writing the original draft, reviewing and editing the
manuscript. Carmen Riggioni and Minghao Chia contributed to
visualization, writing the original draft, reviewing and editing the
manuscript. Niranjan Nagarajan and John EA Common contributed to writing
the original draft, reviewing and editing the manuscript. Heidi H Kong
contributed to reviewing, revising and editing the manuscript. All
authors approved the final version of the manuscript

\textbf{Acknowledgments}

This work was supported by funding from Agency for Science, Technology
and Research (A*STAR) and~A*STAR-EDB-NRF IAF-PP grants~-- H17/01/a0/004
`Skin Research Institute of~Singapore' (J.E.A.C.)~and~H22J1a0040 `Asian
Skin Microbiome Program 2.0' (J.E.A.C. and N.N.); this work was also
supported by the Intramural Research Program of the National Institute
of Arthritis and Musculoskeletal and Skin Diseases, National Institutes
of Health (H.H.K.).~Elizabeth Huiwen Tham is supported by the National
Medical Research Council (NMRC) Transition Award {[}MOH-000269{]} and
the NMRC Clinician-Scientist Award {[}MOH-001415-00{]}.

\textbf{Conflict of Interest Statement}

The authors declared no conflicts of interest



\textbf{Abstract}

The skin microbiome is an extensive community of bacteria, fungi, mites,
and viruses colonizing the skin. Fluctuations in the composition of the
skin microbiome have been observed in atopic dermatitis (AD) and food
allergy (FA), particularly in early life, established disease, and
associated with therapeutics. However, AD is a multifactorial disease
characterized by skin barrier aberrations modulated by genetics,
immunology, and environmental influences, thus the skin microbiome is
not the sole feature of this disease. Future research should focus on
mechanistic understanding of how early life skin microbial shifts may
influence AD and FA onset, to guide potential early intervention
strategies or as microbial biomarkers to identify high-risk infants who
may benefit from possible microbiome-based biotherapeutic strategies.
Harnessing skin microbes as AD biotherapeutics is an emerging field, but
more work is needed to investigate whether this approach can lead to
sustained clinical responses.

\textbf{Keywords}

Atopic dermatitis, Food allergy, Microbiota, Skin microbiome,
Staphylococcus aureus

\textbf{Introduction}

Atopic dermatitis (AD) is a chronic pruritic inflammatory skin condition
characterized by disrupted skin barrier function and immune
dysregulation. Its onset is typically in early life and is more common
in children, afflicting up to 25\%.\textsuperscript{1} AD is a complex
disease with a multifaced burden encompassing physical discomfort, sleep
disturbances, limitations in daily activities and exerts a profound
psychosocial impact on children and their caregivers.\textsuperscript{2}

In addition to these challenges, children with AD often experience
multiple co-morbidities such as food allergies (FA), allergic rhinitis,
asthma, autoimmune disorders, and recurrent skin
infections.\textsuperscript{3, 4} The pathogenesis of AD in children
involves a complex interplay of genetic factors, skin barrier defects,
Th2 cytokine imbalances, allergen sensitization, and microbial
interactions.\textsuperscript{5}

In particular, early onset and severe AD are significant risk factors
for the development of FA in children. The ``Dual Allergy Exposure
Hypothesis'' proposes that allergen exposure, either through the skin or
the gut, during a critical period in early life can lead to the
development of FA.\textsuperscript{6} The concept of primary prevention
of AD has thus gained traction as a strategy to mitigate transcutaneous
sensitization and subsequently reduce the risk of FA and other allergic
disorders in the ``atopic march''.

The skin, being the largest organ in the human body, plays a vital role
in providing barrier protection, sensory regulation, and immune and
thermal homeostasis.\textsuperscript{7} It is colonized by an extensive
community of bacteria, fungi, mites, and viruses thought to interact
with the host to influence health and disease states. Recent advances in
sequencing technology revealing a diverse skin microbial community on
healthy skin and increasing microbial-host interaction studies in humans
and model systems suggest a fine equilibrium exists among pathogens,
commensal organisms, and the immune system. However, in children with
AD, this skin microbiome is altered.

This review highlights the known mechanistic pathways involved in the
development of AD and FA in children, as well as the emerging
understanding of the role of the skin microbiome in pediatric AD and FA.
It also discusses recent studies exploring the potential of the skin
microbiome in the treatment and prevention of these conditions.

\textbf{Search Strategy and selection criteria}

We searched PubMed, Cochrane Library, and Medline for papers published
between January 2012 and December 2022, using the following terms:
``skin microbiome'', ``bacteria'', ``\emph{Staphylococcus aureus} '',
``fungi'', ``mites'', ``atopic dermatitis'', ``eczema'', and ``food
allergy'' in combinations. Articles were also identified through
searches of reference lists of selected key papers in the field. The
search was not limited by language. The final reference list was
selected on the basis of originality, up-to-dateness, impact in the
field, and relevance to the broad scope of this review.

\textbf{Skin microbiome in AD}

AD is characterized by a waxing and waning course, in which worsening of
AD lesions (flares) occur periodically followed by a period of clinical
improvement with treatment.\textsuperscript{5}Microbes on the skin are
thought to play an important role in skin homeostasis by modulating the
immune system,\textsuperscript{8} providing colonization resistance
against pathogens,\textsuperscript{9} or, in the case of
\emph{Staphylococcus aureus (S. aureus),} exacerbating skin
inflammation.\textsuperscript{10}The skin microbiome composition changes
dramatically across the AD flare cycle, with microbial diversity
dropping as disease severity increases, and a concomitant increase in
abundance of \emph{S. aureus} in the majority of
cases.\textsuperscript{11} A predominant \emph{S. aureus}strain is often
observed in the flare state, while heterogenous\emph{Staphylococcus
epidermidis} strain communities are seen in both the flare and
post-flare states. On non-flare AD skin, microbial diversity remains
high; however, the composition and functional potential of the AD
subjects' microbiome are distinct from healthy individuals, highlighting
potential microbiome-related factors that could increase the
susceptibility to flares.\textsuperscript{12} This altered microbiome
signature in the non-flare skin of AD patients is more pronounced in
individuals with high levels of circulating IgE and also associates with
molecular changes in the skin surface microenvironmental
niche.\textsuperscript{13} There is growing evidence that commensal
microbes may play a mechanistic role in skin barrier repair and
attenuate inflammation during AD via AhR-dependent signalling and
glucocorticoid-related pathways.\textsuperscript{14, 15}

The predominance of \emph{S. aureus} strains in flares and relative
reduction of commensal microbes are linked with skin barrier disruption
and inflammation in AD skin.\textsuperscript{16} A meta-analysis
reported that around 70\% of individuals across all ages with AD are
colonized with \emph{S. aureus} on lesional skin, 30-40\% in
non-lesional skin, and 62\% in the nares.\textsuperscript{17} AD
patients have significantly higher odds of \emph{S. aureus} colonization
than healthy controls at all sites compared.\textsuperscript{17}

There is a need for greater understanding of the initiators and drivers
of the altered skin microbiome and why \emph{S. aureus} predominates on
AD skin. The contribution is likely complex and multifactorial, driven
by Th2 skewing of the immune milieu, disruption to the skin barrier by
mutations in genes such as \emph{FLG} , and alterations in lipid and
protein production in the epidermis that increase \emph{S.
aureus}adherence.\textsuperscript{18-20} There is also strong evidence
from genetic disorders that either impact the immune system (such as
inborn errors in immunity), or disrupt skin barrier function (such as
congenital ichthyosis), resulting in overrepresentation
of\emph{Staphylococcus} species as a common feature in microbial
communities.\textsuperscript{21, 22} Thus, both host and microbiome
factors likely contribute to AD pathogenesis in susceptible individuals.

\emph{S. aureus} has long been associated with AD\textsuperscript{23}and
shown to demonstrate its pathogenic effects through various mechanisms
such as disruption of barrier integrity, intrinsic host immune
dysregulation, and expression of virulence genes. (Figure 1) Virulence
factors such as \selectlanguage{greek}α-\selectlanguage{english}toxin, protein A (SpA), lipotechoic acid (LTA), phenol
soluble modulin (PSM)-\selectlanguage{greek}α, \selectlanguage{english}and proteases can damage
keratinocytes.\textsuperscript{24} While AD-associated \emph{S.
aureus}strains have been isolated, several studies have investigated the
differences between \emph{S. aureus} strains isolated from children with
AD as compared to other \emph{S. aureus} strains to potentially identify
specific strains that may contribute to AD skin
disease.\textsuperscript{20, 25, 26}

Viral-host interactions also mediate AD morbidity. AD patients with a
history of \emph{S. aureus} skin infections are at greater risk of
eczema herpeticum (EH), a severe blistering cutaneous infection caused
by herpes virus.\textsuperscript{27, 28} Some mouse and \emph{in
vitro}studies have raised the possibility that \emph{S. aureus} strains
which produce staphylococcal toxic shock syndrome
toxin-1\textsuperscript{29}or \selectlanguage{greek}α-\selectlanguage{english}toxin\textsuperscript{30} may enhance
viral entry. Conversely, AD host factors such as genetics, immune
dysregulation, and barrier defects also increase susceptibility to EH
compared to healthy individuals.

Differences in fungal composition have also been described in AD.
Cross-sectional sequencing studies demonstrated lower relative
abundances of \emph{Malassezia spp} . Correspondingly, the higher
prevalence of non-\emph{Malassezia} fungi such as \emph{Cladosporium,
Alternaria} , \emph{and Aspergillus} in AD skin\textsuperscript{12,
31}may be attributed to environmental selection pressures
as\emph{Malassezia spp} grow best in lipid-rich conditions, which are
deficient in AD skin. Certain \emph{Malassezia} species perform
protective functions, whereas others may induce skin
inflammation.\textsuperscript{32, 33} A small study (n=17) demonstrated
that \emph{Malassezia globosa,} a commensal yeast from healthy adult
volunteers, secretes a protease (\emph{Malassezia globosa} Secreted
Aspartyl Protease 1 - MgSAP1) which disrupts \emph{S. aureus} biofilms
by hydrolyzing SpA.\textsuperscript{34} A murine AD model, however,
showed that \emph{M. pachydermatis, M. sympodialis} , \emph{and M.
furfur} activated IL-23 and IL-17 inflammatory pathways, and this was
corroborated by the presence of \emph{Malassezia} -specific production
of these cytokines by memory T cells in adult AD
patients.\textsuperscript{33} These targeted studies were designed to
investigate the specific inflammation-associated mechanisms exerted by
commensal \emph{Malassezia} spp, mostly in \emph{in vitro} or \emph{in
vivo} models. There is, however, little direct data on how yeast
interact with other skin microbiota or influence human host responses.

Native skin commensals also form part of the innate host defence against
pathogenic organisms. \emph{S. epidermidis} and \emph{Staphylococcus
hominis} are examples of coagulase-negative staphylococci (CoNS) which
stimulate host production of antimicrobial peptides like cathelicidin
and human beta defensin (HBD), and also directly produce PSM-\selectlanguage{greek}γ \selectlanguage{english}and
PSM-\selectlanguage{greek}δ, \selectlanguage{english}which inhibit the growth of pathogenic
bacteria.\textsuperscript{35}

An observational sequencing study (n=100 adult patients) detected
increased abundances of the \emph{Demodex folliculorum} mite on AD skin
compared to healthy controls.\textsuperscript{36} However, no further
mechanistic studies were done to assess the role of \emph{Demodex} mites
in inducing or perpetuating skin inflammation in these patients. While
house dust mites have been shown to trigger inflammation in AD murine
models,\textsuperscript{37} there is little data to show that they
trigger AD flares in AD patients. There is thus insufficient evidence to
conclude if skin mites play a major role in AD development.

\textbf{Skin microbiome markers of AD in early life}

Early life exposure to the external environment may shape host-microbe
interactions that play roles in skin health and atopic disease
onset.\textsuperscript{38} Distinct fluctuations in neonatal and infant
skin physiology in the first year of life influence skin microbiota
colonization patterns. The skin microbiome in healthy neonates is
characterized by the predominance of \emph{Bacillota}
(formerly\emph{Firmicutes} ), such as \emph{Staphylococcus}
and\emph{Streptococcus} , and fewer \emph{Actinomycetota}
(formerly\emph{Actinobacteria} ) (\emph{Cutibacterium}
and\emph{Corynebacterium} ). A small, open, non-randomized,
cross-sectional study found that soon after delivery, vaginally born
neonates (n=4) have skin microbiota that are similar to their mothers'
vaginal fluid, predominantly\emph{Lactobacillus} or \emph{Prevotella}
spp., while neonates born through Caesarean section (n=6) acquire mainly
maternal skin commensals such as \emph{Staphylococcus, Corynebacterium,}
and \emph{Cutibacterium spp} .\textsuperscript{39} In a subsequent
publication where infants were followed up to 30 days of life, the
authors reported that 4 Caesarean-born infants who were exposed to their
mothers' vaginal fluids at birth continued to exhibit skin microbiota
characteristics similar to vaginal-born infants.\textsuperscript{6} A
larger follow-on observational study recruited n=98 vaginal-born infants
and n=79 Caesarean-born infants, 30 of whom were swabbed with maternal
vaginal fluids after birth. Caesarean-born infants who underwent vaginal
seeding had a gut microbiota developmental trajectory up to age 12
months that more closely resembled vaginal-born infants, compared to
those who were not seeded, suggesting that early life vaginal microbiota
transfer had a sustained effect up to 1-year post
intervention.\textsuperscript{7} A subsequent double-blind randomized
controlled trial of 10 vaginal-seeded infants vs 10 controls (seeded
with sterile saline) found that vaginal-seeded infants had significantly
reduced alpha diversity in the skin at day 1, as well as in transitional
stool up to day 30 of life.\textsuperscript{8} There has, however, been
no longitudinal data beyond 1 year of life, nor any data on whether this
intervention had any impact on infant disease outcomes. Furthermore, as
the Caesarean sections were all elective and non-emergent, there is
little known about how other peripartum factors may influence maternal
and infant microbiota and maternal-infant transmission.

Various factors such as maternal microbiome, mode of delivery, and early
environmental exposure may influence the maturation trajectories of the
infant skin microbiome, and from murine models, potentially infant skin
immunology as well. A systematic review by Xiong et al found that
studies examining the link between mode of delivery and AD risk
harboured significant heterogeneity that could be attributed to
differences in country, study design, and method of AD
ascertainment.\textsuperscript{40} No definite conclusions can thus be
made about the impact of delivery mode on AD risk.

Several longitudinal studies have demonstrated early skin microbial
signals that may be predictive of AD onset. A small longitudinal study,
nested within a birth cohort, found that infants who developed AD at age
1 year (n=10) had a much lower abundance of
commensal\emph{Staphylococcus} species detected by 16S rRNA gene
sequencing at 2 months of age relative to controls (n=10)
.\textsuperscript{41} A larger prospective birth cohort study (n=146)
found that early \emph{S. aureus}colonization (by culture-based methods)
in the first few months of life appeared to precede the onset of AD in
infants.\textsuperscript{42}Nakamura et al further observed that infants
in the Chiba birth cohort who had \emph{S. aureus} strains harbouring
dysfunctional mutations in their \emph{Agr} quorum-sensing (QS) system
did not go on to develop AD (n=24), postulating that this functional
\emph{S. aureus} virulence mechanism may be important for AD
pathogenesis.\textsuperscript{43}Further studies are needed to examine
the mechanistic pathways through which early differences in microbiota
composition may influence later disease onset, such as the impact of
microbiota on host immunological responses, skin barrier protein
expression, and barrier function.

Marked pubertal differences in the skin microbiome have been
demonstrated as children sexually mature through Tanner
stages.\textsuperscript{44, 45} Similarly, the skin microbiome
composition of young children with AD (2-12 years, n =59) differed from
adolescents (13-17 years, n =13) and adults (18-62 years, n=56) versus
age-matched nonatopic healthy controls.

Skin microbiome diversity was significantly higher in the non-lesional
skin of AD children than in adolescents/adults, corresponding to similar
patterns in healthy individuals.\textsuperscript{46}
However,\emph{Staphylococcus} was significantly more abundant in
lesional as well as non-lesional skin of children and adolescents with
AD. Skin commensals for AD and control subjects were also age-specific:
such as\emph{Streptococcus} spp enriched in children compared
to\emph{Cutibacterium} and \emph{Corynebacterium} in adults.

There are only a few observational studies describing changes in skin
microbiome signatures in early infancy that may be associated with AD
onset. Further mechanistic studies are needed to deconvolute the
potential role of the skin microbiota in AD pathogenesis and their
interactions with the host skin barrier and immune system in the
pre-clinical disease state.

\textbf{Antibiotic use and infant skin microbiome}

There has been some evidence from meta-analyses for the link between
antibiotic use in pregnancy (n=18 studies)\textsuperscript{47} and early
life (n=22 studies)\textsuperscript{48} and infant AD. These studies
varied considerably in design, ranging from cohort studies to
case-control studies and retrospective medical record reviews, yielding
high heterogeneity. Wan et al\textsuperscript{47} in particular showed
that significant links were demonstrated only for retrospective studies
but not for prospective or cross-sectional studies, suggesting that a
degree of ascertainment bias may exist. Confounding by indication may
also be present in studies where the indication for antibiotic
prescriptions may be due to early skin disease or infections. The
meta-analyses were also not able to delineate the specific at-risk
window in pregnancy or early life where antibiotic administration might
conclusively increase the risk of infant AD.

It has also been shown that the skin microbiome in healthy adults
receiving antibiotic treatment manifested greater changes, as
demonstrated by increased Bray-Curtis dissimilarities after treatment
compared to baseline.\textsuperscript{49} Longer antibiotic courses
induced more profound and persistent changes, suggesting that there was
also a dose/duration-dependent effect.

Antenatal, perinatal, and postnatal antibiotic exposure may
theoretically likewise cause perturbations in the host microbiome and
this has been demonstrated in gut microbiome
studies.\textsuperscript{50} There is, however, limited data describing
the impact of maternal antibiotic exposures on their infants' skin
microbiome and its potential impact on infant AD. Hence, definitive
conclusions on whether the skin microbiome plays any role in the weak
link between maternal and early life antibiotic exposures and infant AD
cannot be made.

\textbf{Skin microbe transmission in households of pediatric AD
patients}

Besides lesional sites of AD, the anterior nares and inguinal creases
are common reservoirs of \emph{S. aureus} . Clinical studies have shown
that \emph{S. aureus} strains can be shared between the reservoirs and
distal skin sites, indicating that skin microbes are spread through
physical transfer or through the airborne route.\textsuperscript{51,
52}The seeding of \emph{S. aureus} between reservoirs and other body
sites may promote recolonization, disrupting optimal AD control.

There is also growing appreciation for the importance of other non-self
reservoirs and skin microbial transmission between individuals in close
contact in perpetuating AD. Studies utilizing 16S or whole genome
sequencing of skin microbiomes have further demonstrated a general
sharing of skin microbes apart from \emph{S. aureus} between members of
the same household.\textsuperscript{52, 53} In a cross-sectional study
of 30 primary caregiver-child pairs (children aged 4- 10 years) in
households with pediatric AD and the same number of age matched control
pairs, Chia et al demonstrated significant microbiome similarities
between the skin of clinically healthy caregivers and the skin of their
children.\textsuperscript{52} A subset of caregivers in households with
pediatric AD also exhibited lower relative abundances of some skin
commensals like \emph{S. hominis} and \emph{Dermacoccus
nishinomiyaensis} . Furthermore, the ratio of \emph{S. aureus}
to\emph{S. hominis} within skin microbiomes was a more sensitive and
specific marker for an individual's (caregiver or child) affiliation to
a house with an AD patient than just \emph{S. aureus} relative
abundances alone, underscoring the importance of additional shared
microbial influences within families. While cross-sectional cohorts have
shed light on possible microbiome sharing between family members,
further studies involving prospective cohorts are necessary to establish
stronger evidence for the role of intra-familial microbial transmission
in the onset, progression, and recurrence of pediatric AD. These studies
are important to establish if the risk of recurrent AD is associated
with the re-acquisition of microbes including \emph{S. aureus} after
their eradication following initial treatment.

Taken together, the current literature supports further investigations
into whether clinically healthy household members should also undergo
decolonization to manage recurrent pediatric AD. A clinical trial has
shown that both \emph{S. aureus} decolonization of all household members
of children below 18 years of age (median age 3.9~years, range,
1.1--17.1~years) with community-acquired methicillin-resistant \emph{S.
aureus} (MRSA) skin and soft tissue infections (SSTI) or individualized
decolonization of only household members with history of SSTI had a
modest effect on the risk of study participants developing future
SSTI,\textsuperscript{54} but no trial has been conducted in the context
of recurrent pediatric AD to date. The ineffectiveness of these
household decolonization strategies could be due to the lack of
decontamination of household surfaces and fomites, which are significant
reservoirs of \emph{S. aureus} , or due to potential complexities with
re-acquisition of \emph{S. aureus} from sources outside the household.
More comprehensive decolonization regimes will need to be trialled to
evaluate the efficacy of expanding treatment beyond the index patient
for managing recurrent pediatric AD.

\textbf{Skin microbiome changes in AD treatment}

Treatment of AD flares reduces disease severity and decreases \emph{S.
aureus} relative abundances with concomitant increase in skin microbiome
diversity including commensal skin flora such as \emph{Corynebacterium
and Cutibacterium} .\textsuperscript{55} Topical corticosteroids and
bleach baths have also been associated with cutaneous microbiota
composition on lesional skin temporarily resembling baseline or similar
to non-lesional skin, although their microbiota remained distinctly
different from healthy control skin.\textsuperscript{56, 57}

More recent therapies have targeted specific inflammatory pathways. The
Th2 inflammatory axis plays a key role in AD
pathology.\textsuperscript{5} During AD pathogenesis, Th2 polarization
leads to increased expression of the cytokines IL-4, IL-13 and
IL-31.\textsuperscript{58, 59} These trigger proinflammatory responses
promoting pruritus, reduced epidermal barrier function, increased
transepidermal water loss, and skin inflammation. Skin barrier defects
facilitate binding of \emph{S. aureus,} while Th2 cytokine signalling
inhibits anti-microbial peptide secretion by
keratinocytes,\textsuperscript{18} potentially contributing to a vicious
cycle of sustained inflammation in chronic AD.

One of the biologics targeting components of this inflammatory axis is
dupilumab, a monoclonal antibody which blocks IL4 receptor alpha
(IL-4R\selectlanguage{greek}α\selectlanguage{english}), leading to inhibition of IL-4/IL-13 signalling. Numerous
clinical trials have shown that dupilumab is effective in alleviating AD
symptoms and reduction in disease scores,\textsuperscript{60} and has
been approved by the FDA for this purpose in both adults and
children.\textsuperscript{61}

Dupilumab therapy is associated with skin microbiome composition
alterations as well. A double-blind, placebo-controlled clinical trial
conducted by Callewaert et al demonstrated that adult patients had
decreased \emph{S. aureus} relative abundance and increased Shannon
diversity as soon as four weeks after dupilumab treatment, correlating
with clinical improvement measured by the Eczema Area and Severity Index
(EASI) and SCORing Atopic Dermatitis (SCORAD)
tools.\textsuperscript{62}While clinical trials showed decreases in
\emph{S. aureus} abundance on patient skin, dupilumab treatment did not
completely eradicate \emph{S. aureus} . Instead, the abundance of
\emph{S. aureus} increased again 32 weeks post
treatment.\textsuperscript{62} Treatment with tralokinumab, an
anti-IL-13 monoclonal antibody, was also associated with reduced\emph{S.
aureus} abundance with concomitant increase in the relative abundances
of CoNS in the lesional skin of adults with moderate-to-severe AD from
the Phase 3 ECZTRA 1 trial {[}ClinicalTrials.gov ID
NCT03131648{]}.\textsuperscript{63} It is still unknown if these changes
in microbiota composition merely reflect transient alterations in host
skin barrier and immune status, or if these changes contribute to
clinical improvement. Future mechanistic work will be helpful in
determining if skin microbiome changes play a role in clinical response
to biologics or merely reflect normalization of epidermal biology.

\textbf{The skin microbiome in food allergy pathogenesis}

Food allergy (FA) is closely associated with AD, particularly in the
early-onset severe phenotype. Murine studies have demonstrated that the
pathogenesis of food allergy may occur through epicutaneous
sensitization to food allergens through the disrupted skin barrier in AD
(Figure 2). In these murine studies, these mechanistic pathways are
postulated to involve activation of dermal antigen-presenting cells upon
exposure of inflamed skin to exogenous food allergens, germinal centre
IgE+ B cell expansion and generation of food allergen-specific IgE and
other pro-inflammatory cytokines (IL-4, IL-5, thymic stromal
lymphopoietin (TSLP) and IL-33).\textsuperscript{64, 65}

Recent studies have increasingly highlighted the association of skin
microbes with the AD-FA axis. Jones et al found that children (n=718;
aged 0--18 years) with AD who were colonized with \emph{S. aureus} ,
particularly MRSA, also had a higher risk of food allergy compared to
healthy controls.\textsuperscript{66}Infants from the Learning About
Peanut Allergy (LEAP) study who were\emph{S. aureus-} colonized during
at least one time-point between 4 and 60 months of age had increased
risk of peanut and egg allergy in the first 5 years of life, independent
of AD severity.\textsuperscript{67} A murine model demonstrated that
combined epicutaneous exposure to staphylococcal enterotoxin B (SEB) and
OVA enhanced OVA-specific IgE and IgG2 antibody responses compared to
OVA exposure alone.\textsuperscript{68} Mice which were cutaneously
sensitized with SEB and peanut allergen extract had significantly
increased peanut-specific Th2 responses compared to mice sensitized with
peanut allergen alone.\textsuperscript{69} These mouse experiments
suggest that SEB may perform an adjunctive role in mediating food
allergy through AD skin.

A cross-sectional metagenomic study (n=62; children aged 4--17 years) of
skin microbiota collected from AD patients with food allergy (ADFA+)
showed an increased \emph{S. aureus} relative abundance on their
non-lesional skin as compared to healthy subjects. \emph{S.
aureus}abundance also positively correlated with transepidermal water
loss in the ADFA+ group but not in AD patients without food allergy
(ADFA-) or healthy groups.\textsuperscript{70} There is, however, a
paucity of studies on the differences in overall skin microbiota
composition (apart from \emph{S. aureus} alone), and the temporal
evolution of the skin microbiome alongside immune dysregulation, in the
development of AD and food allergy.

\textbf{Skin-based interventions for AD and FA prevention}

An increased understanding of the role of the skin barrier and
microbiome in AD and FA pathogenesis has sparked interest in developing
skin-based interventions for allergy prevention. In the past decade,
randomized controlled trials have explored the use of prophylactic skin
interventions from early life to prevent development of AD and FA. A
Cochrane individual participant data (IPD) meta-analysis found no
benefit of a variety of skin interventions inclusive of emollients,
oils, and bathing advice overall for AD and FA
prevention.\textsuperscript{71} Another meta-analysis by Zhong et
al\emph{.} found that prophylactic emollients were effective against AD
development in high-risk infants only and in those without an interval
between treatment cessation and AD outcome
assessment.\textsuperscript{72}

A small study in high-risk infants who received emollients (n=11 in the
intervention arm and n=12 controls) from birth to age 6 months found
greater skin microbiota diversity, lower skin pH, and shifts
in\emph{Streptococcus} abundance on skin, specifically higher \emph{S.
salivarius} and lower \emph{S. mitis} relative abundance, compared to
controls.\textsuperscript{73} The relative abundance of \emph{S.
salivarius} also correlated negatively with skin pH, suggesting that the
lowering of skin pH due to long-term emollient use may either be one of
the mechanisms through which changes in skin microbiota composition
impact AD development or that these microbial fluctuations merely occur
alongside skin barrier changes due to the intervention. Differentiating
between these possibilities could not be achieved from this study alone
and will require in-depth mechanistic studies such as in murine models
to understand the causal interactions between skin emollients,
microbiota and the skin barrier. There have also been no studies
investigating the role of the skin microbiome in FA prevention.

\textbf{Skin microbiome-based approaches for AD treatment}

In contrast to broad-spectrum antibiotic therapies, repurposing
commensal and symbiotic microbes for therapeutic strategies could allow
more targeted antimicrobial effects against pathogenic microbes without
unintended collateral impact on the rest of the healthy microbiota.
Microbiome studies have now investigated numerous microbial mechanisms
by which AD skin could benefit from a microbial driven anti-inflammatory
outcome. The earliest studies utilized a bacterial lysate
of\emph{Vitreoscilla filiformis} as AD therapeutics. The proposed
mechanism was via host antimicrobial peptides and anti-inflammatory
effects. In a randomized, double-blind, vehicle-controlled trial, mild
AD subjects (n=75 aged 6-70 years) who received topical applications
of\emph{V. filiformis} experienced improvements in SCORAD and pruritus
scores, as well as downward trend of \emph{S. aureus} skin burden and
drop-outs related to lack of efficacy.\textsuperscript{74}

A subsequent MRSA skin infection murine study demonstrated that CoNS
species can play an important role in activating other microbes and can
also interact with the epidermis to maintain homeostasis, and interact
or compete with \emph{S. aureus} .\textsuperscript{75} \emph{S.
epidermidis} is an important CoNS that has been shown to reduce skin
inflammation by regulating TLR pathways and can produce sphingomyelinase
to aid in the production of ceramides to maintain the skin barrier in
mouse and \emph{in vitro} models\emph{.} \textsuperscript{76, 77} These
functions highlight the important role \emph{S. epidermidis} has on the
skin and the potential that could be harnessed for AD. However, the use
of \emph{S. epidermidis} without attenuation would be complex, and
potentially controversial, due to its dual roles in protection from
pathogens but also ability to stimulate inflammation or cause systemic
infections in certain situations.\textsuperscript{78}

Transplantation of CoNS commensal microbe \emph{S. hominis} from healthy
patients onto AD skin has been investigated. CoNS strains from healthy
volunteers produced potent AMPs that reduced \emph{S. aureus} on the
skin of 5 adult AD subjects.\textsuperscript{35} A subsequent follow-up
phase 1 clinical trial using the \emph{S. hominis} A9 (ShA9) strain in
54 adult AD patients demonstrated safety; however, eczema severity was
not significantly different when examined among all treated
participants.\textsuperscript{79} A post-hoc analysis showed that a
subgroup of patients who were colonized by \emph{S. aureus} strains
which were sensitive to killing by ShA9 showed significant clinical
improvement compared with vehicle.\textsuperscript{79} A phase 2
clinical trial {[}ClinicalTrials.gov ID: NCT05177328{]} is ongoing to
further investigate this approach.

Another bacteriotherapy approach used \emph{Roseomonas mucosa (R.
mucosa)} , a skin commensal harvested from healthy donors, as topical
therapy for AD. An open-label phase I/II trial with ten adult and 5
pediatric subjects who received skin treatment with \emph{R}
.\emph{mucosa} demonstrated improved disease severity, reduced topical
steroid requirements, and decreased \emph{S.
aureus}burden.\textsuperscript{80} However, the phase II
placebo-controlled clinical trial {[}ClinicalTrials.gov ID:
NCT04936113{]} which combined three strains of \emph{R. mucosa} for a
live therapeutic product (FB-401) in AD patients was terminated because
it failed to demonstrate any significant differences in patients for
achieving the primary outcome of EASI-50 (the proportion of subjects
with a minimum of 50\% improvement in AD disease severity as measured by
the Eczema Area and Severity Index (EASI) score).

Additionally, there have also been recent potential biotherapeutic
approaches using the non-bacterial components of the microbiome such as
bacteriophages to target \emph{S. aureus} but not \emph{S. epidermidis}
.\textsuperscript{81} Bacteriophage endolysin-based therapies have also
been developed as AD therapeutics. Staphefekt SA.100 is a commercialized
topically administered recombinant phage endolysin which was able to
reduce AD symptom and skin inflammation in early phase studies. However,
in a follow-on double-blinded, vehicle-controlled randomized superiority
trial in adults with non-clinically infected moderate-to-severe AD
{[}ClinicalTrials.gov ID: NCT02840955{]}, the endolysin intervention
failed to demonstrate superiority over placebo in topical steroid usage,
clinical efficacy, quality of life, or \emph{S. aureus}
burden.\textsuperscript{82}However, this trial excluded patients with
clinically infected AD and only half of the cohort were colonized with
\emph{S. aureus} prior to enrolment.

Due to the individuality of skin microbiomes at the strain level in both
healthy individuals and AD patients, bacteriotherapy may be effective
only in heavily colonized or clinically infected AD, but may be less
effective in other circumstances. It is therefore likely that these
microbial therapeutic approaches will require careful patient selection
to identify specific subgroups who will benefit from such interventions,
and optimization of therapeutic design to achieve sustained clinical
responses.\textsuperscript{79, 82}

\textbf{Conclusion}

Numerous studies have now reported that the composition of the skin
microbiome is closely associated with AD flares, severity, and response
to various treatment modalities. However, skin microbiota is not the
sole factor in AD where genetics, immunology and environmental
influences also play important roles.

Several gaps in the existing literature remain to be filled and it is
hoped that future studies will address these (Table 1). Many studies
currently demonstrate differences in skin microbiota composition in
cases and controls at a single timepoint, which limits our ability to
make conclusions about causality and temporal progression; or focus on
bacterial species alone but do not explore other microbes such as
viruses and fungi or their interactions with bacteria and the host.
There is also a lack of mechanistic understanding of functional units in
the skin microbiome and whether differences in microbial abundance
impacts clinical disease or are mere bystanders reflecting fluctuations
in clinical disease.

Future research should focus on several broad areas: (1) A mechanistic
understanding of whether skin microbial shifts modulate or merely
reflect AD and FA pathogenesis, treatment response or disease
prevention; (2) Functional analysis of all skin microbes including
bacteria, viruses, fungi and mites in deep metagenomic studies
integrated with culture methods and skin barrier function analysis to
understand their potential interactions with each other to impact
disease phenotypes or progression; (3) Longitudinal studies to identify
the window of opportunity for intervention, if any; (4) Evaluating the
efficacy, sustainability and patient selection for microbe-based
biotherapeutics in disease treatment and prevention. (Table 1).

Several interventional trials that are underway in children with AD
focus mainly on monitoring skin microbiota changes in response to
treatment and microbiota-based interventions, such as probiotics in
topical creams and vaginal microbiota seeding (Table 2). However, apart
from the latter study, the majority of these trials plan only to
document changes in skin microbiota composition as secondary aims. There
is a clear need for more robust studies to fill the gaps described
above, and to move the field away from merely descriptive studies to
understanding the mechanistic role and functions of skin microbiota in
disease pathogenesis and treatment, and to evaluate the potential to
harness them for targeted biotherapeutic interventions or as validated
biomarkers of disease.

\par\null

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Immunomodulatory Treatments for Patients With Atopic Dermatitis: A
Systematic Review and Network Meta-analysis. \emph{JAMA
dermatology}2020; 156: 659-667. DOI: 10.1001/JAMADERMATOL.2020.0796.

61. Press Release: FDA approves Dupixent® (dupilumab) as first biologic
medicine for children aged 6 months to 5 years with moderate-to-severe
atopic dermatitis - Sanofi.

62. Callewaert C, Nakatsuji T, Knight R, et al. IL-4R\selectlanguage{greek}α \selectlanguage{english}Blockade by
Dupilumab Decreases Staphylococcus aureus Colonization and Increases
Microbial Diversity in Atopic Dermatitis. \emph{The Journal of
investigative dermatology} 2020; 140: 191-202.e197. DOI:
10.1016/J.JID.2019.05.024.

63. Beck LA, Bieber T, Weidinger S, et al. Tralokinumab treatment
improves the skin microbiota by increasing the microbial diversity in
adults with moderate-to-severe atopic dermatitis: analysis of microbial
diversity in ECZTRA 1, a randomized controlled trial. \emph{J Am Acad
Dermatol} 2022 2022/12/07. DOI: 10.1016/j.jaad.2022.11.047.

64. Hussain M, Borcard L, Walsh KP, et al. Basophil-derived IL-4
promotes epicutaneous antigen sensitization concomitant with the
development of food allergy. \emph{J Allergy Clin Immunol} 2018; 141:
223-234.e225. 2017/04/10. DOI: 10.1016/j.jaci.2017.02.035.

65. Galand C, Leyva-Castillo JM, Yoon J, et al. IL-33 promotes food
anaphylaxis in epicutaneously sensitized mice by targeting mast
cells.\emph{J Allergy Clin Immunol} 2016; 138: 1356-1366. 2016/07/04.
DOI: 10.1016/j.jaci.2016.03.056.

66. Jones AL, Curran-Everett D and Leung DYM. Food allergy is associated
with Staphylococcus aureus colonization in children with atopic
dermatitis. \emph{J Allergy Clin Immunol} 2016; 137: 1247-1248.e1243.
2016/03/11. DOI: 10.1016/j.jaci.2016.01.010.

67. Tsilochristou O, du Toit G, Sayre PH, et al. Association of
Staphylococcus aureus colonization with food allergy occurs
independently of eczema severity. \emph{J Allergy Clin Immunol} 2019;
144: 494-503. 2019/06/05. DOI: 10.1016/j.jaci.2019.04.025.

68. Savinko T, Lauerma A, Lehtim\selectlanguage{ngerman}äki S, et al. Topical superantigen
exposure induces epidermal accumulation of CD8+ T cells, a mixed
Th1/Th2-type dermatitis and vigorous production of IgE antibodies in the
murine model of atopic dermatitis. \emph{J Immunol} 2005; 175:
8320-8326. 2005/12/13. DOI: 10.4049/jimmunol.175.12.8320.

69. Forbes-Blom E, Camberis M, Prout M, et al. Staphylococcal-derived
superantigen enhances peanut induced Th2 responses in the
skin.\emph{Clin Exp Allergy} 2012; 42: 305-314. 2011/11/19. DOI:
10.1111/j.1365-2222.2011.03861.x.

70. Leung DYM, Calatroni A, Zaramela LS, et al. The nonlesional skin
surface distinguishes atopic dermatitis with food allergy as a unique
endotype. \emph{Sci Transl Med} 2019; 11 2019/02/23. DOI:
10.1126/scitranslmed.aav2685.

71. Kelleher MM, Cro S, Cornelius V, et al. Skin care interventions in
infants for preventing eczema and food allergy. \emph{Cochrane Database
Syst Rev} 2021; 2: Cd013534. 2021/02/06. DOI:
10.1002/14651858.CD013534.pub2.

72. Zhong Y, Samuel M, van Bever H, et al. Reply to correspondence:
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and meta-analysis. \emph{Allergy} 2022; 77: 1934-1935. 2022/06/02. DOI:
10.1111/all.15309.

73. Glatz M, Jo JH, Kennedy EA, et al. Emollient use alters skin barrier
and microbes in infants at risk for developing atopic
dermatitis.\emph{PLoS One} 2018; 13: e0192443. 2018/03/01. DOI:
10.1371/journal.pone.0192443.

74. Gueniche A, Knaudt B, Schuck E, et al. Effects of nonpathogenic
gram-negative bacterium Vitreoscilla filiformis lysate on atopic
dermatitis: a prospective, randomized, double-blind, placebo-controlled
clinical study. \emph{Br J Dermatol} 2008; 159: 1357-1363. 2008/09/18.
DOI: 10.1111/j.1365-2133.2008.08836.x.

75. Paharik AE, Parlet CP, Chung N, et al. Coagulase-Negative
Staphylococcal Strain Prevents Staphylococcus aureus Colonization and
Skin Infection by Blocking Quorum Sensing. \emph{Cell Host Microbe}2017;
22: 746-756.e745. 2017/12/05. DOI: 10.1016/j.chom.2017.11.001.

76. Lai Y, Di Nardo A, Nakatsuji T, et al. Commensal bacteria regulate
Toll-like receptor 3-dependent inflammation after skin injury. \emph{Nat
Med} 2009; 15: 1377-1382. 2009/12/08. DOI: 10.1038/nm.2062.

77. Zheng Y, Hunt RL, Villaruz AE, et al. Commensal Staphylococcus
epidermidis contributes to skin barrier homeostasis by generating
protective ceramides. \emph{Cell Host Microbe} 2022; 30: 301-313.e309.
2022/02/07. DOI: 10.1016/j.chom.2022.01.004.

78. Cau L, Williams MR, Butcher AM, et al. Staphylococcus epidermidis
protease EcpA can be a deleterious component of the skin microbiome in
atopic dermatitis. \emph{J Allergy Clin Immunol} 2021; 147:
955-966.e916. 2020/07/08. DOI: 10.1016/j.jaci.2020.06.024.

79. Nakatsuji T, Hata TR, Tong Y, et al. Development of a human skin
commensal microbe for bacteriotherapy of atopic dermatitis and use in a
phase 1 randomized clinical trial. \emph{Nat Med} 2021; 27: 700-709.
2021/02/24. DOI: 10.1038/s41591-021-01256-2.

80. Myles IA, Earland NJ, Anderson ED, et al. First-in-human topical
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dermatitis.\emph{JCI insight} 2018; 3 2018/05/04. DOI:
10.1172/jci.insight.120608.

81. Shimamori Y, Pramono AK, Kitao T, et al. Isolation and
Characterization of a Novel Phage SaGU1 that Infects Staphylococcus
aureus Clinical Isolates from Patients with Atopic Dermatitis.\emph{Curr
Microbiol} 2021; 78: 1267-1276. 2021/02/28. DOI:
10.1007/s00284-021-02395-y.

82. de Wit J, Totté JEE, van Mierlo MMF, et al. Endolysin treatment
against Staphylococcus aureus in adults with atopic dermatitis:
A~randomized controlled trial. \emph{J Allergy Clin Immunol} 2019; 144:
860-863. 2019/05/31. DOI: 10.1016/j.jaci.2019.05.020.

\textbf{Table 1. Key Research Questions and Future Research Directions}\selectlanguage{english}
\begin{longtable}[]{@{}ll@{}}
\toprule
\textbf{Key Research Questions} & \textbf{Future Research
Directions}\tabularnewline
\midrule
\endhead
Changes in skin microbiota composition & Changes in skin microbiota
composition\tabularnewline
Do shifts in skin microbiota composition impact disease pathogenesis or
do they merely reflect underlying disease processes? & Mechanistic
studies designed to assess the effect of changing skin microbe
abundances on disease pathogenesis Intervention studies to understand
role of microbes in disease pathogenesis\tabularnewline
How do skin microbiota interact with one another, and with the host to
influence disease pathogenesis? & Functional analysis of the
contribution of microbes e.g. bacteria, viruses, fungi and mites
colonizing skin to skin disease Use of deep sequencing methods
integrated with culture methods and measures of skin barrier function to
determine the role of microbes in disease pathogenesis Standardization
of protocols across skin phenotyping studies to allow for comparison of
data Murine models investigating combinations of microbes, and deep
endophenotyping of host responses\tabularnewline
Do skin microbiota alterations in early life impact AD and FA onset in
later childhood If so, what are the mechanisms through which this might
occur? & Larger longitudinal studies with long-term follow up, robust
early life skin barrier measures, and objective allergic outcomes
Mechanistic studies to validate the impact of changes in microbe
composition on disease onset\tabularnewline
Skin microbe-based therapeutic approaches & Skin microbe-based
therapeutic approaches\tabularnewline
Does therapeutic manipulation of skin microbiota prevent AD or FA or
reduce disease severity? If so, what is the window of opportunity for
such interventions? & Randomized controlled trials of early life skin
microbiota manipulation with long-term follow up for allergic disease
onset Detailed collection of skin barrier markers at serial time-points
in early life\tabularnewline
Which patient groups would benefit from biotherapeutic interventions? &
Intervention studies to include different disease phenotypes e.g.
infected AD, positive colonization with target microbe,
etc\tabularnewline
Would disruption of pathogenic skin microbiota transmission between
close contacts improve outcomes? & Randomized controlled trials of
microbe eradication techniques involving close contacts of index
patients\tabularnewline
\bottomrule
\end{longtable}

\textbf{Table 2. Skin Microbiome Clinical Trials in Children}\selectlanguage{english}
\begin{longtable}[]{@{}lllll@{}}
\toprule
\begin{minipage}[b]{0.17\columnwidth}\raggedright\strut
\textbf{NCT Number}\strut
\end{minipage} & \begin{minipage}[b]{0.17\columnwidth}\raggedright\strut
\textbf{Study Title}\strut
\end{minipage} & \begin{minipage}[b]{0.17\columnwidth}\raggedright\strut
\textbf{Subjects}\strut
\end{minipage} & \begin{minipage}[b]{0.17\columnwidth}\raggedright\strut
\textbf{Interventions}\strut
\end{minipage} & \begin{minipage}[b]{0.17\columnwidth}\raggedright\strut
\textbf{Outcome Measures}\strut
\end{minipage}\tabularnewline
\midrule
\endhead
\begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Trials monitoring skin microbiota changes in response to treatment\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Trials monitoring skin microbiota changes in response to treatment\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Trials monitoring skin microbiota changes in response to treatment\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Trials monitoring skin microbiota changes in response to treatment\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Trials monitoring skin microbiota changes in response to treatment\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
NCT01597817\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Efficacy and Safety of a Biofunctional Textile in the Management of
Atopic Dermatitis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Subjects above 12 years of age with atopic dermatitis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Randomized blinded controlled trial Intervention: chitosan coated
textile (cotton long sleeved shirts and pants) Comparator: chitosan-free
cotton long sleeved t-shirts and pants.\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
SCORAD Quality of Life Eczema symptoms Eczema treatment Immunological
markers Skin microbiota (\emph{S. aureus}) Genetic mutations\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
NCT01631617\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Effects of Treatments on Atopic Dermatitis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Cohort 3: subjects 2 -- 50 years of age with atopic dermatitis and
symptoms of active bacterial infection\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Randomized blinded controlled trial Intervention: Cephalexin with dilute
bleach bath Comparator: Cephalexin with placebo bath\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Difference in Shannon Diversity Indices (SDI) from baseline to day
14\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
NCT03376243\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
EARLYEMOLLIENT - Feasibility of Early Emollient Use in Children With
Atopic Eczema\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
50 high-risk neonates from day 1- 21 of life\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Pragmatic, parallel group, assessor-blind randomised open-label
prospective study Intervention: LIPIKAR BAUME AP+ emollient Comparator:
Structured parent education\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Willingness to participate Cumulative incidence of eczema TEWL
Microbiome diversity over time\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
NCT03673059\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Clinical Trial to Assess the Effects of Topical Lotions on Changes in
the Skin Microbiome and Associations With Itch\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Subjects 16-50 years of age with mild to moderate eczema with recent
flare\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Randomized blinded controlled trial Intervention: Cosmetic Moisturizer
Regimen DRUG: OTC Eczema Moisturizer\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
microbiome composition pH changes TEWL Skin hydration EASI score ADSI
score\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
NCT04800185\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Characterizing Skin Microbiome Change in Atopic Dermatitis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Patients 2 years and above with atopic dermatitis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Open label trial DRUG: Crisaborole 2\% topical ointment Comparator:
None\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Skin microbiome before, during and after treatment with crisaborole 2\%
ointment\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
NCT05523986\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Vitamin D Treatment Effect for Atopic Dermatitis in Children\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Children 1-18 years with moderate to severe AD\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Randomized controlled trial Intervention: Vitamin D (2000IU/day) for 6
months Comparator: Placebo\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Vitamin D levels Genotyping Nasal, skin and anal microbiota composition
Total and antigen-specific IgE EASI POEM\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
NCT03614221\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Comparison of Lindioil (Indigo Naturalis Oil Extract) Ointment to
Protopic\selectlanguage{ngerman}® Ointment 0.1\% in Treating Atopic Dermatitis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Patients 16 -- 65 years with atopic dermatitis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Randomized cross-over trial Intevention: Lindioil ointment Comparator:
Protopic 0.1\% ointment\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
EASI-50, EASI-75, EASI-90 Investigator's Global Assessment (IGA) Body
surface area of involvement Length of relapse-free days after treatment
cessation Pruritus symptoms Quality of life Skin microbiome
changes\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
NCT05688735\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Assessment of the Effect of Coconut and Sunflower Seed Oil Derived
Isosorbide Diesters and Colloidal Oatmeal\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Children 2 -- 17 years with active atopic dermatitis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Randomized blinded controlled trial Intervention: Isosorbide Diester
(0.1\% colloidal oatmeal) + topical hydrocortisone 2.5\% ointment
Comparator: Placebo vehicle (with 0.1\% colloidal oatmeal) + topical
hydrocortisone 2.5\% ointment\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
EASI Itch symptoms Topical steroid use TEWL Skin hydration Change in
S\emph{. aureus} abundance on skin\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Trials on Microbiota-based interventions\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Trials on Microbiota-based interventions\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Trials on Microbiota-based interventions\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Trials on Microbiota-based interventions\strut
\end{minipage} & \begin{minipage}[t]{0.17\columnwidth}\raggedright\strut
Trials on Microbiota-based interventions\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
NCT04265716\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Topical \emph{L. reuteri} in Children With Atopic Dermatitis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Children 1 -- 18 years of age with atopic dermatitis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Intervention: Topical probiotic \emph{L. reuteri} Comparator: standard
of care + placebo\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Improvement in skin appearance SCORAD at 16 weeks\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
NCT04771910\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Study of the Skin Microbiome and the Potential of a Topical Probiotic
Cream for Atopic Dermatitis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Patients with atopic dermatitis\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Randomized controlled trial Intervention: Topical cream with live
probiotic (\emph{Lactobacillus}) Comparator: placebo cream\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Skin microbiome composition EASI Skin itch symptoms\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
NCT03928431\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Restoration of Microbiota in Neonates\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Infants of healthy mothers with uncomplicated pregnancies at term\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
Randomized controlled trial Intervention: swab from maternal vagina +
fecal swab on Caesarean-born infants' skin Comparator: clean
saline-soaked gauze\strut
\end{minipage} & \begin{minipage}[t]{0.19\columnwidth}\raggedright\strut
IgE-associated allergic disease at 2 years of age Immunological markers
Microbial composition between groups\strut
\end{minipage}\tabularnewline
\bottomrule
\end{longtable}

Legend: SCORing AD severity (SCORAD); Transepidermal water loss (TEWL),
Eczema Area Severity Index (EASI), Atopic Dermatitis Severity Index
(ADSI), Patient Oriented Eczema Measure (POEM)

\textbf{Figure Legends}

\textbf{Figure 1: Interactions between \emph{Staphylococcus aureus},
native skin commensals and host cells in healthy or diseased skin.}

On healthy skin (left), commensals like
coagulase-negative\emph{Staphylococcus} (CoNS) and the fungi
\emph{Malassezia} secrete a variety of compounds to inhibit the growth
of the pathobiont\emph{Staphylococcus aureus} (\emph{S. aureus} ). CoNS
secrete phenol soluble modulins (PSMs) and auto-inducing peptides, which
inhibit\emph{S. aureus} growth and virulence factor expression
respectively. CoNS can stimulate host epidermal cells to produce
anti-microbial peptides (AMPs) to further restrain \emph{S. aureus}
growth. Both CoNS and commensal \emph{Malassezia} also secrete a variety
of proteases, which disrupt \emph{S. aureus} biofilm formation. These
mechanisms contribute to T cell tolerance and likely optimize barrier
function on healthy skin. On inflamed skin (right), increased \emph{S.
aureus}colonization and biofilm formation can lead to heightened
secretion of virulence factors such as PSMs, toxins and proteases that
damage the stratum corneum. Host AMPs are present in lower amounts or
are rendered less effective due to \emph{S. aureus} activity and Th2
signalling.\emph{S. aureus} can also suppress the growth or activity of
skin commensals. Superantigens released by \emph{S. aureus} can
penetrate the epidermis and trigger dermal dendritic cells to drive T
helper 2 (Th2) polarization and expansion. Excessive numbers of Th2
cells in turn, produce a variety of pro-inflammatory cytokines, which
further exacerbate skin barrier dysfunction, IgE production by B-cells
and mast cell degranulation. While the pre-flare skin (middle) is not
inflamed, there might be decreases in the abundance of commensals which
inhibit\emph{S. aureus} , promoting its transition to a pathogenic
state. These individuals have elevated Th2 responses and IgE compared to
healthy skin, and are pre-disposed to severe itching in subsequent
flares. (Created with BioRender.com)

\textbf{Figure 2. Mechanisms of skin barrier dysfunction in atopic
dermatitis resulting in food allergy.}

Environmental pollutants, detergents, microbial dysbiosis and genetics
such as \emph{FLG} loss of function mutations can lead to disruptions to
the epithelial barrier. Skin barrier impairment leads to skin
inflammation resulting in atopic dermatitis. Epicutaneous exposure to
food allergens in the context of an impaired barrier may trigger food
allergen sensitization through Th2-dependent pathways: Specific resident
dendritic cell (DC) subsets capture allergens in the skin and transport
them to skin-draining lymph nodes where they are presented to CLA+ skin
homing~T cells. IL-4 and IL-13 cytokines promote B-cell isotype
switching to specific IgE (sIgE), and upon differentiating into plasma
cells, yield allergen-specific IgE antibodies. The sIgE bind to
high-affinity Fc\selectlanguage{greek}ε\selectlanguage{english}RI receptors on the surface of mast cells and
basophils. During the sensitization process, a memory pool of
allergen-specific B cells and T helper 2 cells are produced. Upon
subsequent oral antigen exposure (consumption of the allergenic food),
cross-linking of sIgE on the Fc\selectlanguage{greek}ε\selectlanguage{english}RI receptors trigger mast cell
degranulation, release of histamine and other inflammatory mediators,
culminating in the clinical allergic response. The presence of \emph{S.
aureus} enhances pro-inflammatory responses which heighten risk of food
allergy development. \emph{S. aureus} colonization, such as
by\emph{methicillin-resistant S. aureus} (MRSA), and exposure to
staphylococcal enterotoxin B (SEB), has been shown to increase risk of
food allergy (FA) independent of AD severity. \emph{S. aureus} abundance
was also found to be positively correlated with transepidermal water
loss (TEWL) in patients with AD and FA. (Created with BioRender.com)\selectlanguage{english}
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\includegraphics[width=0.70\columnwidth]{figures/Figure-1/Figure-1}

\end{center}
\end{figure}\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/Figure-2/Figure-2}

\end{center}
\end{figure}

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