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During the past decade, the microbiome has emerged as a major contributor to human health.1 It has been suggested in current studies that the early-life microbiome is a crucial factor for proper immune development and long-term health.2, 3 Transient microbial dysbiosis during this time period has been associated with the development of immune-mediated, metabolic, and neurodevelopmental disorders.4 – 7 In addition, increasing evidence has been used to support a vital role of the maternal and intrauterine microbiomes in childhood health and development.8 Collectively, these findings have been used to support the microbiome as a key participant in the Developmental Origins of Health and Disease (DOHaD). In this review, we will discuss the current
research surrounding the maturation of the early-life microbiome and how transient variations in this bacterial consortium can have long-term consequences for human health.
The DOhaD: Where DOes The MicrObiOMe FiT?
The developmental origins hypothesis proposes variations in fetal and infant programming through environmental exposures during a critical window of early life.9 Termed originally as the Barker hypothesis, 10, 11 in which the association between fetal malnutrition and hypertension later in life was a focus, this theory has since expanded to account for many types of early-life exposures and birth outcomes associated with long-term health and development. For example, high birth
The Role of the Microbiome in the Developmental Origins of Health and DiseaseLeah T. Stiemsma, PhD, Karin B. Michels, ScD, PhD
Although the prominent role of the microbiome in human health has been established, the early-life microbiome is now being recognized as a major influence on long-term human health and development. Variations in the composition and functional potential of the early-life microbiome are the result of lifestyle factors, such as mode of birth, breastfeeding, diet, and antibiotic usage. In addition, variations in the composition of the early-life microbiome have been associated with specific disease outcomes, such as asthma, obesity, and neurodevelopmental disorders. This points toward this bacterial consortium as a mediator between early lifestyle factors and health and disease. In addition, variations in the microbial intrauterine environment may predispose neonates to specific health outcomes later in life. A role of the microbiome in the Developmental Origins of Health and Disease is supported in this collective research. Highlighting the early-life critical window of susceptibility associated with microbiome development, we discuss infant microbial colonization, beginning with the maternal-to-fetal exchange of microbes in utero and up through the influence of breastfeeding in the first year of life. In addition, we review the available disease-specific evidence pointing toward the microbiome as a mechanistic mediator in the Developmental Origins of Health and Disease.
abstract
PEDIATRICS Volume 141, number 4, April 2018:e20172437 State-of-the-art review article
To cite: Stiemsma LT and Michels KB. The Role of the Microbiome in the Developmental Origins of Health and Disease. Pediatrics. 2018;141(4): e20172437
Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
Dr Stiemsma conceptualized and outlined the review, conducted the literature search, drafted the initial manuscript, and reviewed and revised the manuscript; Dr Michels supervised the project and critically reviewed and edited the manuscript; and all authors approved the final manuscript as submitted and agreed to be accountable for all aspects of the work.
DOi: https:// doi. org/ 10. 1542/ peds. 2017- 2437
Accepted for publication Nov 29, 2017
Address correspondence to Karin B. Michels, ScD, PhD, Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, 650 Charles E. Young Dr S, Los Angeles, CA 90095. E-mail: [email protected]
PEDIATRICS (ISSN Numbers: Print, 0031-4005; Online, 1098-4275).
Copyright © 2018 by the American Academy of Pediatrics
FiNaNciaL DiscLOsUre: The authors have indicated they have no financial relationships relevant to this article to disclose.
FUNDiNG: Dr Stiemsma is supported by T32 training grant 5T32CA009142-37 from the National Cancer Institute (NCI), National Institutes of Health (NIH). Funded by the National Institues of Health (NIH).
POTeNTiaL cONFLicT OF iNTeresT: The authors have indicated they have no potential conflicts of interest to disclose.
NIH
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weight is associated with an increase in breast and colon cancer risk, 12, 13 and the underlying mechanism of this association may be related to intrauterine exposure to high levels of growth hormones.9
Early-life infections and microbial exposures were not originally associated with DOHaD but were proposed as significant environmental influences on infant immune development in the hygiene hypothesis of allergic disease.14 With the advancement of human microbiome research, a modern extension of the hygiene hypothesis has since been proposed, known as the microflora hypothesis.15 In the microflora hypothesis, it is suggested that early-life environmental exposures alter the development of the human microbiome.15 Shifts in the composition of the microbiome are thought to bias maturation of the immune system toward a hypersensitive and/or hyperinflammatory state.15 For example, the innate and adaptive branches of the immune system are both highly involved in promoting an inflammatory response. However, exposure to microbes typically evokes a T-helper 1–mediated response, which suppresses the T-helper 2 activity often associated with immune-mediated and hypersensitivity reactions.3 Discussion of the mechanisms regulating the interface between the immune system and the microbiota is beyond the scope of this review; please see Tamburini et al3 for a recent in-depth discussion on this topic.
Analogous to DOHaD, an early-life critical window of development has also been proposed for the microbiome. Transient microbial dysbiosis (unhealthy microbial state) during this time frame has been associated with long-term immune and metabolic health issues, 2 meriting its exploration within
the developmental origins field (Fig 1).
earLy-LiFe DeveLOPMeNT OF The MicrObiOMe
The human microbiota is a composite organism, composed of 10 trillion to 100 trillion microbial cells (bacteria, archaea, and microbial eukaryotes) and viruses.16, 17 To highlight the impressive functional potential of the microbiota, the genomic catalog of this super organism, the microbiome, is composed of ∼3.3 million nonredundant genes.16 Although the terms “microbiota” and “microbiome” are descriptive of the microbial composition and genomic catalog, respectively, they are used interchangeably within this research field. The following sections are devoted to delineating the initial colonization and establishment of the human bacterial microbiota in infancy, from conception through the first year of life.
Maternal-to-Fetal Microbial Transfer
Until recently, the intrauterine environment was perceived as sterile.18 However, nonpathogenic bacteria have since been detected by
molecular techniques in the amniotic fluid and placentas of healthy infants, 19, 20 suggesting a maternal-to-fetal exchange of microbes. In addition, through comparisons of the amniotic, placental, and meconium microbiotas, Collado et al21 report that the meconium microbiota of infants delivered via cesarean delivery shares ∼55% of its bacterial taxa with the placenta and amniotic fluid microbiotas. The prenatal maternal microbiome may also modulate the infant immune system. For example, gestation-only colonization with Escherichia coli HA107 was reported to modify the intestinal mucosal innate immune system and transcriptome of the offspring.22
In humans, variations in the placental microbiome composition have been associated with maternal pregnancy-related (stress and gestational diabetes) and neonatal health outcomes (birth weight, preterm birth).7, 23 – 25 The placental microbiome of infants born preterm was also reported to differ in composition according to gestational weight gain, 26 suggesting that this bacterial consortium may mediate
STIEMSMA and MICHELS2
FiGUre 1The infant microbiome is most vulnerable to environmental influences in early life. Maternal to fetal microbial transfer, mode of birth, antibiotics, and diet can alter the colonization and maturation of the early-life microbiome. These lifestyle-induced variations in microbiome composition and function can have prolonged influences on human health and may lead to the development of disease later in life.
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fetal development depending on the health status of the mother.
Isolation of bacteria from the placenta is often associated with a pathophysiological state, which threatens the health of the mother and child. Because of the lack of culture-based analyses of the placental microbiome, there is some controversy surrounding its validity.27 In addition, inclusion of appropriate controls to address background contamination is also lacking in many molecular-based studies characterizing the intrauterine microbiome.28
It is also possible that the placenta does not harbor any viable bacteria but rather is composed of phagocytosed microbial by-products or cell wall components.8, 22, 29 The lack of viable bacteria does not negate the capacity of the placental microbiome to modulate fetal development because interactions with pathogen-associated molecular patterns may still regulate cell differentiation and proliferation.8, 22, 29 In addition, upon implementation of stringent validation strategies for placental metagenomic analyses, the placental microbiome might be referenced as a biomarker for maternal and fetal health and disease. Few studies have been conducted to explore the function of the placental microbiome, 23, 25 emphasizing an opportunity for future research in this area. Analysis of microbial metabolites and the application of metatranscriptomic approaches to characterize the functional capacity of the placental microbiome will be key in defining its role in DOHaD.
vaginal birth: The First step in Postnatal Microbial colonization
Postnatal bacterial colonization of the infant begins during birth, at which time neonates are exposed to the maternal fecal and vaginal microbiotas.30 Within 24 hours of delivery, the microbiotas across various body sites (oral, skin,
meconium, etc) of cesarean delivered infants are initially populated with bacteria residing on the mother’s skin (eg, Staphylococcus spp.), whereas vaginally delivered infants are populated with typical vaginal bacteria (eg, Prevotella, Atopobium spp.).30 In a recent study, Chu et al31 suggest this finding may be specific to the neonatal gut microbiome. In their study of 81 mother and infant dyads, the microbiomes of other body sites (nares, skin, etc) from infants delivered vaginally revealed a bimodal pattern of maternal origin, populated by both the mothers’ vaginal and skin bacteria rather than by one or the other.31 However, it is suggested in both studies that the microbiotas of infants are homogeneously distributed across body sites (eg, meconium, skin, nares, etc) immediately after birth.30
Profiling of the neonatal intestinal microbiome immediately after birth and up to age 2 years suggests that birth mode can result in prolonged infant gut microbial dysbiosis.32 In a study of 43 mother and infant dyads, infants delivered via cesarean delivery exhibited increased phylogenetic diversity immediately after birth.32 However, after 1 month of age, the phylogenetic diversity of infants delivered via cesarean delivery declined below that of vaginally delivered infants.32 Chu et al31 challenge this finding slightly. In their recent study, birth mode was associated with variations in the microbiomes of the nares, skin, and oral cavity immediately after birth but not with variations in the infant meconium microbiome. Researchers of both studies do support the influence of birth mode on neonatal colonization in general; however, more research is needed to determine the influence of this early-life factor on the microbiomes of specific body sites.
Because of the health benefits associated with vaginal birth, 33 Dominguez-bello et al34 conducted
the first study aimed at recolonizing infants delivered via cesarean delivery with vaginal bacteria. After swabbing neonates with maternal vaginal fluids within 2 minutes of birth, the authors report partial restoration of the microbiota of infants delivered via cesarean delivery to that of vaginally delivered infants.34 However, the long-term health effects and composition of the infant microbiome are not yet known.34 Future analysis of these cesarean delivered infants exposed to the vaginal microbiome will be extremely valuable in determining the benefits of vaginally derived bacteria in long-term human health. In addition, the establishment of prospective human studies and animal models attempting similar colonization with vaginal bacteria among offspring delivered via cesarean delivery will be crucial in elucidating the role of vaginal microbes in the development of disease.
breastfeeding Furthers Microbiota Maturation in early Life
As the neonate grows, the homogeneous microbiome populating his or her body diverges into microbe-specific body niches.18, 31 The maturation of the total infant microbiome has been studied for the first year of life, but beyond this time point, most researchers focus specifically on the gut microbiome. Driven in large part by breastfeeding and infant diet, the human gut microbiome continues to mature until the child reaches 2 to 3 years of age, after which its composition stabilizes.35
Breastfeeding seeds the infant gut microbiome through contact with maternal areolar and breast milk microbes and provides key energy sources for many bacteria (human milk oligosaccharides).36 – 39 In a study of 107 mother and infant dyads, infants who were breastfed during the first 30 to 40 days of life
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received a mean of ∼28% of their bacteria from breast milk and ∼10% from maternal areolar skin.38 The authors also report a dose-dependent association between the infant gut microbiome composition and the proportion of daily breastfeeding.38
There is a clear compositional distinction between breastfed and formula-fed infants, with breastfed infants being populated with higher proportions of Bifidobacteria and Lactobacillus spp. and formula-fed infants being populated with a greater prevalence of clostridiales and proteobacteria.32, 40 In addition, formula-fed infants exhibit decreased diversity and bacterial richness even after the first year of life (12–24 months of age).32 In a study of 30 preterm infants, the effect of breastfeeding (versus formula feeding) was also reported to mask the influence of birth weight on the infant microbiome, highlighting breastfeeding as being potentially protective (at least with regard to the infant microbiome) against a traditional DOHaD risk factor.41 Epidemiologic evidence provides further support for the beneficial roles of breastfeeding in promoting infant health. Formula feeding has been associated with an increased risk of various hyperinflammatory and immune-mediated diseases.42, 43 In addition, researchers of a recent epidemiologic study reported that breastfeeding protects against wheezing during the first year of life among infants born to mothers with asthma.43 With the work discussed in this section, we suggest that the microbiome may be a mediator between these associations.
Gestation-associated Maternal Diet shapes the Developing infant Microbiome
Recent evidence has been used to support a significant role of gestation-associated maternal diet in shaping the microbiome of infancy. A maternal high-fat diet during
pregnancy and breastfeeding was reported to induce dysbiosis in the offspring microbiome of Japanese macaques.44 These maternal diet–induced microbial variations persisted in juvenile macaques.44 In addition, a postweaning, low-fat control diet was unable to correct this maternal high-fat diet–induced dysbiosis.44 In a prospective cohort of 26 mother and infant dyads, a high-fat maternal gestational diet was associated with distinct variations in the neonatal gut microbial composition (meconium), which persisted to 4 to 6 weeks of age.45 In a mouse model, a maternal high-fiber diet was associated with increased short-chain fatty acid (SCFA) production in the offspring.46 Emphasizing the immune-modulatory capacity of the maternal diet–driven microbiome during pregnancy, higher frequencies of thymic T-regulatory cells were also found in these pups.46 Finally, demonstrating the effect of maternal diet on the functional capacity of the infant microbiome, piglets born of sows that were fed a western diet (high-energy, high-fat, fructose-based diet) during pregnancy displayed decreased SCFA production.47 In these studies, the importance of the microbiome as a mediator linking gestation-associated maternal diet to infant health is supported, substantiating the role of the microbiome in DOHaD. Future studies may shed more light on the prolonged health and developmental effects of gestation-associated maternal diet.
antibiotics alter infant colonization and Decrease Microbiota Maturation
Perhaps unsurprisingly, pre- and postnatal antibiotic exposure is a major early-life environmental stressor on the infant microbiome. Prenatal maternal antibiotic exposure has been reported to alter the diversity of both the neonatal48 – 50 and maternal51 microbiotas. Intrapartum antibiotic exposure
was also reported to alter the infant oral microbiome composition.52 Specifically, the bacterial families streptococcaceae and gemellaceae and the order lactobacillales were decreased, whereas bacterial families in the proteobacteria phylum were enriched among infants whose mothers received intrapartum antibiotics.52 In addition, among infants whose mothers received antibiotics, the infant oral microbiome composition was further differentiated depending on whether the mother received a cocktail of antibiotics compared with if she received only 1 antibiotic.52
Postnatal antibiotic courses given to the infant in the first 3 to 9 months of life were reported to alter abundances of specific gut bacterial taxa (namely, Ruminococcus and clostridiales).32 In addition, antibiotic use in the first 6 to 12 months of life has been associated with decreased maturation of the infant microbiota.32 This suggests antibiotics may stunt the development of the microbiota if administered during this time period, which could potentially predispose infants to microbiome-associated diseases later in life.32
In epidemiologic studies, it has been suggested that antibiotic-induced dysbiosis in infancy promotes the development of many noncommunicable diseases in later childhood and adulthood (ie, obesity, asthma, inflammatory bowel disease [IBD]).53 – 56 However, these epidemiologic analyses do not address whether these diseases are causally related to early-life antibiotic use or whether they are indicative of early-life immune deficiencies or propensity for infection. Nevertheless, there are some promising animal models and prospective human cohort studies that attempt to address this quandary and provide additional support for the microbiome as a key developmental mediator in DOHaD.
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DysbiOsis-assOciaTeD NONcOMMUNicabLe Diseases PrOviDe aDDiTiONaL sUPPOrT FOr The MicrObiOMe iN DOhaD
The critical Window in early Life
As mentioned at the beginning of this review, DOHaD emphasizes a critical window of susceptibility from conception to early life in which environmental stressors most profoundly affect long-term human health. A similar critical window has emerged for the development of the microbiome. Scientists have narrowed the microbiome early-life critical window to the time period between conception and the first year of life (Fig 1).1 Though more research is needed to confirm this theory, the microbiome’s vulnerability to environmental influences appears to be time varying, more substantial earlier in life and lessening as it matures toward that of an adult (Fig 1). In the following sections, we will discuss disease-specific research (specifically, necrotizing enterocolitis [NEC], asthma and atopic disease, obesity, and neurodevelopmental disorders) that points toward this early-life critical window and further supports the role of the microbiome in DOHaD (summarized in Table 1).
Nec
In addition to the health risks associated with preterm birth, preterm infants display marked neonatal microbial dysbiosis. This dysbiosis enhances their susceptibility to disease, particularly NEC, which may be modified by exposure to antibiotics during this critical time period.57 Through analysis of existing 16S ribosomal RNA gene sequence data, the authors identified differential abundances of proteobacteria, firmicutes, and bacteroidetes, which preceded the onset of NEC.57 Gut dysbiosis characterized by similar variations in bacterial taxa was also reported to precede NEC in a study of 122 extremely
low birth weight neonates.58 The increase in proteobacteria along with increased enterocyte Toll-like receptor 4 activity in these neonates with NEC suggest a hyperinflammatory response to a dysbiotic microbiome.59 However, a recent study was conducted in which researchers identified uropathogenic E coli colonization as a significant risk marker for NEC.59 This suggests an invasive microbial species may be synergistic in driving this dysbiosis-associated disorder. In addition, infants treated with antibiotics for 7–14 days (regardless of NEC status) were enriched for E coli relative to infants treated with antibiotics for 0–6 days.59 This supports a role of neonatal antibiotic-induced dysbiosis in NEC, which may enhance the vulnerability of the neonatal gut microbiome to pathogen invasion. Because of the apparent link between microbial dysbiosis and NEC, probiotic supplementation of preterm neonates is becoming a prominent research area for NEC prevention and treatment.109, 110 In a systematic review and meta-analysis of 26 probiotic intervention studies for NEC, it is suggested that probiotic intervention does prevent NEC.60 However, the particular strains to be used and the effects on high-risk populations (extremely low birth weight infants) requires further study.60 Nonetheless, it may be possible in the near future to optimize the neonatal microbiome to combat development of this disease and prevent associated infant mortality.
asthma and atopic Disease
NEC studies highlight the dynamic relation between the gut microbiome and the developing immune system. However, although the neonatal immune system is on high alert for pathogenic invaders, researchers who have conducted studies of asthma and atopic diseases (food allergies, atopic dermatitis, etc)
suggest its development is strongly influenced by commensal bacteria.
In a recent assessment of the microbiome in asthma development, a more substantial role of the maternal microbiota in fetal development is supported than what was previously thought. In a mouse model of allergic airway inflammation, high-fiber (which has been reported to stimulate production of SCFAs by the microbiome111) or acetate (a SCFA) feeding of pregnant mice modulated the maternal microbiota and protected the subsequent offspring from developing allergic airway disease.73 The authors of this study also provided preliminary evidence of this association in humans; high acetate levels in the serum of pregnant individuals correlated with reduced general practitioner visits for coughing and wheezing in the offspring during the first 12 months of life.73
Postnatal early-life dysbiosis in both the human gut2, 4, 5, 70 and airway78 microbiomes is also associated with asthma and atopic disease development in children. This dysbiosis is characterized by shifts in the prevalence of specific bacterial4, 5 and fungal taxa, 70 which are transient and most prominent between birth and 3 months of life. The majority of human studies in this research area reveal only correlative evidence to link the early-life dysbiosis with asthma. However, Arrieta et al4 provide preliminary evidence of causality related to early-life transient dysbiosis and immune development in the context of asthma. In this study, inoculation of previously germ-free (GF) mice with 4 bacterial species, which were reduced in infants at high risk of asthma, ameliorated allergic airway inflammation in these mice.4
There is also evidence to support a role of the early-life microbiome in food allergies. Azad et al74 report a decrease in microbial diversity at
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STIEMSMA and MICHELS6
TabL
e 1
Stud
ies
in W
hich
Res
earc
hers
Rel
ate
the
Earl
y-Li
fe M
icro
biom
e W
ith H
ealth
Out
com
es in
Lat
er C
hild
hood
and
Adu
lthoo
d
Rese
arch
Obj
ectiv
eSt
udy
Popu
latio
n or
An
imal
Mod
elEa
rly-
Life
Fac
tors
and
Ti
min
g of
Exp
osur
eTi
min
g of
Mic
robi
ome
Anal
ysis
or
Inte
rven
tion
Heal
th O
utco
me
and
Tim
ing
of A
sses
smen
tSu
mm
ary
of F
indi
ngs
Ref.
No.
NEC
To
ass
ess
mic
robi
al
dysb
iosi
s be
fore
NEC
in
a sy
stem
atic
rev
iew
and
m
eta-
anal
ysis
Syst
emat
ic r
evie
w
and
met
a-an
alys
is
of 1
4 hu
man
feca
l m
icro
biom
e st
udie
s of
NEC
None
Vari
atio
ns in
the
mic
robi
ome
befo
re N
EC
deve
lopm
ent
NEC
at ∼
30 w
k po
stco
ncep
tion
Incr
ease
d pr
oteo
bact
eria
and
dec
reas
ed
firm
icut
es a
nd b
acte
roid
etes
pre
cede
d NE
C on
set.
Antib
iotic
s, d
iet,
and
mod
e of
del
iver
y do
con
trib
ute
to m
icro
bial
dy
sbio
sis
asso
ciat
ed w
ith N
EC. H
owev
er,
caus
ality
rel
ated
to th
ese
fact
ors
cann
ot b
e de
term
ined
57
To
det
erm
ine
if 1
or m
ore
gut b
acte
rial
taxa
diff
er
betw
een
case
s of
NEC
and
co
ntro
ls
Pros
pect
ive
hum
an c
ohor
t an
alys
is (
prim
ary
coho
rt, n
= 1
22;
seco
ndar
y co
hort
s,
n =
44)
None
Vari
atio
ns in
the
mic
robi
ome
befo
re N
EC
deve
lopm
ent
NEC
in v
ery
low
bir
th w
t in
fant
sIn
crea
ses
in g
amm
apro
teob
acte
ria
and
decr
ease
s in
neg
ativ
icut
es a
nd c
lost
ridi
a-ne
gativ
icut
es c
lass
es o
ver
time
prec
eded
NE
C de
velo
pmen
t
58
To
enh
ance
str
ain-
leve
l re
solu
tion
of N
EC-
asso
ciat
ed p
atho
gens
by
usi
ng d
eep
shot
gun
met
agen
omic
s se
quen
cing
Pros
pect
ive
hum
an c
ohor
t an
alys
is (
n =
166)
None
Vari
atio
ns in
the
mic
robi
ome
befo
re N
EC
deve
lopm
ent
NEC
in in
fanc
yVa
riat
ions
in th
e m
icro
biom
e w
ere
dete
cted
be
fore
NEC
dev
elop
men
t. Ho
wev
er, a
t 17–
22
d po
stpa
rtum
, inf
ants
with
hig
h an
tibio
tic
trea
tmen
t wer
e en
rich
ed fo
r E
coli.
The
gr
oup
late
r id
entifi
ed u
ropa
thog
enic
E
coli
as a
maj
or r
isk
fact
or fo
r NE
C an
d as
soci
ated
dea
th
59
To
com
pare
the
effic
acy
and
safe
ty o
f ent
eral
pr
obio
tic a
dmin
istr
atio
n in
pre
vent
ing
NEC
Syst
emat
ic r
evie
w a
nd
met
a-an
alys
is o
f 24
rand
omiz
ed o
r qu
asi-
rand
omiz
ed c
ontr
olle
d tr
ials
in h
uman
s
None
Ente
ral p
robi
otic
su
pple
men
tatio
n be
fore
NE
C de
velo
pmen
t
Stag
e II
and
stag
e III
NEC
in
infa
ncy
Ente
ral p
robi
otic
sup
plem
enta
tion
sign
ifica
ntly
red
uced
the
inci
denc
e of
NEC
an
d m
orta
lity
in in
fant
s
60
To
ass
ess
the
inte
stin
al
mic
robi
ota
com
posi
tion
befo
re N
EC d
evel
opm
ent
in in
fant
s w
ho d
evel
oped
NE
C an
d co
ntro
ls
Pros
pect
ive
hum
an c
ohor
t an
alys
is (
n =
38)
None
Vari
atio
ns in
the
mic
robi
ome
befo
re N
EC
deve
lopm
ent
NEC
in in
fanc
yAn
ave
rage
of 7
sam
ples
wer
e co
llect
ed
per
subj
ect a
nd th
e te
mpo
ral c
hang
es
in m
icro
biom
e co
mpo
sitio
n w
ere
asse
ssed
. Thr
ough
out e
arly
life
, bef
ore
the
deve
lopm
ent o
f NEC
, diff
eren
t mic
robi
al
popu
latio
ns d
omin
ate
the
gut a
nd a
re
asso
ciat
ed w
ith N
EC d
evel
opm
ent.
In
addi
tion,
the
mic
robi
ome
com
posi
tiona
l pr
ogre
ssio
n ap
pear
s to
be
asso
ciat
ed w
ith
the
timin
g of
NEC
ons
et
61
To
iden
tify
mic
robi
al a
nd
met
abol
ic b
iom
arke
rs
of N
EC
Nest
ed c
ase-
cont
rol
desi
gn (
n =
35)
None
Vari
atio
ns in
the
mic
robi
ome
befo
re N
EC
deve
lopm
ent
NEC
in in
fanc
yLo
wer
α d
iver
sity
4–9
d p
ostb
irth
was
as
soci
ated
with
NEC
dev
elop
men
t. M
icro
biom
es o
f sub
ject
s te
nded
to c
lust
er
acco
rdin
g to
NEC
sta
tus.
The
se m
icro
bial
va
riat
ions
wer
e as
soci
ated
with
shi
fts
in
urin
e m
etab
olite
s, n
amel
y al
anin
e an
d hi
stid
ine
62
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PEDIATRICS Volume 141, number 4, April 2018 7
Rese
arch
Obj
ectiv
eSt
udy
Popu
latio
n or
An
imal
Mod
elEa
rly-
Life
Fac
tors
and
Ti
min
g of
Exp
osur
eTi
min
g of
Mic
robi
ome
Anal
ysis
or
Inte
rven
tion
Heal
th O
utco
me
and
Tim
ing
of A
sses
smen
tSu
mm
ary
of F
indi
ngs
Ref.
No.
To
det
erm
ine
if gu
t m
icro
biom
e co
mpo
sitio
n ca
n be
use
d to
pre
dict
NE
C se
veri
ty
Pros
pect
ive
hum
an c
ohor
t an
alys
is (
n =
30)
None
Vari
atio
ns in
the
mic
robi
ome
befo
re N
EC
deve
lopm
ent
NEC
in in
fanc
yVa
riat
ions
in th
e m
icro
biom
e w
ere
not
asso
ciat
ed w
ith N
EC s
ever
ity. T
here
wer
e al
so n
o di
ffere
nces
in th
e m
icro
biom
e po
st-
NEC
com
pare
d w
ith c
ontr
ols
63
To
ass
ess
whe
ther
fe
cal m
icro
biot
a tr
ansp
lant
atio
n is
an
effe
ctiv
e tr
eatm
ent o
f NEC
Wild
-type
and
Grx
1−/−
m
ouse
mod
els
of N
ECNo
neFe
cal m
icro
biot
a tr
ansp
lant
fr
om 1
to 4
d p
ostb
irth
NEC
5 d
post
birt
hFe
cal m
icro
biot
a tr
ansp
lant
from
hea
lthy
6–8-
wk-
old
mic
e to
mou
se p
ups
cond
ition
ed
for
NEC
redu
ced
NEC
inci
denc
e an
d se
veri
ty c
ompa
red
with
con
trol
s. T
his
was
de
pend
ent o
n Gr
x1. T
he m
echa
nism
of
actio
n is
pot
entia
lly th
roug
h TL
R-m
edia
ted
infla
mm
atio
n an
d gu
t per
mea
bilit
y
64
To
det
erm
ine
if pa
tient
s at
ris
k fo
r NE
C ca
n be
iden
tified
by
thei
r m
econ
ium
and
ear
ly
post
nata
l mic
robi
ota
Pros
pect
ive
hum
an c
ohor
t an
alys
is (
n =
33)
Earl
y en
tera
l fee
ding
and
br
east
milk
Vari
atio
ns in
mec
oniu
m
mic
robi
ome
and
neon
atal
m
icro
biom
e be
fore
NEC
NEC
in in
fanc
yCl
ostr
idiu
m p
erfr
inge
ns a
nd B
acte
roid
es
dore
i wer
e in
crea
sed
in th
e m
econ
ium
of
infa
nts
who
dev
elop
ed N
EC. C
per
frin
gens
ab
unda
nce
pers
iste
d in
neo
nata
l sto
ol
sam
ples
. The
am
ount
of b
reas
t milk
be
fore
NEC
and
ear
lier
ente
ral f
eedi
ng
was
neg
ativ
ely
asso
ciat
ed w
ith N
EC
and
asso
ciat
ed w
ith in
crea
sed
lact
ate-
prod
ucin
g ba
cilli
65
To
com
pare
ent
eral
ver
sus
pare
nter
al a
ntib
iotic
s in
pre
vent
ing
form
ula-
indu
ced
NEC
lesi
ons
in
pigs
Pigl
et m
odel
of N
ECAn
tibio
tic-in
duce
dEn
tera
l and
par
ente
ral
antib
iotic
trea
tmen
t (fo
r 5
d po
st b
irth
)
NEC
in p
rete
rm p
igle
tsEn
tera
l ant
ibio
tics
prev
ente
d NE
C le
sion
s,
whe
reas
lesi
ons
in p
igle
ts th
at w
ere
trea
ted
with
par
ente
ral a
ntib
iotic
s w
ere
incr
ease
d. E
nter
al a
ntib
iotic
s de
crea
sed
bact
eria
l loa
d an
d ab
unda
nces
of
Gram
-pos
itive
bac
teri
a in
the
inte
stin
e.
It is
sug
gest
ed th
at d
elay
ed c
olon
izat
ion
(par
ticul
arly
with
Gra
m-p
ositi
ve b
acte
ria)
m
ay p
reve
nt N
EC. H
owev
er, a
lthou
gh
mic
robi
ome
vari
atio
ns c
orre
late
with
NEC
, th
ey d
o no
t nec
essa
rily
pre
cede
NEC
66
To
det
erm
ine
if to
tal
pare
nter
al n
utri
tion,
be
fore
the
star
t of
ente
ral f
eedi
ng, c
an
prev
ent N
EC-a
ssoc
iate
d gu
t dys
func
tion
and
infla
mm
atio
n
Pigl
et m
odel
of N
ECEn
tera
l and
tota
l par
ente
ral
nutr
ition
Vari
atio
ns in
the
mic
robi
ome
afte
r fe
edin
g m
etho
ds
NEC
in p
rete
rm p
igle
tsEn
tera
l fee
ding
incr
ease
d m
icro
bial
div
ersi
ty
and
the
abun
danc
e of
Clo
stri
dium
spe
cies
. De
nsity
of C
per
frin
gens
was
ass
ocia
ted
with
NEC
sev
erity
. Mic
robi
ome
vari
atio
ns
corr
elat
e w
ith N
EC b
ut d
o no
t nec
essa
rily
pr
eced
e NE
C
67
To
iden
tify
mic
robi
al p
rofil
es
befo
re N
EC d
iagn
osis
Pros
pect
ive
hum
an c
ohor
t an
alys
is (
n =
369)
None
Vari
atio
ns in
the
mic
robi
ome
befo
re N
EC
diag
nosi
s
NEC
in in
fanc
yId
entifi
catio
n of
2 fe
cal m
icro
biot
a pr
ofile
s as
soci
ated
with
NEC
dev
elop
men
t (C
perf
ring
ens
type
A d
omin
ant a
nd K
lebs
iella
do
min
ant)
68
TabL
e 1
Cont
inue
d
by guest on August 10, 2020www.aappublications.org/newsDownloaded from
STIEMSMA and MICHELS8
Rese
arch
Obj
ectiv
eSt
udy
Popu
latio
n or
An
imal
Mod
elEa
rly-
Life
Fac
tors
and
Ti
min
g of
Exp
osur
eTi
min
g of
Mic
robi
ome
Anal
ysis
or
Inte
rven
tion
Heal
th O
utco
me
and
Tim
ing
of A
sses
smen
tSu
mm
ary
of F
indi
ngs
Ref.
No.
To
cha
ract
eriz
e ep
igen
ome
to m
icro
biom
e cr
osst
alk
at c
ritic
al n
eona
tal s
tage
s of
dev
elop
men
t
Tiss
ue-b
ased
(im
mat
ure
ente
rocy
tes)
and
m
ouse
mod
els
(dex
amet
haso
ne o
r 5-
azac
ytid
ine
to in
duce
ep
igen
etic
cha
nges
)
Pren
atal
dex
amet
haso
ne o
r 5-
azac
ytid
ine
trea
tmen
tM
icro
biom
e to
epi
geno
me
cros
stal
k in
per
inat
al li
feTL
R an
d tig
ht ju
nctio
n-si
gnal
ing
path
way
s in
of
fspr
ing
Pren
atal
dex
amet
haso
ne a
nd a
zacy
tidin
e tr
eatm
ent a
lters
DNA
met
hyla
tion
of ti
ght
junc
tion
and
TLR
gene
s an
d as
soci
ated
in
flam
mat
ory
path
way
s in
fetu
ses
and
guts
of 2
-wk-
old
offs
prin
g. B
oth
pren
atal
ex
posu
res
also
alte
red
the
offs
prin
g m
icro
biom
e. A
zacy
tidin
e tr
eatm
ent i
nduc
es
glob
al d
emet
hyla
tion,
sug
gest
ing
that
the
pre-
and
neo
nata
l epi
geno
me
influ
ence
s ne
onat
al m
icro
bial
col
oniz
atio
n
69
Asth
ma
and
atop
ic d
isea
se
To a
naly
ze th
e m
icro
biom
e of
infa
nts
befo
re a
topi
c di
seas
e de
velo
pmen
t at 1
y
of a
ge
Nest
ed c
ase-
cont
rol
desi
gn (
n =
319)
and
Ov
albu
min
-cha
lleng
ed
mou
se m
odel
s of
as
thm
a
None
Vari
atio
ns in
the
3-m
o-ol
d gu
t mic
robi
ome
Atop
y an
d w
heez
ing
at 1
y
of a
geFo
ur b
acte
rial
taxa
(Fa
ecal
ibac
teri
um,
Lach
nosp
ira,
Vei
llone
lla, a
nd R
othi
a) w
ere
decr
ease
d am
ong
infa
nts
with
ato
py a
nd
whe
ezin
g at
1 y
of a
ge. S
uppl
emen
tatio
n of
as
thm
a-in
duce
d m
ice
with
thes
e 4
bact
eria
am
elio
rate
d ai
rway
infla
mm
atio
n
4
To
ana
lyze
the
mic
robi
ota
of in
fant
s be
fore
ast
hma
deve
lopm
ent b
y 4
y of
age
Nest
ed c
ase-
cont
rol
desi
gn (
n =
319)
None
Vari
atio
ns in
the
3-m
o-ol
d gu
t mic
robi
ome
Asth
ma
by 4
y o
f age
Decr
ease
d La
chno
spir
a/Cl
ostr
idiu
m n
eona
tale
ra
tio a
t 3 m
o of
age
was
ass
ocia
ted
with
as
thm
a by
4 y
of a
ge
5
To
cha
ract
eriz
e th
e ba
cter
ial
and
fung
al m
icro
biom
es
in n
eona
tes
befo
re
asth
ma
deve
lopm
ent a
t 4
y of
age
Pros
pect
ive
hum
an c
ohor
t an
alys
is (
n =
168)
None
Vari
atio
ns in
gut
m
icro
biom
e 35
d
post
birt
h
Asth
ma
at 4
y o
f age
Vari
atio
ns in
bac
teri
al a
nd fu
ngal
taxa
at 3
5 d
post
birt
h as
soci
ated
with
hig
hest
rel
ativ
e ri
sk o
f ast
hma.
Ste
rile
feca
l wat
er fr
om
the
high
est-r
isk
grou
p in
duce
s CD
4+ T-
cell
dysf
unct
ion
70
To
cha
ract
eriz
e th
e ea
rly-
life
criti
cal
win
dow
ass
ocia
ted
with
ex
acer
bate
d al
lerg
ic
airw
ays
resp
onse
s in
m
ice
Oval
bum
in-c
halle
nged
m
ouse
mod
elAn
tibio
tic-in
duce
dPe
rina
tal (
in u
tero
and
th
roug
h w
eani
ng)
Asth
ma
indu
ced
late
r in
life
Peri
nata
l van
com
ycin
exp
osur
e pr
omot
es
expa
nsio
n of
firm
icut
es a
nd e
xace
rbat
es
airw
ay in
flam
mat
ion
in m
ice
71
To
ana
lyze
the
effe
cts
of
peri
nata
l ant
ibio
tic
trea
tmen
t on
deve
lopm
ent
of h
yper
sens
itivi
ty
pneu
mon
itis
Th1/
Th17
-med
iate
d m
ouse
m
odel
Antib
iotic
-indu
ced
Peri
nata
l ant
ibio
tic
expo
sure
Hype
rsen
sitiv
ity
pneu
mon
itis
in
adul
thoo
d
Peri
nata
l str
epto
myc
in p
rom
otes
exp
ansi
on
of b
acte
roid
etes
and
res
ults
in e
xagg
erat
ed
hype
rsen
sitiv
ity p
neum
oniti
s
72
To
cha
ract
eriz
e th
e ce
llula
r m
echa
nism
s as
soci
ated
w
ith d
iet o
r m
icro
biot
a-m
edia
ted
imm
une
regu
latio
n
Wild
-type
, Gpr
43−
/−, a
nd
HDAC
9−/−
hou
se d
ust
mite
mou
se m
odel
s of
AA
D; n
este
d ca
se-
cont
rol d
esig
n (n
= 4
0)
Mat
erna
l ace
tate
or
high
-fib
er d
iet;
mat
erna
l se
rum
leve
ls o
f ace
tate
Pren
atal
ant
ibio
tic
expo
sure
; pre
nata
l ac
etat
e ex
posu
re
AAD
indu
ced
in a
dulth
ood;
co
ughi
ng a
nd w
heez
e by
1
y of
age
High
-fibe
r di
et o
r ac
etat
e fe
edin
g of
dam
s in
pre
gnan
cy p
reve
nts
robu
st A
AD in
ad
ult o
ffspr
ing.
Mat
erna
l ser
um le
vels
of
acet
ate
wer
e in
vers
ely
asso
ciat
ed w
ith
gene
ral p
ract
ition
er v
isits
for
coug
hing
and
w
heez
ing
in th
e fir
st 1
2 m
o of
life
73
TabL
e 1
Cont
inue
d
by guest on August 10, 2020www.aappublications.org/newsDownloaded from
PEDIATRICS Volume 141, number 4, April 2018 9
Rese
arch
Obj
ectiv
eSt
udy
Popu
latio
n or
An
imal
Mod
elEa
rly-
Life
Fac
tors
and
Ti
min
g of
Exp
osur
eTi
min
g of
Mic
robi
ome
Anal
ysis
or
Inte
rven
tion
Heal
th O
utco
me
and
Tim
ing
of A
sses
smen
tSu
mm
ary
of F
indi
ngs
Ref.
No.
To
ana
lyze
the
infa
nt
mic
robi
ota
in a
ssoc
iatio
n w
ith fo
od s
ensi
tizat
ion
Nest
ed c
ase-
cont
rol
desi
gn (
n =
166)
None
Vari
atio
ns in
the
gut
mic
robi
ome
at 3
mo
of
age
Food
sen
sitiv
ity a
t 1 y
of
age
Decr
ease
d α
dive
rsity
and
incr
ease
d en
tero
bact
eria
ceae
/bac
tero
idac
eae
ratio
as
soci
ated
with
food
sen
sitiz
atio
n to
at
leas
t 1 fo
od a
llerg
en (
milk
, egg
, pea
nut,
soy)
at 1
y o
f age
.
74
To
ana
lyze
the
earl
y-lif
e m
icro
biot
a in
ass
ocia
tion
with
res
olut
ion
of c
ow’s
m
ilk a
llerg
y
Nest
ed c
ase-
cont
rol
desi
gn (
n =
226
subj
ects
with
milk
al
lerg
y)
None
Vari
atio
ns in
the
gut
mic
robi
ome
at 3
–6 m
o of
age
Milk
alle
rgy
reso
lutio
n by
8
y of
age
Firm
icut
es a
nd c
lost
ridi
a w
ere
enri
ched
in
mic
robi
omes
of s
ubje
cts
who
se m
ilk
alle
rgy
reso
lved
by
8 y
of a
ge. B
acte
roid
etes
an
d En
tero
bact
er w
ere
enri
ched
am
ong
thos
e w
hose
milk
alle
rgy
did
not r
esol
ve b
y 8
y of
age
75
To
inve
stig
ate
age-
depe
nden
t m
icro
bial
mod
ulat
ion
of
iNKT
s in
mou
se m
odel
s of
IB
D an
d as
thm
a
Oval
bum
in-c
halle
nged
m
ouse
mod
elNo
neEx
posu
re to
mat
erna
l gut
m
icro
biom
e at
bir
thAs
thm
a in
duce
d la
ter
in li
feNe
onat
al e
xpos
ure
to a
con
vent
iona
l m
icro
biot
a (c
ompa
red
with
GF
cond
ition
s)
incr
ease
d iN
KT in
the
lung
s an
d pr
otec
ted
agai
nst a
llerg
ic a
sthm
a in
duce
d in
ad
ulth
ood.
In a
dditi
on, h
ypom
ethy
latio
n of
CXC
L16,
dri
ven
by th
e m
icro
biom
e, w
as
asso
ciat
ed w
ith iN
KT in
duct
ion,
impl
icat
ing
the
mic
robi
ome
in g
ene
regu
latio
n
76
To
ana
lyze
the
role
of t
he
earl
y-lif
e lu
ng m
icro
biot
a in
alle
rgen
-indu
ced
airw
ay
infla
mm
atio
n
Mou
se m
odel
of h
ouse
du
st m
ite–i
nduc
ed
airw
ay in
flam
mat
ion
None
2-w
k w
indo
w o
f su
scep
tibili
ty (
lung
m
icro
biom
e)
Asth
ma
indu
ced
late
r in
life
Vari
atio
ns in
the
lung
mic
robi
ome
(shi
ft fr
om
gam
map
rote
obac
teri
a an
d fir
mic
utes
to
bact
eroi
dete
s) a
ssoc
iate
d w
ith d
ecre
ased
ae
roal
lerg
en r
espo
nsiv
enes
s an
d in
crea
sed
Helio
s− T-
regu
lato
ry c
ells
. Thi
s is
med
iate
d by
PD-
L1. B
lock
age
of P
D-L1
in th
e fir
st 2
wk
of li
fe r
esul
ts in
enh
ance
d al
lerg
ic a
irw
ay
infla
mm
atio
n
77
To
ana
lyze
the
naso
phar
ynge
al
mic
robi
ome
in in
fanc
y in
ass
ocia
tion
with
re
spir
ator
y di
seas
e la
ter
in li
fe
Pros
pect
ive
hum
an c
ohor
t st
udy
(n =
234
)No
neVa
riat
ions
in th
e na
soph
aryn
geal
m
icro
biom
e 7–
9 w
k po
stbi
rth
Chro
nic
whe
ezin
g at
5–1
0 y
of a
geCh
ildre
n w
ho d
evel
oped
chr
onic
whe
ezin
g at
5–
7 y
of a
ge a
nd w
ere
atop
ic b
y ag
e 2
wer
e tw
ice
as li
kely
to h
ave
been
col
oniz
ed w
ith
asym
ptom
atic
Str
epto
cocc
us
78
To
det
erm
ine
if va
riat
ions
in
the
skin
mic
robi
ome
in
earl
y lif
e ar
e as
soci
ated
w
ith a
topi
c de
rmat
itis
Nest
ed c
ase-
cont
rol
desi
gn (
n =
20)
None
Vari
atio
ns in
the
skin
(a
ntec
ubita
l fos
sa)
mic
robi
ome
at 2
mo
of
age
Atop
ic d
erm
atiti
s at
1 y
of
age
Colo
niza
tion
of a
ntec
ubita
l fos
sa a
t 2 m
o of
ag
e w
ith S
taph
yloc
occu
s w
as a
ssoc
iate
d w
ith d
ecre
ased
inci
denc
e of
ato
pic
derm
atiti
s at
1 y
of a
ge
79
To
ana
lyze
ass
ocia
tions
be
twee
n ne
onat
al g
ut
Bifid
obac
teri
um s
peci
es
and
ecze
ma
or a
topy
de
velo
pmen
t in
the
first
ye
ar o
f life
Nest
ed c
ase-
cont
rol
desi
gn (
n =
117)
Colo
niza
tion
patt
erns
in
fluen
ced
by h
ouse
hold
pe
ts, n
umbe
r of
sib
lings
, an
d m
ater
nal a
llerg
ic
stat
us
Vari
atio
ns in
Bi
fidob
acte
rium
spe
cies
at
1 w
k an
d 3
mo
of a
ge
Atop
ic d
erm
atiti
s at
1 y
of
age
Vari
atio
ns in
Bifi
doba
cter
ium
spe
cies
at 1
w
k an
d 3
mo
of a
ge w
ere
asso
ciat
ed w
ith
risk
of e
czem
a at
1 y
of a
ge. H
owev
er, t
he
mic
robi
ome
was
not
ana
lyze
d af
ter
3 m
o of
age
80
TabL
e 1
Cont
inue
d
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Rese
arch
Obj
ectiv
eSt
udy
Popu
latio
n or
An
imal
Mod
elEa
rly-
Life
Fac
tors
and
Ti
min
g of
Exp
osur
eTi
min
g of
Mic
robi
ome
Anal
ysis
or
Inte
rven
tion
Heal
th O
utco
me
and
Tim
ing
of A
sses
smen
tSu
mm
ary
of F
indi
ngs
Ref.
No.
To
ana
lyze
ass
ocia
tions
be
twee
n pr
opor
tions
of
IgA
coat
ing
and
bact
eria
bo
und
to Ig
A in
infa
ncy
and
alle
rgy
deve
lopm
ent
late
r in
life
Nest
ed c
ase-
cont
rol
desi
gn (
n =
48)
None
IgA
and
tota
l bac
teri
al lo
ad
mea
sure
d at
1 w
k an
d 1
y of
age
Asth
ma,
alle
rgic
rh
inoc
onju
nctiv
itis,
al
lerg
ic u
rtic
aria
, and
ec
zem
a by
7 y
of a
ge
At 1
2 m
o of
age
, chi
ldre
n w
ith a
llerg
ic d
isea
se
(par
ticul
arly
ast
hma)
dis
play
ed a
low
er
prop
ortio
n of
IgA
boun
d to
feca
l bac
teri
a.
IgA
reco
gniti
on p
atte
rns
for
the
mic
robi
ota
vari
ed b
etw
een
child
ren
with
alle
rgie
s an
d he
alth
y ch
ildre
n at
1 w
k of
age
81
To
ana
lyze
feca
l mic
robi
al
dive
rsity
and
bac
teri
al
abun
danc
es in
the
first
ye
ar o
f life
in a
ssoc
iatio
n w
ith a
sthm
a an
d al
lerg
ies
late
r in
life
Nest
ed c
ase-
cont
rol
desi
gn (
n =
47)
None
Mic
robi
al d
iver
sity
at 1
mo
of a
geAs
thm
a at
7 y
of a
geCh
ildre
n w
ith a
sthm
a di
spla
yed
low
er o
vera
ll m
icro
bial
div
ersi
ty th
an c
hild
ren
with
out
asth
ma
82
To
inve
stig
ate
the
infa
nt
inte
stin
al m
icro
biot
a co
mpo
sitio
n in
as
soci
atio
n w
ith m
ater
nal
pren
atal
str
ess
and
infa
nt
heal
th
Nest
ed c
ase-
cont
rol
desi
gn (
n =
56)
Pren
atal
str
ess
Vari
atio
ns in
the
mic
robi
ome
at p
ostn
atal
da
ys 7
, 14,
28,
80,
and
110
GI s
ympt
oms
and
alle
rgic
re
spon
se b
y 3
mo
of a
geIn
fant
s ex
pose
d to
pre
nata
l str
ess
disp
laye
d m
ore
GI s
ympt
oms
(38%
com
pare
d w
ith 2
2%)
and
alle
rgic
rea
ctio
ns (
43%
co
mpa
red
with
0%
), w
hich
wer
e as
soci
ated
w
ith v
aria
tions
in th
e m
icro
biom
e. T
his
mic
robi
ome
was
cha
ract
eriz
ed b
y le
ss
lact
ic a
cid
bact
eria
and
Akk
erm
ansi
a an
d gr
eate
r Es
cher
ichi
a, E
nter
obac
ter,
and
Se
rrat
ia
83
Obes
ity a
nd m
etab
olis
m
To a
naly
ze if
the
earl
y-lif
e m
icro
biot
a co
mpo
sitio
n is
as
soci
ated
with
chi
ldho
od
BMI a
nd if
ant
ibio
tic u
se
mod
ifies
this
ass
ocia
tion
Nest
ed c
ase-
cont
rol
desi
gn fr
om 2
coh
orts
(B
ibo
coho
rt, n
= 8
7;
Flor
a co
hort
, n =
75)
Antib
iotic
trea
tmen
tVa
riat
ions
in th
e gu
t m
icro
biom
e at
3 m
o of
ag
e
BMI a
t 5–6
yIn
the
3-m
o-ol
d m
icro
biom
e, r
elat
ive
abun
danc
e of
str
epto
cocc
i was
pos
itive
ly
asso
ciat
ed w
ith B
MI a
t 5–6
y o
f age
, and
re
lativ
e ab
unda
nce
of b
ifido
bact
eria
was
ne
gativ
ely
asso
ciat
ed w
ith B
MI a
t 5–6
y
of a
ge. A
mon
g ch
ildre
n w
ith a
his
tory
of
mul
tiple
ant
ibio
tic c
ours
es, t
he fi
rmic
utes
ph
ylum
was
sig
nific
antly
ass
ocia
ted
with
BM
I. Ho
wev
er, m
icro
biom
e co
mpo
sitio
n w
as
not m
easu
red
at a
ny o
ther
tim
e po
int
84
To
ana
lyze
the
impa
ct o
f di
et o
n th
e ea
rly-
life
mic
robi
ome
in a
pri
mat
e m
odel
Prim
ate
mod
el (
high
-fat
vers
us s
tand
ard
diet
)M
ater
nal h
igh-
fat d
iet
duri
ng p
regn
ancy
and
br
east
feed
ing
Vari
atio
ns in
the
offs
prin
g m
icro
biom
e co
mpo
sitio
nSh
ifts
in m
icro
bial
m
etab
olic
pat
hway
sIn
this
stu
dy, a
link
to a
spe
cific
hea
lth
outc
ome
was
not
est
ablis
hed.
How
ever
, a
mat
erna
l hig
h-fa
t die
t did
alte
r th
e m
icro
biom
e co
mpo
sitio
n of
offs
prin
g m
acaq
ues,
whi
ch p
ersi
sted
in ju
veni
le
mac
aque
s. O
ffspr
ing
disp
laye
d al
tere
d m
etab
olic
pat
hway
s on
the
basi
s of
m
ater
nal d
iet.
Addi
tiona
lly, t
hese
func
tiona
l pa
thw
ays
(am
ino
acid
, car
bohy
drat
e,
and
lipid
met
abol
ism
) co
rrel
ated
with
ab
unda
nces
of s
peci
fic g
ut b
acte
ria
44
TabL
e 1
Cont
inue
d
by guest on August 10, 2020www.aappublications.org/newsDownloaded from
PEDIATRICS Volume 141, number 4, April 2018 11
Rese
arch
Obj
ectiv
eSt
udy
Popu
latio
n or
An
imal
Mod
elEa
rly-
Life
Fac
tors
and
Ti
min
g of
Exp
osur
eTi
min
g of
Mic
robi
ome
Anal
ysis
or
Inte
rven
tion
Heal
th O
utco
me
and
Tim
ing
of A
sses
smen
tSu
mm
ary
of F
indi
ngs
Ref.
No.
To
det
erm
ine
if th
e pl
acen
tal
mic
robi
ome
vari
es in
as
soci
atio
n w
ith b
irth
wt
Pros
pect
ive
hum
an c
ohor
t an
alys
is
(n =
24)
None
Vari
atio
ns in
the
plac
enta
l m
icro
biom
e co
mpo
sitio
nBi
rth
wt
Low
bir
th w
t inf
ants
dis
play
ed lo
wer
gut
m
icro
biom
e ri
chne
ss a
nd v
aria
tions
in
the
abun
danc
es o
f spe
cific
bac
teri
al ta
xa
com
pare
d w
ith n
orm
al b
irth
wt i
nfan
ts.
Lact
obac
illus
per
cent
age
was
pos
itive
ly
corr
elat
ed w
ith b
irth
wt
24
To
ana
lyze
the
effe
ct o
f ea
rly-
life
mic
robi
al
pert
urba
tion
with
an
tibio
tic tr
eatm
ent o
n ho
st m
etab
olis
m a
nd
adip
osity
Mou
se m
odel
(hi
gh-fa
t ve
rsus
sta
ndar
d di
et)
Antib
iotic
-indu
ced
LDP
expo
sure
from
bir
th
thro
ugh
wea
ning
Body
com
posi
tion
in
adul
thoo
dCo
mpa
red
with
con
trol
s an
d m
ice
expo
sed
to
long
-term
LDP
, mic
e ex
pose
d to
LDP
for
4 or
8
wk
afte
r bi
rth
disp
laye
d el
evat
ed c
alor
ic
inta
ke a
nd fa
ster
tota
l mas
s an
d fa
t mas
s ac
cum
ulat
ion.
The
aut
hors
als
o re
port
th
at th
e pe
nici
llin-
sele
cted
mic
robi
ota
can
indu
ce m
etab
olic
cha
nges
whe
n tr
ansf
erre
d to
GF
mic
e
6
To
bet
ter
unde
rsta
nd h
ow
earl
y-lif
e an
tibio
tic u
se
alte
rs th
e gu
t mic
robi
ome
com
posi
tion
and
met
abol
ic d
evel
opm
ent
Mou
se m
odel
(hi
gh fa
t ve
rsus
sta
ndar
d di
et)
Antib
iotic
-indu
ced
Puls
ed a
ntib
iotic
trea
tmen
t co
mpl
eted
sho
rtly
aft
er
wea
ning
Body
com
posi
tion
from
3–
6 w
kEa
rly-
life
puls
ed a
ntib
iotic
trea
tmen
t ac
cele
rate
s to
tal m
ass
and
bone
gro
wth
. Th
e au
thor
s al
so r
epor
t tha
t res
pons
e to
hig
h-fa
t die
t is
alte
red
depe
ndin
g on
th
e pa
rtic
ular
ant
ibio
tic a
nd n
umbe
r of
co
urse
s us
ed to
per
turb
the
mic
robi
ota
85
To
ana
lyze
the
impa
ct o
f m
ater
nal p
repr
egna
ncy
BMI o
n th
e in
fant
gut
m
icro
biom
e co
mpo
sitio
n an
d fu
nctio
nal p
oten
tial
Nest
ed c
ase-
cont
rol
desi
gn (
n =
39)
Mat
erna
l pre
preg
nanc
y ob
esity
Vari
atio
ns in
infa
nt
mic
robi
ome
com
posi
tion
and
func
tion
Infa
nt m
etab
olis
m a
t 18
mo
of a
geFi
rmic
utes
wer
e re
port
ed e
nric
hed
in c
hild
ren
born
to m
othe
rs a
t a n
orm
al w
t, w
here
as
bact
eroi
dete
s w
ere
enri
ched
in in
fant
s bo
rn to
wom
en w
ho w
ere
obes
e. In
this
st
udy,
a li
nk to
an
infa
nt h
ealth
out
com
e w
as n
ot e
stab
lishe
d, b
ut d
iffer
entia
l m
icro
biom
e m
etab
olic
func
tions
that
wer
e ba
sed
on w
heth
er in
fant
s w
ere
born
to
mot
hers
at a
nor
mal
wt o
r to
wom
en w
ho
wer
e ob
ese
was
iden
tified
86
To
inve
stig
ate
the
effe
ct o
f ca
dmiu
m e
xpos
ure
on th
e ea
rly-
life
gut m
icro
biot
a an
d m
etab
olis
m in
ad
ulth
ood
SPF
mou
se m
odel
Cadm
ium
exp
osur
e 1
wk
befo
re p
aren
tal m
atin
gVa
riat
ions
in th
e m
icro
biom
e co
mpo
sitio
n ob
serv
ed a
t 8 w
k an
d at
ad
ulth
ood
(20
wk)
Body
com
posi
tion
mea
sure
d in
adu
lthoo
dCa
dmiu
m e
xpos
ure
in p
aren
tal m
ice
resu
lted
in in
crea
sed
fat a
ccum
ulat
ion
in m
ale
offs
prin
g. A
ltera
tions
in
mic
robi
ome
com
posi
tion
occu
rred
bef
ore
mea
sure
men
ts o
f bod
y co
mpo
sitio
n. In
ad
ditio
n, th
roug
h m
icro
biot
a tr
ansf
er
expe
rim
ents
, the
gro
up r
epor
ted
that
fat
accu
mul
atio
n w
as d
rive
n by
the
cadm
ium
-ex
pose
d m
icro
biom
e
87
To
det
erm
ine
if th
e ea
rly-
life
gut m
icro
biot
a co
mpo
sitio
n is
ass
ocia
ted
with
wt d
evel
opm
ent i
n ea
rly
child
hood
Nest
ed c
ase-
cont
rol
desi
gn (
n =
49)
None
Vari
atio
ns in
the
mic
robi
ome
com
posi
tion
betw
een
6 an
d 12
mo
of a
ge
BMI m
easu
red
at 7
y o
f age
Grea
ter
abun
danc
e of
Sta
phyl
ococ
cus
aure
us
in c
hild
ren
who
wer
e ob
ese
in in
fanc
y.
Grea
ter
abun
danc
es o
f bifi
doba
cter
ia in
ch
ildre
n at
a n
orm
al w
t in
infa
ncy
88
TabL
e 1
Cont
inue
d
by guest on August 10, 2020www.aappublications.org/newsDownloaded from
STIEMSMA and MICHELS12
Rese
arch
Obj
ectiv
eSt
udy
Popu
latio
n or
An
imal
Mod
elEa
rly-
Life
Fac
tors
and
Ti
min
g of
Exp
osur
eTi
min
g of
Mic
robi
ome
Anal
ysis
or
Inte
rven
tion
Heal
th O
utco
me
and
Tim
ing
of A
sses
smen
tSu
mm
ary
of F
indi
ngs
Ref.
No.
To
inve
stig
ate
the
effe
cts
of
earl
y-lif
e fa
ctor
s on
the
traj
ecto
ry o
f gut
mic
robi
al
deve
lopm
ent a
nd
child
hood
adi
posi
ty
Pros
pect
ive
hum
an c
ohor
t an
alys
is (
n =
75)
Gest
atio
nal a
ge a
nd
deliv
ery
mod
eVa
riat
ions
in th
e m
icro
biom
e be
fore
6 m
o of
age
Adip
osity
at 1
8 m
o of
age
Infa
nts
with
hig
h Bi
fidob
acte
rium
and
Co
llins
ella
at a
late
r ag
e di
spla
yed
low
er
adip
osity
at 1
8 m
o of
age
. Inf
ants
who
ac
quir
ed th
ese
taxa
at 6
mo
show
ed th
e lo
wes
t adi
posi
ty a
t 18
mo.
In a
dditi
on,
acqu
isiti
on o
f the
se b
acte
rial
taxa
was
in
fluen
ced
by le
ngth
of g
esta
tion
and
deliv
ery
mod
e
89
To
ana
lyze
the
effe
ct o
f su
bthe
rape
utic
ant
ibio
tic
adm
inis
trat
ion
on th
e gu
t mic
robi
ome
and
host
m
etab
olis
m
Mou
se m
odel
of a
ntib
iotic
-in
duce
d ad
ipos
ityAn
tibio
tic-in
duce
dVa
riat
ions
in th
e m
icro
biom
e m
easu
red
befo
re s
acri
fice
Body
com
posi
tion
mea
sure
d in
adu
lthoo
d (1
6–20
wk)
The
auth
ors
gene
rate
d a
mou
se m
odel
of
adip
osity
by
expo
sing
mic
e in
ear
ly li
fe
to a
ntib
iotic
s. V
aria
tions
in m
icro
bial
co
mpo
sitio
n be
fore
adi
posi
ty m
easu
rem
ent
was
not
ass
esse
d. H
owev
er, t
he a
ntib
iotic
s di
d al
ter
the
mic
robi
ome
com
posi
tion,
SCF
A m
etab
olis
m, a
nd h
epat
ic m
etab
olis
m o
f fa
tty
acid
s an
d lip
ids
90
To
ana
lyze
the
asso
ciat
ion
betw
een
the
earl
y-lif
e gu
t m
icro
biom
e co
mpo
sitio
n an
d BM
I in
child
hood
Pros
pect
ive
hum
an c
ohor
t an
alys
is (
n =
138)
None
Vari
atio
ns in
the
mic
robi
ome
com
posi
tion
with
in th
e fir
st y
ear
of
age
BMI S
D sc
ore
betw
een
1 an
d 3
y of
age
Abun
danc
e of
Bac
tero
ides
frag
ilis
at 3
and
26
wk
of a
ge is
ass
ocia
ted
with
BM
I SD
scor
e be
twee
n 1
and
3 y
of a
ge. A
bund
ance
of
Stap
hylo
cocc
us a
t 3 a
nd 5
2 w
k is
inve
rsel
y as
soci
ated
with
BM
I SD
scor
e be
twee
n 1
and
3 y
91
Neur
odev
elop
men
t
To d
eter
min
e if
limite
d ne
stin
g st
ress
alte
rs
offs
prin
g m
icro
biot
a,
cort
icos
tero
ne le
vels
, and
in
test
inal
per
mea
bilit
y
Rat m
odel
of l
imite
d ne
stin
g st
ress
Lim
ited
nest
ing
stre
ssVa
riat
ions
in th
e gu
t m
icro
biom
e co
mpo
sitio
n 21
d p
ost b
irth
(at
w
eani
ng)
Lim
ited
nest
ing
stre
ss
from
pos
tnat
al d
ays
2–10
Lim
ited-
nest
ing
pups
had
hy
perc
ortic
oste
rone
mia
, enh
ance
d in
test
inal
per
mea
bilit
y, d
ecre
ased
m
icro
bial
div
ersi
ty, a
nd v
aria
tions
in
spec
ific
mic
robi
al ta
xa
92
To
det
erm
ine
if m
ater
nal
high
-fat-d
iet-i
nduc
ed
obes
ity is
ass
ocia
ted
with
so
cial
beh
avio
ral d
efici
ts
and
alte
red
mic
robi
ota
in
the
offs
prin
g
High
-fat d
iet m
ouse
mod
elM
ater
nal h
igh-
fat d
iet
Vari
atio
ns in
the
gut
mic
robi
ome
com
posi
tion
in o
ffspr
ing
Beha
vior
exa
ms
on
7–12
-wk-
old
offs
prin
g m
ice
A m
ater
nal h
igh-
fat d
iet i
nduc
es
com
posi
tiona
l var
iatio
ns in
the
gut
mic
robi
ome
of o
ffspr
ing
mic
e. O
ffspr
ing
mic
e of
mot
hers
on
a hi
gh-fa
t die
t co
hous
ed w
ith m
ice
born
of m
othe
rs r
aise
d on
a r
egul
ar d
iet d
ispl
ayed
nor
mal
soc
ial
beha
vior
. In
addi
tion,
rei
ntro
duct
ion
of
L re
uter
i (la
ckin
g in
offs
prin
g m
ice
of a
m
othe
r on
a h
igh-
fat d
iet)
res
tore
d no
rmal
so
cial
beh
avio
r in
thes
e m
ice
93
TabL
e 1
Cont
inue
d
by guest on August 10, 2020www.aappublications.org/newsDownloaded from
PEDIATRICS Volume 141, number 4, April 2018 13
Rese
arch
Obj
ectiv
eSt
udy
Popu
latio
n or
An
imal
Mod
elEa
rly-
Life
Fac
tors
and
Ti
min
g of
Exp
osur
eTi
min
g of
Mic
robi
ome
Anal
ysis
or
Inte
rven
tion
Heal
th O
utco
me
and
Tim
ing
of A
sses
smen
tSu
mm
ary
of F
indi
ngs
Ref.
No.
To
det
erm
ine
if co
gniti
ve
abili
ty is
ass
ocia
ted
with
pa
rtic
ular
infa
nt g
ut
mic
robi
ota
profi
les
Pros
pect
ive
hum
an c
ohor
t an
alys
is (
n =
89)
Grou
p 2
was
mor
e lik
ely
to h
ave
been
bre
astf
ed,
less
like
ly to
hav
e be
en b
orn
by c
esar
ean
deliv
ery,
and
ass
ocia
ted
with
whi
te e
thni
city
. Ha
ving
old
er s
iblin
gs
was
ass
ocia
ted
with
in
crea
sed
α di
vers
ity
3 gr
oups
of s
ubje
cts
wer
e id
entifi
ed o
n th
e ba
sis
of th
eir
1-y
mic
robi
ome
anal
ysis
Cogn
itive
out
com
es a
t 1
and
2 y
of a
geTh
ree
grou
ps o
f sub
ject
s w
ere
iden
tified
on
the
basi
s of
thei
r m
icro
biom
e.
Grou
p 1
disp
laye
d hi
gh a
bund
ance
of
Faec
alib
acte
rium
, gro
up 2
dis
play
ed
high
abu
ndan
ce o
f Bac
tero
ides
, and
gr
oup
3 di
spla
yed
high
abu
ndan
ce o
f ru
min
ococ
cace
ae. I
ndiv
idua
l Mul
len
scal
es
diffe
red
betw
een
grou
ps. α
div
ersi
ty w
as
nega
tivel
y as
soci
ated
with
indi
vidu
al M
ulle
n sc
ales
at 2
y o
f age
(ex
pres
sive
lang
uage
an
d vi
sual
rec
eptio
n)
94
To
det
erm
ine
if m
ater
nal
pren
atal
str
ess
alte
rs th
e m
icro
bial
intr
aute
rine
en
viro
nmen
t and
beh
avio
r in
offs
prin
g
Mou
se m
odel
of p
rena
tal
stre
ssPr
enat
al s
tres
sVa
riat
ions
in p
lace
ntal
m
icro
biom
e an
d fe
cal
mic
robi
ome
of o
ffspr
ing
Anxi
ety-
like
beha
vior
in
offs
prin
gPr
enat
al m
ater
nal s
tres
s w
as a
ssoc
iate
d w
ith v
aria
tions
in th
e m
icro
biom
e of
da
ms,
offs
prin
g, a
nd in
the
plac
enta
. Ad
ditio
nally
, pre
nata
l str
ess
is a
ssoc
iate
d w
ith in
crea
sed
IL-1
β in
the
plac
enta
and
re
duce
d br
ain-
deri
ved
neur
otro
phic
fact
or
in p
lace
nta
and
adul
t offs
prin
g am
ygda
la
7
To
det
erm
ine
if pr
obio
tic
adm
inis
trat
ion
in e
arly
lif
e m
odifi
es m
ater
nal
sepa
ratio
n-in
duce
d gu
t dy
sfun
ctio
n
Rat m
odel
(st
ress
in
duce
d by
mat
erna
l se
para
tion)
Mat
erna
l sep
arat
ion
in
earl
y lif
e (d
ay 4
to d
ay
19)
Vari
atio
ns in
mic
robi
ome
and
gut f
unct
ion
in
offs
prin
g
Hypo
thal
amus
-pitu
itary
-ad
rena
l axi
s ac
tivity
Incr
ease
d co
rtic
oste
rone
leve
ls a
nd a
ltere
d co
loni
c m
ucos
al b
arri
er fu
nctio
n in
m
ater
nally
sep
arat
ed r
at p
ups.
Ear
ly-li
fe
adm
inis
trat
ion
of p
robi
otic
s (c
ompo
sed
of
Lact
obac
illus
rha
mno
sus
and
Lact
obac
illus
he
lvet
icus
str
ains
) to
rat
pup
s am
elio
rate
s th
ese
findi
ngs
and
pers
ists
to a
dulth
ood
95
To
det
erm
ine
if ea
rly-
life
stre
ss a
lters
the
gut-b
rain
ax
is
Rat m
odel
(st
ress
in
duce
d by
mat
erna
l se
para
tion)
Mat
erna
l sep
arat
ion
in
earl
y lif
eVa
riat
ions
in m
icro
biom
e co
mpo
sitio
n in
rat
pup
sSy
mpt
oms
of p
sych
iatr
ic
diso
rder
s an
d ir
rita
ble
bow
el s
yndr
ome
Incr
ease
d pl
asm
a co
rtic
oste
rone
and
in
crea
sed
tum
or n
ecro
sis
fact
or-α
an
d in
terf
eron
-γ. A
lso,
the
mic
robi
ome
com
posi
tion
vari
ed in
the
mat
erna
lly
sepa
rate
d gr
oup
com
pare
d w
ith th
e ra
ts
that
wer
e no
t mat
erna
lly s
epar
ated
96
To
exa
min
e th
e ef
fect
s of
pr
enat
al a
nd e
arly
-life
ex
posu
re to
pro
pion
ic
acid
and
LPS
on
offs
prin
g gu
t mic
robi
al m
etab
olis
m,
loco
mot
or a
ctiv
ity, a
nd
anxi
ety-
like
beha
vior
Rat m
odel
None
Pre-
and
pos
tnat
al L
PS o
r pr
opio
nic
acid
exp
osur
eBe
havi
or tr
aits
in o
ffspr
ing
Pren
atal
pro
pion
ic a
cid
incr
ease
d an
xiet
y-lik
e be
havi
or in
mal
e an
d fe
mal
e ad
oles
cent
of
fspr
ing.
Pos
tnat
al p
ropi
onic
aci
d in
crea
sed
anxi
ety-
like
beha
vior
in fe
mal
e of
fspr
ing
only
. Pre
nata
l pro
pion
ic a
cid
and
LPS
indu
ced
deve
lopm
enta
l del
ays
(inc
ludi
ng d
elay
s in
eye
ope
ning
)
97
TabL
e 1
Cont
inue
d
by guest on August 10, 2020www.aappublications.org/newsDownloaded from
STIEMSMA and MICHELS14
Rese
arch
Obj
ectiv
eSt
udy
Popu
latio
n or
An
imal
Mod
elEa
rly-
Life
Fac
tors
and
Ti
min
g of
Exp
osur
eTi
min
g of
Mic
robi
ome
Anal
ysis
or
Inte
rven
tion
Heal
th O
utco
me
and
Tim
ing
of A
sses
smen
tSu
mm
ary
of F
indi
ngs
Ref.
No.
To
det
erm
ine
if co
loni
zatio
n by
gut
mic
robi
ota
in
earl
y lif
e im
pact
s br
ain
deve
lopm
ent a
nd a
dult
beha
vior
GF a
nd S
PF m
ouse
mod
els
None
Offs
prin
g of
pre
viou
sly
GF
mic
e co
loni
zed
with
SPF
m
icro
biot
a
Beha
vior
in a
dulth
ood
Adul
t col
oniz
ed o
ffspr
ing
disp
laye
d si
mila
r be
havi
ors
com
pare
d w
ith S
PF m
ice.
The
se
mic
e sp
ent l
ess
time
expl
orin
g th
e op
en
arm
s in
the
maz
e (l
ess
loco
mot
or a
ctiv
ity).
Addi
tiona
lly, c
olon
ized
mic
e ex
pres
sed
less
sy
napt
ophy
sin
and
PSD-
95 in
the
stri
atum
co
mpa
red
with
GF
mic
e, s
ugge
stin
g th
e m
icro
biom
e is
invo
lved
in p
rogr
amm
ing
brai
n de
velo
pmen
t
98
To
det
erm
ine
if a
mat
erna
l hi
gh-fa
t-die
t-alte
red
mic
robi
ome
can
mod
ify
offs
prin
g be
havi
or
Mou
se m
odel
col
oniz
ed
with
mat
erna
l hig
h-fa
t-di
et-s
hape
d m
icro
biot
a
Mat
erna
l hig
h-fa
t die
tFe
mal
e m
ice
tran
spla
nted
w
ith h
igh-
fat d
iet
mic
robi
ome
Beha
vior
trai
ts in
offs
prin
gFe
mal
e m
ice
wer
e tr
ansp
lant
ed w
ith a
hi
gh-fa
t-die
t- or
con
trol
low
-fat-d
iet-
asso
ciat
ed g
ut m
icro
biom
e. O
ffspr
ing
of
thes
e m
ice
disp
laye
d al
tere
d be
havi
or
in a
sex
-dep
ende
nt m
anne
r. Of
fspr
ing
mic
e di
spla
yed
less
str
ess
afte
r m
ater
nal
sepa
ratio
n. M
ale
offs
prin
g di
spla
yed
decr
ease
d ex
plor
ator
y an
d co
gniti
ve
beha
vior
s, w
hich
is in
dica
tive
of in
crea
sed
anxi
ety.
Fem
ale
mic
e di
spla
yed
incr
ease
s in
ad
ipos
ity a
nd b
ody
wt
99
To
ana
lyze
the
mic
robi
al a
nd
mol
ecul
ar m
echa
nism
s th
at u
nder
lie th
e gu
t-bra
in
axis
GF a
nd c
onve
ntio
nally
ra
ised
mou
se m
odel
sNo
neGF
mic
e co
loni
zed
afte
r w
eani
ngNe
uron
al a
ctiv
ity in
the
amyg
dala
Abse
nce
of a
mic
robi
ota
in e
arly
life
res
ults
in
diff
eren
tial g
ene
expr
essi
on, e
xon
usag
e,
RNA
editi
ng, a
nd u
pstr
eam
gen
e re
gula
tion
in th
e am
ygda
la. T
his
was
sim
ilar
to
mic
e w
ho w
ere
rais
ed G
F fo
r th
eir
entir
e liv
es b
ut v
arie
d w
hen
com
pare
d w
ith
conv
entio
naliz
ed m
ice
100
To
exa
min
e w
heth
er
vari
atio
ns in
the
vagi
nal m
icro
biom
e ar
e as
soci
ated
with
var
ied
offs
prin
g pr
ogra
mm
ing
Mou
se m
odel
of p
rena
tal
stre
ssPr
enat
al s
tres
sVa
riat
ions
in th
e m
ater
nal
vagi
nal a
nd n
eona
tal g
ut
mic
robi
ome
Met
abol
ic a
nd n
euro
logi
c pr
ogra
mm
ing
and
in
offs
prin
g
Lact
obac
illus
abu
ndan
ce is
dec
reas
ed in
the
vagi
nal m
icro
biom
e an
d in
neo
nate
s bo
rn
to d
ams
expo
sed
to e
arly
pre
nata
l str
ess.
Ot
her
bact
eria
l pop
ulat
ion
abun
danc
es
also
var
ied
in o
ffspr
ing
expo
sed
to e
arly
pr
enat
al s
tres
s. E
arly
pre
nata
l str
ess
alte
red
met
abol
ic p
rofil
es a
nd a
min
o ac
id
avai
labi
lity
in th
e br
ain
101
Imm
une-
med
iate
d di
seas
es (
IBD,
T1D
, etc
)
To in
vest
igat
e ag
e-de
pend
ent
mic
robi
al m
odul
atio
n of
iN
KTs
in m
ouse
mod
els
of
IBD
and
asth
ma
Mou
se m
odel
of
oxaz
olon
e-in
duce
d co
litis
None
SPF-
colo
niza
tion
duri
ng
preg
nanc
y le
ad to
SPF
-co
loni
zed
offs
prin
g
Colit
is in
duce
d la
ter
in li
feNe
onat
al e
xpos
ure
to a
con
vent
iona
l m
icro
biot
a co
mpa
red
with
GF
cond
ition
s pr
otec
ted
mic
e fr
om o
xazo
lone
-indu
ced
colit
is
76
TabL
e 1
Cont
inue
d
by guest on August 10, 2020www.aappublications.org/newsDownloaded from
PEDIATRICS Volume 141, number 4, April 2018 15
Rese
arch
Obj
ectiv
eSt
udy
Popu
latio
n or
An
imal
Mod
elEa
rly-
Life
Fac
tors
and
Ti
min
g of
Exp
osur
eTi
min
g of
Mic
robi
ome
Anal
ysis
or
Inte
rven
tion
Heal
th O
utco
me
and
Tim
ing
of A
sses
smen
tSu
mm
ary
of F
indi
ngs
Ref.
No.
To
det
erm
ine
if an
d ho
w
earl
y-lif
e ex
posu
re to
an
tibio
tics
chan
ges
susc
eptib
ility
to IB
D
Mou
se m
odel
DSS
-indu
ced
colit
isAn
tibio
tic-in
duce
dLD
P af
ter
wea
ning
Colit
is in
duce
d la
ter
in li
feLD
P-tr
eate
d m
ice
disp
laye
d tr
ansi
ent g
ut
mic
robi
al c
ompo
sitio
nal a
ltera
tions
, in
clud
ing
erad
icat
ion
of s
egm
ente
d fil
amen
tous
bac
teri
a. In
add
ition
, aft
er D
SS-
indu
ced
colit
is, L
DP m
ice
disp
laye
d re
duce
d co
litis
sym
ptom
s, Il
-17
expr
essi
on, a
nd il
eal
Th17
diff
eren
tiatio
n co
mpa
red
with
mic
e ex
pose
d to
met
roni
dazo
le, e
nrofl
oxac
in,
and
cont
rols
. Fin
ally
, the
aut
hors
rep
ort
peni
cilli
n’s
effe
cts
are
depe
nden
t on
erad
iatio
n of
seg
men
ted
filam
ento
us
bact
eria
, im
plic
atin
g th
e m
icro
biom
e as
the
med
iato
r be
twee
n th
is e
arly
life
exp
osur
e an
d co
litis
dev
elop
men
t
102
To
exp
lore
the
influ
ence
of
gut
dys
bios
is in
the
prog
ress
ion
of T
1D
NOD
mou
se m
odel
Antib
iotic
-indu
ced
Antib
iotic
trea
tmen
t in
earl
y lif
e (c
once
ptio
n un
til 4
0 w
k po
stna
tal)
Spon
tane
ous
diab
etes
la
ter
in li
feAn
tibio
tics
wer
e ad
min
iste
red
to N
OD m
ice
from
con
cept
ion
until
40
wk
post
nata
l de
velo
pmen
t. Tr
eatm
ent w
ith a
ntib
iotic
s in
crea
sed
inci
denc
e of
T1D
in m
ale
mic
e.
Antib
iotic
trea
tmen
t als
o re
sulte
d in
nea
r ab
latio
n of
the
gut m
icro
biom
e at
8 w
k of
age
, whi
ch m
ay p
artia
lly e
xpla
in th
e in
crea
sed
T1D
inci
denc
e in
mal
e m
ice
103
To
det
erm
ine
if ex
posu
re to
pr
enat
al a
ntib
iotic
s ca
n pr
otec
t offs
prin
g fr
om
T1D
NOD
mou
se m
odel
Antib
iotic
-indu
ced
Pren
atal
ant
ibio
tic
trea
tmen
t ind
uced
va
riat
ions
in o
ffspr
ing
and
mat
erna
l m
icro
biom
es
Spon
tane
ous
diab
etes
la
ter
in li
fePr
enat
al n
eom
ycin
and
van
com
ycin
trea
tmen
t re
sulte
d in
diff
eren
tial s
hift
s in
the
offs
prin
g an
d m
ater
nal m
icro
biom
es.
Offs
prin
g tr
eate
d pr
enat
ally
with
neo
myc
in
wer
e pr
otec
ted
from
T1D
dev
elop
men
t, w
here
as o
ffspr
ing
trea
ted
pren
atal
ly w
ith
vanc
omyc
in d
ispl
ayed
acc
eler
ated
T1D
de
velo
pmen
t. Th
e an
tibio
tic tr
eatm
ent a
lso
resu
lted
in a
ltere
d im
mun
e pr
ofile
s, s
uch
as in
crea
sed
T-cel
l–m
edia
ted
infla
mm
atio
n in
mic
e tr
eate
d w
ith v
anco
myc
in a
nd
alte
red
antig
en-p
rese
ntin
g ce
ll ph
enot
ypes
in
mic
e tr
eate
d w
ith n
eom
ycin
104
To
det
erm
ine
the
impa
ct o
f ta
rget
ing
Gram
-neg
ativ
e gu
t bac
teri
a at
var
ious
tim
e po
ints
in e
arly
life
on
T1D
deve
lopm
ent
NOD
mou
se m
odel
Antib
iotic
-indu
ced
Pren
atal
ant
ibio
tic
trea
tmen
t ind
uced
va
riat
ions
in o
ffspr
ing
mic
robi
ome
Spon
tane
ous
diab
etes
la
ter
in li
fePr
egna
nt, N
OD m
ice
trea
ted
with
an
antib
iotic
m
ixtu
re (
neom
ycin
, pol
ymyx
in B
, and
st
rept
omyc
in)
wer
e pr
otec
ted
from
T1D
co
mpa
red
with
mic
e tr
eate
d po
stna
tally
. M
icro
biot
a tr
ansf
er fr
om th
ese
mic
e to
un
trea
ted
mic
e re
sulte
d in
pro
tect
ion
from
T1
D
105
TabL
e 1
Cont
inue
d
by guest on August 10, 2020www.aappublications.org/newsDownloaded from
STIEMSMA and MICHELS16
Rese
arch
Obj
ectiv
eSt
udy
Popu
latio
n or
An
imal
Mod
elEa
rly-
Life
Fac
tors
and
Ti
min
g of
Exp
osur
eTi
min
g of
Mic
robi
ome
Anal
ysis
or
Inte
rven
tion
Heal
th O
utco
me
and
Tim
ing
of A
sses
smen
tSu
mm
ary
of F
indi
ngs
Ref.
No.
To
com
pare
the
effe
cts
of p
ulse
d th
erap
eutic
an
tibio
tics
or c
ontin
uous
lo
w-d
ose
antib
iotic
s in
ear
ly li
fe o
n T1
D de
velo
pmen
t
NOD
mou
se m
odel
Antib
iotic
-indu
ced
Puls
ed a
ntib
iotic
trea
tmen
t in
duce
d va
riat
ions
in
6-w
k-ol
d m
icro
biom
e
Spon
tane
ous
diab
etes
la
ter
in li
fePu
lsed
pos
tnat
al tr
eatm
ent w
ith ty
losi
n al
tere
d th
e m
ouse
mic
robi
ome
and
acce
lera
ted
T1D
deve
lopm
ent c
ompa
red
with
mic
e tr
eate
d w
ith s
ubth
erap
eutic
pe
nici
llin
from
pre
gnan
cy to
wee
k 12
106
To
ana
lyze
the
asso
ciat
ion
betw
een
the
infa
nt g
ut
mic
robi
ome
and
T1D
deve
lopm
ent
Pros
pect
ive
hum
an c
ohor
t an
alys
is (
n =
33)
None
Vari
atio
ns in
the
mic
robi
ome
befo
re
diag
nosi
s w
ith T
1D
T1D
diag
nosi
s at
∼3
y of
age
T1D
dise
ase
stat
e w
as d
istin
guis
habl
e by
the
gut m
icro
biom
e co
mpo
sitio
n.
Sero
conv
erte
d su
bjec
ts d
iagn
osed
with
T1D
di
spla
yed
a m
arke
d de
crea
se in
α d
iver
sity
be
fore
dia
gnos
is w
hen
com
pare
d w
ith
sero
conv
erte
d su
bjec
ts n
ot d
iagn
osed
with
T1
D an
d no
nser
ocon
vert
ed s
ubje
cts
107
To
ana
lyze
the
effe
ct o
f pe
ripa
rtum
cef
oper
azon
e ad
min
istr
atio
n on
the
mat
erna
l and
offs
prin
g m
icro
biot
a an
d IB
D in
the
offs
prin
g
SPF
IL-1
0 kn
ock-
out m
ouse
m
odel
com
bine
d w
ith
DSS-
indu
ced
colit
is
Antib
iotic
-indu
ced
Peri
part
um a
ntib
iotic
tr
eatm
ent i
nduc
ed g
ut
dysb
iosi
s in
offs
prin
g th
at p
ersi
sts
to a
dulth
ood
Spon
tane
ous
colit
is la
ter
in li
fePe
ripa
rtum
exp
osur
e to
cef
oper
azon
e in
crea
ses
risk
of s
pont
aneo
us c
oliti
s in
offs
prin
g. A
ntib
iotic
s al
so c
ontr
ibut
e to
imm
une
skew
ing
and
prom
ote
gut
dysb
iosi
s th
at p
ersi
sts
to a
dulth
ood.
Ad
ditio
nally
, as
dem
onst
rate
d by
feca
l tr
ansp
lant
to G
F IL
-10
knoc
k-ou
t dam
s,
imm
une
skew
ing
is m
edia
ted
by th
e an
tibio
tic-in
duce
d dy
sbio
sis
108
To
ana
lyze
the
impa
ct o
f a
mat
erna
l hig
h-fib
er
diet
on
T -reg
ulat
ory
cell
diffe
rent
iatio
n in
the
offs
prin
g
SPF
GPR4
1−/−
mou
se
mod
elM
ater
nal h
igh-
fiber
die
t du
ring
pre
gnan
cy a
nd
brea
stfe
edin
g
Incr
ease
d pl
asm
a SC
FAs
Incr
ease
d th
ymic
and
pe
riph
eral
T-re
gula
tory
ce
lls
Com
pare
d w
ith o
ffspr
ing
from
mat
erna
l mic
e fe
d a
norm
al d
iet,
high
-fibe
r di
et d
urin
g pr
egna
ncy
and
brea
stfe
edin
g re
sulte
d in
in
crea
sed
plas
ma
SCFA
s in
the
offs
prin
g.
Thes
e of
fspr
ing
also
dis
play
ed h
ighe
r fr
eque
ncie
s of
thym
ic a
nd p
erip
hera
l T-r
egul
ator
y ce
lls, w
hich
may
be
prom
pted
by
incr
ease
d SC
FA le
vels
46
AAD,
alle
rgic
air
way
s di
seas
e; C
D4+,
clu
ster
of d
iffer
entia
tion
4; C
XCL1
6, c
hem
okin
e lig
and
16; D
SS, d
extr
an s
odiu
m s
ulfa
te; G
I, ga
stro
inte
stin
al; G
PR41
, G p
rote
in–c
oupl
ed r
ecep
tor
41; G
PR43
, G p
rote
in–c
oupl
ed r
ecep
tor
43; G
rx1,
Glu
tare
doxi
n-1;
HD
AC9,
his
tone
dea
cety
lase
9; I
gA, i
mm
unog
lobu
lin A
; IL-
1β, i
nter
leuk
in 1
bet
a; IL
-10,
inte
rleu
kin
10; I
L-17
, int
erle
ukin
17;
iNKT
, inv
aria
nt n
atur
al k
iller
T c
ell;
LPS,
lipo
poly
sacc
hari
de; N
OD, n
onob
ese
diab
etic
; PD-
L1, p
rogr
amm
ed d
eath
liga
nd-1
; PSD
-95,
po
stsy
napt
ic d
ensi
ty p
rote
in 9
5; R
ef.,
refe
renc
e; T
h1, T
-hel
per
1; T
h17,
T-he
lper
17;
TLR
, Tol
l-lik
e re
cept
or; T
1D, t
ype
1 di
abet
es.
TabL
e 1
Cont
inue
d
by guest on August 10, 2020www.aappublications.org/newsDownloaded from
3 months of age and an increased enterobacteriaceae/bacteroidaceae ratio at 3 months and 1 year of age, which was associated with increased food sensitization among 1-year-old children. Variations in the gut microbiome at 3 and 6 months of age have also been associated with the resolution of a milk allergy by 8 years of age.75 Thus, authors of the current microbiome research for asthma and allergies suggest the time period between birth and 1 year of age as the developmental origins window for this disease. These immune hypersensitivities persist into later childhood and adulthood despite the transient nature of microbial dysbiosis.
Obesity
Similar to asthma and atopic disease, prospective studies reveal early-life gut microbiome compositional variations, which precede the development of obesity.88, 91 A recent study reveals temporal and compositional microbiome associations with early childhood adiposity.89 Specifically, infants with high Streptococcus abundance at 6 months of age displayed increased adiposity at 18 months of age.89 This emphasizes the importance of both microbiome composition and timing of microbiome maturation in the development of childhood obesity.
Mouse model studies have been used to mechanistically support the potential metabolic effects of early-life microbial dysbiosis and emphasize the obesity-inducing abilities of antibiotics. In a study by Cho et al, 90 antibiotics administered to mice in early life resulted in subsequent increases in adiposity and metabolic hormones. Cox et al6 furthered this research by manipulating the early-life microbiota using low-dose penicillin (LDP). Here, they report LDP exposure during early life increased the effect of a high-fat diet on the microbiota, which could
be transferred to GF mice to induce obesity.6 It will be important for future researchers to incorporate both prospective human studies and animal models to determine the microbiome-associated effects of early-life antibiotic exposure on human health.
Neurodevelopmental Disorders
A less intuitive role of the gut microbiome in human health and development is the impact of early-life microbial dysbiosis in neurodevelopment (ie, the gut-brain axis). There is increasing evidence to support early-life microbial compositional variations in stress response and anxiety. In animal models, it is suggested that neonatal stress after maternal separation results in long-term compositional changes to the intestinal microbiota, 95, 96 and treating rat pups with probiotics can counter the resulting elevated corticosterone levels.95 Prenatal exposure to the SCFA, propionic acid, was also reported to increase anxiety-like behavior in mice.97 In a recent study, Gur et al7 report the influence of prenatal maternal stress in mice and its ability to alter both the maternal and neonatal intestinal microbiomes. Adult offspring exposed to prenatal maternal stress also displayed increased anxiety-like behavior.7 Additionally, prenatal stress also induced variations in the placental microbiome.7 This suggests that the intrauterine microbial environment is a potential mediator of maternal prenatal stress and resulting stress in the offspring.
Variations in the gut microbiome have also been associated with many facets of social behavior. Adult offspring of conventionalized dams (previously GF but colonized with the microbiome of specific pathogen–free [SPF] mice) were reported to display decreased motor activity compared with offspring from GF dams.98 Buffington et al93
report impaired social behavior (similar to that observed in autism spectrum disorder) in the offspring of dams that were fed a high-fat diet, which is mediated by variations in the offspring microbiome. In addition, using shotgun metagenomic sequencing, this group identified a significant reduction in Lactobacillus reuteri among the maternal high-fat diet–fed offspring.93 Supplementation of drinking water with L reuteri resulted in restoration of offspring social deficits.93 Notably, the majority of studies with researchers focusing on the early-life critical window in relation to neurodevelopment have been conducted in animal models. However, there is recent evidence to support a role of the infant gut microbiome in cognitive development in humans. Carlson et al94 reported variations in gut microbiome α diversity in 1-year-old children, which correlated with their cognitive abilities measured at age 2. Additional studies in humans will substantiate this evidence. However, it is interesting to note that researchers consistently identify the time period between pregnancy and the first year of life as the most influential in human development.
Collectively, this disease-specific research is used to support a role of the early-life microbiome in fetal and childhood development in a variety of contexts. However, prediagnostic variations in the early-life microbiome composition have been associated with other chronic noncommunicable diseases in later childhood and adulthood (ie, IBD and type 1 diabetes, Table 1).1 In addition, Harris et al112 identified an association between adolescent diet and breast cancer diagnosed in adulthood, suggesting that the timing of susceptibility for the microbiome may also be disease specific. The future of research surrounding the microbiome in DOHaD is thus ripe with opportunity.
PEDIATRICS Volume 141, number 4, April 2018 17 by guest on August 10, 2020www.aappublications.org/newsDownloaded from
cONcLUsiONs aND FUTUre DirecTiONs
In this review, we summarize evidence supporting the role of the microbiome as a fundamental part of human physiology and key to our understanding of DOHaD. Pre- and postbirth exposures alter the microbiome composition and functional potential in the neonate. In turn, this dysbiosis results in a number of health and disease outcomes later in life. Collaborative translational efforts using both animal models and human samples will mechanistically define the extent to which the microbiome plays a causal role during this critical window of developmental plasticity. Multiomics approaches, combining epigenetic, transcriptome, and microbiome analyses in large, prospective, human birth cohorts will enhance our current understanding of how the microbiome may interact with host components to drive aspects of infant development. In addition, as it is becoming clearer that the microbiota (both maternal and placental) can influence fetal development, more research surrounding the vaginal and intrauterine microbiomes is needed to paint a fuller picture of the fetal and neonatal origins of disease. We propose revisiting DOHaD and incorporating the microbiome into our current understanding of the many aspects of early human development associated with long-term health.
reFereNces
1. Stiemsma LT, Reynolds LA, Turvey SE, Finlay BB. The hygiene hypothesis: current perspectives and future therapies. Immunotargets Ther. 2015;4:143–157
2. Stiemsma LT, Turvey SE. Asthma and the microbiome: defining the critical window in early life. Allergy Asthma Clin Immunol. 2017;13:3
3. Tamburini S, Shen N, Wu HC, Clemente JC. The microbiome in early life: implications for health outcomes. Nat Med. 2016;22(7):713–722
4. Arrieta MC, Stiemsma LT, Dimitriu PA, et al; CHILD Study Investigators. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med. 2015;7(307):307ra152
5. Stiemsma LT, Arrieta MC, Dimitriu PA, et al; Canadian Healthy Infant Longitudinal Development (CHILD) Study Investigators. Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma. Clin Sci (Lond). 2016;130(23):2199–2207
6. Cox LM, Yamanishi S, Sohn J, et al. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell. 2014;158(4):705–721
7. Gur TL, Shay L, Palkar AV, et al. Prenatal stress affects placental cytokines and neurotrophins, commensal microbes, and anxiety-like behavior in adult female offspring. Brain Behav Immun. 2017;64:50–58
8. Mueller NT, Bakacs E, Combellick J, Grigoryan Z, Dominguez-Bello MG. The infant microbiome development: mom matters. Trends Mol Med. 2015;21(2):109–117
9. Waterland RA, Michels KB. Epigenetic epidemiology of the developmental origins hypothesis. Annu Rev Nutr. 2007;27:363–388
10. Osmond C, Barker DJ, Winter PD, Fall CH, Simmonds SJ. Early growth and death from cardiovascular disease in women. BMJ. 1993;307(6918):1519–1524
11. Barker DJ, Osmond C. Infant mortality, childhood nutrition, and ischaemic heart disease in England and Wales. Lancet. 1986;1(8489):1077–1081
12. Hjalgrim LL, Westergaard T, Rostgaard K, et al. Birth weight as a risk factor for childhood leukemia: a meta-analysis of 18 epidemiologic studies. Am J Epidemiol. 2003;158(8):724–735
13. Trichopoulos D. Hypothesis: does breast cancer originate in utero? Lancet. 1990;335(8695):939–940
14. Strachan DP. Hay fever, hygiene, and household size. BMJ. 1989;299(6710):1259–1260
15. Shreiner A, Huffnagle GB, Noverr MC. The “Microflora Hypothesis” of allergic disease. Adv Exp Med Biol. 2008;635:113–134
16. Ursell LK, Metcalf JL, Parfrey LW, Knight R. Defining the human microbiome. Nutr Rev. 2012;70(suppl 1):S38–S44
17. Robinson CM, Pfeiffer JK. Viruses and the microbiota. Annu Rev Virol. 2014;1:55–69
18. Arrieta MC, Stiemsma LT, Amenyogbe N, Brown EM, Finlay B. The intestinal microbiome in early life: health and disease. Front Immunol. 2014;5:427
19. Steel JH, Malatos S, Kennea N, et al. Bacteria and inflammatory cells in fetal membranes do not always cause preterm labor. Pediatr Res. 2005;57(3):404–411
20. Satokari R, Grönroos T, Laitinen K, Salminen S, Isolauri E. Bifidobacterium and Lactobacillus DNA in the human placenta. Lett Appl Microbiol. 2009;48(1):8–12
21. Collado MC, Rautava S, Aakko J, Isolauri E, Salminen S. Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci Rep. 2016;6:23129
22. Gomez de Agüero M, Ganal-Vonarburg SC, Fuhrer T, et al. The maternal microbiota drives early postnatal innate immune development. Science. 2016;351(6279):1296–1302
23. Bassols J, Serino M, Carreras-Badosa G, et al. Gestational diabetes is associated with changes in placental microbiota and microbiome. Pediatr Res. 2016;80(6):777–784
STIEMSMA and MICHELS18
abbreviaTiONs
DOHaD: Developmental Origins of Health and Disease
GF: germ freeIBD: inflammatory bowel diseaseLDP: low-dose penicillinNEC: necrotizing enterocolitisSCFA: short-chain fatty acidSPF: specific pathogen free
by guest on August 10, 2020www.aappublications.org/newsDownloaded from
24. Zheng J, Xiao X, Zhang Q, Mao L, Yu M, Xu J. The placental microbiome varies in association with low birth weight in full-term neonates. Nutrients. 2015;7(8):6924–6937
25. Prince AL, Ma J, Kannan PS, et al. The placental membrane microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis. Am J Obstet Gynecol. 2016;214(5):627.e1–627.e16
26. Antony KM, Ma J, Mitchell KB, Racusin DA, Versalovic J, Aagaard K. The preterm placental microbiome varies in association with excess maternal gestational weight gain. Am J Obstet Gynecol. 2015;212(5):653.e1–e16
27. Perez-Muñoz ME, Arrieta MC, Ramer-Tait AE, Walter J. A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome. Microbiome. 2017;5(1):48
28. Lauder AP, Roche AM, Sherrill-Mix S, et al. Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome. 2016;4(1):29
29. Boro P, Kumaresan A, Singh AK, et al. Expression of short chain fatty acid receptors and pro-inflammatory cytokines in utero-placental tissues is altered in cows developing retention of fetal membranes. Placenta. 2014;35(7):455–460
30. Dominguez-Bello MG, Costello EK, Contreras M, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA. 2010;107(26):11971–11975
31. Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD, Aagaard KM. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat Med. 2017;23(3):314–326
32. Bokulich NA, Chung J, Battaglia T, et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med. 2016;8(343):343ra82
33. Sevelsted A, Stokholm J, Bønnelykke K, Bisgaard H. Cesarean section and
chronic immune disorders. Pediatrics. 2015;135(1). Available at: www. pediatrics. org/ cgi/ content/ full/ 135/ 1/ e92
34. Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med. 2016;22(3):250–253
35. Yatsunenko T, Rey FE, Manary MJ, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222–227
36. Cabrera-Rubio R, Collado MC, Laitinen K, Salminen S, Isolauri E, Mira A. The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery. Am J Clin Nutr. 2012;96(3):544–551
37. Harmsen HJ, Wildeboer-Veloo AC, Raangs GC, et al. Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J Pediatr Gastroenterol Nutr. 2000;30(1):61–67
38. Pannaraj PS, Li F, Cerini C, et al. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome. JAMA Pediatr. 2017;171(7):647–654
39. Marcobal A, Barboza M, Froehlich JW, et al. Consumption of human milk oligosaccharides by gut-related microbes. J Agric Food Chem. 2010;58(9):5334–5340
40. Bezirtzoglou E, Tsiotsias A, Welling GW. Microbiota profile in feces of breast- and formula-fed newborns by using fluorescence in situ hybridization (FISH). Anaerobe. 2011;17(6):478–482
41. Gregory KE, Samuel BS, Houghteling P, et al. Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants. Microbiome. 2016;4(1):68
42. Brugman S, Visser JT, Hillebrands JL, Bos NA, Rozing J. Prolonged exclusive breastfeeding reduces autoimmune diabetes incidence and increases regulatory T-cell frequency in bio-breeding diabetes-prone rats. Diabetes Metab Res Rev. 2009;25(4):380–387
43. Azad MB, Vehling L, Lu Z, et al; CHILD Study Investigators. Breastfeeding,
maternal asthma and wheezing in the first year of life: a longitudinal birth cohort study. Eur Respir J. 2017;49(5):1602019
44. Ma J, Prince AL, Bader D, et al. High-fat maternal diet during pregnancy persistently alters the offspring microbiome in a primate model. Nat Commun. 2014;5:3889
45. Chu DM, Antony KM, Ma J, et al. The early infant gut microbiome varies in association with a maternal high-fat diet. Genome Med. 2016;8(1):77
46. Nakajima A, Kaga N, Nakanishi Y, et al. Maternal high fiber diet during pregnancy and lactation influences regulatory T cell differentiation in offspring in mice. J Immunol. 2017;199(10):3516–3524
47. Val-Laillet D, Besson M, Guérin S, et al. A maternal Western diet during gestation and lactation modifies offspring’s microbiota activity, blood lipid levels, cognitive responses, and hippocampal neurogenesis in Yucatan pigs. FASEB J. 2017;31(5):2037–2049
48. Tormo-Badia N, Håkansson Å, Vasudevan K, Molin G, Ahrné S, Cilio CM. Antibiotic treatment of pregnant non-obese diabetic mice leads to altered gut microbiota and intestinal immunological changes in the offspring. Scand J Immunol. 2014;80(4):250–260
49. Corvaglia L, Tonti G, Martini S, et al. Influence of intrapartum antibiotic prophylaxis for Group B Streptococcus on gut microbiota in the first month of life. J Pediatr Gastroenterol Nutr. 2016;62(2):304–308
50. Keski-Nisula L, Kyynäräinen HR, Kärkkäinen U, Karhukorpi J, Heinonen S, Pekkanen J. Maternal intrapartum antibiotics and decreased vertical transmission of Lactobacillus to neonates during birth. Acta Paediatr. 2013;102(5):480–485
51. Khan I, Azhar EI, Abbas AT, et al. Metagenomic analysis of antibiotic-induced changes in gut microbiota in a pregnant rat model. Front Pharmacol. 2016;7:104
52. Gomez-Arango LF, Barrett HL, McIntyre HD, Callaway LK, Morrison M, Dekker Nitert M. Antibiotic treatment at delivery shapes the initial oral
PEDIATRICS Volume 141, number 4, April 2018 19 by guest on August 10, 2020www.aappublications.org/newsDownloaded from
microbiome in neonates. Sci Rep. 2017:7:43481
53. Scott FI, Horton DB, Mamtani R, et al. Administration of antibiotics to children before age 2 years increases risk for childhood obesity. Gastroenterology. 2016;151(1):120–129.e5
54. Hviid A, Svanström H, Frisch M. Antibiotic use and inflammatory bowel diseases in childhood. Gut. 2011;60(1):49–54
55. Shaw SY, Blanchard JF, Bernstein CN. Association between the use of antibiotics in the first year of life and pediatric inflammatory bowel disease. Am J Gastroenterol. 2010;105(12):2687–2692
56. Hoskin-Parr L, Teyhan A, Blocker A, Henderson AJ. Antibiotic exposure in the first two years of life and development of asthma and other allergic diseases by 7.5 yr: a dose-dependent relationship. Pediatr Allergy Immunol. 2013;24(8):762–771
57. Pammi M, Cope J, Tarr PI, et al. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis. Microbiome. 2017;5(1):31
58. Warner BB, Deych E, Zhou Y, et al. Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study. Lancet. 2016;387(10031):1928–1936
59. Ward DV, Scholz M, Zolfo M, et al. Metagenomic sequencing with strain-level resolution implicates uropathogenic E. coli in necrotizing enterocolitis and mortality in preterm infants. Cell Reports. 2016;14(12):2912–2924
60. Aceti A, Gori D, Barone G, et al; Italian Society of Neonatology. Probiotics for prevention of necrotizing enterocolitis in preterm infants: systematic review and meta-analysis. Ital J Pediatr. 2015;41:89
61. Zhou Y, Shan G, Sodergren E, Weinstock G, Walker WA, Gregory KE. Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study. PLoS One. 2015;10(3):e0118632
62. Morrow AL, Lagomarcino AJ, Schibler KR, et al. Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants. Microbiome. 2013;1(1):13
63. Barron LK, Warner BB, Tarr PI, Shannon WD, Deych E, Warner BW. Independence of gut bacterial content and neonatal necrotizing enterocolitis severity. J Pediatr Surg. 2017;52(6):993–998
64. Li X, Li X, Shang Q, et al. Fecal microbiota transplantation (FMT) could reverse the severity of experimental necrotizing enterocolitis (NEC) via oxidative stress modulation. Free Radic Biol Med. 2017;108:32–43
65. Heida FH, van Zoonen AGJF, Hulscher JBF, et al. A necrotizing enterocolitis-associated gut microbiota is present in the meconium: results of a prospective study. Clin Infect Dis. 2016;62(7):863–870
66. Birck MM, Nguyen DN, Cilieborg MS, et al. Enteral but not parenteral antibiotics enhance gut function and prevent necrotizing enterocolitis in formula-fed newborn preterm pigs. Am J Physiol Gastrointest Liver Physiol. 2016;310(5):G323–G333
67. Bjornvad CR, Thymann T, Deutz NE, et al. Enteral feeding induces diet-dependent mucosal dysfunction, bacterial proliferation, and necrotizing enterocolitis in preterm pigs on parenteral nutrition. Am J Physiol Gastrointest Liver Physiol. 2008;295(5):G1092–G1103
68. Sim K, Shaw AG, Randell P, et al. Dysbiosis anticipating necrotizing enterocolitis in very premature infants. Clin Infect Dis. 2015;60(3):389–397
69. Cortese R, Lu L, Yu Y, Ruden D, Claud EC. Epigenome-microbiome crosstalk: a potential new paradigm influencing neonatal susceptibility to disease. Epigenetics. 2016;11(3):205–215
70. Fujimura KE, Sitarik AR, Havstad S, et al. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat Med. 2016;22(10):1187–1191
71. Russell SL, Gold MJ, Willing BP, Thorson L, McNagny KM, Finlay BB. Perinatal antibiotic treatment affects murine microbiota, immune responses
and allergic asthma. Gut Microbes. 2013;4(2):158–164
72. Russell SL, Gold MJ, Reynolds LA, et al. Perinatal antibiotic-induced shifts in gut microbiota have differential effects on inflammatory lung diseases. J Allergy Clin Immunol. 2015;135(1):100–109
73. Thorburn AN, McKenzie CI, Shen S, et al. Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites. Nat Commun. 2015;6:7320
74. Azad MB, Konya T, Guttman DS, et al; CHILD Study Investigators. Infant gut microbiota and food sensitization: associations in the first year of life. Clin Exp Allergy. 2015;45(3):632–643
75. Bunyavanich S, Shen N, Grishin A, et al. Early-life gut microbiome composition and milk allergy resolution. J Allergy Clin Immunol. 2016;138(4):1122–1130
76. Olszak T, An D, Zeissig S, et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science. 2012;336(6080):489–493
77. Gollwitzer ES, Saglani S, Trompette A, et al. Lung microbiota promotes tolerance to allergens in neonates via PD-L1. Nat Med. 2014;20(6):642–647
78. Teo SM, Mok D, Pham K, et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host Microbe. 2015;17(5):704–715
79. Kennedy EA, Connolly J, Hourihane JO, et al. Skin microbiome before development of atopic dermatitis: early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year. J Allergy Clin Immunol. 2017;139(1):166–172
80. Ismail IH, Boyle RJ, Licciardi PV, et al. Early gut colonization by Bifidobacterium breve and B. catenulatum differentially modulates eczema risk in children at high risk of developing allergic disease. Pediatr Allergy Immunol. 2016;27(8):838–846
81. Dzidic M, Abrahamsson TR, Artacho A, et al. Aberrant IgA responses to the gut microbiota during infancy
STIEMSMA and MICHELS20 by guest on August 10, 2020www.aappublications.org/newsDownloaded from
precede asthma and allergy development. J Allergy Clin Immunol. 2017;139(3):1017–1025.e14
82. Abrahamsson TR, Jakobsson HE, Andersson AF, Björkstén B, Engstrand L, Jenmalm MC. Low gut microbiota diversity in early infancy precedes asthma at school age. Clin Exp Allergy. 2014;44(6):842–850
83. Zijlmans MA, Korpela K, Riksen-Walraven JM, de Vos WM, de Weerth C. Maternal prenatal stress is associated with the infant intestinal microbiota. Psychoneuroendocrinology. 2015;53:233–245
84. Korpela K, Zijlmans MA, Kuitunen M, et al. Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use. Microbiome. 2017;5(1):26
85. Nobel YR, Cox LM, Kirigin FF, et al. Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nat Commun. 2015;6:7486
86. Cerdó T, Ruiz A, Jáuregui R, et al. Maternal obesity is associated with gut microbial metabolic potential in offspring during infancy [published online ahead of print August 17, 2017]. J Physiol Biochem. doi: 10. 1007/ s13105- 017- 0577- x
87. Ba Q, Li M, Chen P, et al. Sex-dependent effects of cadmium exposure in early life on gut microbiota and fat accumulation in mice. Environ Health Perspect. 2017;125(3):437–446
88. Kalliomäki M, Collado MC, Salminen S, Isolauri E. Early differences in fecal microbiota composition in children may predict overweight. Am J Clin Nutr. 2008;87(3):534–538
89. Dogra S, Sakwinska O, Soh SE, et al; GUSTO Study Group. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity. MBio. 2015;6(1):e02419–14
90. Cho I, Yamanishi S, Cox L, et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature. 2012;488(7413):621–626
91. Vael C, Verhulst SL, Nelen V, Goossens H, Desager KN. Intestinal microflora and body mass index during the first three years of life: an observational study. Gut Pathog. 2011;3(1):8
92. Moussaoui N, Jacobs JP, Larauche M, et al. Chronic early-life stress in rat pups alters basal corticosterone, intestinal permeability, and fecal microbiota at weaning: influence of sex. J Neurogastroenterol Motil. 2017;23(1):135–143
93. Buffington SA, Di Prisco GV, Auchtung TA, Ajami NJ, Petrosino JF, Costa-Mattioli M. Microbial reconstitution reverses maternal diet-induced social and synaptic deficits in offspring. Cell. 2016;165(7):1762–1775
94. Carlson AL, Xia K, Azcarate-Peril MA, et al. Infant gut microbiome associated with cognitive development. Biol Psychiatry. 2018;83(2):148–159
95. Gareau MG, Jury J, MacQueen G, Sherman PM, Perdue MH. Probiotic treatment of rat pups normalises corticosterone release and ameliorates colonic dysfunction induced by maternal separation. Gut. 2007;56(11):1522–1528
96. O’Mahony SM, Marchesi JR, Scully P, et al. Early life stress alters behavior, immunity, and microbiota in rats: implications for irritable bowel syndrome and psychiatric illnesses. Biol Psychiatry. 2009;65(3):263–267
97. Foley KA, Ossenkopp KP, Kavaliers M, Macfabe DF. Pre- and neonatal exposure to lipopolysaccharide or the enteric metabolite, propionic acid, alters development and behavior in adolescent rats in a sexually dimorphic manner. PLoS One. 2014;9(1):e87072
98. Diaz Heijtz R, Wang S, Anuar F, et al. Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci USA. 2011;108(7):3047–3052
99. Bruce-Keller AJ, Fernandez-Kim SO, Townsend RL, et al. Maternal obese-type gut microbiota differentially impact cognition, anxiety and compulsive behavior in male and female offspring in mice. PLoS One. 2017;12(4):e0175577
100. Stilling RM, Ryan FJ, Hoban AE, et al. Microbes & neurodevelopment—absence of microbiota during early life increases activity-related transcriptional pathways in the amygdala. Brain Behav Immun. 2015;50:209–220
101. Jašarević E, Howerton CL, Howard CD, Bale TL. Alterations in the vaginal microbiome by maternal stress are associated with metabolic reprogramming of the offspring gut and brain. Endocrinology. 2015;156(9):3265–3276
102. Jin S, Zhao D, Cai C, et al. Low-dose penicillin exposure in early life decreases Th17 and the susceptibility to DSS colitis in mice through gut microbiota modification. Sci Rep. 2017;7:43662
103. Candon S, Perez-Arroyo A, Marquet C, et al. Antibiotics in early life alter the gut microbiome and increase disease incidence in a spontaneous mouse model of autoimmune insulin-dependent diabetes [published correction appears in PLoS One. 2016;11(1):e0147888]. PLoS One. 2015;10(5):e0125448
104. Hu Y, Jin P, Peng J, Zhang X, Wong FS, Wen L. Different immunological responses to early-life antibiotic exposure affecting autoimmune diabetes development in NOD mice. J Autoimmun. 2016;72:47–56
105. Hu Y, Peng J, Tai N, et al. Maternal antibiotic treatment protects offspring from diabetes development in nonobese diabetic mice by generation of tolerogenic APCs. J Immunol. 2015;195(9):4176–4184
106. Livanos AE, Greiner TU, Vangay P, et al. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nat Microbiol. 2016;1(11):16140
107. Kostic AD, Gevers D, Siljander H, et al; DIABIMMUNE Study Group. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015;17(2):260–273
108. Miyoshi J, Bobe AM, Miyoshi S, et al. Peripartum antibiotics promote gut dysbiosis, loss of immune tolerance, and inflammatory bowel disease in genetically prone offspring. Cell Reports. 2017;20(2):491–504
109. Millar M, Seale J, Greenland M, et al. The microbiome of infants recruited to a randomised placebo-controlled probiotic trial (PiPS trial). EBioMedicine. 2017;20:255–262
PEDIATRICS Volume 141, number 4, April 2018 21 by guest on August 10, 2020www.aappublications.org/newsDownloaded from
110. Strunk T, Hibbert J, Doherty D, et al. Probiotics and antimicrobial protein and peptide levels in preterm infants. Acta Paediatr. 2017;106(11): 1747–1753
111. Trompette A, Gollwitzer ES, Yadava K, et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med. 2014;20(2):159–166
112. Harris HR, Willett WC, Vaidya RL, Michels KB. An adolescent and early adulthood dietary pattern associated with inflammation and the incidence of breast cancer. Cancer Res. 2017;77(5):1179–1187
STIEMSMA and MICHELS22 by guest on August 10, 2020www.aappublications.org/newsDownloaded from
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Leah T. Stiemsma and Karin B. MichelsThe Role of the Microbiome in the Developmental Origins of Health and Disease
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