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22. American Diabetes Association, Diabetes Care 24, 775778 (2001). 23. S. Marshall, O. Nadeau, K. Yamasaki, J. Biol. Chem. 279, 3531335319 (2004). ACKNOWLEDGMENTS O.L., G.W.H., and R.L.H. designed all experiments; the optogenetics experiments were also designed by Y.A. and J.E.S., and the elecotrophysiological experiments were also designed by I.H. O.L. performed all experiments and analyzed all data but the electrophysiology (I.H.) and the optogenetics (J.E.S.). The optogenetics data were analyzed by J.E.S., Y.A., and O.L. O.L., G.W.H., and R.L.H. wrote the manuscript. We thank G. Schütz for providing the aCaMKII-CreER T2 mice, J. L. Bedont for help with in situ hybridization experiments, and R. H. White for assistance with mating and genotyping. All data necessary to understand and assess the conclusions of the manuscript are in the body of the paper and in the supplementary materials. All primary data are archived on a secure server located in the Department of Neuroscience at Johns Hopkins University (JHU). All data will be made available upon request. G.W.H. receives a share of royalty received by the university on sales of the CTD 110.6 antibody, which are managed by JHU. The research was supported by NIH (grant R01NS036715 to R.L.H. and grants R01DK6167, N01-HV-00240, and P01HL107153 to G.W.H.) and the National Institute on Drug Abuse Intramural Research Program (Y.A.). SUPPLEMENTARY MATERIALS www.sciencemag.org/content/351/6279/1293/suppl/DC1 Materials and Methods Figs. S1 to S9 References (2429) 29 September 2015; accepted 5 February 2016 10.1126/science.aad5494 MICROBIOTA The maternal microbiota drives early postnatal innate immune development Mercedes Gomez de Agüero, 1 * Stephanie C. Ganal-Vonarburg, 1 * Tobias Fuhrer, 2 Sandra Rupp, 1 Yasuhiro Uchimura, 1 Hai Li, 1 Anna Steinert, 1 Mathias Heikenwalder, 3 Siegfried Hapfelmeier, 4 Uwe Sauer, 2 Kathy D. McCoy, 1 * Andrew J. Macpherson 1 *Postnatal colonization of the body with microbes is assumed to be the main stimulus to postnatal immune development. By transiently colonizing pregnant female mice, we show that the maternal microbiota shapes the immune system of the offspring. Gestational colonization increases intestinal group 3 innate lymphoid cells and F4/80 + CD11c + mononuclear cells in the pups. Maternal colonization reprograms intestinal transcriptional profiles of the offspring, including increased expression of genes encoding epithelial antibacterial peptides and metabolism of microbial molecules. Some of these effects are dependent on maternal antibodies that potentially retain microbial molecules and transmit them to the offspring during pregnancy and in milk. Pups born to mothers transiently colonized in pregnancy are better able to avoid inflammatory responses to microbial molecules and penetration of intestinal microbes. D uring pregnancy, the eutherian fetus in- habits a largely sterile environment in utero, protected from infections by mater- nal immunity. Rejection of the allogeneic fetus is avoided through maternal and fe- tal vascular separation, the immune privileged status of the placental trophoblast, and gesta- tional maternal tolerance mechanisms (1). At birth, the situation changes dramatically as body sur- faces become progressively colonized with microbes, directly exposing the immature neonatal immune system to potential pathogens (2, 3). Despite continued protection from the immunoglobulins and antibacterial peptides in milk, the conse- quence of this transition for human health is that most of the worldwide mortality in children up to 5 years old is due to infectious disease (46). Immune system development is both prepro- grammed in neonatal tissues and driven later by exposure to pathogenic and nonpathogenic mi- crobes (3). Germ-free mice have low immuno- globulin concentrations; lymphopenia of lymphoid structures; reduced bone marrow leukocyte pools; and aberrant innate and adaptive immune func- tions (7, 8). It has been widely assumed that most microbiota-driven immune alterations are post- natal effects induced by the neonates own micro- biota (2, 9, 10). Here, we challenge this assumption by asking how the maternal microbiota in preg- nancy alone affects the early postnatal immune system of the offspring. To achieve gestation-only colonization under conditions where the mice deliver their pups spon- taneously at term, we used a system in which pregnant dams are transiently colonized with genetically engineered Escherichia coli HA107 (11). Because this strain does not persist in the intestine, pregnant dams become germ-free again before term and naturally deliver germ-free pups (fig. S1A). Although E. coli is a minor component of the adult human microbiota, it is commoner in the neonatal intestine (12) and a frequent cause of human neonatal sepsis (13). Gestation-only colonization shapes the intestinal mucosal innate immune composition Gestation-only colonization with E. coli HA107 altered the numbers of early postnatal intestinal innate leukocytes in wild-type C57BL/6 mice. At postnatal day 14, there was an increase in small intestinal innate lymphoid cell (ILC) proportions and total numbers compared with germ-free con- trols, particularly the NKp46 + RORgt + ILC3 sub- set (Fig. 1, A and B, and fig. S1B). Small intestinal NKp46 + RORgt + ILC3 are described in germ-free mice (14), but persistently increased following transient gestational colonization, reaching a max- imum in 14- to 21-day-old pups: This increase persisted even after weaning (Fig. 1C and fig. S1C), consistent with increased small intestinal ILC3 content of colonized compared with germ-free mice (15) and the microbiota-dependent mod- ulation of RORgt expression in this subset (16). Increases in the expression of the cytokine interleukin-22 (IL-22) in this population have been observed following permanent colonization or the introduction of segmented filamentous bacteria to the microbiota (17, 18). Total numbers of IL-22expressing cells increased in line with the increased NKp46 + RORgt + ILC3 numbers as a result of gestational colonization, although in- dividual IL-22 expression levels did not change, likely because the pups were born and raised germ-free (fig. S1, D to F). There was also an increase in the small and large intestinal F4/80 + CD11c + mononuclear cells (iMNCs) in day 14 (d14) pups born to gestation- only colonized dams (Fig. 1, D and E, and fig. S2, A to C), whereas the F4/80 + CD11c macrophages, F4/80 lo CD11c + dendritic cells (DCs), and the CD103 + or CD11b + DC subpopulations were not signifi- cantly affected (Fig. 1, D and E, and fig. S2, B to E). The gestational effects on increased F4/80 + CD11c + iMNCs were also maximal between postnatal days 14 to 21, and they persisted until at least 8 weeks of age in the colon (Fig. 1F). Gestational coloniza- tion caused no significant changes in small intestinal ILC2 numbers (fig. S3, A and B) or in other early postnatal innate leukocyte populations in either systemic or intestinal tissues (table S1). These re- sults showed that temporary colonization of a pregnant dam has long-term consequences for certain populations of innate lymphoid and mono- nuclear cells in the intestines of her offspring. We next sought to verify that the effects of gestational E. coli on early postnatal innate leu- kocytes would also be seen with animals stably colonized by a different microbiota both in the mother and after birth. We compared C57BL/6 animals carrying the defined altered Schaedler flora (ASF) of eight microbes with germ-free con- trols. Both small intestinal NKp46 + ILC3 and in- testinal F4/80 + CD11c + MNC populations were increased in pups born to stably colonized ASF 1296 18 MARCH 2016 VOL 351 ISSUE 6279 sciencemag.org SCIENCE 1 Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3010 Bern, Switzerland. 2 Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland. 3 Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany. 4 Institute for Infectious Diseases, University of Bern, 3010 Bern, Switzerland. *These authors contributed equally to this work. Corresponding author: E-mail: [email protected] RESEARCH | RESEARCH ARTICLES on March 18, 2016 Downloaded from on March 18, 2016 Downloaded from on March 18, 2016 Downloaded from on March 18, 2016 Downloaded from on March 18, 2016 Downloaded from on March 18, 2016 Downloaded from on March 18, 2016 Downloaded from
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Page 1: MICROBIOTA Thematernal microbiotadrivesearly … · signatures that are consistent with adapting early postnatal immunity and intestinal function gen-erally to postnatal microbial

22. American Diabetes Association, Diabetes Care 24, 775–778(2001).

23. S. Marshall, O. Nadeau, K. Yamasaki, J. Biol. Chem. 279,35313–35319 (2004).

ACKNOWLEDGMENTS

O.L., G.W.H., and R.L.H. designed all experiments; the optogeneticsexperiments were also designed by Y.A. and J.E.S., and theelecotrophysiological experiments were also designed by I.H.O.L. performed all experiments and analyzed all data but theelectrophysiology (I.H.) and the optogenetics (J.E.S.). Theoptogenetics data were analyzed by J.E.S., Y.A., and O.L. O.L.,

G.W.H., and R.L.H. wrote the manuscript. We thank G. Schütz forproviding the aCaMKII-CreERT2 mice, J. L. Bedont for help with insitu hybridization experiments, and R. H. White for assistance withmating and genotyping. All data necessary to understand andassess the conclusions of the manuscript are in the body of thepaper and in the supplementary materials. All primary data arearchived on a secure server located in the Department ofNeuroscience at Johns Hopkins University (JHU). All data will bemade available upon request. G.W.H. receives a share of royaltyreceived by the university on sales of the CTD 110.6 antibody,which are managed by JHU. The research was supported byNIH (grant R01NS036715 to R.L.H. and grants R01DK6167,

N01-HV-00240, and P01HL107153 to G.W.H.) and the NationalInstitute on Drug Abuse Intramural Research Program (Y.A.).

SUPPLEMENTARY MATERIALS

www.sciencemag.org/content/351/6279/1293/suppl/DC1Materials and MethodsFigs. S1 to S9References (24–29)

29 September 2015; accepted 5 February 201610.1126/science.aad5494

MICROBIOTA

The maternal microbiota drives earlypostnatal innate immune developmentMercedes Gomez de Agüero,1* Stephanie C. Ganal-Vonarburg,1* Tobias Fuhrer,2

Sandra Rupp,1 Yasuhiro Uchimura,1 Hai Li,1 Anna Steinert,1 Mathias Heikenwalder,3

Siegfried Hapfelmeier,4 Uwe Sauer,2 Kathy D. McCoy,1* Andrew J. Macpherson1*†

Postnatal colonization of the body with microbes is assumed to be the main stimulus topostnatal immune development. By transiently colonizing pregnant female mice, we showthat the maternal microbiota shapes the immune system of the offspring. Gestationalcolonization increases intestinal group 3 innate lymphoid cells and F4/80+CD11c+

mononuclear cells in the pups. Maternal colonization reprograms intestinal transcriptionalprofiles of the offspring, including increased expression of genes encoding epithelialantibacterial peptides and metabolism of microbial molecules. Some of these effects aredependent on maternal antibodies that potentially retain microbial molecules and transmitthem to the offspring during pregnancy and in milk. Pups born to mothers transientlycolonized in pregnancy are better able to avoid inflammatory responses to microbialmolecules and penetration of intestinal microbes.

During pregnancy, the eutherian fetus in-habits a largely sterile environment inutero, protected from infections by mater-nal immunity. Rejection of the allogeneicfetus is avoided through maternal and fe-

tal vascular separation, the immune privilegedstatus of the placental trophoblast, and gesta-tionalmaternal tolerancemechanisms (1). At birth,the situation changes dramatically as body sur-faces becomeprogressively colonizedwithmicrobes,directly exposing the immature neonatal immunesystem to potential pathogens (2, 3). Despitecontinued protection from the immunoglobulinsand antibacterial peptides in milk, the conse-quence of this transition for human health is thatmost of the worldwide mortality in children upto 5 years old is due to infectious disease (4–6).Immune system development is both prepro-

grammed in neonatal tissues and driven later byexposure to pathogenic and nonpathogenic mi-crobes (3). Germ-free mice have low immuno-

globulin concentrations; lymphopenia of lymphoidstructures; reduced bonemarrow leukocyte pools;and aberrant innate and adaptive immune func-tions (7, 8). It has beenwidely assumed thatmostmicrobiota-driven immune alterations are post-natal effects induced by the neonate’s ownmicro-biota (2, 9, 10). Here, we challenge this assumptionby asking how the maternal microbiota in preg-nancy alone affects the early postnatal immunesystem of the offspring.To achieve gestation-only colonization under

conditionswhere themice deliver their pups spon-taneously at term, we used a system in whichpregnant dams are transiently colonized withgenetically engineered Escherichia coli HA107(11). Because this strain does not persist in theintestine, pregnant dams become germ-free againbefore term and naturally deliver germ-free pups(fig. S1A). Although E. coli is a minor componentof the adult human microbiota, it is commonerin the neonatal intestine (12) and a frequent causeof human neonatal sepsis (13).

Gestation-only colonization shapesthe intestinal mucosal innateimmune composition

Gestation-only colonization with E. coli HA107altered the numbers of early postnatal intestinalinnate leukocytes in wild-type C57BL/6 mice. Atpostnatal day 14, there was an increase in small

intestinal innate lymphoid cell (ILC) proportionsand total numbers compared with germ-free con-trols, particularly the NKp46+RORgt+ ILC3 sub-set (Fig. 1, A and B, and fig. S1B). Small intestinalNKp46+RORgt+ ILC3 are described in germ-freemice (14), but persistently increased followingtransient gestational colonization, reaching amax-imum in 14- to 21-day-old pups: This increasepersisted even after weaning (Fig. 1C and fig. S1C),consistent with increased small intestinal ILC3content of colonized compared with germ-freemice (15) and the microbiota-dependent mod-ulation of RORgt expression in this subset (16).Increases in the expression of the cytokineinterleukin-22 (IL-22) in this population havebeen observed following permanent colonizationor the introduction of segmented filamentousbacteria to themicrobiota (17, 18). Total numbersof IL-22–expressing cells increased in line withthe increased NKp46+RORgt+ ILC3 numbers asa result of gestational colonization, although in-dividual IL-22 expression levels did not change,likely because the pups were born and raisedgerm-free (fig. S1, D to F).There was also an increase in the small and

large intestinal F4/80+CD11c+ mononuclear cells(iMNCs) in day 14 (d14) pups born to gestation-only colonized dams (Fig. 1, D and E, and fig. S2,A to C), whereas the F4/80+CD11c–macrophages,F4/80loCD11c+ dendritic cells (DCs), and the CD103+

or CD11b+ DC subpopulations were not signifi-cantly affected (Fig. 1, D and E, and fig. S2, B to E).The gestational effects on increased F4/80+CD11c+

iMNCswere alsomaximal betweenpostnatal days14 to 21, and they persisted until at least 8 weeksof age in the colon (Fig. 1F). Gestational coloniza-tion causedno significant changes in small intestinalILC2 numbers (fig. S3, A and B) or in other earlypostnatal innate leukocyte populations in eithersystemic or intestinal tissues (table S1). These re-sults showed that temporary colonization of apregnant dam has long-term consequences forcertain populations of innate lymphoid andmono-nuclear cells in the intestines of her offspring.We next sought to verify that the effects of

gestational E. coli on early postnatal innate leu-kocytes would also be seen with animals stablycolonized by a different microbiota both in themother and after birth. We compared C57BL/6animals carrying the defined altered Schaedlerflora (ASF) of eight microbes with germ-free con-trols. Both small intestinal NKp46+ ILC3 and in-testinal F4/80+CD11c+ MNC populations wereincreased in pups born to stably colonized ASF

1296 18 MARCH 2016 • VOL 351 ISSUE 6279 sciencemag.org SCIENCE

1Maurice Müller Laboratories (DKF), Universitätsklinik fürViszerale Chirurgie und Medizin Inselspital, Murtenstrasse35, University of Bern, 3010 Bern, Switzerland. 2Institute ofMolecular Systems Biology, Swiss Federal Institute ofTechnology (ETH) Zürich, 8093 Zürich, Switzerland. 3Divisionof Chronic Inflammation and Cancer, German Cancer ResearchCenter (DKFZ), Heidelberg, Germany. 4Institute for InfectiousDiseases, University of Bern, 3010 Bern, Switzerland.*These authors contributed equally to this work. †Correspondingauthor: E-mail: [email protected]

RESEARCH | RESEARCH ARTICLES

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Page 2: MICROBIOTA Thematernal microbiotadrivesearly … · signatures that are consistent with adapting early postnatal immunity and intestinal function gen-erally to postnatal microbial

mothers compared with germ-free controls (fig.S4, A and B). Colonization of adult germ-freeC57BL/6 animals with an ASF microbiota for21 days also selectively increased intestinalNKp46+

ILC3 and F4/80+CD11c+ iMNC populations (fig.S4, C and D, and table S2). Given that the ASFmicrobiota does not contain Proteobacteria, weconcluded that the innate leukocyte alterationsseen through gestation-only colonization withE. coli are also present in mice colonized with adefined microbiota, dominated by Bacteroidesdistasonis (19). Nevertheless, given the altera-tions in adaptive immunity when germ-freemiceare permanently colonized with amicrobiota (8),we next assessed the extent of adaptive immunechanges after gestation-only colonization.

Maternal gestational colonizationdoes not affect adaptive immunecomposition of pups

We found that gestation-only colonization didnot alter relative or absolute populations of B orT cells during development in the bone marrow,spleen, or thymus (fig. S5, A and B). Intestinal

and systemic CD4 or CD8 T cell numbers, T cellactivation status (table S3), CD4 subpopulations(fig. S5, C to G), and intestinal microarchitecture(fig. S6) were also generally unaffected. Becauseall the neonatal mice in these experiments weregerm-free, we concluded that the well-knownmicrobiota-driven effects of amplification of Band T cell numbers and resulting reorganizationof lymphoid structures result from postnatal col-onizationwith an endogenousmicrobiota (19–21).

Maternal microbiota induces intestinaltranscriptional reprogramming in offspring

Many functions of the neonatal intestine are de-velopmentally regulated, including transport ofnutrients, salts, and water; barrier function; andsecretion of antibacterial peptides and mucus(22). Because different aspects of intestinal devel-opment determine the ability of the neonate totolerate an incoming microbiota, we questionedwhether the changes in innate leukocytes aftergestational colonization were part of a muchwider range of adaptations triggered bymaternalexposure to intestinal microbes. We carried out

RNA sequencing (RNA-Seq) analysis of wholesmall intestinal mucosal RNA from neonates atday 14. Unsupervised analysis showed a series ofconsistent transcriptional changes in the pupsborn to gestation-only colonized dams comparedwith controls (Fig. 2A). The genetic and proteininteractions inferred from differentially expressedtranscripts (23) included up-regulated gene net-works for cell division and differentiation,mucusand ion channels, and the polymeric immuno-globulin receptor and mononuclear recruitment,as well as for metabolism of xenobiotics, bileacids, complex lipids, and sugars (Fig. 2B). Thesedifferentially expressed genes included signif-icantly increased overall expression of signaturegenes for the different Paneth cell, goblet cell, andearly/late enterocyte precursor epithelial lineages(24, 25) (fig. S7, A to C). Transcripts for the C-lectinReg family and antibacterial defensin peptideswere also significantly increased in the pups ofgestation-only colonized dams compared withcontrols (Fig. 2C and fig. S7D).These results show that the maternal micro-

biota drives wide-rangingmucosal transcriptional

SCIENCE sciencemag.org 18 MARCH 2016 • VOL 351 ISSUE 6279 1297

Fig. 1. Maternal microbial exposure during pregnancy shapes the frequen-cy of intestinal innate lymphoid and mononuclear cell populations in theoffspring. Germ-free C57BL/6 dams were transiently colonized with E. coliHA107 (gestational colonization) or kept germ-free throughout (controls). Alloffspring were analyzed by flow cytometry at day 14 after birth unless indi-cated. (A) Representative dot plots showing Lin– (CD19–CD3–) small intestinallamina propria lymphocytes (upper row) and Lin–RORgt+NKp46– ILC3 (lowerrow). (B) Absolute numbers (geometric mean, sample number n ≥ 5) of theindicated Lin– small intestinal ILC populations. (C) Absolute numbers of

small intestinal Lin–NKp46+RORgt+ ILC3 at indicated time points after birth.Data represent geometricmean±SD,n=3 to 10per timepoint. (D)Representativedot plots showing Lin–MHC-II+ colon lamina propria intestinal mononuclear cells(iMNCs) (upper row) and Lin–MHC-II+CD11c+F4/80lo iMNCs (lower row). (E) Ab-solute numbers (geometric mean, n ≥ 5) of indicated Lin–MHC-II+ iMNCpopulations in the colon. (F) Absolute numbers (geometricmean ± SD, n= 3 to10 per time point) of colon Lin–MHC-II+CD11c+F4/80+ iMNCs at different timepoints after birth. Data are each representative of four independent experi-ments or show pooled data from four experiments. *P ≤ 0.05; **P ≤ 0.01.

RESEARCH | RESEARCH ARTICLES

Page 3: MICROBIOTA Thematernal microbiotadrivesearly … · signatures that are consistent with adapting early postnatal immunity and intestinal function gen-erally to postnatal microbial

signatures that are consistent with adapting earlypostnatal immunity and intestinal function gen-erally to postnatal microbial colonization andthemetabolic consequences of inevitable bile saltand dietary xenobiotic exposure, even in pups borngerm-free. Thus,many aspects ofwhatmight havebeen thought of as canonical host epithelial de-velopment and innate immunity are likely shapedthrough maternal microbial colonization.

Gestational colonization effects dependon maternal antibodies

Live intestinalmicrobes, including E. coliHA107,generally do not penetrate the body further thanthe lymphnodesdraining the intestinalmesentery(26, 27), and we found no culturable organismsin the placenta after treatment in our gestationalcolonization experiments. It was therefore likelythat the effects of maternal gestational microbeson early postnatal innate immunity resulted frompenetration of microbial molecular products, firstto maternal tissues, and subsequently to the fetusor neonate. Supporting this hypothesis, we found

that serum transfer from gestation-only colonizedfemales to unexposed pregnant dams was suffi-cient to shape intestinal NKp46+ ILC3 populationsin the neonates (Fig. 3A and fig. S8, A and B), butnot when immunoglobulin G (IgG) was depletedfrom the serum before transfer, nor when the ser-um was derived from gestationally colonized JH

−/−

antibody-deficient dams (fig. S8, A and B). Giventhe sufficiency of serum IgG transfer, antibodytransfer from themother toher offspringwas likelyimportant to realize some features of early post-natal immune development, because the gestation-only induction of small intestinal NKp46+ ILC3 bythematernalmicrobiota was lost in the antibody-deficient JH

−/− strain (Fig. 3, B andC).Weconfirmedthat this effect was due to the lack of maternalantibodies using a heterozygous strain combina-tion approach (fig. S8C). Nevertheless, not all as-pects ofmaternal microbiota-driven early postnatalimmune system development are antibody depen-dent, because induction of F4/80+CD11c+ iMNCswas preserved despite the lack of neonatal and/ormaternal antibodies (fig. S8, D and E).

Because NKp46+ ILC3 but not CD11c+F4/80+

iMNC increases are mediated through maternalantibody-dependent mechanisms after transientgestational colonization, we predicted that only asubset of the many transcriptional responses at-tributable to epithelial and other intestinal cellswould bematernal antibody-dependent. RNA-Seqanalysis was carried out in d14 ileum to comparethe responses ofC57BL/6wild-type andJH

−/−groups,each of which was compared to germ-free con-trols. Only a subset of up-regulated genes in allnetworkswerematernal antibody-dependent (Fig.3D and fig. S9, A to C). For example, althoughRegIIIa transcript numbers were elevated in thepups of antibody-deficient mothers, maximal up-regulation of RegIIIb and RegIIIg was antibodydependent (Fig. 3E and fig. S9D).

Maternal microbial molecular transfer tothe offspring

Maternal microbiota effects on the pups wereonly seen when the mother was transientlycolonized during pregnancy itself (fig. S10, A

1298 18 MARCH 2016 • VOL 351 ISSUE 6279 sciencemag.org SCIENCE

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Fig. 2. Maternal microbial exposure during pregnancy causes extensivechanges in the intestinal gene expression profile in neonates. Germ-freeC57BL/6 dams were transiently colonized with E. coliHA107 during pregnancy(gestational colonization) or kept germ-free throughout (controls).Whole-tissueRNA from the small intestinewas isolated from the offspringonday 14after birthand used for RNA-Seq (n = 3 per group). (A) Heat map of genes differentially ex-pressed (fold-change≥ 2; adjustedP value padj < 0.001).The color scale shows

the relative expression profiles. (B) Upper:Volcano plot showing fold-change ofgene expression in offspring born to gestationally colonizedmothers comparedto offspring born to controlmothers.Genes with significantly different expressionbetween the two groups (fold-change ≥ 2; padj < 0.01) are highlighted in red;lower: STRINGanalyses for significantly altered transcripts in each case. (C) Fold-change of selected transcripts for antimicrobial peptides between the gesta-tionally colonized and control pups (***padj < 0.001; see also data file S1).

RESEARCH | RESEARCH ARTICLES

Page 4: MICROBIOTA Thematernal microbiotadrivesearly … · signatures that are consistent with adapting early postnatal immunity and intestinal function gen-erally to postnatal microbial

and B). In mice, maternal IgG is transferredacross the placenta and through intestinal up-take from the milk (28), so we used litter-swapexperiments to distinguish between antenataland postnatal effects of the maternal microbiota.Although there was a nonsignificant trend to-ward increased small intestinal NKp46+ ILC3 inneonates born to an unmanipulated mother andnursed by a gestation-only colonized mother,both in utero gestation and postnatal nursing bydams that had been colonized during pregnancywere necessary for significant ILC3 induction(Fig. 4A).These results imply that maternal microbiota-

derived compounds are transferred fromthemoth-er to the offspring and that this process is increasedin the presence of maternal antibodies. We nextconsidered antibody-enhanced retention of bacte-rial products in themother and antibody-mediatedtransfer of bacterial products. The first of theseeffects was demonstrated by following 14C elim-ination from metabolically labeled E. coli HA107in wild-type and antibody-deficient mice. Thepresence of antibodies significantly increasedretention of 14C-labeledmolecules in themesenteric

lymph nodes, spleen, liver, and serum for at least36 hours compared with antibody-deficient con-trols (Fig. 4, B andC, and fig. S11, A toD):Microbialmolecular exposure of the placenta and the fetuswas also enhanced at embryonic day 16 (E16) (Fig.4, D and E). We also found significantly increasedradioactivity originating from maternal micro-bial molecules in the milk, and from postnatalintestinal mucosa and liver of wild-type pups(Fig. 4, F to I). This shows that maternal anti-bodies enhance the retention and transmissionofmicrobialmolecules, although effects other thandirect microbial molecular binding cannot beexcluded. To verify that these compounds arereally ofmicrobial origin rather than the productsof secondary metabolism in the mother, we grewHA107 on [13C]glucose so that bacterial com-pounds became fully labeled with 13C, as judgedby mass spectrometry–shift data. Intestinal 13C-labeled metabolite levels were equivalent wheth-er or not the mother expressed antibodies (fig.S12); however, after intestinal administration of13C-labeled HA107 in C57BL/6 intravenously (i.v.)primed mice, serum contained bacterial metab-olites comigrating with IgG that were absent

from the serum of antibody-deficient mice (fig.S13 and data file S5). Even if HA107 was onlydelivered through the intestinal route, which doesnot induce high-affinity serum IgG (11), therewas evidence of low-affinity IgG coating of E. colithat was absent from serum of untreated germ-free controls or from HA107-treated JH-deficientmice (fig. S14). We therefore concluded that ei-ther sterile bacterial fragments or small moleculescan potentially be bound to maternal IgG afterintestinal exposure.Given that increases in NKp46+ ILC3 and com-

ponents of the mucosal transcriptome were anti-body dependent, whereas F4/80+CD11c+ iMNCswere induced by gestational colonization even inpups of antibody-deficient dams, we assumedthat a number of molecular ligand–receptor sys-tems are driving different aspects of neonataladaptation in response to the maternal micro-biota. Toll-like receptor ligand signaling was notessential for the effect (fig. S15, A and B). Therewas an extensive range of bacterial-derived (13C-labeled) molecules passed from the mother tothe offspring (Fig. 5A and fig. S16), some of whichalso reached neonatal tissues (fig. S16). These

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Fat storage

Cholesterol derived hormone

production

Cholesterol synthesis

Inflammatory signals

Sugar

met

aboli

sm

Metabolism of dietary

xenobiotics/bile acids

Metabolicregulation

Sugar

metabolism Metabolic

regulation

Metabolism of dietary xenobiotics/bile acids

Ion channels/mucus /secretionIon

channels /mucus /secretion

n= 228

n= 85

n=95

Antibody-dependent networks

Antibody-independent

networks

Networks in the absence of antibodies

Sqle

Lss

Sc4mol Cyp51

Idi1

Ryr1

Lrat

Bst1

Defa1

Hmgcr Il1rl1

Rhof

Il1a

Mmp7

Vav2

Abcg5 Adipoq

HpPcsk9

FgaSlc22a1

Slc36a2Retn

CfdHgdHabp2

Dpp4Mgam

Adcy1Vipr1

Atp1b1

Ccl25

Agtr2

Anpep

Ggt1Gpx2

Ppara

Cyp2j13

Hnf4g

Acsm3

Cyp2c66

Cyp2c55Akr1c14

GykAkr1b7

Cyp2j6Ugt2b35 Plb1

Khk

Ugt2b34Slc2a5

Cyp2d26

Slc5a1Cyp3a13

Slc26a6 Sult2b1Sult1d1

Fmo4

Hkdc1

ControlGestational colonization

WT

JH-/-

RORγ t

NK

p46

101

102

103

104

Abs

olut

e ce

ll nu

mbe

r ***

JH-/-WT

n.s.

Treh

Ang4

Sis

Defa20

Oas3H2-Q1

Clca3

Pla2g2a

Tff2Cyp4f14

Chdh

Dmbt1

Zg16

Cyp2c65

Pnliprp2

Cyp3a11

Rdh7Cyp3a25

Ugt2a3

10.97 1.58

56.4 31.0

8.03 3.79

50.1 38.1

9.60 1.18

56.5 32.8

7.54 1.09

57.2 34.2

ControlGestationalcolonization

WT (Gestational colonization vs control) (Gestational colonization vs control)

JH-/-

WTJH -/-

Lo

g2

(fo

ld- c

ha

ng

e)(g

est.

colo

niza

tion

t o c

ontro

l)

-4

-2

0

2

4 *** *** *** *** **

Reg3a Reg3b Reg3g CAMP Hmgb1

WT

Abs

olut

e ce

ll nu

mbe

r

103

104

105 **

Control

Gestationalcolonization HA107 serum

NKp46+ ILC3

NKp46+ ILC3

Fig. 3. Sufficiency of serum transfer and requirement for maternalantibodies for gestational colonization effects. (A) Pregnant germ-freeC57BL/6 dams were transiently colonized (gestational colonization), leftgerm-free (control), or injected i.v. with serum from a germ-free donor pre-viously gavaged with E. coliHA107 (HA107 serum).Total Lin–RORgt+NKp46+

ILC3 (geometric mean, n ≥ 2) in d14 offspring small intestine. (B to E)Germ-free C57BL/6 (WT,wild type) or JH

−/− damswere colonizedwith E. coliHA107 during pregnancy (gestational colonization) or kept germ-free (con-trol). (B) Representative flow cytometry dot plots showing Lin–RORgt+NKp46+

ILC3 in d14 small intestine. (C) Total numbers (geometric mean, n ≥ 3) of

Lin–RORgt+NKp46+ ILC3 in d14 small intestine. (D and E) RNA-Seq of d14distal small intestinal RNA in offspring of JH

−/− and wild-type dams (n = 3 pergroup). (D) STRING analysis comparing genes significantly enriched aftergestational colonization versus germ-free in either WT (black circle) or JH

−/−

(blue circle) strains. Total number of differentially regulated genes areshown. (E) Fold-change of expression of indicated genes in offspring fromgestationally colonized compared to control mothers in WTor JH

−/− strains(***padj < 0.001, see also data files S2 and S3). Data are representative oftwo (A) and three (B and C) independent experiments. (A and C) **P ≤ 0.01;***P ≤ 0.001.

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1300 18 MARCH 2016 • VOL 351 ISSUE 6279 sciencemag.org SCIENCE

n.d.Amino SugarsAmino Acids and DerivativesMonosaccharidesTrisaccharidesOligosaccharidesDisaccharidesFatty Acid EstersFatty Acids and ConjugatesGlycerolipidsGlycerophospholipids

log2(fold-change)Control Gestational C-HA10713

103

104

105

Abs

olut

ece

llnu

mbe

r * *

Control waterColonization

NOD ligandsSCFAs

RIG-I ligands

Gestational treatment:

Control Colonization

I3CSolvent

Gestational treatment:

WT

WT

-log1

0(p-

valu

e)

-log1

0(p-

valu

e)

WT Milk JH Milk-/-

-2 0 2 40

0.5

1

1.5

2

2.5

3

3.5

4

4.5

10

-2 0 2 40

0.5

1

1.5

2

2.5

3

3.5

4

4.5

10

12

49

73

,!"#

$!!"#

76

319

238

Tissue Compound Sum formula WT JH-/-

fold-change p-value fold-change p-value

Milk Kynurenine [+10] C10H12N2O3 7.807 0.0325 2.529 > 0.05

Indolelactic acid [+11] C11H11NO3 6.790 0.0341 n.d.

5-Hydroxy-L-tryptophan [+11] C11H12N2O3 5.248 0.0308 1.791 > 0.05

Hydroxykynurenamine [+9] C9H12N2O2 4.973 0.0278 0.974 > 0.05

Hydroxykynurenine [+10] C10H12N2O4 4.539 0.0406 1.457 > 0.05

5-Methoxytryptamine [+11] C11H14N2O 4.181 0.0380 1.190 > 0.05

5-Methoxytryptophol [+11] C11H13NO2 3.808 0.0109 1.235 > 0.05

Indole-5,6-quinone [+8] C8H5NO2 2.024 0.0019 1.307 0.0057

Neonatal liver Hydroxykynurenine [+10] C10H12N2O4 2.394 < 0.0001 1.679 0.0015

Neonatal spleen Hydroxykynurenine [+10] C10H12N2O4 2.754 < 0.0001 1.656 0.0015

log2(fold-change)Control Gestational C-HA10713

NKp46+ ILC3

NKp46+ ILC3

Abs

olut

ece

llnu

mbe

r

103

104

105

Fig. 5. Profiles of maternal microbial molecules shaping the neonatalimmune system. (A to C) Pregnant germ-free wild-type or JH

−/− mice weregavaged on E10 and E12 with unlabeled E. coli HA107, and on E15 and E16 with13C-labeled E. coli HA107. Maternal milk (gestationally colonized, n = 6 to 8;germ-free control, n = 2) was analyzed by mass spectrometry. (A and B)Volcano plots of fold-change analysis betweenmilk from treated and untreatedWT (A) and JH

−/− (B) dams. Metabolite compound classes are color-coded.Inset histogram: percentage 13C labeling for each significantly altered com-pound (fold-change ≥ 2; P ≤ 0.05): unlabeled (white), ≥25% labeled (gray),100% labeled (black). A total of 395 potentially 13C-labeled compounds were

significantly enriched in the milk of WTdams. (C) Fully labeled metabolites ofthe AhR ligand class present in d1 to d3 milk of WT and JH

−/− femalesgestationally exposed to 13C-HA107. See also data file S4. (D) Pregnantgerm-free C57BL/6 mice were gavaged with indole-3-carbinol (I3C) or sol-vent, or gestationally colonized.Total numbers of Lin–RORgt+NKp46+ ILC3 inthe d14 offspring small intestine (geometric mean, n ≥ 6). (E) Pregnantgerm-free C57BL/6 mice were exposed to short-chain fatty acids (SCFAs),NOD1/2 ligands, or RIG-I ligand or gestationally colonized. Total numbers ofLin–RORgt+NKp46+ ILC3 in d14 offspring small intestine (geometric mean, n ≥3). Data are representative of three (D) independent experiments. *P ≤ 0.05.

102

103

104

105

Mother: Foster:

ctrl HA107 HA107 ctrlctrl HA107 HA107ctrl

Parental MLN

*****

*

***

WT Back-ground

JH-/-

Placenta, E16

******

DP

M/g

*

Back-ground

120h36h8h

*

Abs

olut

e ce

ll nu

mbe

r WTAntibody-deficient

102

103

104

105

Parental liver

DP

M/g

*

Back-ground

120h36h8h

*

10 2

10 3

10 4

10 5

DP

M/g

102

103

104*

DP

M/g

102

103

104

105 ***

WT Back-ground

JH-/-

Fetus, E16

******

p=0.1

WT Back-ground

JH-/-

Maternal milk, d1/2

**

DP

M/g

102

103

104

Offspring liver

DP

M/g

Back-ground

d10/11d6/7d1102

103

104

105

*

Offspring spleen

DP

M/g

Back-ground

d10/11d6/7d1102

103

104

******

***

Offspring small intestine

DP

M/g

Back-ground

d10/11d6/7d1102

103

104

NKp46+ ILC3

WTAntibody-deficient

Fig. 4. Maternal microbial molecules reach the offspring during preg-nancy and after birth. (A) Pregnant germ-free C57BL/6 mice were colo-nized with E. coli HA107 or germ-free (ctrl). Half of each litter was swappedto another group for fostering at birth.Total numbers (geometric mean, n ≥8) of Lin–RORgt+NKp46+ ILC3 in the offspring small intestine on postnatalday 14. (B and C) Adult germ-free WTor Rag1−/− (antibody-deficient) micereceived three gavages of 1010 colony-forming units (CFU) of unlabeled E. coliHA107 and one gavage of 1010 CFU of 14C-labeled E. coli HA107. Radio-activity in the indicated tissues of WT and Rag1−/− adults was monitored

over time. (D to F) Pregnant germ-free C57BL/6 WT or JH−/− mice were

gavaged with 1010 CFU of 14C-labeled E. coli HA107 on E14. Placental or fetaltissues at E16 (D and E) or milk at d1/2 after birth (F) fromWTor JH

−/− micewas analyzed for radioactivity. (G to I) Postnatal tissues from WT offspringwere analyzed for persistence of transferred radioactive maternal microbialproducts. Geometric means are shown. Open circles show backgroundscintillation in offspring from nongavaged mice (B to I). Results are repre-sentative of three (A) or two (D to I) independent experiments. *P ≤ 0.05;**P ≤ 0.01; ***P ≤ 0.001.

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bacterial-derived metabolites present in milk oroffspring tissues from gestationally colonizedmiceincluded natural microbial ligands for the arylhydrocarbon receptor (AhR) or their precursors(Fig. 5, A to C, and table S4) (29). Most of thesebacterial metabolites, including the fully labeledAhR ligands (Fig. 5C), were not enriched in themilk of treated JH

−/− mice (Fig. 5, B and C), al-though these data do not prove that these mol-

ecules are necessarily bound to the antibodies fortransfer. Because AhR-deficientmice have a com-pound phenotype (30), and strain combinationexperiments reveal globally nonredundant signal-ing pathways, we took the approach of treatingpregnant germ-free mice with authentic ligandsfor AhR, short-chain fatty acids, nucleotide-binding oligomerization domain (NOD) ligandsand the retinoic acid–inducible gene I (RIG-I)

ligand. Of these, only the AhR ligand (indole-3-carbinol, I3C) increased NKp46+ ILC3 in theoffspring of the treatedmothers (Fig. 5, D and E).This occurred even in the absence of antibodies,although to a significantly lower extent (fig. S17,A and B). Although this shows that early postnatalNKp46+ ILC3 numbers are increased in responseto aryl hydrocarbons, antibodies are not essentialfor the effect provided that a sufficient dose of

SCIENCE sciencemag.org 18 MARCH 2016 • VOL 351 ISSUE 6279 1301

0

20

40

60

CF

U/o

rgan

PBS JM83 PBS JM83Challenge:

***

Bacteria translocation MLNE. coli JM83

Bacteria translocation MLN B. fragilis

0

20

40

60 **

A B

D

-2 0 2

010

2030

40

log2 (fold-change)

-log1

0 (p

adj)

ControlGestational colonization

50

CF

U/o

rgan

upregulated in gestational

colonized group

upregulated in control

group

Man2b2

Naga

Man2b1Fuca1

Lgmn

Dlk1Dgat2

Fabp4

HexaAmdhd2

Gpihbp1

St3gal5

Cfd

Ces1d

Fuca2

Renbp

Galns

Gusb

Ctsa

Npl

Neu1

Glb1

Gpx3

Slc17a5

G6pcGalk1

Gsta2Cryz

Gaa St3gal1

Ddit3 Hpgds

Bmp7 Cyp2e1Hmox1

Ftl1 Slc46a1

Slc40a1Hif3a

Apoc1Itgb5 Apoc3

Diras1

LtfHgd

Apoc4Spp2

Igfals

Lrrc10b

Apoa4

Entpd3

Fga

Lrrn1

Cfi

Rtn4r

FgbSaa1

Ttr

Pde4c

C9F10

Sucnr1

Rras

Galr2Sst

Cell cycle regulation

Signaling by GPCR

Amino sugar and nucleotide metabolism

Lipid metabolism

Glycosaminoglycan metabolism

Lysosome activity

Adaptation to microbial colonization

Detoxification of oxidative stress

Purinemetabolism

Fignl1Sass6

Zwilch

Lrr1Dsn1

Casc5Kif4Xpo1Sgol2

DckIqgap3 Nuf2

Cenpi Kntc1Kif20a

CenpfKif24 Bub1Ska1

Sgol1

Ckap2 Cenpe

Aurkb

Shcbp1

Bub1b Ccnb2

Tpx2

Spag5

Ccnb1Gca

Asf1b Hirip3Cdc25c

Tex30Nupl1Nup160

Cse1lMlf1ip Nek2 Pbk

Esco2

Topbp1

Cdkn3

AI448607

Ttk Tmem48

Cenpq

Mad2l1

Pola1

Ercc6l

Kif18a

Ankrd32

Cenpk

Rfc4TpteDtl

Exo1 Orc1Mcm8

Rrm2Chek1 Atr

Ccl2

Fbxo5

Atad2Haus6Cdc6 Dbf4Ncapg2

Ccna2

Smc2

Ckap2l Ccne2

E2f8Depdc1a

Noxin

Slc16a12

Insig1 Mki67

Mis18bp1Kif11

Kiaa1524

Hells

Smc4

Kif15

Top2a

Nusap1

AunipHnrnpa1

Ncapg

Kif20b

Aqp4

Aspm

HmmrBlm

Neil3

Rad54l

G2e3

Ppat

Racgap1Prc1

Kif14Plk4

Cep55

Arhgap11aGen1

Paf

Dkc1

Vav3

Polq

Dlgap5

BC055324Ect2Gbp1

Kif23Parpbp

Ska3

Stil

Pla2g4aDiap3

NcaphTrim59

Nox1 HmgcrPrr11 Aurka Kif18b

Melk Rps6ka6

Mitotic prometaphase,, metaphase and anaphase

APC and cell cycle regulation

Cellular growth and proliferationCell death and survival

Centrosome and chromatin

organization

Cell cycle check point

Control Gestational colonization

Gestationaltreatment:

E

Reg3a Reg3b Reg3g

C

Rag1-/-

****

PBS JM83 PBS JM83 PBS JM83 PBS JM83

Bacteria translocation MLNE. coli JM83

Challenge:

GF GF ASF d21 GF

Rag-/-

c-/-

**

GF

0

10

20

30

40

50

CF

U/o

rgan

Control Gestational colonization

B. fragilis B. fragilisChallenge:

Gestationaltreatment:

During pregnancy

101

102

103

104

105

# re

ads 19x

37x

25x

3x

3x

3x

******

PBSJM83PBSJM83

Control

Gestational colonization

Challenge

Fig. 6. Microbial exposure during pregnancy functionally protects theoffspring. (A, B, D, and E) Germ-free C57BL/6 dams were gestationallycolonized or kept germ-free. (A) Day 14 pups were challenged with 105 CFU ofE. coli JM83 or phosphate-buffered saline (PBS). Bacterial titers in mesentericlymph nodes (MLN) were determined at 18 hours (x ± SD, n ≥ 5). (B) Day 14pups were challenged with 1010 CFU of B. fragilis or PBS. Bacterial titers inMLNs were determined at 18 hours (x ± SD, n ≥ 10). (C) Adult germ-freeC57BL/6 Rag1−/− or Rag2−/−gc−/− were colonized for 21 days with ASFor keptgerm-free before challenge with 107 CFUof E. coli JM83 or PBS. Bacterial titers

at 18 hours in MLNs are shown (x ± SD, n ≥ 5). (D and E) Day 14 pups werechallenged with 105 CFU of E. coli JM83 or PBS (n = 3 per group) before smallintestinal RNA-Seq. 18 hours later. STRING analyses for differentially expressedtranscripts (fold-change ≥ 2; padj < 0.01, data file S6) compare challengedpups born to germ-free or gestationally colonizedmothers. (E) Read number ofindicated genes in E. coli– or PBS-challenged offspring (geometricmean, n= 3,***padj < 0.001; see also data files S7 and S8). Data are representative of three(A and C) or two (B) independent experiments. (A to C) *P ≤ 0.05; **P ≤ 0.01;***P ≤ 0.001.

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AhR ligand is transmitted from themother to heroffspring. Indeed, we found that ILC3 increasesinduced by an endogenous ASF microbiota inadult mice were also antibody independent, pre-sumably because endogenous colonization pro-vides a sufficient dose of bacterial ligands (fig.S17C). We concluded that maternal antibodiesassist the transfer of microbial compounds tothe offspring, but are not independently requiredto increase ILC3 numbers. Given the diversity ofmaternal microbial molecular transfer, it remainsprobable that other microbial molecular speciescan also drive early postnatal adaptation.

Gestational colonization effects oninnate immune precursors

The elevated number of intestinal NKp46+ ILC3and F4/80+CD11c+ iMNCs in the offspring bornto gestation-only colonized dams may result fromamplified precursor populations or increased pro-liferation of the mature intestinal population.Neonatal ILC3 precursors (14, 31) were not in-creased in the liver or intestine of E17 fetusesfrom gestationally HA107-colonized mice (fig.S18, A toD).We did detect increased proliferativecapacity of small intestinalNKp46+ ILC3 isolatedfrom 14-day-old pups born to gestation-onlycolonized dams (fig. S18, E and F). F4/80+CD11c+

iMNCs stem from CD11b+CX3CR1intLy6C+ mono-cytes (32, 33), which were significantly increasedin the colon lamina propria of 14-day-old pupsfrom gestationally colonized dams (fig. S18, Gand H).

Functional impact of gestationalcolonization on the early postnatalimmune system

To test whether the integrity of the early post-natal intestine to live microbial challenge wasimproved by gestational colonization, we chal-lenged pups with the replication-competentparent strain of HA107, E. coli JM83. Despiteequal E. coli cecal colonization at 18 hours, onlythe pups of gestationally colonized mothers ordams treated with the AhR ligand I3C couldavoid translocation of JM83 to the mesentericlymph nodes (Fig. 6A and fig. S19, A and B).Because presence of HA107-specific antibodiesmight contribute to E. coli–primed protection,we confirmed these results by challenge withBacteroides fragilis, where HA107-induced anti-bodies do not cross-react (Fig. 6B and fig. S19C).To verify the role of ILC3 in intestinal integrity

(34), we exploited the fact that ILC3 can be in-duced in adults independently of B cells and anti-bodies (fig. S17C and table S5). Comparison ofRag−/− and Rag−/−gc

−/− mice (which lack ILCsas well as B and T cells) showed that ILCs wererequired to mediate the microbiota-driven pro-tection from bacterial translocation during chal-lenge with JM83 (Fig. 6C).Systemic immune responsiveness is also likely

shaped by gestational colonization, as tumor ne-crosis factor–a and IL-6 proinflammatory cytokineproduction was reduced in the pups’ splenocytesafter intraperitoneal lipopolysaccharide (fig.S20). Because ILC3 are a very minor population

in the spleen, the mechanism is likely to be quitedistinct from the gestational effects on intestinalfunction.These functional readouts of gestational colo-

nization only show some of the potential benefitsof maternal microbial molecular exposure in thepups. After challengewith replication-competentE. coli, small intestinal RNA-Seq analysis showedexpression of antioxidant and lysosomal enzymenetworks in the pups of gestation-only colonizeddams, whereas control pups had wide-rangingexpression signatures for cellular proliferation,cytoskeletal organization, and ribosome biosynthe-sis (Fig. 6D and fig. S21A). Expression of somegenes for antimicrobial peptides induced bygestational colonization also increased furtherafter intestinal bacterial challenge (Fig. 6E andfig. S21B).

Conclusion

The maternal microbiota prepares the newbornfor host-microbial mutualism. This results frommicrobial molecular transfer because in our ex-perimental system, live microbes are no longerpresent at birth; we do not detect live microbesin the placenta or the neonate; and the result canbe recapitulated with sterile serum transfer. Inother words, maternal antibodies not only pro-tect the neonate through pathogen neutraliza-tion (4, 5), but also have a more general effectpromoting microbial molecular transfer. Short-chain fatty acids from microbes are known toshape the adult immune system (35, 36).We showhere that ligands for the AhR, known to driveILC3 expansion (37) and limit adult bacterialtranslocation (38), can be derived from the ma-ternal microbiota and shape the composition andfunction of early postnatal immunity.Nevertheless,AhR ligands are unlikely to be the onlymolecularmechanism involved in gestational microbialshaping.Secretory antibodies in the milk are known

to delay the maturation of the early postnatalimmune system and determine long-term intes-tinal microbiota composition (39–41). Here weshow that maternal antibodies also enhance mi-crobial molecular levels in the fetus and the neo-nate. Themolecular constituents of the maternalmicrobiota are able to ready neonatal innate im-munity in time for the tsunami of microbes thatsuccessively colonize the intestine (42, 43). Althoughthese studies were focused on benign microbes, theimmune morphogenesis driven by the maternalmicrobiota is likely also to benefit young mam-mals when they encounter pathogens. Postnatalmicrobial colonization is a pivotal early event inautonomous host-microbialmutualism. Fortunately,the maternal microbiota and maternal immunityprepare the neonate for its inevitable challenges.

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ACKNOWLEDGEMENTS

We thank W.-D. Hardt, C. Mueller, and D. Candinas for criticalinput and support. J. Limenitakis and I. Keller helped withbioinformatic analyses. The data presented in this manuscriptare tabulated in the main paper and in the supplementary materials;sequencing data are available via www.ebi.ac.uk/ena/data/view/PRJEB12398. E. coli HA107 is available from A.J.M. undera material transfer agreement with the University of Bern. TheClean Mouse Facility is supported by the Genaxen Foundation,Inselspital and the University of Bern. This work was funded bythe Swiss National Science Foundation (SNSF 310030B_160262,SNF Sinergia CRSII3_136286, and SNSF Sinergia CRSII3_154414)to A.J.M. K.D.M is supported by a grant from the SNSF(SNSF310030_134902) and the European Research Council(ERC, FP/2007-2013) Agreement no. 281785. S.C.G.-V. was fundedby a Marie Curie Intra-European Fellowship (FP7-PEOPLE-2013-IEFProject No. 627206). S.H. was funded by SNSF grant 310030_138452and the ERC (FP/2007-2013) Agreement no. 281904. The authorshave no conflicts of interest.

SUPPLEMENTARY MATERIALS

www.sciencemag.org/content/351/6279/1296/suppl/DC1Materials and MethodsFigs. S1 to S21Tables S1 to S5References (44–53)Data Files S1 to S8

28 August 2015; accepted 22 January 201610.1126/science.aad2571

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