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Maternal IgA protects against the development of necrotizing enterocolitis in preterm infants

Abstract

Neonates are protected from colonizing bacteria by antibodies secreted into maternal milk. Necrotizing enterocolitis (NEC) is a disease of neonatal preterm infants with high morbidity and mortality that is associated with intestinal inflammation driven by the microbiota1,2,3. The incidence of NEC is substantially lower in infants fed with maternal milk, although the mechanisms that underlie this benefit are not clear4,5,6. Here we show that maternal immunoglobulin A (IgA) is an important factor for protection against NEC. Analysis of IgA binding to fecal bacteria from preterm infants indicated that maternal milk was the predominant source of IgA in the first month of life and that a relative decrease in IgA-bound bacteria is associated with the development of NEC. Sequencing of IgA-bound and unbound bacteria revealed that before the onset of disease, NEC was associated with increasing domination by Enterobacteriaceae in the IgA-unbound fraction of the microbiota. Furthermore, we confirmed that IgA is critical for preventing NEC in a mouse model, in which pups that are reared by IgA-deficient mothers are susceptible to disease despite exposure to maternal milk. Our findings show that maternal IgA shapes the host–microbiota relationship of preterm neonates and that IgA in maternal milk is a critical and necessary factor for the prevention of NEC.

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Data availability

Patient-related data not included in the paper were generated as part of clinical trials and may be subject to patient confidentiality. The human study protocol was approved by the Institutional Review Board (protocol numbers PRO16030078 and PRO09110437) of the University of Pittsburgh. All raw and analyzed sequencing data have been deposited in Sequence Read Archive (accession number PRJNA526906).

Code availability

The algorithm for deconvolution of IgSeq data is available on GitHub (https://github.com/handlab/IgA_Seq_Deconvolution).

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Acknowledgements

We thank the University of Pittsburgh In Situ Hybridization Laboratory for the preparation of tissue slides and the University of Pittsburgh Division of Laboratory Animal Research for assistance with animal husbandry; M. Band, C. Wright, T. Akraiko and the Roy J. Carver Biotechnology Center DNA Sequencing Center at the University of Illinois for assistance with NextGen Sequencing. Igha−/− mice were provided by Y. Belkaid. We thank A. Poholek, L. Konnikova, S. Canna and the members of the Hand and Morowitz laboratories for discussion and critical reading of the manuscript, N. Palm for advice on IgSeq analysis and D. Kostka for advice on deconvolution of IgSeq samples. This project was supported in part by the UPMC Children’s Hospital of Pittsburgh. M.G. is supported by K08DK101608, R03DK111473 and R01DK118568 from the National Institutes of Health, March of Dimes Foundation grant no. 5-FY17-79, the Children’s Discovery Institute of Washington University and St Louis Children’s Hospital. M.J.M. and the collection of samples are supported by R01AI092531. T.W.H. is supported by the Richard King Mellon Foundation Institute for Pediatric Research.

Author information

K.P.G., M.J.M. and T.W.H. designed all of the experiments; K.P.G., B.A.F., J.T.T., J.J. and C.M. performed all of the experiments; C.M. and M.G. assisted with the implementation of the mouse NEC model; microbiome analyses was carried out by K.P.G., B.R.M., M.B.R., A.H.P.B. and T.W.H.; IgSeq analyses and development of deconvolution techniques were performed by K.P.G., M.B.R. and B.R.M.; R.B., M.J.M., M.G. and C.M. collected the preterm infant fecal samples; data analyses and synthesis were performed by K.P.G., B.R.M., M.J.M. and T.W.H.; K.P.G., B.R.M., M.J.M. and T.W.H. wrote the manuscript.

Correspondence to Timothy W. Hand.

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The authors declare no competing interests.

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Peer review information: Joao Monteiro was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended Data

Extended Data Fig. 1 Maternal milk-derived antibodies binding to intestinal bacteria from preterm infants.

a,b, Representative flow plots show binding of intestinal bacteria derived from preterm infants to IgM (a; n = 20) and IgG (b; n = 12) relative to IgA. Numbers in quadrants show the mean percentage ± s.d. of data collected from the cohort in Table 1. c, Percentage IgA staining of intestinal bacteria of a single preterm infant fed exclusively with formula. Source Data

Extended Data Fig. 2 Fraction of intestinal bacteria bound by IgA in preterm infants.

a, Percentage IgA-bound bacteria from longitudinally collected fecal samples from preterm infants in our study. The dotted red lines indicate the date of NEC diagnosis. b, Percentage IgA-bound intestinal bacteria from prospectively collected samples of patients that will develop NEC (n = 10, 39 samples combined) and controls (n = 13, 59 samples combined). Samples from multiple patients are pooled and represented in four-day windows post-delivery to increase the number of samples available for each time window. Box and whisker plots depict the mean (line) the 25th and 75th percentiles (box) and range (whiskers) for each time window. Two-way ANOVA. Source Data

Extended Data Fig. 3 Linear discriminant analysis of the microbiota of infants that will develop NEC and controls.

Linear discriminant effect size analysis comparing pooled samples from controls or infants that will develop NEC before the diagnosis of disease. OTUs that discriminate between patients that will progress to NEC (n = 10, 39 samples combined) and controls (n = 13, 59 samples combined) before disease onset are ranked by the effect size (represented by the linear discriminant analysis score). Source Data

Extended Data Fig. 4 Deconvolution method to decrease the effect of contamination in IgSeq.

a, Representative staining of the abundance of IgA-bound bacteria before (unsorted) or after magnetic separation (IgA+ and IgA) measured by flow cytometry of all samples (NEC samples, n = 39; control samples, n = 59). b, Graphical depiction of our deconvolution methodology. In this schematic, size represents IgA binding (large, IgA+; small, IgA), which can be measured on intact cells, and colors represent two different taxa, which can only be measured by sequencing. c, Percentage of IgA+ bacteria (measured by flow cytometry of unsorted fecal samples) compared to percentage of 16S rRNA reads found in the IgA+ sample (IgA+/IgA+ + IgA). Each dot represents a paired sample derived from the same fecal sample (n = 140). d, The same analysis as in c was carried out on samples after deconvolution (n = 140). c,d, Data were analyzed by linear regression with Pearson’s correlation coefficient and contain samples (n = 42) that were excluded from our prospective NEC analysis as they were collected after the NEC diagnosis, after DOL 40 or complicated by non-NEC illness and/or treatment. Source Data

Extended Data Fig. 5 Longitudinal analysis of the intestinal microbiota of preterm infants.

Stacked bar charts depict the relative abundances of OTUs (unsorted sample, deconvolved IgA+ and IgA fractions) at the family level, from all patients in our study, at all time points analyzed. Patients will develop NEC, n = 10, 39 samples combined; controls, n = 13, 59 samples combined. Source Data

Extended Data Fig. 6 Ratio of IgA to IgA+ reads for low-abundance taxa.

ac, Ratio of reads (IgA/IgA+; log2-transformed values) from paired IgA+ and IgA samples shown for each analyzed DOL. a, Staphylococcaceae reads. b, Streptococcaceae reads. c, Enterococcaceae reads. For all graphs, each patient is shown in a different color and the R2 value is based on a linear regression and Pearson’s correlation coefficient. The number of samples used in each graph varies because instances in which the IgA+ and/or IgA samples had zero reads were excluded. a, NEC samples, n = 10, 30 samples combined; control samples, n = 13, 53 samples combined. b, NEC samples, n = 10, 19 samples combined; control samples, n = 13, 32 samples combined. c, NEC samples, n = 10, 30 samples combined; control samples, n = 13, 51 samples combined. Source Data

Extended Data Fig. 7 Absolute number of bacteria and number of bacteria associated with the dominant taxa in preterm infants.

a, Total number of bacteria in each fecal sample determined by bead-based flow cytometry analysis. Black circles represent controls (n = 8, 43 samples combined); red triangles represent infants that went on to develop NEC (n = 5, 24 samples combined). b, Total number of Enterobacteriaceae in patients that will develop NEC (right) and controls (left). Semi-log non-linear regression. c, Total number of anaerobes in patients that will develop NEC (right) and controls (left). Semi-log non-linear regression. Source Data

Extended Data Fig. 8 Enterobacter spp. is enriched in the IgA+ fraction of breast-fed mouse pups.

Magnetically sorted IgA+ (left) and IgA (right) samples from fecal samples of day 12 (day 5 of NEC protocol) pups (n = 4). Frequency of Enterobacter spp. in each sample is shown as measured by qPCR for Enterobacter spp. (23S rRNA expression) normalized to the relative number of bacteria in each sample (as measured by 16S rRNA expression). AU, arbitrary units. *P = 0.0379 by paired Student’s t-test. Source Data

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Fig. 1: IgA binding to the intestinal bacteria of preterm infants is positively correlated with maternal milk feeding and negatively correlated with the development of NEC.
Fig. 2: Reduced intestinal bacterial diversity driven by increased IgA-unbound Enterobacteriaceae precedes the development of NEC.
Fig. 3: IgA is a necessary component of breast milk for the prevention of the development of experimental NEC.
Extended Data Fig. 1: Maternal milk-derived antibodies binding to intestinal bacteria from preterm infants.
Extended Data Fig. 2: Fraction of intestinal bacteria bound by IgA in preterm infants.
Extended Data Fig. 3: Linear discriminant analysis of the microbiota of infants that will develop NEC and controls.
Extended Data Fig. 4: Deconvolution method to decrease the effect of contamination in IgSeq.
Extended Data Fig. 5: Longitudinal analysis of the intestinal microbiota of preterm infants.
Extended Data Fig. 6: Ratio of IgA to IgA+ reads for low-abundance taxa.
Extended Data Fig. 7: Absolute number of bacteria and number of bacteria associated with the dominant taxa in preterm infants.
Extended Data Fig. 8: Enterobacter spp. is enriched in the IgA+ fraction of breast-fed mouse pups.