16S rRNA gene sequencing data from: Breastmilk IgG engages the neonatal immune system to instruct immune responses to gut antigens

Maternal antibodies fundamentally regulate gut immunity in the developing
infant, yet the mechanisms underlying this process remain elusive. Here,
we show that maternal IgG, ingested in the first week of life, restrains
microbiota-dependent adaptive immune responses weeks later, following
weaning. Antibodies are key regulators of gut microbiota diversity and
composition, prompting us to explore whether alterations in microbiome
assembly correlated with immune dysregulation in maternal
antibody-deficient offspring. 16S rRNA gene sequencing of ileal and
colonic contents did not reveal substantial differences in the diversity
of microbes in each sample (alpha diversity) nor between-group distances
(beta diversity) between age-matched offspring of µMT+/- or µMT-/-
littermate dams and B6 sires. However, the abundance of a small subset of
taxa differed significantly between p7 offspring of µMT+/- and µMT-/-
dams, and this variation increased with age. Thus, the absence of all
breastmilk antibodies correlates with minor alterations in the assembly of
the postnatal microbiome. Analysis of p20 progeny of µMT-/- dams and B6
sires fed sIgG or BSA during the first week of life similarly failed to
reveal significant differences in alpha or beta diversity as a function of
feeding. Instead, litter was a driving factor. Indeed, the provision of
IgG resulted in the differential abundance of only a single ileal taxon
and two colonic taxa, which were distinct from those identified in p21
offspring of µMT+/- and µMT-/- dams. The similarity in microbiota
community structure between IgG and BSA-fed littermates indicates that
breastmilk IgG does not significantly alter the composition of the
developing microbiome.