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. 2023 Jun 13;56(6):1220–1238.e7. doi: 10.1016/j.immuni.2023.04.002

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© 2023 The Author(s)

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

PMC Copyright notice

Rapid establishment of a dense and immunogenic small intestinal core microbiome in absence of adaptive immune maturation

(A) Bacterial density determined by quantitative 16S rRNA gene qRCR normalized to murine Gapdh in total small intestinal (SI) tissue (n = 5, mean + SD, Kruskall-Wallis/Dunn’s multiple comparison to adult).

(B) Anaerobic culture of homogenized small intestinal tissue (n = 4, mean, Mann-Whitney U test).

(C) Bacterial density determined by quantitative 16S rDNA quantitative real-time PCR normalized to murine Gapdh in total colonic tissue (n = 5, mean + SD, Kruskall-Wallis/Dunn’s multiple comparison to adult).

(D) Phylogenetic placement, phylum assignment (inner circle), and relative abundance (outer circle) of metagenome-assembled genomes (MAGs) in the SI luminal content by shotgun sequencing.

(E) Molecular species richness determined in (D) (n = 6, mean, Mann-Whitney U test).

(F) Saturation plot depicting number of MAGs required to cover most of the functional potential (n = 6, median + SD). Knee points indicated with vertical lines.

(G) Knee points of the individual saturation curves indicated in (F) (n = 6, mean + SD, Mann-Whitney U test).

(H) BOTA scores of all MAGs from (D) (n_PND11 = 59, n_Adult = 149 MAGs, violin plot, Mann-Whitney U test).

(I) Cumulative abundance-weighted BOTA scores from (D) (n = 6, mean, Mann-Whitney-U test).

(J) Venn diagram of non-host-derived protein species identified by mass spectrometry in small intestinal luminal material (n = 6).

(K and L) Percentage of M1–M3 of cDC2 in PND11 (K) pIgR^+/− offspring born to pIgR^−/− dams or pIgR^+/+ offspring born to pIgR^+/+ dams (n = 4–5) and (L) wildling (WLD) animals (n = 11–12), (mean + SD; two-way ANOVA/Bonferroni test between genetic groups within the same maturational stage) determined by FACS.

(M) Percentage of M1–M3 of cDC2 in PND12 mice after oral administration of adult intestinal content (adultIC) on PND9-11 (n = 5), (mean + SD; two-way ANOVA/Bonferroni test between treatment groups within the same maturational stage).

(N) Percentage of CD44^hi cells among total PP CD4⁺ T cells in 14-day-old mice after oral administration of adult intestinal content (adultIC) on PND1-9 (n = 6–8; median).

(O–Q) Percentage of M1–M3 of cDC2 in PND12 mice that were administered (O) B. fragilis by oral gavage on PND9-11 (n = 5), (P) 8 h after E. coli OMVs oral gavage (n = 6–7), and (Q) weaning intestinal content (weanIC) by oral gavage on PND9-11 (n = 5–9) (mean + SD, two-way ANOVA/Bonferroni test between treatment groups within the same maturational stage). See also Figure S5 and Tables S1 and S2.