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. Author manuscript; available in PMC: 2022 Aug 11.
Published in final edited form as: Cell Host Microbe. 2021 Jul 21;29(8):1249–1265.e9. doi: 10.1016/j.chom.2021.06.014

Figure 1. Study design, microbiome and ileal gene expression analysis of STR experiment.

Figure 1.

A) Study design. Pregnant NOD/ShiLtJ mice were randomized into six groups. Pups in five groups received atylosin course (1PAT; 1P) from P5-P10 and then were gavaged at P15 with broth alone (1P with broth), or with one of four pools of donor cecal contents in broth (i: CMT containing Pup-P5, ii: Mom-P5, iii: Mom-P0 and iv: Mom-T-P0 cecal contents). One pup group did not receive 1P (Control; C), and mice were gavaged in parallel at P15 with broth alone (C with broth). Mice (n=6-18/group) were followed and sacrificed at P28 and P42 to assess effects of the gavages on the microbiota and on ileal gene expression. B) α-diversity of cecal microbiome at P28 and P42, with rarefaction at 3000 sequences/sample, in mice receiving the different gavages. mean±SD shown, *p<0.05; ***p<0.001; ****p<0.0001; Mann-Whitney U test. C) β-diversity of cecal microbiome in mice receiving the different gavages, as measured by unweighted UniFrac analysis. Groups are: C(Broth), control pups receiving blank broth: 1P(Broth), 1P pups receiving blank broth; CMT(Mom-P0), 1P pups receiving CMT from normal dams at day of birth. **p=0.0017; one-way-ANOVA with Tukey’s HSD post-test for multiple comparisons. D) Volcano plot of RNAseq-based differential ileal gene expression at P42 between C and 1P mice receiving broth alone (upper panel), and between 1P mice receiving Mom-P0 (CMT) and 1P mice receiving broth alone (1P) (lower panel) (n=3 mice/group). In the upper panel, the 10 genes most differentiated by 1P(Broth) are Trim71, Fgf4, Tmprss2, Rarres1, Gdf3 (repressed), and Oasl1, Hyou1, Angptl4, Slfn4, Syvn1 (induced). In the lower panel, the 10 genes most differentiated by CMT(Mom-P0) are Hoxb5-8 (repressed), and Gimd1, Mroh7, Trim38, Gata4, Slc34a3, Peg10 (induced). E) RT-qPCR-based P28 ileal gene expression of Nos2, Muc2, Muc4, Runxl, Foxp3, CD3g, Saa1/2 and TNFα. Group 1: C(Broth), Group 2: 1P(Broth), Group 3: CMT(Mom-P0), Group 4: CMT(Mom-T-P0), 1P pups receiving CMT from dams on the day of birth who were exposed during pregnancy to tylosin. Mean±SD shown; n=6-14 mice/group; *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; Mann-Whitney Utest. Related to Figure S1D, Tables S1,S2.