1. Figure S1. Schematic overview of the analytical approach in this study. For simplification, three individuals, A. B and C, are shown, in which A and B respond FOS-intake to elevate fecal IgA whereas C does not. Time-course data of IgA, metabolites and microbes from each individual were analyzed in the six-step procedures as shown. To evaluate the intra-individual variability, in the first step, we assessed whether FOS supplementation affected gut environment individually (steps I and II). Next, correlation coefficient between IgA and microbe/metabolite profiles was calculated based on the method described in Ref. 24 (step III). To cluster metabolite-microbe correlation profile derived from each individual, individual ID was added, as ID-tag, in front of microbe names (at the family level), then correlation coefficient between microbial composition and metabolic profile was calculated in each individual, and the data obtained from individuals were merged (step IV). Correlation among IgA-metaboilte-microbe commonly observed in FOS responders (i.e. individuals A and B) was selected and constructed the correlation network related to IgA response (steps V and VI).

2. ID1ID2ID3ID4 ID5ID6ID7 Days Before intake FOS After intake Figure S2. The individual fecal IgA profile in time series. The fecal samples were collected more than 2 times during each period.

3. Figure S3. The comparison of Unifrac distance between “within” and “between” diet periods. P values were calculated using Mann-Whitney U test. NS, no significant difference. NS

4. A ID1ID2ID3ID4 ID5 ID6ID7 B ID1ID2ID3ID4 ID5 ID6ID7 Figure S4. Intra-individual profiles in time-dependent gut environment changes. (A) and (B) Score plots from PCA of fecal profile in individual samples are shaded by diet periods. (A) PCA on the fecal profiling data from microbiome analysis and (B) from metabolome analysis.

5. Table S1. The number of fecal samples used in this study and volunteers’ information. The number of fecal samples ID 1 2 3 4 5 6 7 Gender Female Male Female Male Female Age 23 30 25 22 23 25 30 Before FOS 2 3 2 4 3 2 During FOS 7 4 2 3 7 4 After FOS 2 3 2

6. Number of reads% Total number of input sequences383,447 100.0 Filter-passed sequences 222,863 58.1 Reads removed Length outside bounds of 200 and 1000 54,706 14.3 Reads lacking primer sequences 71,675 18.7 Mean qual score below minimum of 25 731 0.2 Denoising and chimeric detected reads 34,203 8.9 Table S2. Summary of quality filtering of the 16S V1-2 sequences produced by 454 pyrosequencing of 7 healthy volunteers.

7. Table S3. Commonly correlated metabolites with IgA and microbes profile in FOS responders, ID4 and ID5. Highly correlated chemical shifts (ppm) and assigned metabolites with IgA and microbial tags commonly in ID4 and ID5 are listed. Multiple correlation analysis suggests the common metabolites may induce fecal IgA production by FOS supplementation. Positive correlation Metabolite- IgA Metabolite-Microbe Source of microbes Chemical shift (ppm)MetaboliteMicrobe 7.42 L- phenylalanineVeillonelaceae ID4 6.97.18L-lysineCoriobacteriaceae ID4 3.986.9TyramineBifidobacteriaceae ID5 3.623.3ButyrateS24-7 ID5 3.33.26Peptostreptococcaceae ID5 2.143.02Alcaligenaceae ID5 2.022.14 1.72.02 1.021.74 0.981.7 1.46 1.02 0.98 Negative correlation Metabolite- IgA Metabolite-Microbe Source of microbes Chemical shift (ppm)MetaboliteMicrobe 7.26 p-cresolRikenellaceae ID4 7.14 Barnesiellaceae ID4 7.1 Mogibacteriaceae ID4 6.827.06Clostridiaceae ID5 1.426.82Desulfovibrionaceae ID5 1.381.58Pasteurellaceae ID4 and ID5 1.11.38 0.91.18 0.861.14 0.820.9 0.780.86 0.82 0.78

8. OTU IDMicrobialfamily Best-hit species Identity (%) Effect of FOS Subject OTU3300RikenellaceaeAlistipesputredinis100Increased ID4 OTU2822BarnesiellaceaeBarnesiellaintestinihomini98Decreased OTU2701CoriobacteriaceaeCoriobacteriaceae bacterium85Decreased OTU2014VeillonellaceaeVeillonella parvula93Decreased OTU2505CoriobacteriaceaeEggerthellalenta99Decreased OTU2830PasteurellaceaeHaemophilusparainfluenzae99Decreased ID4 and ID5 OTU2479 Bifidocateriaceae Bifidobacteriumadolescentis100 Increased ID5 OTU3664 Bifidobacteriumpseudocatenulat um 100 OTU4944 Bifidobacteriumlongum subsp. longum 100 OTU4102Bifidobacteriumstercoris99 OTU4282 Clostridiaceae Clostridium sp. CRIB97 Decreased OTU2098Ruminococcus sp. ZS2-1582 OTU2996Clostridium sp. CRIB98 OTU2435Clostridium sp. A4-7799 OTU4416 Alcaligenaceae Parasutterella excrementihominis 99 Decreased OTU2781Parasutterellasecunda99 OTU2782DesulfovibrionaceaeDesulfomonaspigra98Decreased Table S4. OTUs and assigned indigenous species showing 1 ≥ average reads in the microbial families highly correlated with IgA and metabolites in ID4 and ID5.

9. Table S5. Chemical shifts of fecal metabolites identified by NMR. CodeMetabolite assignment 1 Butyrate CH 2 2.1542.35 t CH 2 1.5522.13m 2 L-lysine CH 3 3.7557.24 t CH 3.0041.94t CH 1.7029.10m 3 L-phenylalanine CH 7.41131.8 m CH 7.36130.6m CH 7.32132.2d CH 3.9858.93dd CH 2 3.2739.21m CH 2 3.1139.07m 4 Tyramine CH 7.24132.1 d CH 2 6.89118.9d 5 p-cresol CH 7.16133.6m CH 6.82118.2dd 6 Acetate CH 3 1.9126.09s 7 Propionate CH 2 2.1733.47q CH 3 1.0412.98t 8 Succinate CH 2 2.4036.88s 9 Lactate CH 3 1.3222.26d 10 L-Valine CH 3.5963.11d CH 2.2631.78m CH 3 1.0320.67d CH 3 0.9719.38d 11 L-Leucine CH 3.7356.24m CH 2 1.7242.62m CH 2 1.7126.91m 12 L-Isoleucine CH 3.6662.30d CH 1.9738.66m CH 2 1.4527.32m CH 3 0.9917.48d Letters indicate multipicity of the peak. s, singlet; d, doublet; dd, doublet of doublets; t, triplet; q, quartet; m, multiplet. Chemical shift (ppm) δ 1 H δ 13 C Multiplicity of 1 H signal