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).

ID1 ID2 ID3 ID4

ID5 ID6 ID7

Days Days Days Days

Days Days Days

Before intake FOSAfter intake

Figure S2. The individual fecal IgA profile in time series. The fecal samples were collected more than 2 times during each period.

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

AID1 ID2 ID3 ID4

ID5 ID6 ID7

BID1 ID2 ID3 ID4

ID5 ID6 ID7

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.

Table S1. The number of fecal samples used in this study and volunteers’ information.

The number of fecal samples

ID

1234567

Gender

FemaleMale

FemaleMaleMaleMale

Female

Age

23302522232530

Before FOS

2332432

During FOS

7423774

After FOS

2322222

Number of reads %

Total number of input sequences 383,447 100.0

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.

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-

IgAMetabolite-Microbe Source of

microbesChemical shift (ppm) Metabolite Microbe

7.42 7.42 L- phenylalanine Veillonelaceae ID46.9 7.18 L-lysine Coriobacteriaceae ID4

3.98 6.9 Tyramine Bifidobacteriaceae ID53.62 3.3 Butyrate S24-7 ID53.3 3.26 Peptostreptococcaceae ID5

2.14 3.02 Alcaligenaceae ID52.02 2.141.7 2.02

1.02 1.740.98 1.7

1.461.02

　 0.98

Negative correlation 　Metabolite-

IgAMetabolite-Microbe Source of

microbesChemical shift (ppm) Metabolite Microbe

7.26 7.26 p-cresol Rikenellaceae ID47.14 7.14 Barnesiellaceae ID47.1 7.1 Mogibacteriaceae ID4

6.82 7.06 Clostridiaceae ID51.42 6.82 Desulfovibrionaceae ID51.38 1.58 Pasteurellaceae ID4 and ID51.1 1.380.9 1.18

0.86 1.140.82 0.90.78 0.86

0.82　 0.78

OTU ID Microbialfamily Best-hit species Identity (%)Effect of

FOSSubject

OTU3300 Rikenellaceae Alistipesputredinis 100 Increased

ID4OTU2822 Barnesiellaceae Barnesiellaintestinihomini 98 DecreasedOTU2701 Coriobacteriaceae Coriobacteriaceae bacterium 85 DecreasedOTU2014 Veillonellaceae Veillonella parvula 93 DecreasedOTU2505 Coriobacteriaceae Eggerthellalenta 99 Decreased

OTU2830 Pasteurellaceae Haemophilusparainfluenzae 99 DecreasedID4 and

ID5OTU2479

Bifidocateriaceae

Bifidobacteriumadolescentis 100

Increased

ID5

OTU3664Bifidobacteriumpseudocatenulatum

100

OTU4944Bifidobacteriumlongum subsp. longum

100

OTU4102 Bifidobacteriumstercoris 99OTU4282

Clostridiaceae

Clostridium sp. CRIB 97

DecreasedOTU2098 Ruminococcus sp. ZS2-15 82OTU2996 Clostridium sp. CRIB 98OTU2435 Clostridium sp. A4-77 99

OTU4416Alcaligenaceae

Parasutterella excrementihominis

99Decreased

OTU2781 Parasutterellasecunda 99OTU2782 Desulfovibrionaceae Desulfomonaspigra 98 Decreased

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.

Table S5. Chemical shifts of fecal metabolites identified by NMR.

Code Metabolite assignment

1 Butyrate CH2 2.15 42.35 t CH2 1.55 22.13 m

2 L-lysine CH3 3.75 57.24 t CH 3.00 41.94 t CH 1.70 29.10 m

3 L-phenylalanine CH 7.41 131.8 m CH 7.36 130.6 m CH 7.32 132.2 d CH 3.98 58.93 dd CH2 3.27 39.21 m CH2 3.11 39.07 m

4 Tyramine CH 7.24 132.1 d CH2 6.89 118.9 d

1 p-cresol CH 7.16 133.6 m CH 6.82 118.2 dd

1 Acetate CH3 1.91 26.09 s• Propionate CH2 2.17 33.47 q

CH3 1.04 12.98 t• Succinate CH2 2.40 36.88 s• Lactate CH3 1.32 22.26 d1 L-Valine CH 3.59 63.11 d

CH 2.26 31.78 m CH3 1.03 20.67 d CH3 0.97 19.38 d

• L-Leucine CH 3.73 56.24 m CH2 1.72 42.62 m CH2 1.71 26.91 m

• L-Isoleucine CH 3.66 62.30 d CH 1.97 38.66 m CH2 1.45 27.32 m CH3 0.99 17.48 dLetters indicate multipicity of the peak. s, singlet; d, doublet; dd, doublet of doublets; t, triplet;

q, quartet; m, multiplet.

Chemical shift (ppm) δ1H δ13C

Multiplicity of 1H signal