Circles (Unit 8) Video – Learn Alberta ?l=0&ID1=AB.MATH.JR.SHAP&ID2=AB.MATH.JR.SHAP.CIRC&lesson=html
ID1
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Transcript of ID1
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