Gut Microbiota α- and β-Diversity, but Not Dietary Patterns, Differ Between Underweight and Normal-Weight Japanese Women Aged 20–39 Years
Abstract
1. Introduction
2. Materials and Methods
2.1. Study Design
2.2. Data Collection
2.3. DNA Extraction and Sequencing
2.4. PCR Amplification
2.5. Library Preparation and Sequencing
2.6. Data Processing and Analysis
2.7. Data Preprocessing
2.8. Statistical Analysis
2.8.1. Alpha Diversity Indices
2.8.2. Nonmetric Multidimensional Scaling (NMDS)
2.8.3. Redundancy Analysis (RDA)
2.8.4. ANOVA-like Differential Expression Tool, Version 2 (AldEx2)
3. Results
3.1. Participant Characteristics
3.2. Alpha Diversity of Dietary and Gut Microbiota Patterns
3.3. Correlations of Alpha Diversity with BMI and Nutrient Intake
3.4. The Beta Diversity of Gut Microbiota Patterns Rather Than Dietary Patterns Differed Between the Normal and Underweight Groups
3.5. The Difference in Bacterial Composition Between the Normal and Underweight Groups Reflects the Beta Diversity of the Gut Microbiota
3.6. Differential Abundance Analysis by ALDEx2
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
PERMANOVA | permutational multivariate analysis of variance |
PERMDISP | permutational analysis of multivariate dispersions |
ALDEx2 | ANOVA-Like Differential Expression (version 2) |
NMDS | nonmetric multidimensional scaling |
RDA | redundancy analysis |
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Variable | Normal Weight Group (C) | Underweight Group (L) | p |
---|---|---|---|
(n = 40) | (n = 40) | ||
Age, years | 27.88 (4.65) | 27.40 (4.49) | 0.65 |
Weight, kg | 53.84 (5.78) | 43.36 (4.15) | <0.001 |
Height, cm | 160.86 (6.05) | 159.17 (5.10) | 0.19 |
BMI, kg/m2 | 20.77 (1.41) | 17.07 (0.97) | <0.001 |
Energy intake, kcal/d | 1650.0 (666.6) | 1564.0 (341.3) | 0.48 |
Carbohydrate, g/d | 212.73 (127.02) | 205.48 (44.24) | 0.74 |
Protein intake, g/d | 55.21 (18.32) | 53.90 (14.70) | 0.73 |
Lipid intake, g/d | 57.10 (15.52) | 55.15 (14.38) | 0.57 |
Dietary fiber, g/d | 10.31 (4.54) | 10.16 (3.33) | 0.87 |
Dietary Pattern | ||||
---|---|---|---|---|
Index | χ2 (df = 1) | p-Value | Cliff’s δ (95% CI) | Magnitude |
Shannon index | 1.06 | 0.30 | −0.13 (−0.37, 0.12) | Negligible |
Simpson’s diversity index | 0.84 | 0.36 | 0.12 (−0.13, 0.35) | Negligible |
Pielou index | 0.37 | 0.54 | −0.079 (−0.32, 0.18) | Negligible |
Gut Microbiota | ||||
Index | χ2 (df = 1) | p-Value | Cliff’s δ (95% CI) | Magnitude |
Shannon index | 20.37 | <0.001 | 0.59 (0.36, 0.75) | large |
Simpson’s diversity index | 18.09 | <0.001 | 0.55 (0.32, 0.72) | large |
Pielou index | 26.4 | <0.001 | 0.67 (0.46, 0.81) | large |
Shannon Index (Diet) | Shannon Index (Gut Microbiota) | |||
---|---|---|---|---|
ρ (95% CI) | p (Two-Tailed) | ρ (95% CI) | p (Two-Tailed) | |
BMI | −0.19 [−0.41, 0.029] | 0.077 | 0.49 [0.30, 0.65] | <0.0001 |
Age | 0.026 [−0.20, 0.25] | 0.82 | 0.00042 [−0.22, 0.23] | 0.97 |
Energy intake | 0.28 [0.062, 0.47] | 0.013 | −0.066 [−0.28, 0.16] | 0.56 |
Carbohydrate intake | 0.20 [−0.017, 0.41] | 0.07 | −0.10 [−0.32, 0.12] | 0.37 |
Protein intake | 0.49 [0.31, 0.64] | <0.0001 | −0.10 [−0.31, 0.2] | 0.36 |
Lipid intake | 0.31 [0.99, 0.50] | 0.0048 | 0.027 [−0.19, 0.25] | 0.81 |
Dietary fiber intake | 0.63 [0.47, 0.75] | <0.0001 | −0.13 [−0.35, 0.095] | 0.24 |
Dietary Pattern | |||||||
---|---|---|---|---|---|---|---|
Section | Metric | C (n = 40) | L (n = 40) | Contrast (Pair) | R2 | F | p |
PERMANOVA | Between-group composition | — | — | — | ≈0 | ≈0 | 0.99 |
PERMDISP (overall) | Dispersion difference | — | — | — | — | 0.44 | 0.52 |
PERMDISP (Tukey) | Pairwise | — | — | −0.013 (−0.050, 0.025) | — | — | 0.51 |
Distance to centroid | Mean (BCa 95% CI) | 0.14 (0.13–0.17) | 0.13 (0.11–0.17) | — | — | — | — |
Distance to centroid | Median (BCa 95% CI) | 0.14 (0.11–0.15) | 0.11 (0.087–0.13) | — | — | — | — |
Dietary pattern | |||||||
Gut Microbiome | |||||||
Section | Metric | C (n = 40) | L (n = 40) | Contrast (Pair) | R2 | F | p |
PERMANOVA | Between-group composition | — | — | — | 0.064 | 5.31 | 0.0001 |
PERMDISP (overall) | Dispersion difference | — | — | — | — | 3.21 | 0.072 |
PERMDISP (Tukey) | Pairwise | — | — | 0.025 (−0.0028, 0.053) | — | — | 0.079 |
Distance to centroid | Mean (BCa 95% CI) | 0.28 (0.27, 0.30) | 0.31 (0.29, 0.33) | — | — | — | — |
Distance to centroid | Median (BCa 95% CI) | 0.27 (0.25, 0.31) | 0.29 (0.27, 0.31) | — | — | — | — |
Section | Metric | Value | Axis | Prop (Fraction) | Prop (%) | p | Term | F | df |
---|---|---|---|---|---|---|---|---|---|
Model summary | Total inertia | 0.28 | |||||||
Model summary | R2 | 0.045 | |||||||
Model summary | Adjusted R2 | 0.032 | |||||||
Model summary | Permutation F | 3.65 | |||||||
Model summary | Permutation p | 0.0005 | |||||||
Model summary | Permutations (N) | ||||||||
9999 | |||||||||
Model summary | Significant axes (p < 0.05) | 1 | |||||||
Model summary | Significant terms (p < 0.05) | 1 | |||||||
Model summary | List of significant terms | BMI group | |||||||
Model summary | R2 | 0.045 | |||||||
Per-axis | RDA1 | 1 | 100.00% | 0.0005 | |||||
Per-term | 0.0005 | BMI group | 3.65 | 1 |
Feature | diff.btw | Effect | wi.ep | wi.eBH | we.ep | we.eBH |
---|---|---|---|---|---|---|
Bacteroides | −0.94 | −0.54 | <0.001 | 0.011 | <0.001 | 0.013 |
Enterocloster | −2.74 | −0.63 | <0.001 | <0.001 | <0.001 | 0.013 |
Erysipelatoclostridium | −2.64 | −0.52 | <0.001 | 0.0085 | <0.001 | 0.015 |
Dorea | 4.89 | 0.63 | <0.001 | 0.019 | <0.001 | 0.024 |
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Yamamoto-Wada, R.; Hiraiwa, E.; Okuma, K.; Yamada, M.; Ushiroda, C.; Deguchi, K.; Naruse, H.; Masuyama, H.; Iizuka, K. Gut Microbiota α- and β-Diversity, but Not Dietary Patterns, Differ Between Underweight and Normal-Weight Japanese Women Aged 20–39 Years. Nutrients 2025, 17, 3265. https://doi.org/10.3390/nu17203265
Yamamoto-Wada R, Hiraiwa E, Okuma K, Yamada M, Ushiroda C, Deguchi K, Naruse H, Masuyama H, Iizuka K. Gut Microbiota α- and β-Diversity, but Not Dietary Patterns, Differ Between Underweight and Normal-Weight Japanese Women Aged 20–39 Years. Nutrients. 2025; 17(20):3265. https://doi.org/10.3390/nu17203265
Chicago/Turabian StyleYamamoto-Wada, Risako, Eri Hiraiwa, Kana Okuma, Masako Yamada, Chihiro Ushiroda, Kanako Deguchi, Hiroyuki Naruse, Hiroaki Masuyama, and Katsumi Iizuka. 2025. "Gut Microbiota α- and β-Diversity, but Not Dietary Patterns, Differ Between Underweight and Normal-Weight Japanese Women Aged 20–39 Years" Nutrients 17, no. 20: 3265. https://doi.org/10.3390/nu17203265
APA StyleYamamoto-Wada, R., Hiraiwa, E., Okuma, K., Yamada, M., Ushiroda, C., Deguchi, K., Naruse, H., Masuyama, H., & Iizuka, K. (2025). Gut Microbiota α- and β-Diversity, but Not Dietary Patterns, Differ Between Underweight and Normal-Weight Japanese Women Aged 20–39 Years. Nutrients, 17(20), 3265. https://doi.org/10.3390/nu17203265