Table 1 Population characteristics, divided between yoghurt consumers and non-consumers. P values were generated using linear mixed effect models where yoghurt consumption was used a predictor and age, sex and BMI were included as fixed effects and family structure as a random effect (M1), M2 was calculated by adding HEI as covariate to M1. * P-value obtained from Fisher’s exact test to evaluate enrichment of a given phenotype (smoking or type 2 diabetes) in the yoghurt consumer group

Yoghurt intake (1–5 times a week)

1900

0

Yoghurt intake (> 5 times a week)

1125

0

Total yoghurt intake (times/week)

4.67 ± 3.08

0.03 ± 0.08

Age (year)

67.6 ± 12.6

65.8 ± 14.3

Sex (% Female)

0.937

0.857

Smoking history (%)

45.73%

50.70%

0.005*

 T2DM (%)

6.99%

9.50%

0.12*

 BMI (kg/m²)

25.43 ± 0.08

25.22 ± 0.13

0.402

 Body weight (kg)

67.45 ± 0.24

67.32 ± 0.39

0.211

 Body fat mass (%)

47.27 ± 0.62

49.09 ± 1.08

0.547

 Visceral fat mass (g)

539.51 ± 6.60

573.72 ± 11.46

0.009

 Fasting glucose (mmol/L)

4.83 ± 0.01

4.83 ± 0.02

0.307

 Fasting insulin (pmol/L)

39.57 ± 0.16

38.73 ± 0.28

0.031

 C-reactive protein (mg/l)

1.85 ± 0.05

1.96 ± 0.08

0.157

 Alanine aminotransferase (Ul/L)

20.83 ± 0.18

20.99 ± 0.28

0.433

 HEI

59.97 ± 9.03

57.22 ± 11.08

2.72x10⁻¹⁰

 Whole fruit

4.93 ± 0.46

4.64 ± 1.03

3.72 x10⁻³⁰

 Total fruit

4.89 ± 0.51

4.49 ± 1.09

9.75 x10⁻⁴⁶

 Whole grains

8.16 ± 2.64

6.74 ± 3.41

2.7 x10⁻³⁵

 Dairy

5.58 ± 2.34

5.30 ± 2.7

0.002

 Total protein

2.23 ± 0.65

2.35 ± 0.78

4.58 x10⁻⁰⁹

 Sea plant protein

4.30 ± 0.94

4.39 ± 0.99

0.001

 Greens and beans

4.52 ± 0.94

4.53 ± 0.99

0.907

 Total vegetable

3.75 ± 1.22

3.77 ± 1.29

0.269

 Fatty acids

3.76 ± 2.40

3.62 ± 2.73

0.467

 Refined grains

1.10 ± 2.65

1.05 ± 2.73

0.592

 Sodium

7.84 ± 2.05

8.02 ± 2.25

0.061

 Empty calories

8.86 ± 4.82

8.24 ± 5.63

0.072

 16S rRNA gene sequencing (n)

1057

400

 Shotgun metagenomic sequencing (n)

400

144

 Faecal metabolomic (n)

309

110