Table 1 Variability of the studied gut microbiota and stool components before antibiotic treatment administration in the 22 healthy volunteers included in the CEREMI trial

Bacterial microbiota

 Bacterial counts (log₁₀ CFU/g)

22

11.3

0.19

1.7

0.14

1.2

 Bacterial microbiome richness (MGS/g)

22

269.7

64.69

24.0

16.01

5.9

 Enterobacterales counts (log₁₀ CFU/g)

22

7.5

1.37

18.3

1.00

13.3

Resistance

 Global resistome richness (copies/g)

22

820.1

159.50

19.5

69.75

8.5

 β-lactamasome abundance (log₁₀)

22

 − 0.8

0.03

3.8

0.02

2.5

 β-lactamase activity (log₁₀ nmol/min.g)

22

1.2

0.59

49.2

0.20

16.7

Phage microbiota

 Phage microbiome richness (contigs/g)

21

1226.6

271.81

22.2

91.37

7.5

Fungal microbiota

 Fungal load (log₁₀)

21

 − 5.2

0.72

13.9

1.27

24.4

 Fungal microbiome richness (fungal OTUs/g)

22

25.6

4.77

18.6

9.13

35.7

 C. albicans DNA concentration (log₁₀)

21

 − 5.0

0.81

16.2

0.47

9.4

Metabolome

 Metabolome richness (chemical species/g)

22

1472.7

 < 0.01

0.0

98.85

6.7

 Cholesterol conversion rate (log₁₀)

22

 − 0.6

1.03

171.7

0.49

81.7

 Bile acids transformation capacity (log₁₀)

22

 − 0.1

0.09

90.0

0.06

60.0