Table 1 Description of the Illumina MiSeq seqencing runs and the sequence data sets (Set#1 to Set#5 represented in Fig. 1C). For each data set, the table includes minimum (min), maximum (max), mean, median and total number of microbial reads per sample, and number of samples and Amplicon Sequence Variants (ASVs) after all quality filters. The total number of samples before quality filters is given into brackets

Run1

Set#1

V5–V6 region of the bacterial 16S

223

27,008.08

25,427

77,777

5,509,649

204 [216]

7994

Run2

All sets

V5–V6 region of the bacterial 16S

1877

14,934.57

13,900

49,186

4,062,204

272 [291]

8582

Set#2

2597

16,452.09

15,320

49,186

2,484,265

151 [162]

4953

Set#3

1877

11,675.1

10,428

31,533

361,928

31 [36]

1393

Set#4

2700

13,720.46

13,385.5

24,499

960,432

70 [72]

2649

Set#5

3696

12,778.95

10,538

25,180

255,579

20 [21]

2725

Run 1 + Run 2

All sets

223

20,108.93

18,370.5

77,777

9,571,853

476 [507]

13,173

Run3

Set#1

Fungal ITS1 region

2555

29,429.85

24,368

90,458

6,062,549

206 [216]

5951

Run4

All sets

Fungal ITS1 region

1002

29,698.18

27,848

93,873

8,523,378

287 [291]

8700

Set#2

3176

32,634.37

28,617

93,873

5,254,134

161 [162]

5498

Set#3

5392

27,488.14

23,614

82,485

989,573

36 [36]

1574

Set#4

5220

27,000.31

27,334

48,015

1,944,022

72 [72]

2736

Set#5

1002

18,647.17

15,351.5

41,041

335,649

18 [21]

2906

Run 3 + Run 4

All sets

1002

29,586.06

26,327

93,873

14,585,927

493 [507]

11,242