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Table 1 Data about calves (origin, signalment, history, clinical examination) and number of reads of each sample

From: Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves

ID

Farm

Age (months)

Sex

Weight (kg)

Previous episodes of BRD

Spontaneous cough

Nasal discharge

Abnormal lung sounds

Read number NS sample

Read number TTA sample

1a

TO1

14

M

400

3 months before sampling

Repeated

Cloudy and bilateral

Wheezes and crackles on the left side of the thorax

NP

53,494

2b

CN1

6

M

180

No

Absent

Absent

Absent

NP

7902

3a

CN1

6

M

180

1 month before sampling

Occasional

Absent

Wheezes and crackles on both sides of the thorax

NP

47,115

4b

CN1

6

M

180

No

Absent

Absent

Absent

NP

18,855

5b

CN1

6

M

180

No

Absent

Absent

Absent

NP

81,564

6a

CN2

6

M

180

No

Absent

Cloudy and unilateral

Absent

36,160

129,750

7b

CN2

6

M

180

No

Absent

Absent

Absent

28,543

118,454

8b

CN2

6

M

180

No

Absent

Absent

Absent

31,232

61,778

9a

CN2

6

M

180

No

Absent

Cloudy and bilateral

Wheezes and crackles on both sides of the thorax

DNA < 5 ng/μl

DNA < 5 ng/μl

10a

VC1

5

F

150

No

Repeated

Absent

Wheezes and crackles on both sides of the thorax

40,694

142,459

11a

VC1

5

F

150

2 months before sampling

Absent

Absent

Wheezes and crackles on both sides of the thorax

12,952

DNA < 5 ng/μl

12b

VC1

5

F

150

No

Absent

Absent

Absent

5988

DNA < 5 ng/μl

13a

VC1

5

M

150

No

Absent

Absent

Wheezes and crackles on both sides of the thorax

24,070

26,910

14b

TO2

6

M

200

No

Absent

Absent

Absent

DNA < 5 ng/μl

68,954

15b

TO2

6

F

200

No

Absent

Absent

Absent

20,464

40,790

16a

TO2

6

F

200

No

Absent

Absent

Wheezes and crackles on the right side of the thorax

167,198

107,679

17a

TO2

6

F

200

No

Absent

Cloudy and bilateral

Absent

DNA < 5 ng/μl

143,886

18b

TO2

6

M

200

No

Absent

Absent

Absent

3932

55,630

19b

TO2

6

M

200

No

Absent

Absent

Absent

DNA < 5 ng/μl

1,825c

20b

TO2

6

M

200

No

Absent

Absent

Absent

154,004

4585

21b

TO3

5

M

170

No

Absent

Absent

Absent

1,536c

6833

22b

TO3

5

M

170

No

Absent

Absent

Absent

159c

189c

  1. ID = animal’s identification number. Farm origin = farms are indicated with the provincial code (TO Torino, CN Cuneo, VC Vercelli) and progressively numerated. Sex: M = male, F = female. Read number = number of reads for each sample. TTA = trans-tracheal aspiration sample. NS = nasal swab sample. NP = not performed. DNA < 5 ng/μ = samples with DNA concentration lower than 5 ng/μl and not sequenced
  2. aCalves with clinical signs of BRD
  3. bHealthy calves
  4. cSamples with less than 2500 reads excluded from the final analysis