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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