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Table 1 Differentially abundant microbial groups (metagenomics sequencing-based) in the URT of beef calves

From: Effect of maternal separation and transportation stress on the bovine upper respiratory tract microbiome and the immune response to resident opportunistic pathogens

Comparisons

Microbial group

Sampling time point (median, IQR %)

P-value

D0

D2

D4

D8

D14

D28

All samples

Bacteria (D)

97.1, 0.8b

97.9, 1.1b

97.5, 0.7b

96.1, 4.4a

97.1, 3.4b

97.2, 1.4b

0.01

 

Viruses (D)

1.1, 0.9b

0.6, 0.6a

0.8, 0.6a

2.1, 4.7b

1.4, 3.2b

1.7, 1.4b

 < 0.01

 

Actinobacteria (P)

0.4, 0.1a

0.4, 0.3a

0.5, 0.2

0.5, 0.2

0.4, 0.2a

0.6,0.3b

 < 0.01

 

Bacteroidetes (P)

0.1, 0.2a

0.1, 0.1a

0.2, 0.4a

0.2, 0.4a

0.2, 0.3a

0.7, 1.6b

 < 0.01

 

Firmicutes (P)

0.2, 0.1a

0.2, 0.1a

0.2, 0.1a

0.3, 0.2

0.2, 0.2a

0.4, 0.4b

 < 0.01

 

Tenericutes (P)

0.5, 0.8

1.0, 1.6

0.3, 1.2

1.4, 2.2a

0.4, 0.7b

0.1, 0.2b

 < 0.01

 

Mannheimia (G)

0, 0.01a

0.02, 0.1

0.2, 0.7b

0.02, 0.04

0.01, 0.03a

0, 0.02a

 < 0.01

 

Pasteurella (G)

0, 0.01a

0.02, 0.1b

0.04, 0.07b

0.01, 0.02b

0, 0.02a

0, 0.01a

 < 0.01

 

Moraxella (G)

0.005, 0.02a

0.1, 0.2b

0.1, 0.3b

0.03, 0.1ab

0.01, 0.05

0.02, 0.08

0.02

 

Histophilus (G)

0, 0.01a

0.02, 0.04b

0.06, 0.04b

0, 0.02b

0, 0.02b

0.005, 0.01

 < 0.01

Weaned only

Mannheimia (G)

0, 0a

0.02, 0.04

0.3, 0.6b

0.02, 0.08

0, 0.002a

0.005, 0.01

 < 0.01

Weaned + Transport only

Histophilus (G)

0.02, 0.02

0.03, 0.04

0.06, 0.02a

0, 0b

0, 0.03b

0.005, 0.02

0.02

 

Microvirus (G)

94.8, 9.2a

86.7, 6.2b

93.9, 6.0a

98.5, 1.4a

96.4, 2.0a

96.9, 2.0b

 < 0.01

  1. D, domain (median as a % of all assigned domains); P, Phylum (median as a % of all assigned phyla within bacteria), G, Genus (median as a % of all assigned genera within bacteria or viruses); IQR, inter quartile ration
  2. a,bMedian with different superscripts are different at P < 0.05 (Post-hoc test for multiple comparisons of sampling time point using pairwise Wilcox test)