Additional file 1 of Identification of bovine respiratory disease through the nasal microbiome
Creators: name: Centeno-Martinez, Ruth Eunice
name: Glidden, Natalie
name: Mohan, Suraj
name: Davidson, Josiah Levi
name: Fernández-Juricic, Esteban
name: Boerman, Jacquelyn P.
name: Schoonmaker, Jon
name: Pillai, Deepti
name: Koziol, Jennifer
name: Ault, Aaron
name: Verma, Mohit S.
name: Johnson, Timothy A.
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional File 1. Supplementary Results. Figure S1. Top 10 most abundant genera present in the DNA extraction negative controls used as a negative control in the DNA extraction and sequencing step. Figure S2. Holstein steer nasal microbiome alpha diversity relative to the date of collection. Figure S3. Variation in the cattle’s nasal alpha diversity estimated relative to the average daily temperature (°F). Figure S4. Average relative abundance of the 10 most abundant phyla (a), family (b), and genera (c) present in the nasal microbiome of BRD and healthy animals. Figure S5. Variable importance measured by random forest indicated by the mean decrease accuracy. Figure S6. Visual representation of the positive ASV co-occurrence analysis in the healthy group (n = 74) with a probability of occurrence in the same sample &gt; 0.9. Figure S7. Visual representation of the positive ASV co-occurrence analysis in the BRD group (n = 57) with a probability of occurrence in the same sample &gt; 0.9. Figure S8. Visual representation of the negative ASV co-occurrence analysis of the healthy group (n = 74) with a probability of occurrence in the same sample &lt; 0.05. Figure S9. Visual representation of the negative ASV co-occurrence analysis in the BRD group (n = 57) with a probability of occurrence in the same sample &lt; 0.05. Table S1. Variation in the cattle’s nasal alpha diversity relative to the animal age (months) analyzed using General Linear Mixed Model. Table S2. Sample average distance to the centroids of the BRD and healthy groups. Table S3. Prevalence of ASVs assigned as P. multocida, H. somni and M. bovis the nasal cavity of BRD (n = 75) and healthy (n = 74) groups based on 16S rRNA gene sequencing. Table S4. Prevalence of the genera Pasteurella, Histophilus, Mannheimia or Mycoplasma in the nasal cavity of Holstein steers (n=131) and between BRD (n = 75) and healthy (n = 74) animals based on 16S rRNA gene sequencing. Table S5. Positive ASV pair combinations present in 73 out of 74 healthy samples with a probability of occurrence in the same sample &gt; 0.9. Table S6. Co-occurrence analysis with positive ASV pair combinations present in 56 out of 57 BRD samples with a probability of occurrence in the same sample of 1. Table S7. Co-occurrence analysis showing negative ASV pair combinations that are not likely to co-exist in the heathy group with a probability &lt; 0.04. Table S8. Co-occurrence analysis showing negative ASV pair combinations that are not likely to co-exist in the BRD group with a probability &lt; 0.04. Table S9. Evaluation of Pasteurella multocida, Histophilus somni, Mannheimia haemolytica and Mycoplasma bovis using qPCR assays.