Additional file 1 of The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs
Creators: name: Gaire, Tara N.
name: Odland, Carissa
name: Zhang, Bingzhou
name: Ray, Tui
name: Doster, Enrique
name: Nerem, Joel
name: Dee, Scott
name: Davies, Peter
name: Noyes, Noelle
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Physiology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 1: Figure S1. Boxplots of the raw sequence read counts by time point and treatment group (Minimal—dark grey, Moderate—blue and Intensive—red color). Horizontal lines forming each box represent the first quartile, median and third quartile, while whiskers denote 1.5x the interquartile range. Figure S2. Proportion of host (Sus scrofa) to non-host reads per sample (x-axis) by treatment groups for each time point. Figure S3. Relative abundance of resistance by type (drugs, biocides, multi-compounds and metals) in composite fecal samples, separated by treatment group (panels) and sampling time point (weaning/transport to market). Figure S4. Microbiome composition (NMDS—non metric multidimensional scaling, Bray-Curtis dissimilarity) at phylum level (stress=0.09) by A) sampling time point (ANOSIM—Analysis of similarities P=0.001, PERMANOVA—Permutational multivariate analysis of variance R2=49%, P=0.001). B) by treatment (ANOSIM P=0.238, PERMANOVA R2 &lt;1%, P=0.113). C) microbiome composition at class level (stress=0.10) by sampling time point (ANOSIM P=0.001, PERMANOVA R2=47%, P=0.001). D) by treatment (ANOSIM P=0.388, PERMANOVA R2 &lt;1%, P=0.167). Ellipse indicates 95% confidence interval for distance around centroids of the group. Figure S5. Log-fold change (logFC, x-axes) of microbial phyla for A) each treatment group (Minimal, Moderate and Intensive) comparing sequential sampling time points (i.e., positive logFC values indicate higher abundance in the later time point compared to the earlier time point) and B) between treatment groups (Minimal, Moderate and Intensive) for each sampling time point. Each dot represents a microbial phylum in the group and red dots represent genera that are significantly different between comparison groups (i.e., logFC≥±1, mean abundance ≥ 3, BH adjusted P&lt; 0.05). Figure S6. Log-fold change (logFC, x-axes) of microbial genera for A) each treatment group (Minimal, Moderate and Intensive) comparing sequential time points (i.e., positive logFC values indicate higher abundance in the later time point compared to the earlier sampling time point) and B) between treatment groups (Minimal, Moderate and Intensive) for each time point. Each dot represents a microbial genera in the group and red dots represent genera that are significantly different between comparison groups (i.e., logFC≥±1, mean abundance ≥ 3, BH adjusted P&lt; 0.05). Figure S7. Model fit for number of Dirichlet mixture components (DMM), K using the Laplace approximation, A) microbiome at genus level and B) resistome at ARG level. Figure S8. 100% stacked bar of top 10 taxa (microbial genera) within each DMM cluster. Figure S9. Resistome composition (NMDS, Bray-Curtis dissimilarity) at class level (stress=0.048) by A) sampling time point (ANOSIM P=0.001, PERMANOVA R2=56%, P=0.001). B) by treatment (ANOSIM P=0.487, PERMANOVA R2&lt;1%, P=0.502). C) Resistome composition at mechanism level (stress=0.066) by sampling time point (ANOSIM P=0.001, PERMANOVA R2=54.8%, P=0.001). D) by treatment (ANOSIM P=0.08, PERMANOVA R2 &lt;1%, P=0.344). Ellipse indicates 95% confidence interval for distance around centroids of the group. Figure S10. Number of reads aligned to resistome (i.e ARGs) (cumulative sum scaling normalized) in the MEGARes database by time point and treatment group (represented by colored dots). Horizontal lines forming each box represent the first quartile, median and third quartile, while whiskers denote 1.5x the interquartile range. Each sample is represented by a dot with horizontal jitter. Figure S11. Effect of sampling time point on the multivariate dispersion of A) resistome at ARG level and B) microbiome at genus level. Both resistome and microbiome beta-diversity are measured as the distance to their group centroid (using Bray-Curtis distance). Figure S12. Boxplot of A) Number of samples for each resistotype depicted as a function of enterotypes (microbiome DMM cluster), B) ARG diversity of treatment group for each time point according to the resistotypes. Table S1. List of AMR mechanisms for each AMR class presented in heatmap Fig. 7. Table S2. List of low abundant ARGs that were detected post-PRRSv challenge in moderate and intensive treatment groups.