Additional file 1 of Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models
Creators: name: Liu, Fang
name: Smith, Allen D.
name: Solano-Aguilar, Gloria
name: Wang, Thomas T. Y.
name: Pham, Quynhchi
name: Beshah, Ethiopia
name: Tang, Qingjuan
name: Urban, Joseph F.
name: Xue, Changhu
name: Li, Robert W.
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Figure S1. A PCA plot showing that krill oil (KO), COX2 inhibitor (celecoxib) and IKK2 inhibitor (TPCA1) induced distinct transcriptome patterns in human THP1 cells differentiated using phorbol 12-myristate 13-acetate (PMA). Figure S2. MA plots (log ratio vs mean average) for the visualization of differences in global transcriptome features of THP1 cells under different treatment conditions. The percentage denotes the number of up (red) or down (green) regulated genes induced by various compounds at a false discovery rate (FDR) &lt; 0.05. Figure S3. Heatmaps showing genes in Chemokine (A) and Nod-like receptor signaling (B) pathways significantly inhibited by krill oil and other inhibitors at FDR &lt; 0.05. Figure S4. Krill oil acted synergistically with COX2 and IKK2 inhibitors in increasing the expression of PPARG and FABP5 in human THP1 cells differentiated using PMA. Figure S5. The expression of IL17RA was significantly inhibited by krill oil in human THP1 cells in vitro. Figure S6. The number of bacteria engulfed by human macrophage phagocytosis was marginally increased by krill oil in vitro. Figure S7. A. A heat map showing the genes displaying a significant difference in abundance in the four experimental groups in the proximal colon tissue in pigs in response to Trichuris suis infection and dietary supplements. SC: uninfected pigs fed SO. SI: infected pigs fed SO. KC: uninfected pigs fed KO. KI: infected pigs fed KO. B. Modules-trait relationships in the signed consensus network. The correlation between pathophysiological traits, worm count, gut histamine levels, and gut fatty acid (FA_22:6) measurements, and the module eigengene value was calculated based on Pearson correlation. C. A scatterplot showing gene significance (y-axis) vs. module membership (x-axis) in the purple module. D. Transcription factors significantly enriched in the purple module in the signed consensus network. Figure S8. ANOSIM analysis of beta diversity in the porcine proximal colon microbiome. Figure S9. Global microbial interaction networks inferred using a Random Matrix Theory (RMT) based algorithm in the porcine proximal colon microbial community. Figure S10. Microbial signatures or balances associated with acetate and eicosapentaenoic acid (EPA) concentrations in proximal colon contents in pigs. Figure S11. Select pathways significantly correlated with soybean (SO) and krill oil (KO) supplementation. Figure S12. Taxa significantly correlated with gut luminal concentrations of histamine, 1-methyhistamine, and/or cir-urocanate in a Citrobacter rodentium induced murine colitis model. Figure S13.Citrobacter rodentium infection in mice had a significant impact on gut microbial diversity. Table S1. Composition analysis of krill oil and soybean oil used in the study. Table S2. Top 20 genera selected by Random Forests that distinguish the infection status in a porcine model. Table S3. Serum long chain polyunsaturated fatty acid (LCFA) in pigs. KO: krill oil. SO: soybean oil. HMDB: The Human Metabolome Database. Table S4. The metabolites related to Histidine Metabolism was significantly affected by krill oil supplement (KO) in pigs infected by Trichuris suis.