Additional file 1 of Selected commensals educate the intestinal vascular and immune system for immunocompetence

Additional file 1: Figure S1. Microbiota determines neutrophil mediated elimination of C. rodentium. (A) Fecal CFU in C. rodentium infected SPF and GF mice, after fecal microbiota transplant (FMT) from SPF mice. (B) C. rodentium-carriers were gavaged on day 22 p.i with an overnight (O/N) aerobic culture of feces from SPF animals, CFUs were determined. (C) Fecal CFUs of C. rodentium in indicated mice. (D) Kinetic of colonic neutrophils absolute cell numbers (ACN) during the course of C. rodentium infection. (E) Neutrophil frequencies in the colonic lamina propria of indicated mice at day 8 and10 p.i. (F) ACN of neutrophils in the blood of indicated mice at day 8 and 10 p.i. (G) Frequencies of LFA-1+ neutrophils in the blood and colon of C. rodentium infected mice. For C. rodentium infection: animals were orally infected with (109 CFU/ml) C. rodentium. Data shown are means ±SD and representative of at least two independent experiments, each symbol represents the individual value for one mouse (G-I). One-way ANOVA was used: ****p < 0.0001; ** p ≤ 0.01; * p ≤ 0.05; ns, not significant. Figure S2. Commensal triggered gene expression and macroscopic changes of the colon. (A) Volcano plot showing fold-change of gene expression in colonic endothelial cells of OMM12 and OMM12 +MC2 (log2-fold change≥1; p-adj < 0.05). STRING analysis for significantly upregulated transcripts in colonic endothelial cells of OMM12 (left) and OMM12 + MC2 (right) mice. (B) Representative immunostaining and quantification of VEGFa expression (brown staining) in the ileum of indicated mice. (C) Macroscopic alterations and colon length in response to the microbiota. (D) Quantification of colonic crypt length in indicated mice, each symbol represents one crypt (n=3). (E) OMM12+MC2 bacteria were visualized by FISH in medial colon (red, bacteria; blue, DAPI). (F) STRING analysis of differentially expressed genes (log2-fold change ≥1; p-adj < 0.05) in complete colon of OMM12 after colonisation with MC2 (n = 4 replicates per group). For C. rodentium infection: animals were orally infected with (109 CFU/ml) C. rodentium. Data shown are means ±SD; at least two independent experiments were performed, each symbol represents the individual value for one mouse (A, C-F). One-way ANOVA was used: ****p < 0.0001; ** p ≤ 0.01; * p ≤ 0.05; ns, not significant. Figure S3. Effects of GF mice monocolonization with E. coli or C. amalonaticus. (A) Fecal C. rodentium CFUs in GF and colonized mice after oral infection with C. rodentium. (B) Frequencies of ICAM1+, CD146+ and MadCAM1+ colonic endothelial cells in indicated animals. (C) Relative abundance (RA) of LP-isolated CD45-CD31+ colonic endothelial cells. (D) Representative images and quantification of whole mount staining in indicated mice. Partial vascularized crypts were quantified by insertion of contour surface modules (gray areas). (E) Intravital, multi-photon microscopy of small intestinal blood capillaries after i.v. injection of Qtracker™ 655. Vessel areas were quantified with trace image processing to make morphometric measurements within a bounding box (BB). Scale bar: 30μm. Results are representative of 4-5 experiments. Data represent mean ±SD of 2-3 independent experiments, each symbol represents the value for one mouse (A, B, D-F). Dotted line represents the reference range for OMM12 mice (D-G). One-way ANOVA was used: ****p < 0.0001; ** p ≤ 0.01; * p ≤ 0.05; ns, not significant. Figure S4. Gene networks from Fig. 4. STRING analysis for significantly upregulated transcripts in the colon of GF (A) and OMM12 mice (B)

Additional file 2 of Selected commensals educate the intestinal vascular and immune system for immunocompetence

Additional file 2: Supplemental Table 1. Results of virulence factor and antibiotic resistance gene prediction based on blastp&VFDB and RGI&CARD

Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2.

COVID-19 is a respiratory illness caused by a novel coronavirus called SARS-CoV-2. The viral spike (S) protein engages the human angiotensin-converting enzyme 2 (ACE2) receptor to invade host cells with ~10-15-fold higher affinity compared to SARS-CoV S-protein, making it highly infectious. Here, we assessed if ACE2 polymorphisms can alter host susceptibility to SARS-CoV-2 by affecting this interaction. We analyzed over 290,000 samples representing &gt;400 population groups from public genomic datasets and identified multiple ACE2 protein-altering variants. Using reported structural data, we identified natural ACE2 variants that could potentially affect virus-host interaction and thereby alter host susceptibility. These include variants S19P, I21V, E23K, K26R, T27A, N64K, T92I, Q102P and H378R that were predicted to increase susceptibility, while variants K31R, N33I, H34R, E35K, E37K, D38V, Y50F, N51S, M62V, K68E, F72V, Y83H, G326E, G352V, D355N, Q388L and D509Y were predicted to be protective variants that show decreased binding to S-protein. Using biochemical assays, we confirmed that K31R and E37K had decreased affinity, and K26R and T92I variants showed increased affinity for S-protein when compared to wildtype ACE2. Consistent with this, soluble ACE2 K26R and T92I were more effective in blocking entry of S-protein pseudotyped virus suggesting that ACE2 variants can modulate susceptibility to SARS-CoV-2

Additional file 3 of Selected commensals educate the intestinal vascular and immune system for immunocompetence

Additional file 3

Integrated genomic analysis reveals mutated ELF3 as a potential gallbladder cancer vaccine candidate

Gallbladder cancer incidence shows characteristic geographic patterns. Here the authors perform a genomic analysis of gallbladder cancers in patients from countries with high incidence (South Korea, India and Chile) and identify ELF3 and other significantly mutated genes not previously associated with gallbladder cancer