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Abbreviations CON: Control CNCbl10: Cyanocobalamin at 10 g/ml CNCbl40: Cyanocobalamin at 40 g/ml MeCbl10: Methylcobalamin at 10 g/ml MeCbl40: Methylcobalamin at 40 g/ml EHEC: Enterohemorrhagic Escherichia coli SURV: Survival experiment EPC: Early-stage pathogen colonization experiment PBS: Phosphate-buffered saline SAMSA2: Simple annotation of metatranscriptomes by sequence analysis 2.0 SCFA: Short-chain fatty acid INF: Interferon gamma IL: Interleukins KC: Keratinocytes-derived chemokine TNF: Tumor necrosis factor alpha GM-CSF: Granulocyte-macrophage colony-stimulating factor MMP9: Matrix metalloproteinase-9 RANTES: Regulated on activation normal T cell expressed and secreted IP10: Interferon gamma-induced protein-10 MCP1: Monocyte chemoattractant protein-1 MIP: Macrophage inflammatory proteins ASV: Amplicon sequencing variant BHI: Brain heart infusion

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Pneumonia requires antibiotics and respiratory support when needed