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M. abscessus occupies a wider nutritional niche than M. marinum. A Heat map of M. abscessus stress gene expression derived from RNAseq of M. abscessus at 6 dpi in zebrafish embryos compared to baseline in vitro 7H9 broth cultured M. abscessus. Values are log2 fold change, all genes are differentially expressed between in vivo and in vitro groups (see Supplementary File 1). B Heat map of in vivo M. abscessus lipid metabolism gene expression compared to in vitro 7H9 broth cultured M. abscessus. Values are log2 fold change, all genes are differentially expressed between in vivo and in vitro groups (see Supplementary File 1). C Quantification of M. abscessus growth in 7H9 media supplemented with carbon sources. Single experiment with technical triplicates. D Quantification of M. abscessus and M. marinum growth in 7H9 media diluted to 10% with PBS and supplemented with in vitro caseum. M. marinum culture was performed for 4 days prior to Day 00 when M. abscessus is added to the co-culture conditions. Data is representative of three independent experiments. E Representative images of M. abscessus and M. marinum growth in 7H9 media diluted to 10% with PBS and supplemented with in vitro caseum. M. marinum culture was performed for 4 days prior to Day 00 when M. abscessus is added to the co-culture conditions. F Quantification of M. marinum growth in 163 individual embryos from 0 to 3 dpsi with M. abscessus. R squared value calculated by linear regression, slope equation Y = −0.07066*X + 32.79, P = 0.0481.
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