Phage resistance and apparent lysogenization of Mycobacterium smegmatis due to infection with mycobacteriophage D29 results in the emergence of new variations of the pyruvylated, acylated trehaloses described by Saadat and Ballou, J. Biol. Chem. 258 (1983) 1813-1818. Thin-layer chromatography of the glycolipids from two strains of phage-resistant M. smegmatis (mc(2)22 and mc(2)11) and comparison with those from phage-sensitive strains revealed a new, more mobile glycolipid in each case. The structures of these acyltrehalose-containing lipooligosaccharides were elucidated by a combination of gas-liquid chromatography-mass spectrometry, methylation analysis, H-1 and C-13 NMR spectroscopy, and fast-atom bombardment mass spectrometry. The glycolipid from M. smegmatis mc(2)22 is beta-D-glcp-(1 --> 3)-4,6-O-(1-methoxycarbonylethylidene)-beta-D-Glcp-(1 --> 4)-beta-D-Glcp-(1 --> 6)-2-O-acyl-(alpha-D-Glcp-(1 <-> 1)-3,4-di-O-acyl-alpha-D-Glcp and that from M. smegmatis mc(2)11 is 4,6-O-(1-methoxycarbonylethylidene)-3-O-Me-beta -D-Glcp-(1 --> 3)-4,6-0-(1-methoxycarbonylethylidene)-beta -D-Glcp-(1 --> 4)-P-DGlcp-(1 -->, 6)-2-O-acyl-alpha-D-Glcp-(1 <-> 1)-3,4-di-O-acyl-alpha-D-Glcp. These differ from the original pyruvylated glycolipids of Saadat and Ballou in the extent of their O-acylation and O-methylation. The findings are the first example of the definition of a chemical basis for phage resistance and presumed lysogeny in mycobacteria, and show parallels to related changes in gram-negative enteric bacteria.